diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md
index 532a0fc64..b19eaa0e7 100644
--- a/reports/anvil-edge/README.md
+++ b/reports/anvil-edge/README.md
@@ -13,4 +13,4 @@ After each successful deployment, automated tool tests are also run against the
Latest tool tests for each chunk:
-
+
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json
index 098f9827a..73123b4d0 100644
--- a/reports/anvil-edge/tool-tests/chunks.json
+++ b/reports/anvil-edge/tool-tests/chunks.json
@@ -49,11 +49,11 @@
"date2": "Thu Aug 22 18:43:08 2024"
},
"8": {
- "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-23-06-10-1/results.html",
- "date1": "Fri Aug 23 06:25:56 2024",
- "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-23-06-10-1/tools.yml",
- "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-16-06-10-1/results.html",
- "date2": "Fri Aug 16 06:25:00 2024"
+ "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.html",
+ "date1": "Fri Aug 30 06:25:36 2024",
+ "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/tools.yml",
+ "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-23-06-10-1/results.html",
+ "date2": "Fri Aug 23 06:25:56 2024"
},
"9": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-23-18-15-1/results.html",
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/chunk.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/chunk.json
new file mode 100644
index 000000000..320f55161
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/chunk.json
@@ -0,0 +1,7 @@
+{
+ "8": {
+ "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.html",
+ "date1": "Fri Aug 30 06:25:36 2024",
+ "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/tools.yml"
+ }
+}
\ No newline at end of file
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/chunk.txt
new file mode 100644
index 000000000..f6c939318
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/chunk.txt
@@ -0,0 +1,27 @@
+-t collection_column_join --tool-version 071084070619
+-t collection_column_join --tool-version 58228a4d58fe
+-t deeptools_plot_coverage --tool-version 56bce3c82278
+-t trim_galore --tool-version 084bbd8ba7b8
+-t minimap2 --tool-version f54f5baedfdd
+-t flye --tool-version 3ee0ef312022
+-t poretools_tabular --tool-version 2cb2feb94f0e
+-t hisat2 --tool-version 26371a1df031
+-t hisat2 --tool-version f4af63aaf57a
+-t samtools_merge --tool-version 740ce0a18f0d
+-t samtools_merge --tool-version 36677f429310
+-t bam_to_sam --tool-version 88eedb4abea0
+-t anndata_export --tool-version 707023fa62fe
+-t anndata_export --tool-version 0cb889db0910
+-t alevin --tool-version 04b494623f8e
+-t alevin --tool-version e4c01dcece8b
+-t scanpy_plot --tool-version aa0c474463c2
+-t scanpy_plot --tool-version a8f865950ac4
+-t scanpy_run_pca --tool-version 988edd5fa902
+-t scanpy_run_pca --tool-version ce93e630b55a
+-t table_compute --tool-version 60ff16842fcd
+-t lofreq_viterbi --tool-version aa35ee7f3ab2
+-t bcftools_convert_to_vcf --tool-version fec517907949
+-t bcftools_plugin_fill_an_ac --tool-version 582f8b13873d
+-t vcfaddinfo --tool-version 6ea73d6151ec
+-t vcfleftalign --tool-version 29f9b782727e
+-t ivar_consensus --tool-version 78bbd17d0703
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/05f1cc2cc180b061.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/05f1cc2cc180b061.json
new file mode 100644
index 000000000..289bc4308
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/05f1cc2cc180b061.json
@@ -0,0 +1,132 @@
+{
+ "model_class": "Job",
+ "id": "05f1cc2cc180b061",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:18:05.746212",
+ "update_time": "2024-08-30T07:18:24.999336",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-dltns",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/6/b/2/dataset_6b225a08-de2e-4ffc-8cdd-52a766782281.dat' && cp '/galaxy/server/database/objects/d/4/7/dataset_d478885a-4e93-45c0-b833-35a1871257f0.dat' ./mate1.fastq.gz && gunzip ./mate1.fastq.gz && cp '/galaxy/server/database/objects/f/1/1/dataset_f11bdbe6-877d-4608-9a9f-4897fa921a3a.dat' ./mate2.fastq.gz && gunzip ./mate2.fastq.gz && ln -s '/galaxy/server/database/objects/e/f/b/dataset_efb5abf0-017c-45c6-a694-2548c0bf2885.dat' ./alevinmap.tsv && salmon alevin -l A -i ./index -1 ./mate1.fastq -2 ./mate2.fastq -o ./output -p \"${GALAXY_SLOTS:-4}\" --chromium --tgMap ./alevinmap.tsv --numCellBootstraps '2' --keepCBFraction '1.0' --dumpFeatures --dumpMtx --freqThreshold '5' && gunzip output/alevin/quants_mat.mtx.gz && gunzip output/alevin/quants_tier_mat.gz && gunzip output/alevin/quants_mean_mat.gz && gunzip output/alevin/quants_var_mat.gz && gunzip output/aux_info/fld.gz && gunzip output/aux_info/observed_bias.gz && gunzip output/aux_info/observed_bias_3p.gz",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "optional": "{\"dumpBfh\": false, \"dumpFeatures\": true, \"dumpMtx\": true, \"dumpUmiGraph\": false, \"expectCells\": \"\", \"forceCells\": \"\", \"freqThreshold\": \"5\", \"keepCBFraction\": \"1.0\", \"lowRegionMinNumBarcodes\": \"\", \"maxNumBarcodes\": \"\", \"minScoreFraction\": \"\", \"mrna\": null, \"noDedup\": false, \"numCellBootstraps\": \"2\", \"rrna\": null, \"whitelist\": null}",
+ "allout": "false",
+ "protocol": "\"--chromium\"",
+ "pairstraight": "{\"__current_case__\": 0, \"file1\": {\"values\": [{\"id\": 307, \"src\": \"hda\"}]}, \"file2\": {\"values\": [{\"id\": 308, \"src\": \"hda\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"readselect\": \"paired\"}",
+ "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 306, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}"
+ },
+ "inputs": {
+ "tgmap": {
+ "id": "9e7b4465e6d5f5e7",
+ "src": "hda",
+ "uuid": "efb5abf0-017c-45c6-a694-2548c0bf2885"
+ },
+ "pairstraight|file2": {
+ "id": "fda5818e8a5af745",
+ "src": "hda",
+ "uuid": "f11bdbe6-877d-4608-9a9f-4897fa921a3a"
+ },
+ "pairstraight|file1": {
+ "id": "626a64c6bb868c48",
+ "src": "hda",
+ "uuid": "d478885a-4e93-45c0-b833-35a1871257f0"
+ },
+ "refTranscriptSource|s_index|fasta": {
+ "id": "ade34174ea908ec9",
+ "src": "hda",
+ "uuid": "6b225a08-de2e-4ffc-8cdd-52a766782281"
+ }
+ },
+ "outputs": {
+ "quants_mat_cols_txt": {
+ "id": "388a4dbdf6225b5e",
+ "src": "hda",
+ "uuid": "1a811432-4941-4735-89b6-0b87a7d26d61"
+ },
+ "quants_mat_rows_txt": {
+ "id": "016a9ecab36a8a33",
+ "src": "hda",
+ "uuid": "c7f8267e-25a2-43e5-a3f4-10e21ab11301"
+ },
+ "quants_mat_mtx": {
+ "id": "c8642ef18f13529c",
+ "src": "hda",
+ "uuid": "4671a059-2f13-4e16-8224-26fb87dbe063"
+ },
+ "raw_cb_frequency_txt": {
+ "id": "a201e7513402edc5",
+ "src": "hda",
+ "uuid": "94e23446-c99d-4f28-a2cb-5fa9f42586a3"
+ },
+ "quants_tier_mat": {
+ "id": "bfc105b661dbaf2b",
+ "src": "hda",
+ "uuid": "40387756-8171-4ba3-8458-7ab7a2278eae"
+ },
+ "featureDump_txt": {
+ "id": "37bf2b8aff708392",
+ "src": "hda",
+ "uuid": "5d1ce308-ef04-4307-9e22-c8afb94d4dd3"
+ },
+ "whitelist_txt": {
+ "id": "6c555ae15f749b36",
+ "src": "hda",
+ "uuid": "a6c6b15d-d965-42c7-90f5-7facba229951"
+ },
+ "quants_mean_mat": {
+ "id": "8e3bc46515971f80",
+ "src": "hda",
+ "uuid": "6792f8c2-0020-42fd-88a6-5e3b7636f0cc"
+ },
+ "quants_var_mat": {
+ "id": "9e66f7e372adc5d1",
+ "src": "hda",
+ "uuid": "c93c16f0-360c-41cc-861d-e1487fada4f7"
+ },
+ "quants_boot_rows_txt": {
+ "id": "fa46b69b3b6eb2d0",
+ "src": "hda",
+ "uuid": "48ae43a8-3804-451f-a40b-b5aecb38069a"
+ },
+ "expected_bias": {
+ "id": "ef008abdd885cd3a",
+ "src": "hda",
+ "uuid": "ffa68773-a1bf-4d2f-9216-17af90d27a79"
+ },
+ "observed_bias": {
+ "id": "9157b567b4405058",
+ "src": "hda",
+ "uuid": "a86985fb-67bf-41e0-998e-a27b9b05cfa5"
+ },
+ "observed_bias_3p": {
+ "id": "787f20cab39ce662",
+ "src": "hda",
+ "uuid": "8b2746d8-9a97-45ef-ae2e-c59c49c368c3"
+ },
+ "flenDist_txt": {
+ "id": "91ee28930f1e2eb4",
+ "src": "hda",
+ "uuid": "3fe922e2-673c-42a8-beee-075481887097"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": [],
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/0c5fa726f67a9d66.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/0c5fa726f67a9d66.json
new file mode 100644
index 000000000..70cb26e69
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/0c5fa726f67a9d66.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "0c5fa726f67a9d66",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T08:08:57.544623",
+ "update_time": "2024-08-30T08:09:08.432695",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-gbnn4",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/428/registry.xml' '/galaxy/server/database/jobs_directory/000/428/upload_params.json' '575:/galaxy/server/database/objects/6/2/f/dataset_62fe37e2-b0b2-480f-b892-54951abafd69_files:/galaxy/server/database/objects/6/2/f/dataset_62fe37e2-b0b2-480f-b892-54951abafd69.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_wbhaifrf\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"examples.7.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_bm5uwcw3\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "3f4b647bf56e33ca",
+ "src": "hda",
+ "uuid": "62fe37e2-b0b2-480f-b892-54951abafd69"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/1a18e3937393327c.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/1a18e3937393327c.json
new file mode 100644
index 000000000..f1e51cf95
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/1a18e3937393327c.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "1a18e3937393327c",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:10:09.396045",
+ "update_time": "2024-08-30T07:10:21.898947",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-vjp9c",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/215/registry.xml' '/galaxy/server/database/jobs_directory/000/215/upload_params.json' '252:/galaxy/server/database/objects/f/b/3/dataset_fb332dc3-820f-46f1-8eea-4845812e8cc6_files:/galaxy/server/database/objects/f/b/3/dataset_fb332dc3-820f-46f1-8eea-4845812e8cc6.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_p0t1tx49\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"test_input_1_a.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_24plaftt\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "fbce319d75744a7b",
+ "src": "hda",
+ "uuid": "fb332dc3-820f-46f1-8eea-4845812e8cc6"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/1d8f058f735ff10d.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/1d8f058f735ff10d.json
new file mode 100644
index 000000000..82eaa37d0
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/1d8f058f735ff10d.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "1d8f058f735ff10d",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T08:12:30.055518",
+ "update_time": "2024-08-30T08:12:41.098379",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-8qrrf",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/441/registry.xml' '/galaxy/server/database/jobs_directory/000/441/upload_params.json' '588:/galaxy/server/database/objects/9/8/e/dataset_98ed1a65-6b35-4a0a-ac5d-7b298e0ec81c_files:/galaxy/server/database/objects/9/8/e/dataset_98ed1a65-6b35-4a0a-ac5d-7b298e0ec81c.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_rml7sg47\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"examples.1.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_4qijso58\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "030993b6c9043e4c",
+ "src": "hda",
+ "uuid": "98ed1a65-6b35-4a0a-ac5d-7b298e0ec81c"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/21b4b2693acea78a.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/21b4b2693acea78a.json
new file mode 100644
index 000000000..b862223cd
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/21b4b2693acea78a.json
@@ -0,0 +1,55 @@
+{
+ "model_class": "Job",
+ "id": "21b4b2693acea78a",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:46:42.485838",
+ "update_time": "2024-08-30T07:46:50.637279",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-tkf98",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "cp '/galaxy/server/database/objects/0/2/8/dataset_028d334c-30f9-4a11-bf97-1c28532bdb15.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/348/configs/tmpm3gqvmnt' > '/galaxy/server/database/objects/4/f/f/dataset_4ff53f62-2edd-4994-9b63-8c6fdba8fa14.dat' && python '/galaxy/server/database/jobs_directory/000/348/configs/tmpm3gqvmnt' >> '/galaxy/server/database/objects/4/f/f/dataset_4ff53f62-2edd-4994-9b63-8c6fdba8fa14.dat' && ls . >> '/galaxy/server/database/objects/4/f/f/dataset_4ff53f62-2edd-4994-9b63-8c6fdba8fa14.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "advanced_common": "{\"show_log\": true}",
+ "method": "{\"__current_case__\": 11, \"log\": false, \"method\": \"pl.pca_variance_ratio\", \"n_pcs\": \"5\"}",
+ "format": "\"png\""
+ },
+ "inputs": {
+ "adata": {
+ "id": "c948ff00108a577e",
+ "src": "hda",
+ "uuid": "028d334c-30f9-4a11-bf97-1c28532bdb15"
+ }
+ },
+ "outputs": {
+ "hidden_output": {
+ "id": "4503b172d2db2f67",
+ "src": "hda",
+ "uuid": "4ff53f62-2edd-4994-9b63-8c6fdba8fa14"
+ },
+ "out_png": {
+ "id": "ede55d2d793e0163",
+ "src": "hda",
+ "uuid": "01f05daa-b8de-4d7b-9289-78fff472829d"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/21b90fd529ee415c.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/21b90fd529ee415c.json
new file mode 100644
index 000000000..a5ccfb00b
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/21b90fd529ee415c.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "21b90fd529ee415c",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:53:12.952166",
+ "update_time": "2024-08-30T06:53:23.793967",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-d95r9",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/108/registry.xml' '/galaxy/server/database/jobs_directory/000/108/upload_params.json' '134:/galaxy/server/database/objects/b/a/4/dataset_ba49f66c-4b64-4a84-9bae-c70b6907ed6a_files:/galaxy/server/database/objects/b/a/4/dataset_ba49f66c-4b64-4a84-9bae-c70b6907ed6a.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_lf9dzrw0\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"phiX.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_59g85rop\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "13df7a486c8004eb",
+ "src": "hda",
+ "uuid": "ba49f66c-4b64-4a84-9bae-c70b6907ed6a"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/22f19ad876838d6e.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/22f19ad876838d6e.json
new file mode 100644
index 000000000..7769e8404
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/22f19ad876838d6e.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "22f19ad876838d6e",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:38:14.914742",
+ "update_time": "2024-08-30T06:38:25.867061",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-lsfhf",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/60/registry.xml' '/galaxy/server/database/jobs_directory/000/60/upload_params.json' '70:/galaxy/server/database/objects/e/9/8/dataset_e98b8b1b-2512-49ec-9bee-167e0eb32a22_files:/galaxy/server/database/objects/e/9/8/dataset_e98b8b1b-2512-49ec-9bee-167e0eb32a22.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params__26am7l8\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"bwa-mem-mt-genome.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_olvzsjet\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "8fe67bcff76f53cb",
+ "src": "hda",
+ "uuid": "e98b8b1b-2512-49ec-9bee-167e0eb32a22"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/34b4dc44e77155a2.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/34b4dc44e77155a2.json
new file mode 100644
index 000000000..f79a2ac1e
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/34b4dc44e77155a2.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "34b4dc44e77155a2",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:27:50.557615",
+ "update_time": "2024-08-30T07:28:00.667703",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-rhlh6",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/288/registry.xml' '/galaxy/server/database/jobs_directory/000/288/upload_params.json' '395:/galaxy/server/database/objects/6/4/b/dataset_64bbb10f-79f8-45be-ab39-fd1c5e078cdd_files:/galaxy/server/database/objects/6/4/b/dataset_64bbb10f-79f8-45be-ab39-fd1c5e078cdd.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_yy_nt8oj\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"pbmc68k_reduced.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_z8xrey0r\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "bc3f7c1e67c329a8",
+ "src": "hda",
+ "uuid": "64bbb10f-79f8-45be-ab39-fd1c5e078cdd"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/359f65ffc3abb465.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/359f65ffc3abb465.json
new file mode 100644
index 000000000..b4963447e
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/359f65ffc3abb465.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "359f65ffc3abb465",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T08:01:38.096930",
+ "update_time": "2024-08-30T08:01:48.842112",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-7wggl",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/400/registry.xml' '/galaxy/server/database/jobs_directory/000/400/upload_params.json' '547:/galaxy/server/database/objects/e/3/3/dataset_e33f879e-6325-45ca-ac53-d08492fb8a75_files:/galaxy/server/database/objects/e/3/3/dataset_e33f879e-6325-45ca-ac53-d08492fb8a75.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_bwit_g9d\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"small.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_23bkdpys\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "ab909a96e8ef0e49",
+ "src": "hda",
+ "uuid": "e33f879e-6325-45ca-ac53-d08492fb8a75"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/361b5ee0a3110f70.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/361b5ee0a3110f70.json
new file mode 100644
index 000000000..3c727f090
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/361b5ee0a3110f70.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "361b5ee0a3110f70",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:09:57.679739",
+ "update_time": "2024-08-30T07:10:08.777849",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-zqtdx",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/212/registry.xml' '/galaxy/server/database/jobs_directory/000/212/upload_params.json' '249:/galaxy/server/database/objects/d/b/1/dataset_db1f61ee-1bad-4c4f-9840-b622b8fd3e2b_files:/galaxy/server/database/objects/d/b/1/dataset_db1f61ee-1bad-4c4f-9840-b622b8fd3e2b.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_c0bocqkl\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"test_input_1_a.sam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9allzmmq\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "ce3120272ed58015",
+ "src": "hda",
+ "uuid": "db1f61ee-1bad-4c4f-9840-b622b8fd3e2b"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/377e92f1cc29a047.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/377e92f1cc29a047.json
new file mode 100644
index 000000000..e77d3b3f5
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/377e92f1cc29a047.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "377e92f1cc29a047",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:38:26.604047",
+ "update_time": "2024-08-30T06:38:37.614299",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-b8rnn",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/63/registry.xml' '/galaxy/server/database/jobs_directory/000/63/upload_params.json' '73:/galaxy/server/database/objects/6/2/a/dataset_62a40ad7-1acb-45d3-8ea3-5805759ece39_files:/galaxy/server/database/objects/6/2/a/dataset_62a40ad7-1acb-45d3-8ea3-5805759ece39.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_s0jwkt8x\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"bwa-mem-mt-genome.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_5yd3_xxv\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "cf3f663fd647142e",
+ "src": "hda",
+ "uuid": "62a40ad7-1acb-45d3-8ea3-5805759ece39"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/3d7c835c180678a2.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/3d7c835c180678a2.json
new file mode 100644
index 000000000..9405d410a
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/3d7c835c180678a2.json
@@ -0,0 +1,55 @@
+{
+ "model_class": "Job",
+ "id": "3d7c835c180678a2",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:44:59.336865",
+ "update_time": "2024-08-30T07:45:08.277328",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-dvjvq",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "cp '/galaxy/server/database/objects/4/3/1/dataset_431cd7d3-482b-4484-8e61-6f19e0d801c7.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/342/configs/tmp753tuud7' > '/galaxy/server/database/objects/1/e/a/dataset_1eadb9f6-ba74-4228-9017-a1d3f92184e2.dat' && python '/galaxy/server/database/jobs_directory/000/342/configs/tmp753tuud7' >> '/galaxy/server/database/objects/1/e/a/dataset_1eadb9f6-ba74-4228-9017-a1d3f92184e2.dat' && ls . >> '/galaxy/server/database/objects/1/e/a/dataset_1eadb9f6-ba74-4228-9017-a1d3f92184e2.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "advanced_common": "{\"show_log\": true}",
+ "method": "{\"__current_case__\": 7, \"highly_variable_genes\": true, \"log\": false, \"method\": \"pl.highly_variable_genes\"}",
+ "format": "\"png\""
+ },
+ "inputs": {
+ "adata": {
+ "id": "86d5a32cd72d8f1f",
+ "src": "hda",
+ "uuid": "431cd7d3-482b-4484-8e61-6f19e0d801c7"
+ }
+ },
+ "outputs": {
+ "hidden_output": {
+ "id": "038608c16b6b728c",
+ "src": "hda",
+ "uuid": "1eadb9f6-ba74-4228-9017-a1d3f92184e2"
+ },
+ "out_png": {
+ "id": "3fd2877a377cc9dd",
+ "src": "hda",
+ "uuid": "f49059eb-0e91-4d98-8d4a-f5fc3d6f4b86"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "WARNING: saving figure to file filter_genes_dispersion.png\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "WARNING: saving figure to file filter_genes_dispersion.png\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/3fd2877a377cc9dd.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/3fd2877a377cc9dd.json
new file mode 100644
index 000000000..425fd5021
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/3fd2877a377cc9dd.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "3fd2877a377cc9dd",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T08:19:51.879185",
+ "update_time": "2024-08-30T08:20:02.025663",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-m2mmd",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/475/registry.xml' '/galaxy/server/database/jobs_directory/000/475/upload_params.json' '622:/galaxy/server/database/objects/d/7/5/dataset_d7594d8e-1075-48dc-95b5-4d0ddef8e978_files:/galaxy/server/database/objects/d/7/5/dataset_d7594d8e-1075-48dc-95b5-4d0ddef8e978.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_2542anyg\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"vcflib-phix.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_q24s_k04\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "731cc57dc90c197e",
+ "src": "hda",
+ "uuid": "d7594d8e-1075-48dc-95b5-4d0ddef8e978"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/428d6406e93d9d09.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/428d6406e93d9d09.json
new file mode 100644
index 000000000..230128826
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/428d6406e93d9d09.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "428d6406e93d9d09",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:59:59.086382",
+ "update_time": "2024-08-30T07:00:11.576392",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-vbdvp",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/151/registry.xml' '/galaxy/server/database/jobs_directory/000/151/upload_params.json' '183:/galaxy/server/database/objects/5/1/a/dataset_51a04810-d6fc-4af6-918e-d1de60bc26a3_files:/galaxy/server/database/objects/5/1/a/dataset_51a04810-d6fc-4af6-918e-d1de60bc26a3.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_4yzlxniv\"",
+ "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}",
+ "dbkey": "\"phiX\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"hisat_input_1_forward.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_69yb3c19\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fastqsanger\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "8007b0341c73cffe",
+ "src": "hda",
+ "uuid": "51a04810-d6fc-4af6-918e-d1de60bc26a3"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/436da20d1fd8461d.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/436da20d1fd8461d.json
new file mode 100644
index 000000000..aab3cb5c6
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/436da20d1fd8461d.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "436da20d1fd8461d",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:26:09.763371",
+ "update_time": "2024-08-30T06:26:36.948713",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-fwxc2",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/1/registry.xml' '/galaxy/server/database/jobs_directory/000/1/upload_params.json' '1:/galaxy/server/database/objects/d/9/4/dataset_d94506d8-abb4-434d-8b4c-a10626ee8844_files:/galaxy/server/database/objects/d/9/4/dataset_d94506d8-abb4-434d-8b4c-a10626ee8844.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_q94_am2k\"",
+ "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"in_1.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ufkr5lo7\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"tabular\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "436da20d1fd8461d",
+ "src": "hda",
+ "uuid": "d94506d8-abb4-434d-8b4c-a10626ee8844"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/46776bb661fa2c92.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/46776bb661fa2c92.json
new file mode 100644
index 000000000..c90851805
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/46776bb661fa2c92.json
@@ -0,0 +1,50 @@
+{
+ "model_class": "Job",
+ "id": "46776bb661fa2c92",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:59:34.324053",
+ "update_time": "2024-08-30T07:59:40.977481",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-99bnf",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "cp '/galaxy/server/database/jobs_directory/000/392/configs/tmpkqrz7igg' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"tabular\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "precision": "\"2\"",
+ "out_opts": "[\"ignore_nas\", \"output_headers_row\"]",
+ "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 538, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 3, \"dimension\": \"0\", \"matrixapply_func\": {\"__current_case__\": 0, \"custom_func\": \"vec.sum()+vec.median()\", \"vector_op\": \"custom\"}, \"mode\": \"matrixapply\"}}"
+ },
+ "inputs": {
+ "singtabop|input": {
+ "id": "0f26b673bb300aef",
+ "src": "hda",
+ "uuid": "7ebd7be0-44b0-4ba6-bb5b-0e2a6c2b096e"
+ }
+ },
+ "outputs": {
+ "table": {
+ "id": "87b9749fc51dc6b8",
+ "src": "hda",
+ "uuid": "428beca5-fbff-4bb4-8f0f-460f30c31e4b"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/47fccb329a775a72.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/47fccb329a775a72.json
new file mode 100644
index 000000000..a74cfc154
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/47fccb329a775a72.json
@@ -0,0 +1,55 @@
+{
+ "model_class": "Job",
+ "id": "47fccb329a775a72",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:24:12.485692",
+ "update_time": "2024-08-30T07:24:20.888017",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-cb9pp",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "cp '/galaxy/server/database/objects/9/4/f/dataset_94f285ad-837d-4681-bf47-c61fe11a2421.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/275/configs/tmpyqdazgx_' > '/galaxy/server/database/objects/b/e/b/dataset_bebe4fa6-8af1-4a63-bf55-18cc062a5e40.dat' && python '/galaxy/server/database/jobs_directory/000/275/configs/tmpyqdazgx_' >> '/galaxy/server/database/objects/b/e/b/dataset_bebe4fa6-8af1-4a63-bf55-18cc062a5e40.dat' && ls . >> '/galaxy/server/database/objects/b/e/b/dataset_bebe4fa6-8af1-4a63-bf55-18cc062a5e40.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "advanced_common": "{\"show_log\": true}",
+ "method": "{\"__current_case__\": 3, \"groupby\": \"\", \"key_variables\": {\"__current_case__\": 2, \"keys\": \"n_genes, percent_mito, n_counts\", \"type\": \"custom\"}, \"log\": false, \"method\": \"pl.violin\", \"rotation\": \"\", \"seaborn_violinplot\": {\"bw\": \"scott\", \"color\": \"AliceBlue\", \"linewidth\": \"0.0\", \"orient\": null, \"saturation\": \"0.75\"}, \"use_raw\": false, \"violin_plot\": {\"multi_panel\": {\"__current_case__\": 0, \"height\": \"20\", \"multi_panel\": \"True\", \"width\": \"20\"}, \"scale\": \"width\", \"stripplot\": {\"__current_case__\": 0, \"jitter\": {\"__current_case__\": 0, \"jitter\": \"True\", \"size\": \"1.0\"}, \"stripplot\": \"True\"}}, \"xlabel\": \"\"}",
+ "format": "\"png\""
+ },
+ "inputs": {
+ "adata": {
+ "id": "1325463534297ec8",
+ "src": "hda",
+ "uuid": "94f285ad-837d-4681-bf47-c61fe11a2421"
+ }
+ },
+ "outputs": {
+ "hidden_output": {
+ "id": "44f6cd6d9970c8f1",
+ "src": "hda",
+ "uuid": "bebe4fa6-8af1-4a63-bf55-18cc062a5e40"
+ },
+ "out_png": {
+ "id": "ecfb059196fefc44",
+ "src": "hda",
+ "uuid": "b88d4b8f-0092-479d-a19a-13bd288120bb"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "WARNING: saving figure to file violin.png\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "WARNING: saving figure to file violin.png\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/4c4a43e5488d989e.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/4c4a43e5488d989e.json
new file mode 100644
index 000000000..b6ab12d1e
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/4c4a43e5488d989e.json
@@ -0,0 +1,48 @@
+{
+ "model_class": "Job",
+ "id": "4c4a43e5488d989e",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_tabular/poretools_tabular/0.6.1a1.0",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:47:51.703323",
+ "update_time": "2024-08-30T06:48:19.437621",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-sc9p2",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "poretools tabular --type all '/galaxy/server/database/objects/8/b/4/dataset_8b4e79eb-d7da-4a1c-8ecf-bc88f4747513.dat' > '/galaxy/server/database/objects/9/c/7/dataset_9c7bac0e-8f5d-4c5a-b85a-595023598175.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"fast5.tar\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "type": "\"all\""
+ },
+ "inputs": {
+ "input": {
+ "id": "3cfb09a11cdf160e",
+ "src": "hda",
+ "uuid": "8b4e79eb-d7da-4a1c-8ecf-bc88f4747513"
+ }
+ },
+ "outputs": {
+ "output": {
+ "id": "21b90fd529ee415c",
+ "src": "hda",
+ "uuid": "9c7bac0e-8f5d-4c5a-b85a-595023598175"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/5fcfe86f7ffa46b0.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/5fcfe86f7ffa46b0.json
new file mode 100644
index 000000000..62fbed0c3
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/5fcfe86f7ffa46b0.json
@@ -0,0 +1,55 @@
+{
+ "model_class": "Job",
+ "id": "5fcfe86f7ffa46b0",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:43:17.443377",
+ "update_time": "2024-08-30T07:43:26.000334",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-t72mg",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "cp '/galaxy/server/database/objects/0/f/f/dataset_0fff1026-5e52-4116-813a-f8fa32fb486b.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/336/configs/tmplolqd15_' > '/galaxy/server/database/objects/6/0/5/dataset_605abc07-b52e-4a1f-b241-a307f90fdbc7.dat' && python '/galaxy/server/database/jobs_directory/000/336/configs/tmplolqd15_' >> '/galaxy/server/database/objects/6/0/5/dataset_605abc07-b52e-4a1f-b241-a307f90fdbc7.dat' && ls . >> '/galaxy/server/database/objects/6/0/5/dataset_605abc07-b52e-4a1f-b241-a307f90fdbc7.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "advanced_common": "{\"show_log\": true}",
+ "method": "{\"__current_case__\": 5, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 0, \"height\": \"3\", \"test\": \"yes\", \"width\": \"10\"}, \"gene_symbols\": \"symbol\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_pcolor\": {\"alpha\": \"\", \"cmap\": \"Accent\", \"edgecolors\": \"face\", \"snap\": false, \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.matrixplot\", \"num_categories\": \"7\", \"swap_axes\": false, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 1, \"type\": \"custom\", \"var_names\": \"Fog1,EKLF,SCL\"}}",
+ "format": "\"png\""
+ },
+ "inputs": {
+ "adata": {
+ "id": "3c04a6000b1da1cb",
+ "src": "hda",
+ "uuid": "0fff1026-5e52-4116-813a-f8fa32fb486b"
+ }
+ },
+ "outputs": {
+ "hidden_output": {
+ "id": "14756a0451bf8376",
+ "src": "hda",
+ "uuid": "605abc07-b52e-4a1f-b241-a307f90fdbc7"
+ },
+ "out_png": {
+ "id": "46da947090ba3225",
+ "src": "hda",
+ "uuid": "eb3a0c42-824c-44f6-9b05-4d7ba8bbccf2"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/6a8e2e23745f6c0d.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/6a8e2e23745f6c0d.json
new file mode 100644
index 000000000..d6a4fc4cb
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/6a8e2e23745f6c0d.json
@@ -0,0 +1,117 @@
+{
+ "model_class": "Job",
+ "id": "6a8e2e23745f6c0d",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:17:03.331734",
+ "update_time": "2024-08-30T07:17:36.251221",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-86zh2",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/4/5/1/dataset_451a0b29-4870-431d-a23b-c988bab22363.dat' && cp '/galaxy/server/database/objects/1/a/2/dataset_1a2f8863-f68f-443f-b699-30dd31bb8bd2.dat' ./mate1.fastq.gz && gunzip ./mate1.fastq.gz && cp '/galaxy/server/database/objects/3/b/4/dataset_3b4e7a84-86bd-416a-be49-d7906a308a10.dat' ./mate2.fastq.gz && gunzip ./mate2.fastq.gz && ln -s '/galaxy/server/database/objects/d/4/7/dataset_d47d26a4-50b8-4eda-b849-7215b4a38ed9.dat' ./alevinmap.tsv && salmon alevin -l A -i ./index -1 ./mate1.fastq -2 ./mate2.fastq -o ./output -p \"${GALAXY_SLOTS:-4}\" --chromium --tgMap ./alevinmap.tsv --keepCBFraction '1.0' --dumpFeatures --dumpMtx --freqThreshold '5' && gunzip output/alevin/quants_mat.mtx.gz && gunzip output/alevin/quants_tier_mat.gz && gunzip output/aux_info/fld.gz && gunzip output/aux_info/observed_bias.gz && gunzip output/aux_info/observed_bias_3p.gz",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "optional": "{\"dumpBfh\": false, \"dumpFeatures\": true, \"dumpMtx\": true, \"dumpUmiGraph\": false, \"expectCells\": \"\", \"forceCells\": \"\", \"freqThreshold\": \"5\", \"keepCBFraction\": \"1.0\", \"lowRegionMinNumBarcodes\": \"\", \"maxNumBarcodes\": \"\", \"minScoreFraction\": \"\", \"mrna\": null, \"noDedup\": false, \"numCellBootstraps\": \"\", \"rrna\": null, \"whitelist\": null}",
+ "allout": "false",
+ "protocol": "\"--chromium\"",
+ "pairstraight": "{\"__current_case__\": 0, \"file1\": {\"values\": [{\"id\": 292, \"src\": \"hda\"}]}, \"file2\": {\"values\": [{\"id\": 293, \"src\": \"hda\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"readselect\": \"paired\"}",
+ "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 291, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}"
+ },
+ "inputs": {
+ "tgmap": {
+ "id": "1aa19454e64c7484",
+ "src": "hda",
+ "uuid": "d47d26a4-50b8-4eda-b849-7215b4a38ed9"
+ },
+ "pairstraight|file2": {
+ "id": "5bc74392f7594846",
+ "src": "hda",
+ "uuid": "3b4e7a84-86bd-416a-be49-d7906a308a10"
+ },
+ "pairstraight|file1": {
+ "id": "af80223b2b724185",
+ "src": "hda",
+ "uuid": "1a2f8863-f68f-443f-b699-30dd31bb8bd2"
+ },
+ "refTranscriptSource|s_index|fasta": {
+ "id": "012fd79ff5050b2e",
+ "src": "hda",
+ "uuid": "451a0b29-4870-431d-a23b-c988bab22363"
+ }
+ },
+ "outputs": {
+ "flenDist_txt": {
+ "id": "486aa39a6bf52933",
+ "src": "hda",
+ "uuid": "dcf12db7-0384-4c1b-be0b-3d6e8ef259a6"
+ },
+ "observed_bias_3p": {
+ "id": "5ac3666d409c110b",
+ "src": "hda",
+ "uuid": "3337ddbb-9487-4295-b72a-fefc1d492340"
+ },
+ "observed_bias": {
+ "id": "e3d896b61542c76c",
+ "src": "hda",
+ "uuid": "4c89e969-36a0-417f-988d-212aed1d2f0e"
+ },
+ "expected_bias": {
+ "id": "6be82dcbc2b5c0e1",
+ "src": "hda",
+ "uuid": "605bede0-1ba5-4aac-a283-894d4dbace9f"
+ },
+ "whitelist_txt": {
+ "id": "e55f906e1cc2896a",
+ "src": "hda",
+ "uuid": "50a9d3a7-ac5d-45e2-a231-16802e002d2d"
+ },
+ "featureDump_txt": {
+ "id": "d8e603da1c3f291d",
+ "src": "hda",
+ "uuid": "2f1b4796-f864-4f17-a104-8ab3a14e599d"
+ },
+ "quants_tier_mat": {
+ "id": "9f85906923485bec",
+ "src": "hda",
+ "uuid": "488aa477-3c64-4653-bfc7-3b5dd7cbb46f"
+ },
+ "quants_mat_rows_txt": {
+ "id": "b1ea0f569f8c6a70",
+ "src": "hda",
+ "uuid": "04f2e6b4-2f29-4350-abea-3f6acbfcb840"
+ },
+ "quants_mat_cols_txt": {
+ "id": "8f5e193507069e81",
+ "src": "hda",
+ "uuid": "01509744-1c0d-41ad-872b-7fd345d8e00b"
+ },
+ "raw_cb_frequency_txt": {
+ "id": "8931930f797580d2",
+ "src": "hda",
+ "uuid": "417be05d-9ff2-44ce-9baa-103b79f362b4"
+ },
+ "quants_mat_mtx": {
+ "id": "7b400f26a531a182",
+ "src": "hda",
+ "uuid": "4115e486-79b1-49b4-8678-221d29d0be9a"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": [],
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/7037a4c267c5edd7.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/7037a4c267c5edd7.json
new file mode 100644
index 000000000..07cdf25b0
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/7037a4c267c5edd7.json
@@ -0,0 +1,55 @@
+{
+ "model_class": "Job",
+ "id": "7037a4c267c5edd7",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:48:24.546670",
+ "update_time": "2024-08-30T07:48:34.008567",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-zfbtm",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "cp '/galaxy/server/database/objects/e/7/8/dataset_e789b880-5a55-444c-9de0-f8669cb1d20b.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/354/configs/tmpjx966dm_' > '/galaxy/server/database/objects/5/0/3/dataset_503a0a8a-bc5c-44ed-9989-2bd133af09b7.dat' && python '/galaxy/server/database/jobs_directory/000/354/configs/tmpjx966dm_' >> '/galaxy/server/database/objects/5/0/3/dataset_503a0a8a-bc5c-44ed-9989-2bd133af09b7.dat' && ls . >> '/galaxy/server/database/objects/5/0/3/dataset_503a0a8a-bc5c-44ed-9989-2bd133af09b7.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "advanced_common": "{\"show_log\": true}",
+ "method": "{\"__current_case__\": 14, \"arrows\": false, \"color\": \"paul15_clusters\", \"edges\": {\"__current_case__\": 0, \"edges\": \"True\", \"edges_color\": \"AliceBlue\", \"edges_width\": \"0.1\"}, \"groups\": \"\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.umap\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": true, \"use_raw\": false}",
+ "format": "\"png\""
+ },
+ "inputs": {
+ "adata": {
+ "id": "11b59b2c17e03455",
+ "src": "hda",
+ "uuid": "e789b880-5a55-444c-9de0-f8669cb1d20b"
+ }
+ },
+ "outputs": {
+ "hidden_output": {
+ "id": "3717c512ea73d94f",
+ "src": "hda",
+ "uuid": "503a0a8a-bc5c-44ed-9989-2bd133af09b7"
+ },
+ "out_png": {
+ "id": "72b2436f04e95d20",
+ "src": "hda",
+ "uuid": "8448e2d6-a0d8-46c9-8710-690c3176a608"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "WARNING: saving figure to file umap.png\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "WARNING: saving figure to file umap.png\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/72a670fdd9745f64.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/72a670fdd9745f64.json
new file mode 100644
index 000000000..625b78946
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/72a670fdd9745f64.json
@@ -0,0 +1,50 @@
+{
+ "model_class": "Job",
+ "id": "72a670fdd9745f64",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T08:13:01.039586",
+ "update_time": "2024-08-30T08:13:06.409117",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-qcnng",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "cp '/galaxy/server/database/jobs_directory/000/443/configs/tmpcjkn_n50' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"tabular\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "precision": "\"6\"",
+ "out_opts": "[\"ignore_nas\", \"output_headers_col\", \"output_headers_row\"]",
+ "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 589, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 5, \"elem_val\": {\"__current_case__\": 0, \"element_op\": \"None\"}, \"element\": {\"__current_case__\": 0, \"mode\": \"replace\", \"replace_value\": \"a'+'b\"}, \"mode\": \"element\"}}"
+ },
+ "inputs": {
+ "singtabop|input": {
+ "id": "a2b9d4075a0a3357",
+ "src": "hda",
+ "uuid": "e5b37657-8aba-4ad8-a582-15e3ccbb3d06"
+ }
+ },
+ "outputs": {
+ "table": {
+ "id": "622f164698930e73",
+ "src": "hda",
+ "uuid": "2f950d36-c84c-4e37-a4ec-8c08fbc6e99d"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/796656e048485a18.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/796656e048485a18.json
new file mode 100644
index 000000000..cd81f3e4a
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/796656e048485a18.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "796656e048485a18",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:15:45.135534",
+ "update_time": "2024-08-30T07:15:56.084225",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-j2v88",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/239/registry.xml' '/galaxy/server/database/jobs_directory/000/239/upload_params.json' '284:/galaxy/server/database/objects/6/1/6/dataset_6161fb94-6665-4b99-aab2-7e81e372fd92_files:/galaxy/server/database/objects/6/1/6/dataset_6161fb94-6665-4b99-aab2-7e81e372fd92.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_fssugbbb\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"krumsiek11.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_i91u66py\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "e1ff8013427b61ef",
+ "src": "hda",
+ "uuid": "6161fb94-6665-4b99-aab2-7e81e372fd92"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/84d1b775e9099f9d.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/84d1b775e9099f9d.json
new file mode 100644
index 000000000..8d83c4f12
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/84d1b775e9099f9d.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "84d1b775e9099f9d",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:38:38.333772",
+ "update_time": "2024-08-30T06:38:49.745643",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-27pz6",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/66/registry.xml' '/galaxy/server/database/jobs_directory/000/66/upload_params.json' '76:/galaxy/server/database/objects/a/2/a/dataset_a2a02334-000b-4dad-940f-a3df033f79e8_files:/galaxy/server/database/objects/a/2/a/dataset_a2a02334-000b-4dad-940f-a3df033f79e8.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_schlm_5p\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"bwa-mem-mt-genome.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_5r_64r4v\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "60ddc0345154ae3c",
+ "src": "hda",
+ "uuid": "a2a02334-000b-4dad-940f-a3df033f79e8"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8a731c16879c5339.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8a731c16879c5339.json
new file mode 100644
index 000000000..85f540ef2
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8a731c16879c5339.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "8a731c16879c5339",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:12:41.577643",
+ "update_time": "2024-08-30T07:12:52.287739",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-zmdcx",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/228/registry.xml' '/galaxy/server/database/jobs_directory/000/228/upload_params.json' '265:/galaxy/server/database/objects/2/4/e/dataset_24eead86-4558-4dc5-8836-9aa681e597cd_files:/galaxy/server/database/objects/2/4/e/dataset_24eead86-4558-4dc5-8836-9aa681e597cd.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_qt_8hj6l\"",
+ "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"bam_to_sam_in1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_pwyiniuc\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"bam\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "4da2065af1ae5859",
+ "src": "hda",
+ "uuid": "24eead86-4558-4dc5-8836-9aa681e597cd"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8becb61cdaf1d973.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8becb61cdaf1d973.json
new file mode 100644
index 000000000..2451ee907
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8becb61cdaf1d973.json
@@ -0,0 +1,117 @@
+{
+ "model_class": "Job",
+ "id": "8becb61cdaf1d973",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:18:59.582456",
+ "update_time": "2024-08-30T07:19:08.794666",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-8t7z8",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/3/5/3/dataset_353764c1-1cfe-4c8f-b099-a53fde25eac3.dat' && cp '/galaxy/server/database/objects/e/c/2/dataset_ec2745fc-152f-480d-a157-d3a71a001fdd.dat' ./mate1.fastq.gz && gunzip ./mate1.fastq.gz && cp '/galaxy/server/database/objects/4/a/c/dataset_4acd8139-316f-405a-b521-1504259236e3.dat' ./mate2.fastq.gz && gunzip ./mate2.fastq.gz && ln -s '/galaxy/server/database/objects/3/8/f/dataset_38f8f740-d542-43e8-9a12-fab69aa5a6c6.dat' ./alevinmap.tsv && salmon alevin -l A -i ./index -1 ./mate1.fastq -2 ./mate2.fastq -o ./output -p \"${GALAXY_SLOTS:-4}\" --chromium --tgMap ./alevinmap.tsv --keepCBFraction '1.0' --dumpFeatures --dumpMtx --freqThreshold '5' && gunzip output/alevin/quants_mat.mtx.gz && gunzip output/alevin/quants_tier_mat.gz && gunzip output/aux_info/fld.gz && gunzip output/aux_info/observed_bias.gz && gunzip output/aux_info/observed_bias_3p.gz",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "optional": "{\"dumpBfh\": false, \"dumpFeatures\": true, \"dumpMtx\": true, \"dumpUmiGraph\": false, \"expectCells\": \"\", \"forceCells\": \"\", \"freqThreshold\": \"5\", \"keepCBFraction\": \"1.0\", \"lowRegionMinNumBarcodes\": \"\", \"maxNumBarcodes\": \"\", \"minScoreFraction\": \"\", \"mrna\": null, \"noDedup\": false, \"numCellBootstraps\": \"\", \"rrna\": null, \"whitelist\": null}",
+ "allout": "false",
+ "protocol": "\"--chromium\"",
+ "pairstraight": "{\"__current_case__\": 0, \"file1\": {\"values\": [{\"id\": 325, \"src\": \"hda\"}]}, \"file2\": {\"values\": [{\"id\": 326, \"src\": \"hda\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"readselect\": \"paired\"}",
+ "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 324, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}"
+ },
+ "inputs": {
+ "tgmap": {
+ "id": "c25c738b3ca009dd",
+ "src": "hda",
+ "uuid": "38f8f740-d542-43e8-9a12-fab69aa5a6c6"
+ },
+ "pairstraight|file2": {
+ "id": "7abcafbf17910b1a",
+ "src": "hda",
+ "uuid": "4acd8139-316f-405a-b521-1504259236e3"
+ },
+ "pairstraight|file1": {
+ "id": "2d152befef641600",
+ "src": "hda",
+ "uuid": "ec2745fc-152f-480d-a157-d3a71a001fdd"
+ },
+ "refTranscriptSource|s_index|fasta": {
+ "id": "4e3c5faea0b03fb3",
+ "src": "hda",
+ "uuid": "353764c1-1cfe-4c8f-b099-a53fde25eac3"
+ }
+ },
+ "outputs": {
+ "flenDist_txt": {
+ "id": "30c4be037d80c86f",
+ "src": "hda",
+ "uuid": "3e7f3a0a-28be-4a4d-906d-fe3bf8ada75c"
+ },
+ "observed_bias_3p": {
+ "id": "0c6b8f360b3ddec5",
+ "src": "hda",
+ "uuid": "f74134bc-65b3-40c1-862c-fcf5ccf59c7a"
+ },
+ "observed_bias": {
+ "id": "5fcfe86f7ffa46b0",
+ "src": "hda",
+ "uuid": "43288e68-e362-454f-b443-b21d63452bb2"
+ },
+ "expected_bias": {
+ "id": "d6dfb20f580df4aa",
+ "src": "hda",
+ "uuid": "09d3f2a1-62c8-49a7-8e27-4e6c29b0d232"
+ },
+ "whitelist_txt": {
+ "id": "254446c4c22f43e3",
+ "src": "hda",
+ "uuid": "f2c40745-f91c-4bf8-9ac3-fee675d2e410"
+ },
+ "featureDump_txt": {
+ "id": "77d4106665353fec",
+ "src": "hda",
+ "uuid": "8dde9a0e-ca09-46d2-9aa1-2dbd272c551e"
+ },
+ "quants_tier_mat": {
+ "id": "9de2ed719293250f",
+ "src": "hda",
+ "uuid": "5741b4b2-c750-426e-823a-1c9208d908ff"
+ },
+ "quants_mat_rows_txt": {
+ "id": "b6117c47805ab753",
+ "src": "hda",
+ "uuid": "26c32f61-5b2e-4062-b0d3-0056ee6f62d7"
+ },
+ "quants_mat_cols_txt": {
+ "id": "dbaa233cd776bf88",
+ "src": "hda",
+ "uuid": "d2d7575d-1563-4bd3-8473-72bcfacd400b"
+ },
+ "raw_cb_frequency_txt": {
+ "id": "6ddf7485813f25a4",
+ "src": "hda",
+ "uuid": "2c2a735a-3341-4a59-9c4c-580e007309aa"
+ },
+ "quants_mat_mtx": {
+ "id": "37044600c9a534ea",
+ "src": "hda",
+ "uuid": "a600499f-c74d-4365-b3f4-22cfb83e0c7f"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 4194304\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:4194304\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 1005\nFalse junctions count = 1098\nHash table size = 2103\nCandidate marks count = 9186\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 6382\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 1005\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 1016896 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n",
+ "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:02.029] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:02.029] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:02.030] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:02.085] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:02.092] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.333 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 878.1 us\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:02.549] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:02.556] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:03.265] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\nLogs will be written to ./output/logs\n[2024-08-30 07:19:03.295] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:03.295] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:03.295] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:03.295] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:03.295] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:03.295] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:03.295] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:03.299] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:03.300] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:03.300] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:03.310] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:03.363] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:03.363] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:03.366] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:03.388] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:03.408] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:03.446] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:03.449] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:03.576] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:03.597] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:03.597] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.2347 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.089 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 8.44 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 806.25 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.6259 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2949 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.7425 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2667 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 18.15 us\n-----------------------------------------\n[2024-08-30 07:19:03.597] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:03.713] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:03.714] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:03.726] [jointLog] [info] done\n[2024-08-30 07:19:03.726] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:03.726] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:04.660] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:04.660] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:04.661] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:04.661] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:04.661] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:04.681] [alevinLog] [info] Starting optimizer\n\n\n[2024-08-30 07:19:04.827] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:04.827] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 46 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 520 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 740 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1392 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1878 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2455 cells (\u001b[31m48%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2757 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2849 cells (\u001b[31m56%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4019 cells (\u001b[31m79%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4158 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:04.861] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:04.864] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:04.864] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:04.893] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 4194304\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:4194304\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 1005\nFalse junctions count = 1098\nHash table size = 2103\nCandidate marks count = 9186\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 6382\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 1005\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 1016896 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n",
+ "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:02.029] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:02.029] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:02.030] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:02.085] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:02.092] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.333 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 878.1 us\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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0 min 0 sec\r[Building BooPHF] 97.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 97.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 97.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 97.9 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 97.9 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 98.1 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 98.1 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 98.4 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 98.4 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:02.549] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:02.556] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:03.265] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\nLogs will be written to ./output/logs\n[2024-08-30 07:19:03.295] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:03.295] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:03.295] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:03.295] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:03.295] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:03.295] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:03.295] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:03.299] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:03.300] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:03.300] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:03.310] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:03.363] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:03.363] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:03.366] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:03.388] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:03.408] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:03.446] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:03.449] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:03.576] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:03.597] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:03.597] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.2347 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.089 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 8.44 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 806.25 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.6259 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2949 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.7425 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2667 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 18.15 us\n-----------------------------------------\n[2024-08-30 07:19:03.597] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:03.713] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:03.714] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:03.726] [jointLog] [info] done\n[2024-08-30 07:19:03.726] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:03.726] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:04.660] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:04.660] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:04.661] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:04.661] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:04.661] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:04.681] [alevinLog] [info] Starting optimizer\n\n\n[2024-08-30 07:19:04.827] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:04.827] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 46 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 520 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 740 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1392 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1878 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2455 cells (\u001b[31m48%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2757 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2849 cells (\u001b[31m56%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4019 cells (\u001b[31m79%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4158 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:04.861] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:04.864] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:04.864] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:04.893] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8c1ced6614b907de.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8c1ced6614b907de.json
new file mode 100644
index 000000000..1c3c17505
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8c1ced6614b907de.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "8c1ced6614b907de",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:54:36.632378",
+ "update_time": "2024-08-30T06:54:47.026297",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-r7xgs",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/117/registry.xml' '/galaxy/server/database/jobs_directory/000/117/upload_params.json' '147:/galaxy/server/database/objects/0/9/c/dataset_09cb9ac0-ddd2-4901-b4b4-9b1a8b78a684_files:/galaxy/server/database/objects/0/9/c/dataset_09cb9ac0-ddd2-4901-b4b4-9b1a8b78a684.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_w8pm597v\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"phiX.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ksv0r6rj\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "67453b38f2e8d00e",
+ "src": "hda",
+ "uuid": "09cb9ac0-ddd2-4901-b4b4-9b1a8b78a684"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8e847d9dfbfeb264.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8e847d9dfbfeb264.json
new file mode 100644
index 000000000..712abf4ad
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8e847d9dfbfeb264.json
@@ -0,0 +1,132 @@
+{
+ "model_class": "Job",
+ "id": "8e847d9dfbfeb264",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:19:38.654355",
+ "update_time": "2024-08-30T07:19:47.984098",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-66klb",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/a/7/d/dataset_a7d7a68b-2d9d-43be-84b3-5e0a29daca52.dat' && cp '/galaxy/server/database/objects/b/3/d/dataset_b3d76027-3bf6-419c-8740-dfb8fd98d42e.dat' ./mate1.fastq.gz && gunzip ./mate1.fastq.gz && cp '/galaxy/server/database/objects/3/2/0/dataset_320c4220-2796-4964-9dd7-f66cb3de56d7.dat' ./mate2.fastq.gz && gunzip ./mate2.fastq.gz && ln -s '/galaxy/server/database/objects/b/7/9/dataset_b7990462-bf24-4758-a858-5ca1105d8a0f.dat' ./alevinmap.tsv && salmon alevin -l A -i ./index -1 ./mate1.fastq -2 ./mate2.fastq -o ./output -p \"${GALAXY_SLOTS:-4}\" --chromium --tgMap ./alevinmap.tsv --numCellBootstraps '2' --keepCBFraction '1.0' --dumpFeatures --dumpMtx --freqThreshold '5' && gunzip output/alevin/quants_mat.mtx.gz && gunzip output/alevin/quants_tier_mat.gz && gunzip output/alevin/quants_mean_mat.gz && gunzip output/alevin/quants_var_mat.gz && gunzip output/aux_info/fld.gz && gunzip output/aux_info/observed_bias.gz && gunzip output/aux_info/observed_bias_3p.gz",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "optional": "{\"dumpBfh\": false, \"dumpFeatures\": true, \"dumpMtx\": true, \"dumpUmiGraph\": false, \"expectCells\": \"\", \"forceCells\": \"\", \"freqThreshold\": \"5\", \"keepCBFraction\": \"1.0\", \"lowRegionMinNumBarcodes\": \"\", \"maxNumBarcodes\": \"\", \"minScoreFraction\": \"\", \"mrna\": null, \"noDedup\": false, \"numCellBootstraps\": \"2\", \"rrna\": null, \"whitelist\": null}",
+ "allout": "false",
+ "protocol": "\"--chromium\"",
+ "pairstraight": "{\"__current_case__\": 0, \"file1\": {\"values\": [{\"id\": 340, \"src\": \"hda\"}]}, \"file2\": {\"values\": [{\"id\": 341, \"src\": \"hda\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"readselect\": \"paired\"}",
+ "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 339, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}"
+ },
+ "inputs": {
+ "tgmap": {
+ "id": "3d7c835c180678a2",
+ "src": "hda",
+ "uuid": "b7990462-bf24-4758-a858-5ca1105d8a0f"
+ },
+ "pairstraight|file2": {
+ "id": "196609ee608737c3",
+ "src": "hda",
+ "uuid": "320c4220-2796-4964-9dd7-f66cb3de56d7"
+ },
+ "pairstraight|file1": {
+ "id": "7aa45690986c8ca7",
+ "src": "hda",
+ "uuid": "b3d76027-3bf6-419c-8740-dfb8fd98d42e"
+ },
+ "refTranscriptSource|s_index|fasta": {
+ "id": "0c12e840c4d79636",
+ "src": "hda",
+ "uuid": "a7d7a68b-2d9d-43be-84b3-5e0a29daca52"
+ }
+ },
+ "outputs": {
+ "quants_mat_mtx": {
+ "id": "104956edfbaff3c3",
+ "src": "hda",
+ "uuid": "a96a4be9-d72b-4502-97d0-037b5dd80899"
+ },
+ "whitelist_txt": {
+ "id": "f36a30d804e3b144",
+ "src": "hda",
+ "uuid": "2f45c52e-8282-4be4-98c7-3f0151abef4c"
+ },
+ "quants_mean_mat": {
+ "id": "9a7b950bd7b252ef",
+ "src": "hda",
+ "uuid": "f5356659-96a4-4427-9e0a-bc994351f10b"
+ },
+ "quants_var_mat": {
+ "id": "8b8962ff66dcf869",
+ "src": "hda",
+ "uuid": "4ea99ba7-6bf6-45b6-a664-9eb78d4db813"
+ },
+ "quants_boot_rows_txt": {
+ "id": "fe996e4549e22ea0",
+ "src": "hda",
+ "uuid": "ebb6f28b-d48d-4a11-8053-ee49d7eb97a6"
+ },
+ "expected_bias": {
+ "id": "97064a582cfc27ff",
+ "src": "hda",
+ "uuid": "f2c71495-5722-4d3d-b464-407c256a5de9"
+ },
+ "observed_bias": {
+ "id": "7037a4c267c5edd7",
+ "src": "hda",
+ "uuid": "20392db3-2bfb-4f6b-812a-c97c003e8376"
+ },
+ "observed_bias_3p": {
+ "id": "659977122a1a0a55",
+ "src": "hda",
+ "uuid": "cd02928e-dde5-4ba0-b043-7e461d3b589d"
+ },
+ "flenDist_txt": {
+ "id": "e6a4e8500837d9f4",
+ "src": "hda",
+ "uuid": "9d1c0182-b7ae-4430-9bb5-b0499f08109f"
+ },
+ "raw_cb_frequency_txt": {
+ "id": "809be3818664cddc",
+ "src": "hda",
+ "uuid": "3b9ca3a7-19b4-4cf5-83cc-65a7ea13564a"
+ },
+ "quants_mat_cols_txt": {
+ "id": "adcd02e067b1f957",
+ "src": "hda",
+ "uuid": "1a041a9e-df43-4524-b396-75bb48592e18"
+ },
+ "quants_mat_rows_txt": {
+ "id": "8e4662dca1bc59a1",
+ "src": "hda",
+ "uuid": "6c66a81a-c4fe-44c5-8433-ec829eadb69c"
+ },
+ "quants_tier_mat": {
+ "id": "4288384dd8475222",
+ "src": "hda",
+ "uuid": "eeb55ef8-e4d0-4bbd-9e7e-efad995cdbae"
+ },
+ "featureDump_txt": {
+ "id": "21b4b2693acea78a",
+ "src": "hda",
+ "uuid": "53de9e0c-b52f-4b8e-8e55-a3e8acc1a44f"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 4194304\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:4194304\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 1005\nFalse junctions count = 730\nHash table size = 1735\nCandidate marks count = 8052\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 6382\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 1005\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 1016896 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n",
+ "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:40.641] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:40.641] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:40.642] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:40.696] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:40.703] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:40.925] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:40.926] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.7824 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 1.37 ms\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:41.148] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:41.156] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###Logs will be written to ./output/logs\n[2024-08-30 07:19:41.893] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\n[2024-08-30 07:19:41.924] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:41.924] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:41.924] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:41.924] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:41.924] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:41.924] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:41.924] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ numCellBootstraps ] => { 2 }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:41.929] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:41.931] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:41.931] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:41.942] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:41.997] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:41.997] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:42.001] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:42.022] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:42.043] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:42.081] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:42.084] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:42.213] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:42.234] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:42.234] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.4834 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.2083 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 11.98 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 930.92 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.8072 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2416 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.3634 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2181 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 9.31 us\n-----------------------------------------\n[2024-08-30 07:19:42.234] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:42.351] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:42.352] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:42.365] [jointLog] [info] done\n[2024-08-30 07:19:42.366] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:42.366] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:43.302] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:43.302] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:43.302] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:43.303] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:43.303] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:43.314] [alevinLog] [info] Starting optimizer\n\n\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 86 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 140 cells (\u001b[31m3%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 331 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 491 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 673 cells (\u001b[31m13%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 799 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 886 cells (\u001b[31m17%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 944 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1042 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1153 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1205 cells (\u001b[31m24%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2044 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3181 cells (\u001b[31m62%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4134 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4362 cells (\u001b[31m85%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4790 cells (\u001b[31m94%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:43.460] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.460] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:43.522] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:43.525] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:43.526] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:43.553] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 4194304\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:4194304\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 1005\nFalse junctions count = 730\nHash table size = 1735\nCandidate marks count = 8052\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 6382\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 1005\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 1016896 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n",
+ "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:40.641] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:40.641] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:40.642] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:40.696] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:40.703] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:40.925] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:40.926] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.7824 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 1.37 ms\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:41.148] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:41.156] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###Logs will be written to ./output/logs\n[2024-08-30 07:19:41.893] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\n[2024-08-30 07:19:41.924] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:41.924] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:41.924] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:41.924] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:41.924] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:41.924] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:41.924] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ numCellBootstraps ] => { 2 }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:41.929] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:41.931] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:41.931] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:41.942] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:41.997] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:41.997] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:42.001] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:42.022] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:42.043] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:42.081] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:42.084] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:42.213] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:42.234] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:42.234] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.4834 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.2083 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 11.98 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 930.92 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.8072 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2416 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.3634 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2181 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 9.31 us\n-----------------------------------------\n[2024-08-30 07:19:42.234] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:42.351] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:42.352] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:42.365] [jointLog] [info] done\n[2024-08-30 07:19:42.366] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:42.366] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:43.302] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:43.302] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:43.302] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:43.303] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:43.303] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:43.314] [alevinLog] [info] Starting optimizer\n\n\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 86 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 140 cells (\u001b[31m3%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 331 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 491 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 673 cells (\u001b[31m13%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 799 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 886 cells (\u001b[31m17%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 944 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1042 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1153 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1205 cells (\u001b[31m24%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2044 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3181 cells (\u001b[31m62%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4134 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4362 cells (\u001b[31m85%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4790 cells (\u001b[31m94%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:43.460] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.460] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:43.522] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:43.525] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:43.526] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:43.553] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8f0e3ed7f9185b2e.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8f0e3ed7f9185b2e.json
new file mode 100644
index 000000000..e5b1aa070
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/8f0e3ed7f9185b2e.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "8f0e3ed7f9185b2e",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:35:48.157395",
+ "update_time": "2024-08-30T06:35:59.002767",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-v2wpm",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/48/registry.xml' '/galaxy/server/database/jobs_directory/000/48/upload_params.json' '54:/galaxy/server/database/objects/3/c/a/dataset_3caaa1dd-4dcc-45ff-b308-2c2e32713d9a_files:/galaxy/server/database/objects/3/c/a/dataset_3caaa1dd-4dcc-45ff-b308-2c2e32713d9a.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_w8xks62h\"",
+ "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"bwa-mem-fastq2.fq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ah14agck\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fastqsanger.gz\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "85ab19e9b0965386",
+ "src": "hda",
+ "uuid": "3caaa1dd-4dcc-45ff-b308-2c2e32713d9a"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/962284acfddf59f3.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/962284acfddf59f3.json
new file mode 100644
index 000000000..8de958e3e
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/962284acfddf59f3.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "962284acfddf59f3",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:32:47.743306",
+ "update_time": "2024-08-30T06:32:58.216119",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-twnt2",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/35/registry.xml' '/galaxy/server/database/jobs_directory/000/35/upload_params.json' '39:/galaxy/server/database/objects/e/0/0/dataset_e006d6d2-047a-4741-9389-afa40e9ae5b9_files:/galaxy/server/database/objects/e/0/0/dataset_e006d6d2-047a-4741-9389-afa40e9ae5b9.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_w4b3e3c9\"",
+ "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"sanger_full_range_original_sanger.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_xdy96vrb\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fastqsanger.gz\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "146acc7fcb1e613d",
+ "src": "hda",
+ "uuid": "e006d6d2-047a-4741-9389-afa40e9ae5b9"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/9ab7433e8dc2dd11.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/9ab7433e8dc2dd11.json
new file mode 100644
index 000000000..7c939768f
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/9ab7433e8dc2dd11.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "9ab7433e8dc2dd11",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T08:15:08.472499",
+ "update_time": "2024-08-30T08:15:19.867384",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-bqksn",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/453/registry.xml' '/galaxy/server/database/jobs_directory/000/453/upload_params.json' '600:/galaxy/server/database/objects/b/4/8/dataset_b48f9b60-1f81-4a90-ac4e-4ae53a3b6854_files:/galaxy/server/database/objects/b/4/8/dataset_b48f9b60-1f81-4a90-ac4e-4ae53a3b6854.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_n_l9sfao\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"pBR322.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_l0576uvs\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "0ec21021f2f0a75c",
+ "src": "hda",
+ "uuid": "b48f9b60-1f81-4a90-ac4e-4ae53a3b6854"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/9cd2ea9e0fa020ae.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/9cd2ea9e0fa020ae.json
new file mode 100644
index 000000000..d79592a3e
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/9cd2ea9e0fa020ae.json
@@ -0,0 +1,56 @@
+{
+ "model_class": "Job",
+ "id": "9cd2ea9e0fa020ae",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:05:53.505379",
+ "update_time": "2024-08-30T07:05:59.658893",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-fm7pt",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/5/2/d/dataset_52d2be35-52cf-4590-a306-85aba8da3c7b.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/7/b/4/dataset_7b47d477-51c8-4336-8843-1baefab9f8c3.dat' > input_f.fastq && seqtk seq -2 '/galaxy/server/database/objects/7/b/4/dataset_7b47d477-51c8-4336-8843-1baefab9f8c3.dat' > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/d/5/4/dataset_d54d3050-5220-4f35-9a58-b3a92d1aa263.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}",
+ "sum": "{\"new_summary\": false, \"summary_file\": false}",
+ "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 223, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}",
+ "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 222, \"src\": \"hda\"}]}, \"source\": \"history\"}"
+ },
+ "inputs": {
+ "library|input_1": {
+ "id": "8956761243b33003",
+ "src": "hda",
+ "uuid": "7b47d477-51c8-4336-8843-1baefab9f8c3"
+ },
+ "reference_genome|history_item": {
+ "id": "99f189e7e8c10e7f",
+ "src": "hda",
+ "uuid": "52d2be35-52cf-4590-a306-85aba8da3c7b"
+ }
+ },
+ "outputs": {
+ "output_alignments": {
+ "id": "3cb1bb014a0d8afa",
+ "src": "hda",
+ "uuid": "d54d3050-5220-4f35-9a58-b3a92d1aa263"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 20%\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n bucket 2: 10%\n Calculating Z arrays for bucket 4\n bucket 1: 30%\n Entering block accumulator loop for bucket 3:\n bucket 1: 40%\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 1: 50%\n bucket 3: 10%\n bucket 2: 20%\n bucket 1: 60%\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 5\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 3: 20%\n bucket 1: 70%\n bucket 2: 30%\nGetting block 7 of 60\n Calculating Z arrays for bucket 6\n bucket 5: 10%\n bucket 1: 80%\n bucket 3: 30%\n bucket 2: 40%\n bucket 1: 90%\n bucket 4: 10%\n bucket 2: 50%\nGetting block 8 of 60\n bucket 4: 20%\n bucket 5: 20%\n Reserving size (126) for bucket 8\n bucket 1: 100%\n bucket 4: 30%\n Reserving size (126) for bucket 7\n bucket 2: 60%\n bucket 4: 40%\n bucket 5: 30%\n Calculating Z arrays for bucket 7\n bucket 2: 70%\n bucket 3: 40%\n Calculating Z arrays for bucket 8\n bucket 4: 50%\n bucket 2: 80%\n bucket 5: 40%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Entering block accumulator loop for bucket 7:\n bucket 2: 90%\n bucket 5: 50%\n bucket 3: 50%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 8:\n bucket 2: 100%\n bucket 7: 10%\n bucket 4: 60%\n bucket 5: 60%\n bucket 3: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 7: 20%\n bucket 6: 10%\n bucket 8: 10%\n bucket 5: 70%\n bucket 3: 70%\n bucket 4: 70%\n bucket 6: 20%\n bucket 7: 30%\n bucket 8: 20%\n bucket 5: 80%\n bucket 4: 80%\n bucket 6: 30%\n bucket 7: 40%\n bucket 4: 90%\n bucket 8: 30%\n bucket 3: 80%\n bucket 6: 40%\n bucket 7: 50%\n bucket 4: 100%\n bucket 5: 90%\n bucket 8: 40%\n bucket 3: 90%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 7: 60%\n bucket 8: 50%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 3: 100%\n bucket 6: 50%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 7: 70%\n bucket 6: 60%\n bucket 8: 60%\n bucket 7: 80%\n bucket 6: 70%\n bucket 8: 70%\n bucket 7: 90%\n Sorting block time: 00:00:00\n bucket 6: 80%\n bucket 7: 100%\n bucket 8: 80%\nReturning block of 43 for bucket 1\n Sorting block of length 75 for bucket 7\n bucket 8: 90%\n bucket 6: 90%\n bucket 8: 100%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\nGetting block 11 of 60\n bucket 9: 60%\n bucket 10: 40%\n Reserving size (126) for bucket 11\n bucket 10: 50%\n Calculating Z arrays for bucket 11\n bucket 9: 70%\n bucket 10: 60%\n bucket 9: 80%\n bucket 10: 70%\n Entering block accumulator loop for bucket 11:\n bucket 9: 90%\n bucket 10: 80%\n bucket 11: 10%\n bucket 9: 100%\n bucket 10: 90%\n Sorting block of length 124 for bucket 9\n bucket 11: 20%\n (Using difference cover)\n bucket 10: 100%\n bucket 11: 30%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n bucket 12: 20%\n Entering block accumulator loop for bucket 13:\n bucket 12: 30%\n bucket 13: 10%\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 40%\n bucket 12: 70%\n bucket 13: 50%\n Entering block accumulator loop for bucket 14:\n bucket 12: 80%\n bucket 13: 60%\n bucket 14: 10%\n bucket 12: 90%\n bucket 13: 70%\n bucket 14: 20%\n bucket 12: 100%\n bucket 13: 80%\n bucket 14: 30%\n Sorting block of length 82 for bucket 12\n bucket 13: 90%\n (Using difference cover)\n bucket 14: 40%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 30%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n bucket 15: 40%\n bucket 16: 10%\n Entering block accumulator loop for bucket 17:\n bucket 15: 50%\n bucket 16: 20%\n bucket 17: 10%\n bucket 15: 60%\n bucket 16: 30%\n bucket 17: 20%\n bucket 16: 40%\n bucket 17: 30%\n bucket 15: 70%\n bucket 16: 50%\n bucket 17: 40%\n bucket 16: 60%\n bucket 15: 80%\n bucket 17: 50%\n bucket 16: 70%\n bucket 15: 90%\n bucket 17: 60%\n bucket 16: 80%\n bucket 15: 100%\n bucket 17: 70%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 90%\n bucket 17: 80%\n bucket 16: 100%\n bucket 17: 90%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 20%\n Entering block accumulator loop for bucket 19:\n bucket 18: 30%\n bucket 19: 10%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 19: 50%\n bucket 19: 60%\n bucket 18: 80%\n bucket 19: 70%\n bucket 18: 90%\n bucket 19: 80%\n bucket 18: 100%\n bucket 19: 90%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\nGetting block 22 of 60\n bucket 20: 10%\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n Entering block accumulator loop for bucket 22:\n bucket 20: 50%\n Entering block accumulator loop for bucket 21:\n bucket 22: 10%\n bucket 20: 60%\n bucket 21: 10%\n bucket 20: 70%\n bucket 22: 20%\n bucket 20: 80%\n bucket 21: 20%\n bucket 22: 30%\n bucket 20: 90%\n bucket 21: 30%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 22: 50%\n bucket 21: 60%\n bucket 22: 60%\n bucket 21: 70%\n bucket 22: 70%\n bucket 21: 80%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 24: 10%\n bucket 23: 30%\n bucket 24: 20%\n bucket 23: 40%\n bucket 24: 30%\n bucket 23: 50%\n bucket 24: 40%\n bucket 23: 60%\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 26\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 27:\n bucket 25: 10%\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 25: 20%\n bucket 26: 10%\n bucket 27: 20%\n bucket 25: 30%\n bucket 26: 20%\n bucket 27: 30%\n bucket 25: 40%\n bucket 27: 40%\n bucket 26: 30%\n bucket 25: 50%\n bucket 27: 50%\n bucket 26: 40%\n bucket 27: 60%\n bucket 25: 60%\n bucket 27: 70%\n bucket 26: 50%\n bucket 25: 70%\n bucket 27: 80%\n bucket 26: 60%\n bucket 25: 80%\n bucket 26: 70%\n bucket 27: 90%\n bucket 25: 90%\n bucket 26: 80%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\nGetting block 29 of 60\n bucket 28: 100%\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 30%\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 30: 40%\n bucket 30: 50%\n bucket 31: 10%\n bucket 30: 60%\n bucket 31: 20%\n bucket 30: 70%\n bucket 30: 80%\n bucket 31: 30%\n bucket 30: 90%\n bucket 31: 40%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n Entering block accumulator loop for bucket 33:\n bucket 32: 20%\n bucket 33: 10%\n bucket 32: 30%\n bucket 33: 20%\n bucket 32: 40%\n bucket 33: 30%\n bucket 32: 50%\n bucket 33: 40%\n bucket 32: 60%\n bucket 33: 50%\n bucket 32: 70%\n bucket 33: 60%\n bucket 32: 80%\n bucket 33: 70%\n bucket 32: 90%\n bucket 33: 80%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n bucket 35: 10%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 35: 30%\n bucket 34: 50%\n bucket 35: 40%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\nGetting block 36 of 60\n bucket 34: 90%\n bucket 35: 70%\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 34: 100%\n bucket 35: 80%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n Entering block accumulator loop for bucket 36:\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Entering block accumulator loop for bucket 38:\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n bucket 38: 20%\n Entering block accumulator loop for bucket 39:\n bucket 38: 30%\n bucket 39: 10%\n bucket 38: 40%\n bucket 39: 20%\n bucket 38: 50%\n bucket 39: 30%\n bucket 38: 60%\n bucket 39: 40%\n bucket 38: 70%\n bucket 38: 80%\n bucket 39: 50%\n bucket 38: 90%\n bucket 39: 60%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\n bucket 41: 20%\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 41: 50%\n bucket 40: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n bucket 41: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\nGetting block 43 of 60\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 60%\n bucket 42: 70%\n Entering block accumulator loop for bucket 44:\n bucket 42: 80%\n Entering block accumulator loop for bucket 43:\n bucket 42: 90%\n bucket 44: 10%\n bucket 42: 100%\n bucket 43: 10%\n Sorting block of length 119 for bucket 42\n bucket 44: 20%\n (Using difference cover)\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 44: 80%\n bucket 43: 90%\n bucket 44: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n Entering block accumulator loop for bucket 46:\n bucket 45: 20%\n bucket 45: 30%\n bucket 46: 10%\n bucket 45: 40%\n bucket 46: 20%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 46: 40%\n bucket 45: 70%\n bucket 46: 50%\n bucket 45: 80%\n bucket 46: 60%\n bucket 45: 90%\n bucket 46: 70%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n bucket 46: 80%\n bucket 46: 90%\n (Using difference cover)\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n Entering block accumulator loop for bucket 50:\n bucket 49: 50%\n bucket 49: 60%\n bucket 50: 10%\n bucket 49: 70%\n bucket 50: 20%\n bucket 49: 80%\n bucket 50: 30%\n bucket 49: 90%\n bucket 50: 40%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n bucket 51: 20%\n Entering block accumulator loop for bucket 52:\n bucket 51: 30%\n bucket 52: 10%\n bucket 51: 40%\n bucket 52: 20%\n bucket 52: 30%\n bucket 51: 50%\n bucket 52: 40%\n bucket 52: 50%\n bucket 51: 60%\n bucket 52: 60%\n bucket 51: 70%\n bucket 52: 70%\n bucket 51: 80%\n bucket 52: 80%\n bucket 52: 90%\n bucket 51: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n Entering block accumulator loop for bucket 54:\n bucket 53: 20%\n bucket 54: 10%\n bucket 53: 30%\n bucket 54: 20%\n bucket 53: 40%\n bucket 54: 30%\n bucket 53: 50%\n bucket 54: 40%\n bucket 53: 60%\n bucket 54: 50%\n bucket 53: 70%\n bucket 54: 60%\n bucket 54: 70%\n bucket 53: 80%\n bucket 54: 80%\n bucket 53: 90%\n bucket 54: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 56:\n bucket 55: 10%\n bucket 56: 10%\n bucket 55: 20%\n bucket 56: 20%\n bucket 55: 30%\n bucket 56: 30%\n bucket 55: 40%\n bucket 56: 40%\n bucket 55: 50%\n bucket 56: 50%\n bucket 55: 60%\n bucket 56: 60%\n bucket 55: 70%\n bucket 56: 70%\n bucket 55: 80%\n bucket 56: 80%\n bucket 55: 90%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n Entering block accumulator loop for bucket 58:\n bucket 57: 20%\n bucket 57: 30%\n bucket 58: 10%\n bucket 57: 40%\n bucket 57: 50%\n bucket 58: 20%\n bucket 57: 60%\n bucket 58: 30%\n bucket 57: 70%\n bucket 58: 40%\n bucket 57: 80%\n bucket 58: 50%\n bucket 57: 90%\n bucket 57: 100%\n bucket 58: 60%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 59: 20%\n bucket 60: 20%\n bucket 59: 30%\n bucket 60: 30%\n bucket 59: 40%\n bucket 60: 40%\n bucket 59: 50%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n bucket 59: 100%\n (Using difference cover)\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n",
+ "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 20%\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n bucket 2: 10%\n Calculating Z arrays for bucket 4\n bucket 1: 30%\n Entering block accumulator loop for bucket 3:\n bucket 1: 40%\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 1: 50%\n bucket 3: 10%\n bucket 2: 20%\n bucket 1: 60%\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 5\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 3: 20%\n bucket 1: 70%\n bucket 2: 30%\nGetting block 7 of 60\n Calculating Z arrays for bucket 6\n bucket 5: 10%\n bucket 1: 80%\n bucket 3: 30%\n bucket 2: 40%\n bucket 1: 90%\n bucket 4: 10%\n bucket 2: 50%\nGetting block 8 of 60\n bucket 4: 20%\n bucket 5: 20%\n Reserving size (126) for bucket 8\n bucket 1: 100%\n bucket 4: 30%\n Reserving size (126) for bucket 7\n bucket 2: 60%\n bucket 4: 40%\n bucket 5: 30%\n Calculating Z arrays for bucket 7\n bucket 2: 70%\n bucket 3: 40%\n Calculating Z arrays for bucket 8\n bucket 4: 50%\n bucket 2: 80%\n bucket 5: 40%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Entering block accumulator loop for bucket 7:\n bucket 2: 90%\n bucket 5: 50%\n bucket 3: 50%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 8:\n bucket 2: 100%\n bucket 7: 10%\n bucket 4: 60%\n bucket 5: 60%\n bucket 3: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 7: 20%\n bucket 6: 10%\n bucket 8: 10%\n bucket 5: 70%\n bucket 3: 70%\n bucket 4: 70%\n bucket 6: 20%\n bucket 7: 30%\n bucket 8: 20%\n bucket 5: 80%\n bucket 4: 80%\n bucket 6: 30%\n bucket 7: 40%\n bucket 4: 90%\n bucket 8: 30%\n bucket 3: 80%\n bucket 6: 40%\n bucket 7: 50%\n bucket 4: 100%\n bucket 5: 90%\n bucket 8: 40%\n bucket 3: 90%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 7: 60%\n bucket 8: 50%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 3: 100%\n bucket 6: 50%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 7: 70%\n bucket 6: 60%\n bucket 8: 60%\n bucket 7: 80%\n bucket 6: 70%\n bucket 8: 70%\n bucket 7: 90%\n Sorting block time: 00:00:00\n bucket 6: 80%\n bucket 7: 100%\n bucket 8: 80%\nReturning block of 43 for bucket 1\n Sorting block of length 75 for bucket 7\n bucket 8: 90%\n bucket 6: 90%\n bucket 8: 100%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\nGetting block 11 of 60\n bucket 9: 60%\n bucket 10: 40%\n Reserving size (126) for bucket 11\n bucket 10: 50%\n Calculating Z arrays for bucket 11\n bucket 9: 70%\n bucket 10: 60%\n bucket 9: 80%\n bucket 10: 70%\n Entering block accumulator loop for bucket 11:\n bucket 9: 90%\n bucket 10: 80%\n bucket 11: 10%\n bucket 9: 100%\n bucket 10: 90%\n Sorting block of length 124 for bucket 9\n bucket 11: 20%\n (Using difference cover)\n bucket 10: 100%\n bucket 11: 30%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n bucket 12: 20%\n Entering block accumulator loop for bucket 13:\n bucket 12: 30%\n bucket 13: 10%\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 40%\n bucket 12: 70%\n bucket 13: 50%\n Entering block accumulator loop for bucket 14:\n bucket 12: 80%\n bucket 13: 60%\n bucket 14: 10%\n bucket 12: 90%\n bucket 13: 70%\n bucket 14: 20%\n bucket 12: 100%\n bucket 13: 80%\n bucket 14: 30%\n Sorting block of length 82 for bucket 12\n bucket 13: 90%\n (Using difference cover)\n bucket 14: 40%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 30%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n bucket 15: 40%\n bucket 16: 10%\n Entering block accumulator loop for bucket 17:\n bucket 15: 50%\n bucket 16: 20%\n bucket 17: 10%\n bucket 15: 60%\n bucket 16: 30%\n bucket 17: 20%\n bucket 16: 40%\n bucket 17: 30%\n bucket 15: 70%\n bucket 16: 50%\n bucket 17: 40%\n bucket 16: 60%\n bucket 15: 80%\n bucket 17: 50%\n bucket 16: 70%\n bucket 15: 90%\n bucket 17: 60%\n bucket 16: 80%\n bucket 15: 100%\n bucket 17: 70%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 90%\n bucket 17: 80%\n bucket 16: 100%\n bucket 17: 90%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 20%\n Entering block accumulator loop for bucket 19:\n bucket 18: 30%\n bucket 19: 10%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 19: 50%\n bucket 19: 60%\n bucket 18: 80%\n bucket 19: 70%\n bucket 18: 90%\n bucket 19: 80%\n bucket 18: 100%\n bucket 19: 90%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\nGetting block 22 of 60\n bucket 20: 10%\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n Entering block accumulator loop for bucket 22:\n bucket 20: 50%\n Entering block accumulator loop for bucket 21:\n bucket 22: 10%\n bucket 20: 60%\n bucket 21: 10%\n bucket 20: 70%\n bucket 22: 20%\n bucket 20: 80%\n bucket 21: 20%\n bucket 22: 30%\n bucket 20: 90%\n bucket 21: 30%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 22: 50%\n bucket 21: 60%\n bucket 22: 60%\n bucket 21: 70%\n bucket 22: 70%\n bucket 21: 80%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 24: 10%\n bucket 23: 30%\n bucket 24: 20%\n bucket 23: 40%\n bucket 24: 30%\n bucket 23: 50%\n bucket 24: 40%\n bucket 23: 60%\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 26\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 27:\n bucket 25: 10%\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 25: 20%\n bucket 26: 10%\n bucket 27: 20%\n bucket 25: 30%\n bucket 26: 20%\n bucket 27: 30%\n bucket 25: 40%\n bucket 27: 40%\n bucket 26: 30%\n bucket 25: 50%\n bucket 27: 50%\n bucket 26: 40%\n bucket 27: 60%\n bucket 25: 60%\n bucket 27: 70%\n bucket 26: 50%\n bucket 25: 70%\n bucket 27: 80%\n bucket 26: 60%\n bucket 25: 80%\n bucket 26: 70%\n bucket 27: 90%\n bucket 25: 90%\n bucket 26: 80%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\nGetting block 29 of 60\n bucket 28: 100%\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 30%\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 30: 40%\n bucket 30: 50%\n bucket 31: 10%\n bucket 30: 60%\n bucket 31: 20%\n bucket 30: 70%\n bucket 30: 80%\n bucket 31: 30%\n bucket 30: 90%\n bucket 31: 40%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n Entering block accumulator loop for bucket 33:\n bucket 32: 20%\n bucket 33: 10%\n bucket 32: 30%\n bucket 33: 20%\n bucket 32: 40%\n bucket 33: 30%\n bucket 32: 50%\n bucket 33: 40%\n bucket 32: 60%\n bucket 33: 50%\n bucket 32: 70%\n bucket 33: 60%\n bucket 32: 80%\n bucket 33: 70%\n bucket 32: 90%\n bucket 33: 80%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n bucket 35: 10%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 35: 30%\n bucket 34: 50%\n bucket 35: 40%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\nGetting block 36 of 60\n bucket 34: 90%\n bucket 35: 70%\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 34: 100%\n bucket 35: 80%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n Entering block accumulator loop for bucket 36:\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Entering block accumulator loop for bucket 38:\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n bucket 38: 20%\n Entering block accumulator loop for bucket 39:\n bucket 38: 30%\n bucket 39: 10%\n bucket 38: 40%\n bucket 39: 20%\n bucket 38: 50%\n bucket 39: 30%\n bucket 38: 60%\n bucket 39: 40%\n bucket 38: 70%\n bucket 38: 80%\n bucket 39: 50%\n bucket 38: 90%\n bucket 39: 60%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\n bucket 41: 20%\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 41: 50%\n bucket 40: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n bucket 41: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\nGetting block 43 of 60\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 60%\n bucket 42: 70%\n Entering block accumulator loop for bucket 44:\n bucket 42: 80%\n Entering block accumulator loop for bucket 43:\n bucket 42: 90%\n bucket 44: 10%\n bucket 42: 100%\n bucket 43: 10%\n Sorting block of length 119 for bucket 42\n bucket 44: 20%\n (Using difference cover)\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 44: 80%\n bucket 43: 90%\n bucket 44: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n Entering block accumulator loop for bucket 46:\n bucket 45: 20%\n bucket 45: 30%\n bucket 46: 10%\n bucket 45: 40%\n bucket 46: 20%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 46: 40%\n bucket 45: 70%\n bucket 46: 50%\n bucket 45: 80%\n bucket 46: 60%\n bucket 45: 90%\n bucket 46: 70%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n bucket 46: 80%\n bucket 46: 90%\n (Using difference cover)\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n Entering block accumulator loop for bucket 50:\n bucket 49: 50%\n bucket 49: 60%\n bucket 50: 10%\n bucket 49: 70%\n bucket 50: 20%\n bucket 49: 80%\n bucket 50: 30%\n bucket 49: 90%\n bucket 50: 40%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n bucket 51: 20%\n Entering block accumulator loop for bucket 52:\n bucket 51: 30%\n bucket 52: 10%\n bucket 51: 40%\n bucket 52: 20%\n bucket 52: 30%\n bucket 51: 50%\n bucket 52: 40%\n bucket 52: 50%\n bucket 51: 60%\n bucket 52: 60%\n bucket 51: 70%\n bucket 52: 70%\n bucket 51: 80%\n bucket 52: 80%\n bucket 52: 90%\n bucket 51: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n Entering block accumulator loop for bucket 54:\n bucket 53: 20%\n bucket 54: 10%\n bucket 53: 30%\n bucket 54: 20%\n bucket 53: 40%\n bucket 54: 30%\n bucket 53: 50%\n bucket 54: 40%\n bucket 53: 60%\n bucket 54: 50%\n bucket 53: 70%\n bucket 54: 60%\n bucket 54: 70%\n bucket 53: 80%\n bucket 54: 80%\n bucket 53: 90%\n bucket 54: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 56:\n bucket 55: 10%\n bucket 56: 10%\n bucket 55: 20%\n bucket 56: 20%\n bucket 55: 30%\n bucket 56: 30%\n bucket 55: 40%\n bucket 56: 40%\n bucket 55: 50%\n bucket 56: 50%\n bucket 55: 60%\n bucket 56: 60%\n bucket 55: 70%\n bucket 56: 70%\n bucket 55: 80%\n bucket 56: 80%\n bucket 55: 90%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n Entering block accumulator loop for bucket 58:\n bucket 57: 20%\n bucket 57: 30%\n bucket 58: 10%\n bucket 57: 40%\n bucket 57: 50%\n bucket 58: 20%\n bucket 57: 60%\n bucket 58: 30%\n bucket 57: 70%\n bucket 58: 40%\n bucket 57: 80%\n bucket 58: 50%\n bucket 57: 90%\n bucket 57: 100%\n bucket 58: 60%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 59: 20%\n bucket 60: 20%\n bucket 59: 30%\n bucket 60: 30%\n bucket 59: 40%\n bucket 60: 40%\n bucket 59: 50%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n bucket 59: 100%\n (Using difference cover)\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n",
+ "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/9f23ed907fcd9227.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/9f23ed907fcd9227.json
new file mode 100644
index 000000000..3c72858d2
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/9f23ed907fcd9227.json
@@ -0,0 +1,68 @@
+{
+ "model_class": "Job",
+ "id": "9f23ed907fcd9227",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:14:29.561141",
+ "update_time": "2024-08-30T07:14:35.923452",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-6rj5z",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "cat '/galaxy/server/database/jobs_directory/000/234/configs/tmpg13_klky' && python '/galaxy/server/database/jobs_directory/000/234/configs/tmpg13_klky'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"h5ad\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"input\": {\"values\": [{\"id\": 270, \"src\": \"hda\"}]}, \"output_format\": \"tabular\"}"
+ },
+ "inputs": {
+ "hd5_format|input": {
+ "id": "7dac24e6043aac32",
+ "src": "hda",
+ "uuid": "5fd5ccaa-790f-4841-a49a-6ac2a4bb62ad"
+ }
+ },
+ "outputs": {
+ "tabular_varm": {
+ "id": "47fccb329a775a72",
+ "src": "hda",
+ "uuid": "5354394a-bd73-4491-b463-2b272f151ebb"
+ },
+ "tabular_var": {
+ "id": "aed4c4d4d47034ab",
+ "src": "hda",
+ "uuid": "7e1029fd-c4aa-4a10-8e33-b73c82cdbcf2"
+ },
+ "tabular_obsm": {
+ "id": "d055f39f4ce4ec90",
+ "src": "hda",
+ "uuid": "f828518b-277c-4120-b3cf-345878219ece"
+ },
+ "tabular_obs": {
+ "id": "1074ffdf1ba4644d",
+ "src": "hda",
+ "uuid": "20c1b0c2-3a92-42c3-9081-fdf29853039c"
+ },
+ "tabular_x": {
+ "id": "d7f111b001e819c5",
+ "src": "hda",
+ "uuid": "68ecf80c-373d-4552-a227-32affe9d7c4d"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read('/galaxy/server/database/objects/5/f/d/dataset_5fd5ccaa-790f-4841-a49a-6ac2a4bb62ad.dat')\nadata.write_csvs('.', sep=\"\\t\", skip_data = False)\n ",
+ "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nwriting .csv files to .\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read('/galaxy/server/database/objects/5/f/d/dataset_5fd5ccaa-790f-4841-a49a-6ac2a4bb62ad.dat')\nadata.write_csvs('.', sep=\"\\t\", skip_data = False)\n ",
+ "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nwriting .csv files to .\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/aeb32d475429697d.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/aeb32d475429697d.json
new file mode 100644
index 000000000..99dc3113d
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/aeb32d475429697d.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "aeb32d475429697d",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:07:44.324332",
+ "update_time": "2024-08-30T07:07:56.300347",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-9jw6l",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/198/registry.xml' '/galaxy/server/database/jobs_directory/000/198/upload_params.json' '235:/galaxy/server/database/objects/9/7/3/dataset_97350fe4-6f46-448f-b2c6-5df2fae44f27_files:/galaxy/server/database/objects/9/7/3/dataset_97350fe4-6f46-448f-b2c6-5df2fae44f27.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_74nbhiia\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"test_input_1_a.sam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_vrii5mku\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "d7a4e5f649573174",
+ "src": "hda",
+ "uuid": "97350fe4-6f46-448f-b2c6-5df2fae44f27"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b05101e16344c673.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b05101e16344c673.json
new file mode 100644
index 000000000..5bc0dc931
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b05101e16344c673.json
@@ -0,0 +1,54 @@
+{
+ "model_class": "Job",
+ "id": "b05101e16344c673",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T08:14:56.028466",
+ "update_time": "2024-08-30T08:15:07.093029",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-mxx4r",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "ln -s '/galaxy/server/database/objects/1/4/7/dataset_147b9d98-7c47-4639-9741-93de3e07aa31.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && lofreq viterbi --ref 'reference.fa' --defqual 2 --out tmp.bam '/galaxy/server/database/objects/c/2/4/dataset_c249f127-0c77-4e45-b325-b1943a1d8603.dat' && samtools sort --no-PG -T \"${TMPDIR:-.}\" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/galaxy/server/database/objects/f/a/e/dataset_fae0696e-1915-48ba-a79d-695a0d7647c8.dat' tmp.bam",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "adv_options": "{\"bq2_handling\": {\"__current_case__\": 0, \"defqual\": \"2\", \"replace_bq2\": \"keep\"}, \"keepflags\": false}",
+ "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 597, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"
+ },
+ "inputs": {
+ "reference_source|ref": {
+ "id": "4524c3857055ff8a",
+ "src": "hda",
+ "uuid": "147b9d98-7c47-4639-9741-93de3e07aa31"
+ },
+ "reads": {
+ "id": "e2df7eb2735479d5",
+ "src": "hda",
+ "uuid": "c249f127-0c77-4e45-b325-b1943a1d8603"
+ }
+ },
+ "outputs": {
+ "realigned": {
+ "id": "07fa4861902ecd27",
+ "src": "hda",
+ "uuid": "fae0696e-1915-48ba-a79d-695a0d7647c8"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b5720daccddf660f.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b5720daccddf660f.json
new file mode 100644
index 000000000..2d2344032
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b5720daccddf660f.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "b5720daccddf660f",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:26:23.455757",
+ "update_time": "2024-08-30T07:26:33.341247",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-hh5fx",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/283/registry.xml' '/galaxy/server/database/jobs_directory/000/283/upload_params.json' '388:/galaxy/server/database/objects/5/b/3/dataset_5b3273c0-7e21-4f8a-a4e1-e8f74de91919_files:/galaxy/server/database/objects/5/b/3/dataset_5b3273c0-7e21-4f8a-a4e1-e8f74de91919.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_hcqtu9yd\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"krumsiek11.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_nk1c0n39\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "4a8a75b94f6b4c18",
+ "src": "hda",
+ "uuid": "5b3273c0-7e21-4f8a-a4e1-e8f74de91919"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b5e7acd40b18fa7b.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b5e7acd40b18fa7b.json
new file mode 100644
index 000000000..3fa666d5a
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b5e7acd40b18fa7b.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "b5e7acd40b18fa7b",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:28:56.110609",
+ "update_time": "2024-08-30T06:29:06.499261",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-7nk5q",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/20/registry.xml' '/galaxy/server/database/jobs_directory/000/20/upload_params.json' '20:/galaxy/server/database/objects/6/f/e/dataset_6fe96657-f127-47ba-95ab-d8f1d4b99986_files:/galaxy/server/database/objects/6/f/e/dataset_6fe96657-f127-47ba-95ab-d8f1d4b99986.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_nl9h678j\"",
+ "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"in_3_headerless.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_0z63bq99\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"tabular\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "b5e7acd40b18fa7b",
+ "src": "hda",
+ "uuid": "6fe96657-f127-47ba-95ab-d8f1d4b99986"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b7c5dfe00a988157.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b7c5dfe00a988157.json
new file mode 100644
index 000000000..e8900044c
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/b7c5dfe00a988157.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "b7c5dfe00a988157",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:04:12.412928",
+ "update_time": "2024-08-30T07:04:23.345630",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-9j679",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/178/registry.xml' '/galaxy/server/database/jobs_directory/000/178/upload_params.json' '214:/galaxy/server/database/objects/2/4/7/dataset_247690e0-e2bf-4817-ab7a-249627892625_files:/galaxy/server/database/objects/2/4/7/dataset_247690e0-e2bf-4817-ab7a-249627892625.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_560vjd7s\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"phiX.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_8t8es73m\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "5faa833b35d38e4d",
+ "src": "hda",
+ "uuid": "247690e0-e2bf-4817-ab7a-249627892625"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ba59fb127ab9c9a0.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ba59fb127ab9c9a0.json
new file mode 100644
index 000000000..586c7ef03
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ba59fb127ab9c9a0.json
@@ -0,0 +1,50 @@
+{
+ "model_class": "Job",
+ "id": "ba59fb127ab9c9a0",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T08:06:49.842604",
+ "update_time": "2024-08-30T08:06:56.849711",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-8ckl9",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "cp '/galaxy/server/database/jobs_directory/000/418/configs/tmppwwam7w4' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"tabular\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "precision": "\"6\"",
+ "out_opts": "[\"ignore_nas\", \"output_headers_col\", \"output_headers_row\"]",
+ "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 564, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 5, \"elem_val\": {\"__current_case__\": 0, \"element_op\": \"None\"}, \"element\": {\"__current_case__\": 3, \"custom_expr\": \"elem < 10\", \"mode\": \"custom\"}, \"mode\": \"element\"}}"
+ },
+ "inputs": {
+ "singtabop|input": {
+ "id": "ec5cb66180e61371",
+ "src": "hda",
+ "uuid": "eef7e83a-3c0d-4338-822d-db83b205e465"
+ }
+ },
+ "outputs": {
+ "table": {
+ "id": "c0e50146fb12a33b",
+ "src": "hda",
+ "uuid": "a9b8eb66-a327-419a-b138-11e1561d0c52"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/bc3f7c1e67c329a8.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/bc3f7c1e67c329a8.json
new file mode 100644
index 000000000..6eb266741
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/bc3f7c1e67c329a8.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "bc3f7c1e67c329a8",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T08:00:17.200993",
+ "update_time": "2024-08-30T08:00:27.676201",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-7tncq",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/395/registry.xml' '/galaxy/server/database/jobs_directory/000/395/upload_params.json' '542:/galaxy/server/database/objects/e/3/b/dataset_e3b2c203-5acc-4204-b38a-5cee35919135_files:/galaxy/server/database/objects/e/3/b/dataset_e3b2c203-5acc-4204-b38a-5cee35919135.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_vqw1qxsh\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"mat1.umi.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_1pb4nc4x\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "70137aa08a68180b",
+ "src": "hda",
+ "uuid": "e3b2c203-5acc-4204-b38a-5cee35919135"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/bd78b872588b7227.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/bd78b872588b7227.json
new file mode 100644
index 000000000..8f2201bd1
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/bd78b872588b7227.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "bd78b872588b7227",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:52:23.689301",
+ "update_time": "2024-08-30T06:52:33.499207",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-dc62f",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/101/registry.xml' '/galaxy/server/database/jobs_directory/000/101/upload_params.json' '127:/galaxy/server/database/objects/8/5/c/dataset_85c234fe-90cb-42e6-95ee-d2653e2e35a1_files:/galaxy/server/database/objects/8/5/c/dataset_85c234fe-90cb-42e6-95ee-d2653e2e35a1.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_dw7olok3\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"phiX.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_pkn09i3t\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "f219fc94d8d8fc77",
+ "src": "hda",
+ "uuid": "85c234fe-90cb-42e6-95ee-d2653e2e35a1"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ce1cbbe8e1a86205.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ce1cbbe8e1a86205.json
new file mode 100644
index 000000000..4be10eede
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ce1cbbe8e1a86205.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "ce1cbbe8e1a86205",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T08:06:57.691762",
+ "update_time": "2024-08-30T08:07:08.024845",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-c75rl",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/419/registry.xml' '/galaxy/server/database/jobs_directory/000/419/upload_params.json' '566:/galaxy/server/database/objects/1/4/1/dataset_141fc887-2bc4-4e5c-b323-9029ea5b9d72_files:/galaxy/server/database/objects/1/4/1/dataset_141fc887-2bc4-4e5c-b323-9029ea5b9d72.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params__bc7h7il\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"examples.3p2.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_fn0uu2r_\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "56fdcdb629ace6fd",
+ "src": "hda",
+ "uuid": "141fc887-2bc4-4e5c-b323-9029ea5b9d72"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/d3a9677d1e16a3d5.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/d3a9677d1e16a3d5.json
new file mode 100644
index 000000000..98fc36657
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/d3a9677d1e16a3d5.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "d3a9677d1e16a3d5",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:56:51.758395",
+ "update_time": "2024-08-30T07:57:01.787896",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-l6b2g",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/382/registry.xml' '/galaxy/server/database/jobs_directory/000/382/upload_params.json' '529:/galaxy/server/database/objects/3/3/b/dataset_33bbf5dc-a63d-4c98-a582-a803bee7cefb_files:/galaxy/server/database/objects/3/3/b/dataset_33bbf5dc-a63d-4c98-a582-a803bee7cefb.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_r__v013a\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"small.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_zjg3i1kd\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "c1be5ce75d285981",
+ "src": "hda",
+ "uuid": "33bbf5dc-a63d-4c98-a582-a803bee7cefb"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/d4950de95ae89100.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/d4950de95ae89100.json
new file mode 100644
index 000000000..804d6391d
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/d4950de95ae89100.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "d4950de95ae89100",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:26:37.642035",
+ "update_time": "2024-08-30T06:26:49.134075",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-6wmpg",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/4/registry.xml' '/galaxy/server/database/jobs_directory/000/4/upload_params.json' '4:/galaxy/server/database/objects/6/4/6/dataset_646d7486-32a0-43e1-a2e7-b42d63168252_files:/galaxy/server/database/objects/6/4/6/dataset_646d7486-32a0-43e1-a2e7-b42d63168252.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_nmgrjeie\"",
+ "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"in_1_headerless.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_94_pvs73\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"tabular\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "d4950de95ae89100",
+ "src": "hda",
+ "uuid": "646d7486-32a0-43e1-a2e7-b42d63168252"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/dbb2a50ca8aeae6b.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/dbb2a50ca8aeae6b.json
new file mode 100644
index 000000000..189f2d8a5
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/dbb2a50ca8aeae6b.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "dbb2a50ca8aeae6b",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:24:59.421405",
+ "update_time": "2024-08-30T07:25:11.287673",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-wwklx",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/278/registry.xml' '/galaxy/server/database/jobs_directory/000/278/upload_params.json' '381:/galaxy/server/database/objects/b/b/2/dataset_bb280ab0-9c5c-4f4e-aa55-965b38412002_files:/galaxy/server/database/objects/b/b/2/dataset_bb280ab0-9c5c-4f4e-aa55-965b38412002.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_jpt_6750\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"pp.filter_genes_dispersion.krumsiek11-seurat.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_t31olua4\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "91460c972fdbcae8",
+ "src": "hda",
+ "uuid": "bb280ab0-9c5c-4f4e-aa55-965b38412002"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/e346a3559628fca7.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/e346a3559628fca7.json
new file mode 100644
index 000000000..0c2c3b75d
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/e346a3559628fca7.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "e346a3559628fca7",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:36:44.814710",
+ "update_time": "2024-08-30T06:36:55.763468",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-zvjsg",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/53/registry.xml' '/galaxy/server/database/jobs_directory/000/53/upload_params.json' '63:/galaxy/server/database/objects/e/a/e/dataset_eaefe1ce-fb37-4c71-857e-0bc2f82b44e2_files:/galaxy/server/database/objects/e/a/e/dataset_eaefe1ce-fb37-4c71-857e-0bc2f82b44e2.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_m61vgt75\"",
+ "files_metadata": "{\"__current_case__\": 82, \"file_type\": \"fastqsanger.gz\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"bwa-mem-fastq2.fq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_7wyi198b\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fastqsanger.gz\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "377e92f1cc29a047",
+ "src": "hda",
+ "uuid": "eaefe1ce-fb37-4c71-857e-0bc2f82b44e2"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/e8f7dfe617d3d30f.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/e8f7dfe617d3d30f.json
new file mode 100644
index 000000000..444010255
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/e8f7dfe617d3d30f.json
@@ -0,0 +1,67 @@
+{
+ "model_class": "Job",
+ "id": "e8f7dfe617d3d30f",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:30:20.105845",
+ "update_time": "2024-08-30T06:30:26.135287",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-2nvgn",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "sh '/galaxy/server/database/jobs_directory/000/28/configs/tmp0t0fdsl_'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"tabular\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "include_outputs": null,
+ "fill_char": "\".\"",
+ "old_col_in_header": "false",
+ "has_header": "\"0\"",
+ "identifier_column": "\"1\""
+ },
+ "inputs": {
+ "input_tabular3": {
+ "id": "39deb344202734c1",
+ "src": "hda",
+ "uuid": "4da0d27b-dee3-46af-b0ea-45b09f4f4036"
+ },
+ "input_tabular2": {
+ "id": "bc8f6ddfdaa2e232",
+ "src": "hda",
+ "uuid": "91b258a3-8740-4a1a-8671-fe2760398161"
+ },
+ "input_tabular1": {
+ "id": "00a2fd257179f2fd",
+ "src": "hda",
+ "uuid": "c8e5f52f-1e6e-4ecc-ada9-1187773a8dbd"
+ },
+ "input_tabular": {
+ "id": "00a2fd257179f2fd",
+ "src": "hda",
+ "uuid": "c8e5f52f-1e6e-4ecc-ada9-1187773a8dbd"
+ }
+ },
+ "outputs": {
+ "tabular_output": {
+ "id": "e8f7dfe617d3d30f",
+ "src": "hda",
+ "uuid": "c60d6d58-40d9-41d2-8f2e-73769113349b"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/e9af9b83d77bdec3.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/e9af9b83d77bdec3.json
new file mode 100644
index 000000000..d44221857
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/e9af9b83d77bdec3.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "e9af9b83d77bdec3",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:53:09.401499",
+ "update_time": "2024-08-30T07:53:20.980055",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-jwt8p",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/369/registry.xml' '/galaxy/server/database/jobs_directory/000/369/upload_params.json' '516:/galaxy/server/database/objects/e/6/5/dataset_e65b56c5-d549-4e10-a074-18dbd3ced117_files:/galaxy/server/database/objects/e/6/5/dataset_e65b56c5-d549-4e10-a074-18dbd3ced117.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_ktqwn_fs\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"tl.rank_genes_groups.krumsiek11.h5ad\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_jfqo955q\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "6a145a33bdfb6674",
+ "src": "hda",
+ "uuid": "e65b56c5-d549-4e10-a074-18dbd3ced117"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/edd26a7a13f06c11.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/edd26a7a13f06c11.json
new file mode 100644
index 000000000..2b4c43e23
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/edd26a7a13f06c11.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "edd26a7a13f06c11",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:26:50.109091",
+ "update_time": "2024-08-30T06:27:01.144104",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-m5d4d",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/8/registry.xml' '/galaxy/server/database/jobs_directory/000/8/upload_params.json' '8:/galaxy/server/database/objects/f/0/d/dataset_f0d2d2fd-82b3-4fc8-b86a-ea9836604946_files:/galaxy/server/database/objects/f/0/d/dataset_f0d2d2fd-82b3-4fc8-b86a-ea9836604946.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_svatdgbb\"",
+ "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"in_2.tabular\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_xz_v65ak\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"tabular\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "edd26a7a13f06c11",
+ "src": "hda",
+ "uuid": "f0d2d2fd-82b3-4fc8-b86a-ea9836604946"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/edfb9d0cfea2ba20.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/edfb9d0cfea2ba20.json
new file mode 100644
index 000000000..c84c0a75e
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/edfb9d0cfea2ba20.json
@@ -0,0 +1,61 @@
+{
+ "model_class": "Job",
+ "id": "edfb9d0cfea2ba20",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:51:14.463932",
+ "update_time": "2024-08-30T06:51:28.344770",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-d4fv8",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/e/6/c/dataset_e6c6903b-b451-422e-ad48-3ddd5467e448.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/8/7/f/dataset_87f76930-c2d2-47eb-bd5b-cc95f566edb4.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/1/7/6/dataset_1769e135-20e6-4d81-884c-f5ed7b68bedf.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/d/1/9/dataset_d192bf07-81d7-403a-bcdd-7d131622b82a.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}",
+ "sum": "{\"new_summary\": false, \"summary_file\": false}",
+ "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 121, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 122, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}",
+ "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 120, \"src\": \"hda\"}]}, \"source\": \"history\"}"
+ },
+ "inputs": {
+ "library|input_2": {
+ "id": "96ac5aa6b750add6",
+ "src": "hda",
+ "uuid": "1769e135-20e6-4d81-884c-f5ed7b68bedf"
+ },
+ "library|input_1": {
+ "id": "375e718d538c5a3b",
+ "src": "hda",
+ "uuid": "87f76930-c2d2-47eb-bd5b-cc95f566edb4"
+ },
+ "reference_genome|history_item": {
+ "id": "fe260f14d51542d3",
+ "src": "hda",
+ "uuid": "e6c6903b-b451-422e-ad48-3ddd5467e448"
+ }
+ },
+ "outputs": {
+ "output_alignments": {
+ "id": "ffde76bc567fd181",
+ "src": "hda",
+ "uuid": "d192bf07-81d7-403a-bcdd-7d131622b82a"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n bucket 1: 20%\nGetting block 3 of 60\n bucket 1: 30%\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\nGetting block 4 of 60\n Calculating Z arrays for bucket 3\n bucket 1: 40%\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n bucket 1: 50%\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 4\n bucket 1: 60%\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 3:\n bucket 1: 70%\nGetting block 6 of 60\n bucket 2: 10%\n Entering block accumulator loop for bucket 5:\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 3: 10%\n Reserving size (126) for bucket 6\n bucket 1: 80%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 1: 90%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 7\n bucket 2: 20%\n Entering block accumulator loop for bucket 4:\n bucket 3: 20%\n bucket 2: 30%\n Entering block accumulator loop for bucket 7:\n Entering block accumulator loop for bucket 6:\n bucket 4: 10%\n bucket 1: 100%\n Calculating Z arrays for bucket 8\n bucket 7: 10%\n Sorting block of length 42 for bucket 1\n bucket 4: 20%\n bucket 6: 10%\n bucket 7: 20%\n bucket 2: 40%\n bucket 4: 30%\n bucket 6: 20%\n bucket 2: 50%\n Entering block accumulator loop for bucket 8:\n (Using difference cover)\n bucket 6: 30%\n bucket 2: 60%\n bucket 7: 30%\n bucket 4: 40%\n bucket 3: 30%\n bucket 7: 40%\n bucket 6: 40%\n bucket 5: 10%\n bucket 2: 70%\n bucket 8: 10%\n bucket 3: 40%\n bucket 6: 50%\n bucket 5: 20%\n bucket 2: 80%\n bucket 4: 50%\n bucket 3: 50%\n bucket 6: 60%\n bucket 2: 90%\n bucket 8: 20%\n bucket 5: 30%\n bucket 2: 100%\n bucket 3: 60%\n bucket 8: 30%\n bucket 6: 70%\n bucket 7: 50%\n bucket 5: 40%\n bucket 4: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 8: 40%\n Sorting block time: 00:00:00\n bucket 5: 50%\n bucket 3: 70%\n bucket 6: 80%\n bucket 4: 70%\n bucket 7: 60%\n bucket 5: 60%\n bucket 8: 50%\n bucket 4: 80%\n bucket 7: 70%\n bucket 6: 90%\n bucket 5: 70%\n bucket 4: 90%\n bucket 8: 60%\nReturning block of 43 for bucket 1\n bucket 7: 80%\n bucket 8: 70%\n bucket 3: 80%\n bucket 6: 100%\n bucket 4: 100%\n bucket 7: 90%\n bucket 8: 80%\n bucket 5: 80%\n bucket 3: 90%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 3: 100%\n bucket 5: 90%\n bucket 8: 90%\n bucket 5: 100%\n Sorting block of length 106 for bucket 3\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\n Sorting block of length 68 for bucket 4\n bucket 8: 100%\nReturning block of 85 for bucket 2\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 9: 50%\n bucket 10: 50%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 60%\n bucket 9: 60%\n bucket 10: 70%\n bucket 9: 70%\n Entering block accumulator loop for bucket 11:\n bucket 9: 80%\n bucket 10: 80%\n bucket 11: 10%\n bucket 9: 90%\n bucket 10: 90%\n bucket 11: 20%\n bucket 9: 100%\n bucket 10: 100%\n bucket 11: 30%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block of length 124 for bucket 9\n bucket 11: 40%\n bucket 11: 50%\n (Using difference cover)\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 12 of 60\n Reserving size (126) for bucket 12\nGetting block 14 of 60\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Entering block accumulator loop for bucket 12:\n Calculating Z arrays for bucket 13\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 12: 10%\n Entering block accumulator loop for bucket 13:\n bucket 12: 20%\n bucket 13: 10%\n bucket 12: 30%\n Entering block accumulator loop for bucket 14:\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 12: 60%\n bucket 13: 50%\n bucket 14: 20%\n bucket 13: 60%\n bucket 12: 70%\n bucket 14: 30%\n bucket 13: 70%\n bucket 12: 80%\n bucket 14: 40%\n bucket 13: 80%\n bucket 12: 90%\n bucket 13: 90%\n bucket 14: 50%\n bucket 12: 100%\n bucket 13: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 14: 60%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Entering block accumulator loop for bucket 15:\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 15: 10%\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 20%\n bucket 15: 30%\n Entering block accumulator loop for bucket 17:\n bucket 15: 40%\n bucket 17: 10%\n bucket 15: 50%\n Entering block accumulator loop for bucket 16:\n bucket 17: 20%\n bucket 15: 60%\n bucket 16: 10%\n bucket 15: 70%\n bucket 17: 30%\n bucket 16: 20%\n bucket 15: 80%\n bucket 17: 40%\n bucket 16: 30%\n bucket 15: 90%\n bucket 17: 50%\n bucket 16: 40%\n bucket 15: 100%\n bucket 17: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 50%\n bucket 17: 70%\n bucket 16: 60%\n bucket 17: 80%\n bucket 16: 70%\n bucket 17: 90%\n bucket 16: 80%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n bucket 19: 70%\n bucket 20: 50%\n bucket 19: 80%\n bucket 20: 60%\n bucket 19: 90%\n bucket 20: 70%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 22:\n bucket 21: 10%\n bucket 22: 10%\n bucket 21: 20%\n bucket 22: 20%\n bucket 21: 30%\n bucket 22: 30%\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 22: 50%\n bucket 21: 60%\n bucket 22: 60%\n bucket 21: 70%\n bucket 22: 70%\n bucket 21: 80%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n bucket 22: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\nGetting block 24 of 60\n bucket 23: 20%\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 23: 30%\n Entering block accumulator loop for bucket 24:\n bucket 23: 40%\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 23: 50%\n bucket 24: 20%\n bucket 25: 10%\n bucket 23: 60%\n bucket 24: 30%\n bucket 23: 70%\n bucket 24: 40%\n bucket 25: 20%\n bucket 23: 80%\n bucket 24: 50%\n bucket 23: 90%\n bucket 24: 60%\n bucket 25: 30%\n bucket 23: 100%\n bucket 24: 70%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 25: 40%\n bucket 24: 80%\n bucket 25: 50%\n bucket 24: 90%\n bucket 25: 60%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 26: 10%\n bucket 27: 20%\n bucket 26: 20%\n bucket 27: 30%\n bucket 26: 30%\n bucket 27: 40%\n bucket 26: 40%\n bucket 27: 50%\n bucket 26: 50%\n bucket 27: 60%\n bucket 26: 60%\n bucket 27: 70%\n bucket 26: 70%\n bucket 27: 80%\n bucket 26: 80%\n bucket 27: 90%\n bucket 26: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 30:\n bucket 29: 10%\n bucket 30: 10%\n bucket 29: 20%\n bucket 30: 20%\n bucket 30: 30%\n bucket 29: 30%\n bucket 30: 40%\n bucket 29: 40%\n bucket 30: 50%\n bucket 29: 50%\n bucket 30: 60%\n bucket 29: 60%\n bucket 30: 70%\n bucket 29: 70%\n bucket 30: 80%\n bucket 29: 80%\n bucket 30: 90%\n bucket 29: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 10%\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 30%\n bucket 33: 10%\n bucket 32: 40%\n bucket 33: 20%\n bucket 32: 50%\n bucket 33: 30%\n bucket 32: 60%\n bucket 33: 40%\n bucket 32: 70%\n bucket 33: 50%\n bucket 32: 80%\n bucket 33: 60%\n bucket 32: 90%\n bucket 33: 70%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 60%\n bucket 34: 70%\n Entering block accumulator loop for bucket 35:\n bucket 34: 80%\n bucket 35: 10%\n bucket 34: 90%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 20%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 30%\n Entering block accumulator loop for bucket 36:\n bucket 35: 40%\n bucket 36: 10%\n bucket 35: 50%\n bucket 36: 20%\n bucket 35: 60%\n bucket 36: 30%\n bucket 35: 70%\n bucket 36: 40%\n bucket 35: 80%\n bucket 36: 50%\n bucket 35: 90%\n bucket 36: 60%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 70%\n bucket 36: 80%\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n Entering block accumulator loop for bucket 38:\n bucket 37: 20%\n bucket 38: 10%\n bucket 37: 30%\n bucket 38: 20%\n bucket 37: 40%\n bucket 38: 30%\n bucket 37: 50%\n bucket 38: 40%\n bucket 37: 60%\n bucket 38: 50%\n bucket 37: 70%\n bucket 38: 60%\n bucket 37: 80%\n bucket 38: 70%\n bucket 37: 90%\n bucket 38: 80%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 39: 30%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n bucket 39: 40%\n bucket 39: 50%\n Entering block accumulator loop for bucket 40:\n bucket 39: 60%\n bucket 40: 10%\n bucket 39: 70%\n bucket 40: 20%\n bucket 39: 80%\n bucket 40: 30%\n bucket 39: 90%\n bucket 40: 40%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\nGetting block 41 of 60\n bucket 40: 90%\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n Sorting block time: 00:00:00\n bucket 41: 20%\nReturning block of 126 for bucket 39\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 80%\n bucket 42: 90%\n Entering block accumulator loop for bucket 43:\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 50%\n Entering block accumulator loop for bucket 45:\n bucket 44: 60%\n bucket 45: 10%\n bucket 44: 70%\n bucket 45: 20%\n bucket 44: 80%\n bucket 45: 30%\n bucket 44: 90%\n bucket 44: 100%\n bucket 45: 40%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Entering block accumulator loop for bucket 47:\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n Entering block accumulator loop for bucket 48:\n bucket 47: 20%\n bucket 48: 10%\n bucket 47: 30%\n bucket 48: 20%\n bucket 47: 40%\n bucket 48: 30%\n bucket 47: 50%\n bucket 48: 40%\n bucket 47: 60%\n bucket 48: 50%\n bucket 47: 70%\n bucket 48: 60%\n bucket 47: 80%\n bucket 48: 70%\nGetting block 49 of 60\n bucket 48: 80%\n bucket 47: 90%\n Reserving size (126) for bucket 49\n bucket 48: 90%\n Calculating Z arrays for bucket 49\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n bucket 50: 30%\n Calculating Z arrays for bucket 51\n bucket 50: 40%\n Entering block accumulator loop for bucket 51:\n bucket 50: 50%\n bucket 51: 10%\n bucket 50: 60%\n bucket 51: 20%\n bucket 50: 70%\n bucket 51: 30%\n bucket 50: 80%\n bucket 51: 40%\n bucket 50: 90%\n bucket 51: 50%\n bucket 50: 100%\n bucket 51: 60%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\nGetting block 53 of 60\n bucket 52: 10%\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 20%\n bucket 52: 30%\n Entering block accumulator loop for bucket 53:\n bucket 52: 40%\n bucket 52: 50%\n bucket 53: 10%\n bucket 52: 60%\n bucket 53: 20%\n bucket 52: 70%\n bucket 53: 30%\n bucket 52: 80%\n bucket 53: 40%\n bucket 53: 50%\n bucket 52: 90%\n bucket 53: 60%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\nGetting block 56 of 60\n bucket 55: 30%\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 55: 40%\n Entering block accumulator loop for bucket 56:\n bucket 55: 50%\n Entering block accumulator loop for bucket 57:\n bucket 56: 10%\n bucket 55: 60%\n bucket 57: 10%\n bucket 56: 20%\n bucket 55: 70%\n bucket 57: 20%\n bucket 55: 80%\n bucket 56: 30%\n bucket 55: 90%\n bucket 57: 30%\n bucket 56: 40%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 57: 40%\n bucket 56: 50%\n bucket 57: 50%\n bucket 56: 60%\n bucket 57: 60%\n bucket 56: 70%\n bucket 57: 70%\n bucket 56: 80%\n bucket 57: 80%\n bucket 56: 90%\n bucket 57: 90%\n bucket 56: 100%\n bucket 57: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n Sorting block time: 00:00:00\n bucket 59: 60%\nReturning block of 114 for bucket 58\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n",
+ "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n bucket 1: 20%\nGetting block 3 of 60\n bucket 1: 30%\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\nGetting block 4 of 60\n Calculating Z arrays for bucket 3\n bucket 1: 40%\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n bucket 1: 50%\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 4\n bucket 1: 60%\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 3:\n bucket 1: 70%\nGetting block 6 of 60\n bucket 2: 10%\n Entering block accumulator loop for bucket 5:\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 3: 10%\n Reserving size (126) for bucket 6\n bucket 1: 80%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 1: 90%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 7\n bucket 2: 20%\n Entering block accumulator loop for bucket 4:\n bucket 3: 20%\n bucket 2: 30%\n Entering block accumulator loop for bucket 7:\n Entering block accumulator loop for bucket 6:\n bucket 4: 10%\n bucket 1: 100%\n Calculating Z arrays for bucket 8\n bucket 7: 10%\n Sorting block of length 42 for bucket 1\n bucket 4: 20%\n bucket 6: 10%\n bucket 7: 20%\n bucket 2: 40%\n bucket 4: 30%\n bucket 6: 20%\n bucket 2: 50%\n Entering block accumulator loop for bucket 8:\n (Using difference cover)\n bucket 6: 30%\n bucket 2: 60%\n bucket 7: 30%\n bucket 4: 40%\n bucket 3: 30%\n bucket 7: 40%\n bucket 6: 40%\n bucket 5: 10%\n bucket 2: 70%\n bucket 8: 10%\n bucket 3: 40%\n bucket 6: 50%\n bucket 5: 20%\n bucket 2: 80%\n bucket 4: 50%\n bucket 3: 50%\n bucket 6: 60%\n bucket 2: 90%\n bucket 8: 20%\n bucket 5: 30%\n bucket 2: 100%\n bucket 3: 60%\n bucket 8: 30%\n bucket 6: 70%\n bucket 7: 50%\n bucket 5: 40%\n bucket 4: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 8: 40%\n Sorting block time: 00:00:00\n bucket 5: 50%\n bucket 3: 70%\n bucket 6: 80%\n bucket 4: 70%\n bucket 7: 60%\n bucket 5: 60%\n bucket 8: 50%\n bucket 4: 80%\n bucket 7: 70%\n bucket 6: 90%\n bucket 5: 70%\n bucket 4: 90%\n bucket 8: 60%\nReturning block of 43 for bucket 1\n bucket 7: 80%\n bucket 8: 70%\n bucket 3: 80%\n bucket 6: 100%\n bucket 4: 100%\n bucket 7: 90%\n bucket 8: 80%\n bucket 5: 80%\n bucket 3: 90%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 3: 100%\n bucket 5: 90%\n bucket 8: 90%\n bucket 5: 100%\n Sorting block of length 106 for bucket 3\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\n Sorting block of length 68 for bucket 4\n bucket 8: 100%\nReturning block of 85 for bucket 2\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 9: 50%\n bucket 10: 50%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 60%\n bucket 9: 60%\n bucket 10: 70%\n bucket 9: 70%\n Entering block accumulator loop for bucket 11:\n bucket 9: 80%\n bucket 10: 80%\n bucket 11: 10%\n bucket 9: 90%\n bucket 10: 90%\n bucket 11: 20%\n bucket 9: 100%\n bucket 10: 100%\n bucket 11: 30%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block of length 124 for bucket 9\n bucket 11: 40%\n bucket 11: 50%\n (Using difference cover)\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 12 of 60\n Reserving size (126) for bucket 12\nGetting block 14 of 60\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Entering block accumulator loop for bucket 12:\n Calculating Z arrays for bucket 13\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 12: 10%\n Entering block accumulator loop for bucket 13:\n bucket 12: 20%\n bucket 13: 10%\n bucket 12: 30%\n Entering block accumulator loop for bucket 14:\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 12: 60%\n bucket 13: 50%\n bucket 14: 20%\n bucket 13: 60%\n bucket 12: 70%\n bucket 14: 30%\n bucket 13: 70%\n bucket 12: 80%\n bucket 14: 40%\n bucket 13: 80%\n bucket 12: 90%\n bucket 13: 90%\n bucket 14: 50%\n bucket 12: 100%\n bucket 13: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 14: 60%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Entering block accumulator loop for bucket 15:\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 15: 10%\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 20%\n bucket 15: 30%\n Entering block accumulator loop for bucket 17:\n bucket 15: 40%\n bucket 17: 10%\n bucket 15: 50%\n Entering block accumulator loop for bucket 16:\n bucket 17: 20%\n bucket 15: 60%\n bucket 16: 10%\n bucket 15: 70%\n bucket 17: 30%\n bucket 16: 20%\n bucket 15: 80%\n bucket 17: 40%\n bucket 16: 30%\n bucket 15: 90%\n bucket 17: 50%\n bucket 16: 40%\n bucket 15: 100%\n bucket 17: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 50%\n bucket 17: 70%\n bucket 16: 60%\n bucket 17: 80%\n bucket 16: 70%\n bucket 17: 90%\n bucket 16: 80%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n bucket 19: 70%\n bucket 20: 50%\n bucket 19: 80%\n bucket 20: 60%\n bucket 19: 90%\n bucket 20: 70%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 22:\n bucket 21: 10%\n bucket 22: 10%\n bucket 21: 20%\n bucket 22: 20%\n bucket 21: 30%\n bucket 22: 30%\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 22: 50%\n bucket 21: 60%\n bucket 22: 60%\n bucket 21: 70%\n bucket 22: 70%\n bucket 21: 80%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n bucket 22: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\nGetting block 24 of 60\n bucket 23: 20%\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 23: 30%\n Entering block accumulator loop for bucket 24:\n bucket 23: 40%\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 23: 50%\n bucket 24: 20%\n bucket 25: 10%\n bucket 23: 60%\n bucket 24: 30%\n bucket 23: 70%\n bucket 24: 40%\n bucket 25: 20%\n bucket 23: 80%\n bucket 24: 50%\n bucket 23: 90%\n bucket 24: 60%\n bucket 25: 30%\n bucket 23: 100%\n bucket 24: 70%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 25: 40%\n bucket 24: 80%\n bucket 25: 50%\n bucket 24: 90%\n bucket 25: 60%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 26: 10%\n bucket 27: 20%\n bucket 26: 20%\n bucket 27: 30%\n bucket 26: 30%\n bucket 27: 40%\n bucket 26: 40%\n bucket 27: 50%\n bucket 26: 50%\n bucket 27: 60%\n bucket 26: 60%\n bucket 27: 70%\n bucket 26: 70%\n bucket 27: 80%\n bucket 26: 80%\n bucket 27: 90%\n bucket 26: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 30:\n bucket 29: 10%\n bucket 30: 10%\n bucket 29: 20%\n bucket 30: 20%\n bucket 30: 30%\n bucket 29: 30%\n bucket 30: 40%\n bucket 29: 40%\n bucket 30: 50%\n bucket 29: 50%\n bucket 30: 60%\n bucket 29: 60%\n bucket 30: 70%\n bucket 29: 70%\n bucket 30: 80%\n bucket 29: 80%\n bucket 30: 90%\n bucket 29: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 10%\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 30%\n bucket 33: 10%\n bucket 32: 40%\n bucket 33: 20%\n bucket 32: 50%\n bucket 33: 30%\n bucket 32: 60%\n bucket 33: 40%\n bucket 32: 70%\n bucket 33: 50%\n bucket 32: 80%\n bucket 33: 60%\n bucket 32: 90%\n bucket 33: 70%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 60%\n bucket 34: 70%\n Entering block accumulator loop for bucket 35:\n bucket 34: 80%\n bucket 35: 10%\n bucket 34: 90%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 20%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 30%\n Entering block accumulator loop for bucket 36:\n bucket 35: 40%\n bucket 36: 10%\n bucket 35: 50%\n bucket 36: 20%\n bucket 35: 60%\n bucket 36: 30%\n bucket 35: 70%\n bucket 36: 40%\n bucket 35: 80%\n bucket 36: 50%\n bucket 35: 90%\n bucket 36: 60%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 70%\n bucket 36: 80%\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n Entering block accumulator loop for bucket 38:\n bucket 37: 20%\n bucket 38: 10%\n bucket 37: 30%\n bucket 38: 20%\n bucket 37: 40%\n bucket 38: 30%\n bucket 37: 50%\n bucket 38: 40%\n bucket 37: 60%\n bucket 38: 50%\n bucket 37: 70%\n bucket 38: 60%\n bucket 37: 80%\n bucket 38: 70%\n bucket 37: 90%\n bucket 38: 80%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 39: 30%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n bucket 39: 40%\n bucket 39: 50%\n Entering block accumulator loop for bucket 40:\n bucket 39: 60%\n bucket 40: 10%\n bucket 39: 70%\n bucket 40: 20%\n bucket 39: 80%\n bucket 40: 30%\n bucket 39: 90%\n bucket 40: 40%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\nGetting block 41 of 60\n bucket 40: 90%\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n Sorting block time: 00:00:00\n bucket 41: 20%\nReturning block of 126 for bucket 39\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 80%\n bucket 42: 90%\n Entering block accumulator loop for bucket 43:\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 50%\n Entering block accumulator loop for bucket 45:\n bucket 44: 60%\n bucket 45: 10%\n bucket 44: 70%\n bucket 45: 20%\n bucket 44: 80%\n bucket 45: 30%\n bucket 44: 90%\n bucket 44: 100%\n bucket 45: 40%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Entering block accumulator loop for bucket 47:\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n Entering block accumulator loop for bucket 48:\n bucket 47: 20%\n bucket 48: 10%\n bucket 47: 30%\n bucket 48: 20%\n bucket 47: 40%\n bucket 48: 30%\n bucket 47: 50%\n bucket 48: 40%\n bucket 47: 60%\n bucket 48: 50%\n bucket 47: 70%\n bucket 48: 60%\n bucket 47: 80%\n bucket 48: 70%\nGetting block 49 of 60\n bucket 48: 80%\n bucket 47: 90%\n Reserving size (126) for bucket 49\n bucket 48: 90%\n Calculating Z arrays for bucket 49\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n bucket 50: 30%\n Calculating Z arrays for bucket 51\n bucket 50: 40%\n Entering block accumulator loop for bucket 51:\n bucket 50: 50%\n bucket 51: 10%\n bucket 50: 60%\n bucket 51: 20%\n bucket 50: 70%\n bucket 51: 30%\n bucket 50: 80%\n bucket 51: 40%\n bucket 50: 90%\n bucket 51: 50%\n bucket 50: 100%\n bucket 51: 60%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\nGetting block 53 of 60\n bucket 52: 10%\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 20%\n bucket 52: 30%\n Entering block accumulator loop for bucket 53:\n bucket 52: 40%\n bucket 52: 50%\n bucket 53: 10%\n bucket 52: 60%\n bucket 53: 20%\n bucket 52: 70%\n bucket 53: 30%\n bucket 52: 80%\n bucket 53: 40%\n bucket 53: 50%\n bucket 52: 90%\n bucket 53: 60%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\nGetting block 56 of 60\n bucket 55: 30%\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 55: 40%\n Entering block accumulator loop for bucket 56:\n bucket 55: 50%\n Entering block accumulator loop for bucket 57:\n bucket 56: 10%\n bucket 55: 60%\n bucket 57: 10%\n bucket 56: 20%\n bucket 55: 70%\n bucket 57: 20%\n bucket 55: 80%\n bucket 56: 30%\n bucket 55: 90%\n bucket 57: 30%\n bucket 56: 40%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 57: 40%\n bucket 56: 50%\n bucket 57: 50%\n bucket 56: 60%\n bucket 57: 60%\n bucket 56: 70%\n bucket 57: 70%\n bucket 56: 80%\n bucket 57: 80%\n bucket 56: 90%\n bucket 57: 90%\n bucket 56: 100%\n bucket 57: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n Sorting block time: 00:00:00\n bucket 59: 60%\nReturning block of 114 for bucket 58\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n",
+ "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ef008abdd885cd3a.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ef008abdd885cd3a.json
new file mode 100644
index 000000000..3e8529828
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ef008abdd885cd3a.json
@@ -0,0 +1,55 @@
+{
+ "model_class": "Job",
+ "id": "ef008abdd885cd3a",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:38:24.567114",
+ "update_time": "2024-08-30T07:38:32.877832",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-ws2hs",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "cp '/galaxy/server/database/objects/f/e/3/dataset_fe3ffb95-001a-4a55-b79a-4f4072b4ef6a.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/320/configs/tmps3r7mftg' > '/galaxy/server/database/objects/2/2/c/dataset_22ce5b42-d8a4-4170-b761-77f189e3767c.dat' && python '/galaxy/server/database/jobs_directory/000/320/configs/tmps3r7mftg' >> '/galaxy/server/database/objects/2/2/c/dataset_22ce5b42-d8a4-4170-b761-77f189e3767c.dat' && ls . >> '/galaxy/server/database/objects/2/2/c/dataset_22ce5b42-d8a4-4170-b761-77f189e3767c.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "__input_ext": "\"input\"",
+ "dbkey": "\"?\"",
+ "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+ "advanced_common": "{\"show_log\": true}",
+ "method": "{\"__current_case__\": 1, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 0, \"height\": \"3\", \"test\": \"yes\", \"width\": \"10\"}, \"gene_symbols\": \"\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_imshow\": {\"alpha\": \"\", \"cmap\": \"YlGnBu\", \"interpolation\": \"None\", \"origin\": \"upper\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.heatmap\", \"num_categories\": \"7\", \"show_gene_labels\": false, \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 0, \"type\": \"all\"}}",
+ "format": "\"png\""
+ },
+ "inputs": {
+ "adata": {
+ "id": "1d8f058f735ff10d",
+ "src": "hda",
+ "uuid": "fe3ffb95-001a-4a55-b79a-4f4072b4ef6a"
+ }
+ },
+ "outputs": {
+ "hidden_output": {
+ "id": "72a670fdd9745f64",
+ "src": "hda",
+ "uuid": "22ce5b42-d8a4-4170-b761-77f189e3767c"
+ },
+ "out_png": {
+ "id": "8997e7210843ec1f",
+ "src": "hda",
+ "uuid": "667c1706-7673-489d-a10b-68ba33924306"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/f219fc94d8d8fc77.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/f219fc94d8d8fc77.json
new file mode 100644
index 000000000..8539649f5
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/f219fc94d8d8fc77.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "f219fc94d8d8fc77",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:56:00.011958",
+ "update_time": "2024-08-30T06:56:11.319786",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-knw5c",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/127/registry.xml' '/galaxy/server/database/jobs_directory/000/127/upload_params.json' '158:/galaxy/server/database/objects/e/2/f/dataset_e2fc8f3f-7598-4893-901f-c5e5113c7473_files:/galaxy/server/database/objects/e/2/f/dataset_e2fc8f3f-7598-4893-901f-c5e5113c7473.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_sr6c6v81\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"phiX.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_o6tpotw3\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "bace94d214f3fc50",
+ "src": "hda",
+ "uuid": "e2fc8f3f-7598-4893-901f-c5e5113c7473"
+ }
+ },
+ "copied_from_job_id": null,
+ "output_collections": {},
+ "tool_stdout": "",
+ "tool_stderr": "",
+ "job_stdout": null,
+ "job_stderr": null,
+ "stdout": "",
+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/f84bfcca59a27fdd.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/f84bfcca59a27fdd.json
new file mode 100644
index 000000000..fd8b5b662
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/f84bfcca59a27fdd.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "f84bfcca59a27fdd",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:50:37.447957",
+ "update_time": "2024-08-30T06:50:49.201174",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-m9vlq",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/91/registry.xml' '/galaxy/server/database/jobs_directory/000/91/upload_params.json' '117:/galaxy/server/database/objects/0/d/0/dataset_0d0dcbb2-baf4-4b24-8b66-b561061e66e0_files:/galaxy/server/database/objects/0/d/0/dataset_0d0dcbb2-baf4-4b24-8b66-b561061e66e0.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_juaccm4c\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"phiX.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_5vb8omhj\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "8c1ced6614b907de",
+ "src": "hda",
+ "uuid": "0d0dcbb2-baf4-4b24-8b66-b561061e66e0"
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+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/f91b2de9e5168308.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/f91b2de9e5168308.json
new file mode 100644
index 000000000..6cacc7d83
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/f91b2de9e5168308.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "f91b2de9e5168308",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:09:44.815987",
+ "update_time": "2024-08-30T07:09:56.092440",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-rh8cw",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/210/registry.xml' '/galaxy/server/database/jobs_directory/000/210/upload_params.json' '247:/galaxy/server/database/objects/b/2/9/dataset_b29df14e-59c9-491a-999d-9fed401f02a7_files:/galaxy/server/database/objects/b/2/9/dataset_b29df14e-59c9-491a-999d-9fed401f02a7.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_eq0yuhoi\"",
+ "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"test_input_1_a_regex.sam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_lw8t9h5t\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"auto\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "b822f195decf577e",
+ "src": "hda",
+ "uuid": "b29df14e-59c9-491a-999d-9fed401f02a7"
+ }
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+ "stderr": "",
+ "job_messages": null,
+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/fb4c3b841421ac3f.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/fb4c3b841421ac3f.json
new file mode 100644
index 000000000..678d91271
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/fb4c3b841421ac3f.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "fb4c3b841421ac3f",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T07:01:31.068925",
+ "update_time": "2024-08-30T07:01:41.923798",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-gtkp9",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/161/registry.xml' '/galaxy/server/database/jobs_directory/000/161/upload_params.json' '193:/galaxy/server/database/objects/7/d/b/dataset_7db06aac-567f-496b-aae2-6c3eb2b38312_files:/galaxy/server/database/objects/7/d/b/dataset_7db06aac-567f-496b-aae2-6c3eb2b38312.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params_cciuuu8x\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"phiX.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_hdcmtt_v\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "5016efe808daa744",
+ "src": "hda",
+ "uuid": "7db06aac-567f-496b-aae2-6c3eb2b38312"
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+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ffa36cfcb4321d19.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ffa36cfcb4321d19.json
new file mode 100644
index 000000000..97c78e0ae
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/errors/ffa36cfcb4321d19.json
@@ -0,0 +1,45 @@
+{
+ "model_class": "Job",
+ "id": "ffa36cfcb4321d19",
+ "history_id": "436da20d1fd8461d",
+ "tool_id": "upload1",
+ "state": "error",
+ "exit_code": null,
+ "create_time": "2024-08-30T06:58:29.768104",
+ "update_time": "2024-08-30T06:58:41.143915",
+ "galaxy_version": "24.1",
+ "external_id": "gxy-6n4mv",
+ "handler": null,
+ "job_runner_name": null,
+ "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/141/registry.xml' '/galaxy/server/database/jobs_directory/000/141/upload_params.json' '173:/galaxy/server/database/objects/c/f/7/dataset_cf7586ac-2066-4763-9b97-a956f997b741_files:/galaxy/server/database/objects/c/f/7/dataset_cf7586ac-2066-4763-9b97-a956f997b741.dat'",
+ "user_email": "tests@fake.org",
+ "command_version": null,
+ "params": {
+ "paramfile": "\"/galaxy/server/database/tmp/upload_params__dn560m0\"",
+ "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+ "dbkey": "\"?\"",
+ "force_composite": "\"false\"",
+ "files": "[{\"NAME\": \"phiX.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_pjygj9b6\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+ "file_count": "\"auto\"",
+ "file_type": "\"fasta\""
+ },
+ "inputs": {},
+ "outputs": {
+ "output0": {
+ "id": "689bab7197243cdc",
+ "src": "hda",
+ "uuid": "cf7586ac-2066-4763-9b97-a956f997b741"
+ }
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+ "dependencies": [],
+ "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/job-metrics.csv b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/job-metrics.csv
new file mode 100644
index 000000000..082ddcaa4
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/job-metrics.csv
@@ -0,0 +1,479 @@
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diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/jobs.txt b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/jobs.txt
new file mode 100644
index 000000000..7d31eca1a
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/jobs.txt
@@ -0,0 +1,478 @@
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diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.html b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.html
new file mode 100644
index 000000000..562ef6308
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.html
@@ -0,0 +1,291 @@
+
+
+
+ Test Results (powered by Planemo)
+
+
+
+
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+
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+
+
+
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\ No newline at end of file
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.json b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.json
new file mode 100644
index 000000000..fef006bcf
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.json
@@ -0,0 +1 @@
+{"version": "0.1", "suitename": "Galaxy Tool Tests", "results": {"total": 209, "errors": 39, "failures": 21, "skips": 4}, "tests": [{"id": "alevin/1.5.1+galaxy0-0", "has_data": true, "data": {"tool_id": "alevin", "tool_version": "1.5.1+galaxy0", "test_index": 0, "time_seconds": 63.753140926361084, "inputs": {"refTranscriptSource|s_index|fasta": {"src": "hda", "id": "012fd79ff5050b2e"}, "refTranscriptSource|TranscriptSource": "history", "pairstraight|file1": {"src": "hda", "id": "af80223b2b724185"}, "pairstraight|file2": {"src": "hda", "id": "5bc74392f7594846"}, "pairstraight|readselect": "paired", "protocol": "--chromium", "tgmap": {"src": "hda", "id": "1aa19454e64c7484"}, "optional|dumpFeatures": true, "optional|dumpMtx": true, "optional|keepCBFraction": "1", "optional|freqThreshold": "5"}, "job": {"model_class": "Job", "id": "6a8e2e23745f6c0d", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:17:03.331734", "update_time": "2024-08-30T07:17:36.251221", "galaxy_version": "24.1", "external_id": "gxy-86zh2", "handler": null, "job_runner_name": null, "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/4/5/1/dataset_451a0b29-4870-431d-a23b-c988bab22363.dat' && cp '/galaxy/server/database/objects/1/a/2/dataset_1a2f8863-f68f-443f-b699-30dd31bb8bd2.dat' ./mate1.fastq.gz && gunzip ./mate1.fastq.gz && cp '/galaxy/server/database/objects/3/b/4/dataset_3b4e7a84-86bd-416a-be49-d7906a308a10.dat' ./mate2.fastq.gz && gunzip ./mate2.fastq.gz && ln -s '/galaxy/server/database/objects/d/4/7/dataset_d47d26a4-50b8-4eda-b849-7215b4a38ed9.dat' ./alevinmap.tsv && salmon alevin -l A -i ./index -1 ./mate1.fastq -2 ./mate2.fastq -o ./output -p \"${GALAXY_SLOTS:-4}\" --chromium --tgMap ./alevinmap.tsv --keepCBFraction '1.0' --dumpFeatures --dumpMtx --freqThreshold '5' && gunzip output/alevin/quants_mat.mtx.gz && gunzip output/alevin/quants_tier_mat.gz && gunzip output/aux_info/fld.gz && gunzip output/aux_info/observed_bias.gz && gunzip output/aux_info/observed_bias_3p.gz", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "optional": "{\"dumpBfh\": false, \"dumpFeatures\": true, \"dumpMtx\": true, \"dumpUmiGraph\": false, \"expectCells\": \"\", \"forceCells\": \"\", \"freqThreshold\": \"5\", \"keepCBFraction\": \"1.0\", \"lowRegionMinNumBarcodes\": \"\", \"maxNumBarcodes\": \"\", \"minScoreFraction\": \"\", \"mrna\": null, \"noDedup\": false, \"numCellBootstraps\": \"\", \"rrna\": null, \"whitelist\": null}", "allout": "false", "protocol": "\"--chromium\"", "pairstraight": "{\"__current_case__\": 0, \"file1\": {\"values\": [{\"id\": 292, \"src\": \"hda\"}]}, \"file2\": {\"values\": [{\"id\": 293, \"src\": \"hda\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"readselect\": \"paired\"}", "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 291, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}"}, "inputs": {"refTranscriptSource|s_index|fasta": {"id": "012fd79ff5050b2e", "src": "hda", "uuid": "451a0b29-4870-431d-a23b-c988bab22363"}, "pairstraight|file1": {"id": "af80223b2b724185", "src": "hda", "uuid": "1a2f8863-f68f-443f-b699-30dd31bb8bd2"}, "pairstraight|file2": {"id": "5bc74392f7594846", "src": "hda", "uuid": "3b4e7a84-86bd-416a-be49-d7906a308a10"}, "tgmap": {"id": "1aa19454e64c7484", "src": "hda", "uuid": "d47d26a4-50b8-4eda-b849-7215b4a38ed9"}}, "outputs": {"quants_mat_mtx": {"id": "7b400f26a531a182", "src": "hda", "uuid": "4115e486-79b1-49b4-8678-221d29d0be9a"}, "raw_cb_frequency_txt": {"id": "8931930f797580d2", "src": "hda", "uuid": "417be05d-9ff2-44ce-9baa-103b79f362b4"}, "quants_mat_cols_txt": {"id": "8f5e193507069e81", "src": "hda", "uuid": "01509744-1c0d-41ad-872b-7fd345d8e00b"}, "quants_mat_rows_txt": {"id": "b1ea0f569f8c6a70", "src": "hda", "uuid": "04f2e6b4-2f29-4350-abea-3f6acbfcb840"}, "quants_tier_mat": {"id": "9f85906923485bec", "src": "hda", "uuid": "488aa477-3c64-4653-bfc7-3b5dd7cbb46f"}, "featureDump_txt": {"id": "d8e603da1c3f291d", "src": "hda", "uuid": "2f1b4796-f864-4f17-a104-8ab3a14e599d"}, "whitelist_txt": {"id": "e55f906e1cc2896a", "src": "hda", "uuid": "50a9d3a7-ac5d-45e2-a231-16802e002d2d"}, "expected_bias": {"id": "6be82dcbc2b5c0e1", "src": "hda", "uuid": "605bede0-1ba5-4aac-a283-894d4dbace9f"}, "observed_bias": {"id": "e3d896b61542c76c", "src": "hda", "uuid": "4c89e969-36a0-417f-988d-212aed1d2f0e"}, "observed_bias_3p": {"id": "5ac3666d409c110b", "src": "hda", "uuid": "3337ddbb-9487-4295-b72a-fefc1d492340"}, "flenDist_txt": {"id": "486aa39a6bf52933", "src": "hda", "uuid": "dcf12db7-0384-4c1b-be0b-3d6e8ef259a6"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "alevin/1.5.1+galaxy0-0", "has_data": true, "data": {"tool_id": "alevin", "tool_version": "1.5.1+galaxy0", "test_index": 0, "time_seconds": 43.00548601150513, "inputs": {"refTranscriptSource|s_index|fasta": {"src": "hda", "id": "4e3c5faea0b03fb3"}, "refTranscriptSource|TranscriptSource": "history", "pairstraight|file1": {"src": "hda", "id": "2d152befef641600"}, "pairstraight|file2": {"src": "hda", "id": "7abcafbf17910b1a"}, "pairstraight|readselect": "paired", "protocol": "--chromium", "tgmap": {"src": "hda", "id": "c25c738b3ca009dd"}, "optional|dumpFeatures": true, "optional|dumpMtx": true, "optional|keepCBFraction": "1", "optional|freqThreshold": "5"}, "job": {"model_class": "Job", "id": "8becb61cdaf1d973", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:18:59.582456", "update_time": "2024-08-30T07:19:08.794666", "galaxy_version": "24.1", "external_id": "gxy-8t7z8", "handler": null, "job_runner_name": null, "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/3/5/3/dataset_353764c1-1cfe-4c8f-b099-a53fde25eac3.dat' && cp '/galaxy/server/database/objects/e/c/2/dataset_ec2745fc-152f-480d-a157-d3a71a001fdd.dat' ./mate1.fastq.gz && gunzip ./mate1.fastq.gz && cp '/galaxy/server/database/objects/4/a/c/dataset_4acd8139-316f-405a-b521-1504259236e3.dat' ./mate2.fastq.gz && gunzip ./mate2.fastq.gz && ln -s '/galaxy/server/database/objects/3/8/f/dataset_38f8f740-d542-43e8-9a12-fab69aa5a6c6.dat' ./alevinmap.tsv && salmon alevin -l A -i ./index -1 ./mate1.fastq -2 ./mate2.fastq -o ./output -p \"${GALAXY_SLOTS:-4}\" --chromium --tgMap ./alevinmap.tsv --keepCBFraction '1.0' --dumpFeatures --dumpMtx --freqThreshold '5' && gunzip output/alevin/quants_mat.mtx.gz && gunzip output/alevin/quants_tier_mat.gz && gunzip output/aux_info/fld.gz && gunzip output/aux_info/observed_bias.gz && gunzip output/aux_info/observed_bias_3p.gz", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "optional": "{\"dumpBfh\": false, \"dumpFeatures\": true, \"dumpMtx\": true, \"dumpUmiGraph\": false, \"expectCells\": \"\", \"forceCells\": \"\", \"freqThreshold\": \"5\", \"keepCBFraction\": \"1.0\", \"lowRegionMinNumBarcodes\": \"\", \"maxNumBarcodes\": \"\", \"minScoreFraction\": \"\", \"mrna\": null, \"noDedup\": false, \"numCellBootstraps\": \"\", \"rrna\": null, \"whitelist\": null}", "allout": "false", "protocol": "\"--chromium\"", "pairstraight": "{\"__current_case__\": 0, \"file1\": {\"values\": [{\"id\": 325, \"src\": \"hda\"}]}, \"file2\": {\"values\": [{\"id\": 326, \"src\": \"hda\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"readselect\": \"paired\"}", "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 324, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}"}, "inputs": {"refTranscriptSource|s_index|fasta": {"id": "4e3c5faea0b03fb3", "src": "hda", "uuid": "353764c1-1cfe-4c8f-b099-a53fde25eac3"}, "pairstraight|file1": {"id": "2d152befef641600", "src": "hda", "uuid": "ec2745fc-152f-480d-a157-d3a71a001fdd"}, "pairstraight|file2": {"id": "7abcafbf17910b1a", "src": "hda", "uuid": "4acd8139-316f-405a-b521-1504259236e3"}, "tgmap": {"id": "c25c738b3ca009dd", "src": "hda", "uuid": "38f8f740-d542-43e8-9a12-fab69aa5a6c6"}}, "outputs": {"quants_mat_mtx": {"id": "37044600c9a534ea", "src": "hda", "uuid": "a600499f-c74d-4365-b3f4-22cfb83e0c7f"}, "raw_cb_frequency_txt": {"id": "6ddf7485813f25a4", "src": "hda", "uuid": "2c2a735a-3341-4a59-9c4c-580e007309aa"}, "quants_mat_cols_txt": {"id": "dbaa233cd776bf88", "src": "hda", "uuid": "d2d7575d-1563-4bd3-8473-72bcfacd400b"}, "quants_mat_rows_txt": {"id": "b6117c47805ab753", "src": "hda", "uuid": "26c32f61-5b2e-4062-b0d3-0056ee6f62d7"}, "quants_tier_mat": {"id": "9de2ed719293250f", "src": "hda", "uuid": "5741b4b2-c750-426e-823a-1c9208d908ff"}, "featureDump_txt": {"id": "77d4106665353fec", "src": "hda", "uuid": "8dde9a0e-ca09-46d2-9aa1-2dbd272c551e"}, "whitelist_txt": {"id": "254446c4c22f43e3", "src": "hda", "uuid": "f2c40745-f91c-4bf8-9ac3-fee675d2e410"}, "expected_bias": {"id": "d6dfb20f580df4aa", "src": "hda", "uuid": "09d3f2a1-62c8-49a7-8e27-4e6c29b0d232"}, "observed_bias": {"id": "5fcfe86f7ffa46b0", "src": "hda", "uuid": "43288e68-e362-454f-b443-b21d63452bb2"}, "observed_bias_3p": {"id": "0c6b8f360b3ddec5", "src": "hda", "uuid": "f74134bc-65b3-40c1-862c-fcf5ccf59c7a"}, "flenDist_txt": {"id": "30c4be037d80c86f", "src": "hda", "uuid": "3e7f3a0a-28be-4a4d-906d-fe3bf8ada75c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 4194304\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:4194304\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 1005\nFalse junctions count = 1098\nHash table size = 2103\nCandidate marks count = 9186\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 6382\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 1005\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 1016896 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:02.029] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:02.029] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:02.030] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:02.085] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:02.092] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.333 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 878.1 us\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:02.549] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:02.556] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:03.265] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\nLogs will be written to ./output/logs\n[2024-08-30 07:19:03.295] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:03.295] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:03.295] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:03.295] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:03.295] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:03.295] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:03.295] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:03.299] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:03.300] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:03.300] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:03.310] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:03.363] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:03.363] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:03.366] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:03.388] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:03.408] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:03.446] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:03.449] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:03.576] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:03.597] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:03.597] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.2347 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.089 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 8.44 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 806.25 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.6259 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2949 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.7425 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2667 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 18.15 us\n-----------------------------------------\n[2024-08-30 07:19:03.597] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:03.713] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:03.714] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:03.726] [jointLog] [info] done\n[2024-08-30 07:19:03.726] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:03.726] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:04.660] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:04.660] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:04.661] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:04.661] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:04.661] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:04.681] [alevinLog] [info] Starting optimizer\n\n\n[2024-08-30 07:19:04.827] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:04.827] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 46 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 520 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 740 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1392 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1878 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2455 cells (\u001b[31m48%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2757 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2849 cells (\u001b[31m56%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4019 cells (\u001b[31m79%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4158 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:04.861] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:04.864] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:04.864] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:04.893] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n", "job_stdout": null, "job_stderr": null, "stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 4194304\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:4194304\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 1005\nFalse junctions count = 1098\nHash table size = 2103\nCandidate marks count = 9186\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 6382\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 1005\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 1016896 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:02.029] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:02.029] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:02.030] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:02.085] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:02.092] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.333 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 878.1 us\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:02.549] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:02.556] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:03.265] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\nLogs will be written to ./output/logs\n[2024-08-30 07:19:03.295] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:03.295] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:03.295] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:03.295] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:03.295] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:03.295] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:03.295] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:03.299] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:03.300] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:03.300] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:03.310] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:03.363] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:03.363] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:03.366] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:03.388] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:03.408] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:03.446] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:03.449] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:03.576] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:03.597] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:03.597] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.2347 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.089 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 8.44 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 806.25 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.6259 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2949 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.7425 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2667 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 18.15 us\n-----------------------------------------\n[2024-08-30 07:19:03.597] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:03.713] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:03.714] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:03.726] [jointLog] [info] done\n[2024-08-30 07:19:03.726] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:03.726] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:04.660] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:04.660] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:04.661] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:04.661] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:04.661] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:04.681] [alevinLog] [info] Starting optimizer\n\n\n[2024-08-30 07:19:04.827] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:04.827] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 46 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 520 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 740 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1392 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1878 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2455 cells (\u001b[31m48%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2757 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2849 cells (\u001b[31m56%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4019 cells (\u001b[31m79%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4158 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:04.861] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:04.864] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:04.864] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:04.893] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, exit_code: None, stderr: Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:02.029] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:02.029] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:02.030] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:02.085] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:02.092] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.333 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 878.1 us\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:02.549] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:02.556] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:03.265] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\nLogs will be written to ./output/logs\n[2024-08-30 07:19:03.295] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:03.295] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:03.295] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:03.295] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:03.295] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:03.295] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:03.295] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:03.299] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:03.300] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:03.300] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:03.310] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:03.363] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:03.363] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:03.366] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:03.388] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:03.408] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:03.446] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:03.449] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:03.576] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:03.597] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:03.597] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.2347 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.089 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 8.44 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 806.25 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.6259 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2949 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.7425 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2667 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 18.15 us\n-----------------------------------------\n[2024-08-30 07:19:03.597] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:03.713] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:03.714] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:03.726] [jointLog] [info] done\n[2024-08-30 07:19:03.726] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:03.726] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:04.660] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:04.660] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:04.661] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:04.661] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:04.661] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:04.681] [alevinLog] [info] Starting optimizer\n\n\n[2024-08-30 07:19:04.827] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:04.827] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 46 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 520 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 740 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1392 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1878 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2455 cells (\u001b[31m48%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2757 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2849 cells (\u001b[31m56%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4019 cells (\u001b[31m79%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4158 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:04.861] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:04.864] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:04.864] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:04.893] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, exit_code: None, stderr: Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:02.029] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:02.029] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:02.030] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:02.049] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:02.059] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:02.085] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:02.092] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.333 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 878.1 us\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:02.549] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:02.556] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:03.265] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\nLogs will be written to ./output/logs\n[2024-08-30 07:19:03.295] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:03.295] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:03.295] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:03.295] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:03.295] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:03.295] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:03.295] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:03.299] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:03.300] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:03.300] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:03.310] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:03.363] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:03.363] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:03.366] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:03.388] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:03.408] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:03.446] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:03.449] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:03.576] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:03.576] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:03.576] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:03.597] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:03.597] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.2347 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.089 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 8.44 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 806.25 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.6259 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2949 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.7425 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2667 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 18.15 us\n-----------------------------------------\n[2024-08-30 07:19:03.597] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:03.713] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:03.714] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:03.726] [jointLog] [info] done\n[2024-08-30 07:19:03.726] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:03.726] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:04.660] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:04.660] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:04.661] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:04.661] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:04.661] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:04.681] [alevinLog] [info] Starting optimizer\n\n\n[2024-08-30 07:19:04.827] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:04.827] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 46 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 328 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 520 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 740 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1392 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1878 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2455 cells (\u001b[31m48%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2757 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2849 cells (\u001b[31m56%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4019 cells (\u001b[31m79%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4158 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:04.835] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:04.861] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:04.864] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:04.864] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:04.872] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:04.893] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n."], "status": "failure"}}, {"id": "alevin/1.5.1+galaxy0-1", "has_data": true, "data": {"tool_id": "alevin", "tool_version": "1.5.1+galaxy0", "test_index": 1, "time_seconds": 48.7509605884552, "inputs": {"refTranscriptSource|s_index|fasta": {"src": "hda", "id": "ade34174ea908ec9"}, "refTranscriptSource|TranscriptSource": "history", "pairstraight|file1": {"src": "hda", "id": "626a64c6bb868c48"}, "pairstraight|file2": {"src": "hda", "id": "fda5818e8a5af745"}, "pairstraight|readselect": "paired", "protocol": "--chromium", "tgmap": {"src": "hda", "id": "9e7b4465e6d5f5e7"}, "optional|dumpFeatures": true, "optional|dumpMtx": true, "optional|numCellBootstraps": "2", "optional|keepCBFraction": "1", "optional|freqThreshold": "5"}, "job": {"model_class": "Job", "id": "05f1cc2cc180b061", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:18:05.746212", "update_time": "2024-08-30T07:18:24.999336", "galaxy_version": "24.1", "external_id": "gxy-dltns", "handler": null, "job_runner_name": null, "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/6/b/2/dataset_6b225a08-de2e-4ffc-8cdd-52a766782281.dat' && cp '/galaxy/server/database/objects/d/4/7/dataset_d478885a-4e93-45c0-b833-35a1871257f0.dat' ./mate1.fastq.gz && gunzip ./mate1.fastq.gz && cp '/galaxy/server/database/objects/f/1/1/dataset_f11bdbe6-877d-4608-9a9f-4897fa921a3a.dat' ./mate2.fastq.gz && gunzip ./mate2.fastq.gz && ln -s '/galaxy/server/database/objects/e/f/b/dataset_efb5abf0-017c-45c6-a694-2548c0bf2885.dat' ./alevinmap.tsv && salmon alevin -l A -i ./index -1 ./mate1.fastq -2 ./mate2.fastq -o ./output -p \"${GALAXY_SLOTS:-4}\" --chromium --tgMap ./alevinmap.tsv --numCellBootstraps '2' --keepCBFraction '1.0' --dumpFeatures --dumpMtx --freqThreshold '5' && gunzip output/alevin/quants_mat.mtx.gz && gunzip output/alevin/quants_tier_mat.gz && gunzip output/alevin/quants_mean_mat.gz && gunzip output/alevin/quants_var_mat.gz && gunzip output/aux_info/fld.gz && gunzip output/aux_info/observed_bias.gz && gunzip output/aux_info/observed_bias_3p.gz", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "optional": "{\"dumpBfh\": false, \"dumpFeatures\": true, \"dumpMtx\": true, \"dumpUmiGraph\": false, \"expectCells\": \"\", \"forceCells\": \"\", \"freqThreshold\": \"5\", \"keepCBFraction\": \"1.0\", \"lowRegionMinNumBarcodes\": \"\", \"maxNumBarcodes\": \"\", \"minScoreFraction\": \"\", \"mrna\": null, \"noDedup\": false, \"numCellBootstraps\": \"2\", \"rrna\": null, \"whitelist\": null}", "allout": "false", "protocol": "\"--chromium\"", "pairstraight": "{\"__current_case__\": 0, \"file1\": {\"values\": [{\"id\": 307, \"src\": \"hda\"}]}, \"file2\": {\"values\": [{\"id\": 308, \"src\": \"hda\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"readselect\": \"paired\"}", "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 306, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}"}, "inputs": {"refTranscriptSource|s_index|fasta": {"id": "ade34174ea908ec9", "src": "hda", "uuid": "6b225a08-de2e-4ffc-8cdd-52a766782281"}, "pairstraight|file1": {"id": "626a64c6bb868c48", "src": "hda", "uuid": "d478885a-4e93-45c0-b833-35a1871257f0"}, "pairstraight|file2": {"id": "fda5818e8a5af745", "src": "hda", "uuid": "f11bdbe6-877d-4608-9a9f-4897fa921a3a"}, "tgmap": {"id": "9e7b4465e6d5f5e7", "src": "hda", "uuid": "efb5abf0-017c-45c6-a694-2548c0bf2885"}}, "outputs": {"flenDist_txt": {"id": "91ee28930f1e2eb4", "src": "hda", "uuid": "3fe922e2-673c-42a8-beee-075481887097"}, "observed_bias_3p": {"id": "787f20cab39ce662", "src": "hda", "uuid": "8b2746d8-9a97-45ef-ae2e-c59c49c368c3"}, "observed_bias": {"id": "9157b567b4405058", "src": "hda", "uuid": "a86985fb-67bf-41e0-998e-a27b9b05cfa5"}, "expected_bias": {"id": "ef008abdd885cd3a", "src": "hda", "uuid": "ffa68773-a1bf-4d2f-9216-17af90d27a79"}, "quants_boot_rows_txt": {"id": "fa46b69b3b6eb2d0", "src": "hda", "uuid": "48ae43a8-3804-451f-a40b-b5aecb38069a"}, "quants_var_mat": {"id": "9e66f7e372adc5d1", "src": "hda", "uuid": "c93c16f0-360c-41cc-861d-e1487fada4f7"}, "quants_mean_mat": {"id": "8e3bc46515971f80", "src": "hda", "uuid": "6792f8c2-0020-42fd-88a6-5e3b7636f0cc"}, "whitelist_txt": {"id": "6c555ae15f749b36", "src": "hda", "uuid": "a6c6b15d-d965-42c7-90f5-7facba229951"}, "featureDump_txt": {"id": "37bf2b8aff708392", "src": "hda", "uuid": "5d1ce308-ef04-4307-9e22-c8afb94d4dd3"}, "quants_tier_mat": {"id": "bfc105b661dbaf2b", "src": "hda", "uuid": "40387756-8171-4ba3-8458-7ab7a2278eae"}, "quants_mat_rows_txt": {"id": "016a9ecab36a8a33", "src": "hda", "uuid": "c7f8267e-25a2-43e5-a3f4-10e21ab11301"}, "quants_mat_cols_txt": {"id": "388a4dbdf6225b5e", "src": "hda", "uuid": "1a811432-4941-4735-89b6-0b87a7d26d61"}, "raw_cb_frequency_txt": {"id": "a201e7513402edc5", "src": "hda", "uuid": "94e23446-c99d-4f28-a2cb-5fa9f42586a3"}, "quants_mat_mtx": {"id": "c8642ef18f13529c", "src": "hda", "uuid": "4671a059-2f13-4e16-8224-26fb87dbe063"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "alevin/1.5.1+galaxy0-1", "has_data": true, "data": {"tool_id": "alevin", "tool_version": "1.5.1+galaxy0", "test_index": 1, "time_seconds": 39.128270864486694, "inputs": {"refTranscriptSource|s_index|fasta": {"src": "hda", "id": "0c12e840c4d79636"}, "refTranscriptSource|TranscriptSource": "history", "pairstraight|file1": {"src": "hda", "id": "7aa45690986c8ca7"}, "pairstraight|file2": {"src": "hda", "id": "196609ee608737c3"}, "pairstraight|readselect": "paired", "protocol": "--chromium", "tgmap": {"src": "hda", "id": "3d7c835c180678a2"}, "optional|dumpFeatures": true, "optional|dumpMtx": true, "optional|numCellBootstraps": "2", "optional|keepCBFraction": "1", "optional|freqThreshold": "5"}, "job": {"model_class": "Job", "id": "8e847d9dfbfeb264", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:19:38.654355", "update_time": "2024-08-30T07:19:47.984098", "galaxy_version": "24.1", "external_id": "gxy-66klb", "handler": null, "job_runner_name": null, "command_line": "mkdir ./index && mkdir ./output && salmon index -i ./index --kmerLen '31' --gencode --transcripts '/galaxy/server/database/objects/a/7/d/dataset_a7d7a68b-2d9d-43be-84b3-5e0a29daca52.dat' && cp '/galaxy/server/database/objects/b/3/d/dataset_b3d76027-3bf6-419c-8740-dfb8fd98d42e.dat' ./mate1.fastq.gz && gunzip ./mate1.fastq.gz && cp '/galaxy/server/database/objects/3/2/0/dataset_320c4220-2796-4964-9dd7-f66cb3de56d7.dat' ./mate2.fastq.gz && gunzip ./mate2.fastq.gz && ln -s '/galaxy/server/database/objects/b/7/9/dataset_b7990462-bf24-4758-a858-5ca1105d8a0f.dat' ./alevinmap.tsv && salmon alevin -l A -i ./index -1 ./mate1.fastq -2 ./mate2.fastq -o ./output -p \"${GALAXY_SLOTS:-4}\" --chromium --tgMap ./alevinmap.tsv --numCellBootstraps '2' --keepCBFraction '1.0' --dumpFeatures --dumpMtx --freqThreshold '5' && gunzip output/alevin/quants_mat.mtx.gz && gunzip output/alevin/quants_tier_mat.gz && gunzip output/alevin/quants_mean_mat.gz && gunzip output/alevin/quants_var_mat.gz && gunzip output/aux_info/fld.gz && gunzip output/aux_info/observed_bias.gz && gunzip output/aux_info/observed_bias_3p.gz", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "optional": "{\"dumpBfh\": false, \"dumpFeatures\": true, \"dumpMtx\": true, \"dumpUmiGraph\": false, \"expectCells\": \"\", \"forceCells\": \"\", \"freqThreshold\": \"5\", \"keepCBFraction\": \"1.0\", \"lowRegionMinNumBarcodes\": \"\", \"maxNumBarcodes\": \"\", \"minScoreFraction\": \"\", \"mrna\": null, \"noDedup\": false, \"numCellBootstraps\": \"2\", \"rrna\": null, \"whitelist\": null}", "allout": "false", "protocol": "\"--chromium\"", "pairstraight": "{\"__current_case__\": 0, \"file1\": {\"values\": [{\"id\": 340, \"src\": \"hda\"}]}, \"file2\": {\"values\": [{\"id\": 341, \"src\": \"hda\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"readselect\": \"paired\"}", "refTranscriptSource": "{\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 339, \"src\": \"hda\"}]}, \"kmer\": \"31\", \"phash\": false}}"}, "inputs": {"refTranscriptSource|s_index|fasta": {"id": "0c12e840c4d79636", "src": "hda", "uuid": "a7d7a68b-2d9d-43be-84b3-5e0a29daca52"}, "pairstraight|file1": {"id": "7aa45690986c8ca7", "src": "hda", "uuid": "b3d76027-3bf6-419c-8740-dfb8fd98d42e"}, "pairstraight|file2": {"id": "196609ee608737c3", "src": "hda", "uuid": "320c4220-2796-4964-9dd7-f66cb3de56d7"}, "tgmap": {"id": "3d7c835c180678a2", "src": "hda", "uuid": "b7990462-bf24-4758-a858-5ca1105d8a0f"}}, "outputs": {"flenDist_txt": {"id": "e6a4e8500837d9f4", "src": "hda", "uuid": "9d1c0182-b7ae-4430-9bb5-b0499f08109f"}, "observed_bias_3p": {"id": "659977122a1a0a55", "src": "hda", "uuid": "cd02928e-dde5-4ba0-b043-7e461d3b589d"}, "observed_bias": {"id": "7037a4c267c5edd7", "src": "hda", "uuid": "20392db3-2bfb-4f6b-812a-c97c003e8376"}, "expected_bias": {"id": "97064a582cfc27ff", "src": "hda", "uuid": "f2c71495-5722-4d3d-b464-407c256a5de9"}, "quants_boot_rows_txt": {"id": "fe996e4549e22ea0", "src": "hda", "uuid": "ebb6f28b-d48d-4a11-8053-ee49d7eb97a6"}, "quants_var_mat": {"id": "8b8962ff66dcf869", "src": "hda", "uuid": "4ea99ba7-6bf6-45b6-a664-9eb78d4db813"}, "quants_mean_mat": {"id": "9a7b950bd7b252ef", "src": "hda", "uuid": "f5356659-96a4-4427-9e0a-bc994351f10b"}, "whitelist_txt": {"id": "f36a30d804e3b144", "src": "hda", "uuid": "2f45c52e-8282-4be4-98c7-3f0151abef4c"}, "featureDump_txt": {"id": "21b4b2693acea78a", "src": "hda", "uuid": "53de9e0c-b52f-4b8e-8e55-a3e8acc1a44f"}, "quants_tier_mat": {"id": "4288384dd8475222", "src": "hda", "uuid": "eeb55ef8-e4d0-4bbd-9e7e-efad995cdbae"}, "quants_mat_rows_txt": {"id": "8e4662dca1bc59a1", "src": "hda", "uuid": "6c66a81a-c4fe-44c5-8433-ec829eadb69c"}, "quants_mat_cols_txt": {"id": "adcd02e067b1f957", "src": "hda", "uuid": "1a041a9e-df43-4524-b396-75bb48592e18"}, "raw_cb_frequency_txt": {"id": "809be3818664cddc", "src": "hda", "uuid": "3b9ca3a7-19b4-4cf5-83cc-65a7ea13564a"}, "quants_mat_mtx": {"id": "104956edfbaff3c3", "src": "hda", "uuid": "a96a4be9-d72b-4502-97d0-037b5dd80899"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 4194304\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:4194304\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 1005\nFalse junctions count = 730\nHash table size = 1735\nCandidate marks count = 8052\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 6382\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 1005\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 1016896 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:40.641] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:40.641] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:40.642] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:40.696] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:40.703] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:40.925] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:40.926] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.7824 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 1.37 ms\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:41.148] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:41.156] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###Logs will be written to ./output/logs\n[2024-08-30 07:19:41.893] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\n[2024-08-30 07:19:41.924] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:41.924] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:41.924] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:41.924] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:41.924] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:41.924] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:41.924] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ numCellBootstraps ] => { 2 }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:41.929] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:41.931] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:41.931] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:41.942] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:41.997] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:41.997] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:42.001] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:42.022] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:42.043] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:42.081] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:42.084] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:42.213] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:42.234] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:42.234] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.4834 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.2083 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 11.98 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 930.92 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.8072 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2416 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.3634 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2181 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 9.31 us\n-----------------------------------------\n[2024-08-30 07:19:42.234] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:42.351] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:42.352] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:42.365] [jointLog] [info] done\n[2024-08-30 07:19:42.366] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:42.366] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:43.302] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:43.302] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:43.302] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:43.303] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:43.303] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:43.314] [alevinLog] [info] Starting optimizer\n\n\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 86 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 140 cells (\u001b[31m3%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 331 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 491 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 673 cells (\u001b[31m13%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 799 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 886 cells (\u001b[31m17%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 944 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1042 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1153 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1205 cells (\u001b[31m24%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2044 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3181 cells (\u001b[31m62%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4134 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4362 cells (\u001b[31m85%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4790 cells (\u001b[31m94%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:43.460] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.460] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:43.522] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:43.525] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:43.526] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:43.553] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n", "job_stdout": null, "job_stderr": null, "stdout": "Threads = 2\nVertex length = 31\nHash functions = 5\nFilter size = 4194304\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:4194304\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 1005\nFalse junctions count = 730\nHash table size = 1735\nCandidate marks count = 8052\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 6382\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 1005\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 1016896 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "stderr": "Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:40.641] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:40.641] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:40.642] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:40.696] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:40.703] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:40.925] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:40.926] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.7824 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 1.37 ms\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:41.148] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:41.156] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###Logs will be written to ./output/logs\n[2024-08-30 07:19:41.893] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\n[2024-08-30 07:19:41.924] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:41.924] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:41.924] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:41.924] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:41.924] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:41.924] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:41.924] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ numCellBootstraps ] => { 2 }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:41.929] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:41.931] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:41.931] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:41.942] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:41.997] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:41.997] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:42.001] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:42.022] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:42.043] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:42.081] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:42.084] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:42.213] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:42.234] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:42.234] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.4834 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.2083 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 11.98 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 930.92 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.8072 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2416 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.3634 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2181 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 9.31 us\n-----------------------------------------\n[2024-08-30 07:19:42.234] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:42.351] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:42.352] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:42.365] [jointLog] [info] done\n[2024-08-30 07:19:42.366] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:42.366] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:43.302] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:43.302] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:43.302] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:43.303] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:43.303] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:43.314] [alevinLog] [info] Starting optimizer\n\n\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 86 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 140 cells (\u001b[31m3%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 331 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 491 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 673 cells (\u001b[31m13%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 799 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 886 cells (\u001b[31m17%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 944 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1042 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1153 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1205 cells (\u001b[31m24%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2044 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3181 cells (\u001b[31m62%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4134 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4362 cells (\u001b[31m85%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4790 cells (\u001b[31m94%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:43.460] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.460] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:43.522] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:43.525] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:43.526] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:43.553] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, exit_code: None, stderr: Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:40.641] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:40.641] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:40.642] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:40.696] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:40.703] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:40.925] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:40.926] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.7824 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 1.37 ms\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:41.148] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:41.156] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###Logs will be written to ./output/logs\n[2024-08-30 07:19:41.893] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\n[2024-08-30 07:19:41.924] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:41.924] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:41.924] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:41.924] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:41.924] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:41.924] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:41.924] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ numCellBootstraps ] => { 2 }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:41.929] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:41.931] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:41.931] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:41.942] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:41.997] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:41.997] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:42.001] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:42.022] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:42.043] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:42.081] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:42.084] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:42.213] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:42.234] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:42.234] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.4834 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.2083 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 11.98 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 930.92 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.8072 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2416 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.3634 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2181 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 9.31 us\n-----------------------------------------\n[2024-08-30 07:19:42.234] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:42.351] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:42.352] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:42.365] [jointLog] [info] done\n[2024-08-30 07:19:42.366] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:42.366] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:43.302] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:43.302] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:43.302] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:43.303] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:43.303] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:43.314] [alevinLog] [info] Starting optimizer\n\n\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 86 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 140 cells (\u001b[31m3%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 331 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 491 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 673 cells (\u001b[31m13%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 799 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 886 cells (\u001b[31m17%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 944 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1042 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1153 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1205 cells (\u001b[31m24%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2044 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3181 cells (\u001b[31m62%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4134 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4362 cells (\u001b[31m85%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4790 cells (\u001b[31m94%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:43.460] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.460] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:43.522] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:43.525] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:43.526] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:43.553] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/bgruening/alevin/alevin/1.5.1+galaxy0, exit_code: None, stderr: Version Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###[2024-08-30 07:19:40.641] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2024-08-30 07:19:40.641] [jLog] [info] building index\nout : ./index\n[2024-08-30 07:19:40.642] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] Removed 1 transcripts that were sequence duplicates of indexed transcripts.\n[2024-08-30 07:19:40.662] [puff::index::jointLog] [warning] If you wish to retain duplicate transcripts, please use the `--keepDuplicates` flag\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2024-08-30 07:19:40.668] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 322 cleaned references\n[2024-08-30 07:19:40.696] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2024-08-30 07:19:40.703] [puff::index::jointLog] [info] ntHll estimated 164678 distinct k-mers, setting filter size to 2^22\nallowedIn: 18\nMax Junction ID: 1201\nseen.size():9617 kmerInfo.size():1202\napproximateContigTotalLength: 145043\ncounters for complex kmers:\n(prec>1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0\ncontig count: 1412 element count: 235270 complex nodes: 8\n# of ones in rank vector: 1411\n[2024-08-30 07:19:40.925] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2024-08-30 07:19:40.926] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 235270\n-----------------------------------------\n| Loading contigs | Time = 1.7824 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading contig boundaries | Time = 1.37 ms\n-----------------------------------------\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n1411\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] contig count for validation: 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of contig vec entries: 6088\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] bits per offset entry 13\n[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Done constructing the contig vector. 1412\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] # segments = 1411\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] total length = 235270\n[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] Reading the reference files ...\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] positional integer width = 18\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] seqSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] rankSize = 235270\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] edgeVecSize = 0\n[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] num keys = 192940\n\r[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 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sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] mphf size = 0.121223 MB\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk size = 117635\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 0 = [0, 117644)\n[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] finished populating pos vector\n[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] writing index components\n[2024-08-30 07:19:41.148] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2024-08-30 07:19:41.156] [jLog] [info] done building index\nVersion Info: ### PLEASE UPGRADE SALMON ###\n### A newer version of salmon with important bug fixes and improvements is available. ####\n###\nThe newest version, available at https://github.com/COMBINE-lab/salmon/releases\ncontains new features, improvements, and bug fixes; please upgrade at your\nearliest convenience.\n###\nSign up for the salmon mailing list to hear about new versions, features and updates at:\nhttps://oceangenomics.com/subscribe\n###Logs will be written to ./output/logs\n[2024-08-30 07:19:41.893] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline\n[2024-08-30 07:19:41.924] [jointLog] [info] setting maxHashResizeThreads to 8\n[2024-08-30 07:19:41.924] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2024-08-30 07:19:41.924] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.\n[2024-08-30 07:19:41.924] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2024-08-30 07:19:41.924] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. \n[2024-08-30 07:19:41.924] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.\n[2024-08-30 07:19:41.924] [jointLog] [info] Using default value of 0.87 for minScoreFraction in Alevin\nUsing default value of 0.6 for consensusSlack in Alevin\n### alevin (dscRNA-seq quantification) v1.5.1\n### [ program ] => salmon \n### [ command ] => alevin \n### [ libType ] => { A }\n### [ index ] => { ./index }\n### [ mates1 ] => { ./mate1.fastq }\n### [ mates2 ] => { ./mate2.fastq }\n### [ output ] => { ./output }\n### [ threads ] => { 8 }\n### [ chromium ] => { }\n### [ tgMap ] => { ./alevinmap.tsv }\n### [ numCellBootstraps ] => { 2 }\n### [ keepCBFraction ] => { 1.0 }\n### [ dumpFeatures ] => { }\n### [ dumpMtx ] => { }\n### [ freqThreshold ] => { 5 }\n\n\n[2024-08-30 07:19:41.929] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)\n[2024-08-30 07:19:41.931] [alevinLog] [info] Filled with 322 txp to gene entries \n[2024-08-30 07:19:41.931] [alevinLog] [info] Found all transcripts to gene mappings\n[2024-08-30 07:19:41.942] [alevinLog] [info] Processing barcodes files (if Present) \n\n \n\n\n[2024-08-30 07:19:41.997] [alevinLog] [info] Done barcode density calculation.\n[2024-08-30 07:19:41.997] [alevinLog] [info] # Barcodes Used: \u001b[32m125000\u001b[0m / \u001b[31m125000\u001b[0m.\n[2024-08-30 07:19:42.001] [alevinLog] [info] Forcing to use 15126 cells\n[2024-08-30 07:19:42.022] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads\n[2024-08-30 07:19:42.043] [alevinLog] [info] Total \u001b[32m5104\u001b[0m(has \u001b[32m501\u001b[0m low confidence) barcodes\n[2024-08-30 07:19:42.081] [alevinLog] [info] Done True Barcode Sampling\n[2024-08-30 07:19:42.084] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done populating Z matrix\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total 0 CB got sequence corrected\n[2024-08-30 07:19:42.213] [alevinLog] [info] Done indexing Barcodes\n[2024-08-30 07:19:42.213] [alevinLog] [info] Total Unique barcodes found: 15126\n[2024-08-30 07:19:42.213] [alevinLog] [info] Used Barcodes except Whitelist: 0\n[2024-08-30 07:19:42.234] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify\n\n[2024-08-30 07:19:42.234] [alevinLog] [info] parsing read library format\n-----------------------------------------\n| Loading contig table | Time = 1.4834 ms\n-----------------------------------------\nsize = 1412\n-----------------------------------------\n| Loading contig offsets | Time = 1.2083 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 11.98 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 930.92 us\n-----------------------------------------\nsize = 235270\nNumber of ones: 1411\nNumber of ones per inventory item: 512\nInventory entries filled: 3\n-----------------------------------------\n| Loading contig boundaries | Time = 1.8072 ms\n-----------------------------------------\nsize = 235270\n-----------------------------------------\n| Loading sequence | Time = 1.2416 ms\n-----------------------------------------\nsize = 192940\n-----------------------------------------\n| Loading positions | Time = 1.3634 ms\n-----------------------------------------\nsize = 570828\n-----------------------------------------\n| Loading reference sequence | Time = 1.2181 ms\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 9.31 us\n-----------------------------------------\n[2024-08-30 07:19:42.234] [jointLog] [info] There is 1 library.\n[2024-08-30 07:19:42.351] [jointLog] [info] Loading pufferfish index\n[2024-08-30 07:19:42.352] [jointLog] [info] Loading dense pufferfish index.\n[2024-08-30 07:19:42.365] [jointLog] [info] done\n[2024-08-30 07:19:42.366] [jointLog] [info] Index contained 322 targets\n[2024-08-30 07:19:42.366] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n[2024-08-30 07:19:43.302] [jointLog] [info] Computed 41 rich equivalence classes for further processing\n[2024-08-30 07:19:43.302] [jointLog] [info] Counted 96 total reads in the equivalence classes \n[2024-08-30 07:19:43.302] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2024-08-30 07:19:43.303] [jointLog] [info] Mapping rate = 0.0768%\n\n[2024-08-30 07:19:43.303] [jointLog] [info] finished quantifyLibrary()\n[2024-08-30 07:19:43.314] [alevinLog] [info] Starting optimizer\n\n\n\u001b[A\r\r\u001b[32mAnalyzed 36 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 42 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 47 cells (\u001b[31m1%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 86 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 93 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 95 cells (\u001b[31m2%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 140 cells (\u001b[31m3%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 231 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 262 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 276 cells (\u001b[31m5%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 285 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 297 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 331 cells (\u001b[31m6%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 385 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 403 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 409 cells (\u001b[31m8%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 436 cells (\u001b[31m9%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 491 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 519 cells (\u001b[31m10%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 575 cells (\u001b[31m11%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 609 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 614 cells (\u001b[31m12%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 673 cells (\u001b[31m13%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 702 cells (\u001b[31m14%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 780 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 789 cells (\u001b[31m15%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 799 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 802 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 805 cells (\u001b[31m16%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 886 cells (\u001b[31m17%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 937 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 944 cells (\u001b[31m18%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 960 cells (\u001b[31m19%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1036 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1042 cells (\u001b[31m20%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1101 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1119 cells (\u001b[31m22%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1153 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1205 cells (\u001b[31m24%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1156 cells (\u001b[31m23%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1393 cells (\u001b[31m27%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1444 cells (\u001b[31m28%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1528 cells (\u001b[31m30%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1570 cells (\u001b[31m31%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1721 cells (\u001b[31m34%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1771 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1803 cells (\u001b[31m35%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1842 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1820 cells (\u001b[31m36%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1898 cells (\u001b[31m37%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1922 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 1957 cells (\u001b[31m38%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2044 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2064 cells (\u001b[31m40%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2210 cells (\u001b[31m43%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2229 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2266 cells (\u001b[31m44%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2336 cells (\u001b[31m46%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2660 cells (\u001b[31m52%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2769 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2781 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 2775 cells (\u001b[31m54%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3004 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3021 cells (\u001b[31m59%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3087 cells (\u001b[31m60%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3181 cells (\u001b[31m62%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3319 cells (\u001b[31m65%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3603 cells (\u001b[31m71%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3799 cells (\u001b[31m74%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 3927 cells (\u001b[31m77%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4089 cells (\u001b[31m80%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4127 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4133 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4134 cells (\u001b[31m81%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4220 cells (\u001b[31m83%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4267 cells (\u001b[31m84%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4362 cells (\u001b[31m85%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 4790 cells (\u001b[31m94%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n\u001b[A\r\r\u001b[32mAnalyzed 5103 cells (\u001b[31m100%\u001b[32m of all).\u001b[0m\n[2024-08-30 07:19:43.460] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.460] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 96.00 UMI after deduplicating.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 BiDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 UniDirected Edges.\n[2024-08-30 07:19:43.477] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read\n[2024-08-30 07:19:43.522] [alevinLog] [info] Clearing EqMap; Might take some time.\n[2024-08-30 07:19:43.525] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping\n[2024-08-30 07:19:43.526] [alevinLog] [info] Starting dumping cell v gene counts in mtx format\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished dumping counts into mtx\n[2024-08-30 07:19:43.532] [alevinLog] [info] Finished optimizer\n[2024-08-30 07:19:43.553] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :\n\nFound no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details\n\n."], "status": "failure"}}, {"id": "anndata_export/0.7.5+galaxy1-0", "has_data": true, "data": {"tool_id": "anndata_export", "tool_version": "0.7.5+galaxy1", "test_index": 0, "time_seconds": 45.00760817527771, "inputs": {"hd5_format|input": {"src": "hda", "id": "734c9a626bb2c838"}, "hd5_format|output_format": "loom", "hd5_format|filetype": "anndata"}, "job": {"model_class": "Job", "id": "8916ff9dbfc5c821", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:13:44.926733", "update_time": "2024-08-30T07:14:10.060803", "galaxy_version": "24.1", "external_id": "gxy-425l2", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/232/configs/tmpkm3z1gge' && python '/galaxy/server/database/jobs_directory/000/232/configs/tmpkm3z1gge'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"input\": {\"values\": [{\"id\": 268, \"src\": \"hda\"}]}, \"output_format\": \"loom\"}"}, "inputs": {"hd5_format|input": {"id": "734c9a626bb2c838", "src": "hda", "uuid": "114758e8-1604-4c3e-9ffc-a72473a598e9"}}, "outputs": {"loom_output": {"id": "0e58dc256cff5b8c", "src": "hda", "uuid": "a999bed7-e6f6-42cd-a710-571be5ab25c8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read('/galaxy/server/database/objects/1/1/4/dataset_114758e8-1604-4c3e-9ffc-a72473a598e9.dat')\nadata.write_loom('anndata.loom')\n ", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read('/galaxy/server/database/objects/1/1/4/dataset_114758e8-1604-4c3e-9ffc-a72473a598e9.dat')\nadata.write_loom('anndata.loom')\n ", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:13:56", "plugin": "core", "name": "end_epoch", "raw_value": "1725002036.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:13:55", "plugin": "core", "name": "start_epoch", "raw_value": "1725002035.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_export/0.7.5+galaxy1-0", "has_data": true, "data": {"tool_id": "anndata_export", "tool_version": "0.7.5+galaxy1", "test_index": 0, "time_seconds": 32.890965700149536, "inputs": {"hd5_format|input": {"src": "hda", "id": "dc0a06c42acc497a"}, "hd5_format|output_format": "loom", "hd5_format|filetype": "anndata"}, "job": {"model_class": "Job", "id": "0c5fbcc3fb28465b", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:15:30.673051", "update_time": "2024-08-30T07:15:44.083562", "galaxy_version": "24.1", "external_id": "gxy-hw6m7", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/238/configs/tmpmwo_i30l' && python '/galaxy/server/database/jobs_directory/000/238/configs/tmpmwo_i30l'", "user_email": "tests@fake.org", "command_version": "anndata version: 0.7.5\n\nloompy version: 2.0.17", "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"input\": {\"values\": [{\"id\": 282, \"src\": \"hda\"}]}, \"output_format\": \"loom\"}"}, "inputs": {"hd5_format|input": {"id": "dc0a06c42acc497a", "src": "hda", "uuid": "80d3bf79-5c7d-4fea-bb3b-be1ad1cc113d"}}, "outputs": {"loom_output": {"id": "b5720daccddf660f", "src": "hda", "uuid": "81812f4c-ccef-46d4-97fb-71e38518478e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read('/galaxy/server/database/objects/8/0/d/dataset_80d3bf79-5c7d-4fea-bb3b-be1ad1cc113d.dat')\nadata.write_loom('anndata.loom')\n ", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read('/galaxy/server/database/objects/8/0/d/dataset_80d3bf79-5c7d-4fea-bb3b-be1ad1cc113d.dat')\nadata.write_loom('anndata.loom')\n ", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:15:33", "plugin": "core", "name": "end_epoch", "raw_value": "1725002133.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:15:32", "plugin": "core", "name": "start_epoch", "raw_value": "1725002132.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_export/0.7.5+galaxy1-1", "has_data": true, "data": {"tool_id": "anndata_export", "tool_version": "0.7.5+galaxy1", "test_index": 1, "time_seconds": 26.085141897201538, "inputs": {"hd5_format|input": {"src": "hda", "id": "7dac24e6043aac32"}, "hd5_format|output_format": "tabular", "hd5_format|filetype": "anndata"}, "job": {"model_class": "Job", "id": "9f23ed907fcd9227", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:14:29.561141", "update_time": "2024-08-30T07:14:35.923452", "galaxy_version": "24.1", "external_id": "gxy-6rj5z", "handler": null, "job_runner_name": null, "command_line": "cat '/galaxy/server/database/jobs_directory/000/234/configs/tmpg13_klky' && python '/galaxy/server/database/jobs_directory/000/234/configs/tmpg13_klky'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"h5ad\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"input\": {\"values\": [{\"id\": 270, \"src\": \"hda\"}]}, \"output_format\": \"tabular\"}"}, "inputs": {"hd5_format|input": {"id": "7dac24e6043aac32", "src": "hda", "uuid": "5fd5ccaa-790f-4841-a49a-6ac2a4bb62ad"}}, "outputs": {"tabular_x": {"id": "d7f111b001e819c5", "src": "hda", "uuid": "68ecf80c-373d-4552-a227-32affe9d7c4d"}, "tabular_obs": {"id": "1074ffdf1ba4644d", "src": "hda", "uuid": "20c1b0c2-3a92-42c3-9081-fdf29853039c"}, "tabular_obsm": {"id": "d055f39f4ce4ec90", "src": "hda", "uuid": "f828518b-277c-4120-b3cf-345878219ece"}, "tabular_var": {"id": "aed4c4d4d47034ab", "src": "hda", "uuid": "7e1029fd-c4aa-4a10-8e33-b73c82cdbcf2"}, "tabular_varm": {"id": "47fccb329a775a72", "src": "hda", "uuid": "5354394a-bd73-4491-b463-2b272f151ebb"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read('/galaxy/server/database/objects/5/f/d/dataset_5fd5ccaa-790f-4841-a49a-6ac2a4bb62ad.dat')\nadata.write_csvs('.', sep=\"\\t\", skip_data = False)\n ", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nwriting .csv files to .\n", "job_stdout": null, "job_stderr": null, "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read('/galaxy/server/database/objects/5/f/d/dataset_5fd5ccaa-790f-4841-a49a-6ac2a4bb62ad.dat')\nadata.write_csvs('.', sep=\"\\t\", skip_data = False)\n ", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nwriting .csv files to .\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nwriting .csv files to .\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nwriting .csv files to .\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nwriting .csv files to .\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nwriting .csv files to .\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nwriting .csv files to .\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nwriting .csv files to .\n."], "status": "failure"}}, {"id": "anndata_export/0.7.5+galaxy1-1", "has_data": true, "data": {"tool_id": "anndata_export", "tool_version": "0.7.5+galaxy1", "test_index": 1, "time_seconds": 11.4048011302948, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "anndata_export/0.7.5+galaxy1-2", "has_data": true, "data": {"tool_id": "anndata_export", "tool_version": "0.7.5+galaxy1", "test_index": 2, "time_seconds": 33.897966623306274, "inputs": {"hd5_format|input": {"src": "hda", "id": "1363b55294005436"}, "hd5_format|filetype": "loom"}, "job": {"model_class": "Job", "id": "453ccadf86e223bb", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:14:56.000705", "update_time": "2024-08-30T07:15:09.373028", "galaxy_version": "24.1", "external_id": "gxy-q7v7x", "handler": null, "job_runner_name": null, "command_line": "mkdir ./output && mkdir ./attributes && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/0cb889db0910/anndata_export/loompy_to_tsv.py' -f '/galaxy/server/database/objects/8/7/b/dataset_87b29f87-ba0d-42c7-888b-c306b4e8dced.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"loom\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 1, \"filetype\": \"loom\", \"input\": {\"values\": [{\"id\": 276, \"src\": \"hda\"}]}}"}, "inputs": {"hd5_format|input": {"id": "1363b55294005436", "src": "hda", "uuid": "87b29f87-ba0d-42c7-888b-c306b4e8dced"}}, "outputs": {"__new_primary_file_attribute_tsvs|col_attr.tsv__": {"id": "54464ef7c0297c1f", "src": "hda", "uuid": "c83a5054-347f-458a-a834-b23e194c0731"}, "__new_primary_file_attribute_tsvs|row_attr.tsv__": {"id": "dbb2a50ca8aeae6b", "src": "hda", "uuid": "e182aea8-1878-42d0-9e55-97a6aef6836c"}, "__new_primary_file_layer_tsvs|extralayer.tsv__": {"id": "7fa970f7987f7789", "src": "hda", "uuid": "b3ecca46-9a43-48b5-ac82-a938aba204eb"}, "__new_primary_file_layer_tsvs|mainmatrix.tsv__": {"id": "52c051c290ff1f7a", "src": "hda", "uuid": "87ccdf66-1aa3-42b1-8809-ed7b5f115526"}, "__new_primary_file_layer_tsvs|thirdlayer.tsv__": {"id": "d67a6cfa691905d8", "src": "hda", "uuid": "8b0f5b5f-42b6-41bd-9d0f-6520af368e3c"}}, "copied_from_job_id": null, "output_collections": {"attribute_tsvs": {"src": "hdca", "id": "1f05aabc0d0c3dd8"}, "layer_tsvs": {"src": "hdca", "id": "d4950de95ae89100"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:14:58", "plugin": "core", "name": "end_epoch", "raw_value": "1725002098.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:14:57", "plugin": "core", "name": "start_epoch", "raw_value": "1725002097.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "anndata_export/0.7.5+galaxy1-2", "has_data": true, "data": {"tool_id": "anndata_export", "tool_version": "0.7.5+galaxy1", "test_index": 2, "time_seconds": 35.67020654678345, "inputs": {"hd5_format|input": {"src": "hda", "id": "005c3fb317fece93"}, "hd5_format|filetype": "loom"}, "job": {"model_class": "Job", "id": "f687fb6becdc363e", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/anndata_export/0.7.5+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:16:16.384821", "update_time": "2024-08-30T07:16:30.625893", "galaxy_version": "24.1", "external_id": "gxy-qm2bk", "handler": null, "job_runner_name": null, "command_line": "mkdir ./output && mkdir ./attributes && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/anndata_export/0cb889db0910/anndata_export/loompy_to_tsv.py' -f '/galaxy/server/database/objects/3/c/2/dataset_3c206d0f-9ab7-473f-9b88-b3f0d081ec75.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"loom\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "hd5_format": "{\"__current_case__\": 1, \"filetype\": \"loom\", \"input\": {\"values\": [{\"id\": 285, \"src\": \"hda\"}]}}"}, "inputs": {"hd5_format|input": {"id": "005c3fb317fece93", "src": "hda", "uuid": "3c206d0f-9ab7-473f-9b88-b3f0d081ec75"}}, "outputs": {"__new_primary_file_attribute_tsvs|col_attr.tsv__": {"id": "3ca30fd587d4e879", "src": "hda", "uuid": "982b9abf-4860-43a4-968a-23e76c23a9a3"}, "__new_primary_file_attribute_tsvs|row_attr.tsv__": {"id": "ba9aa0c87b6e4cac", "src": "hda", "uuid": "f1085286-359b-4198-92aa-9e3f9301ce6a"}, "__new_primary_file_layer_tsvs|extralayer.tsv__": {"id": "34b4dc44e77155a2", "src": "hda", "uuid": "6abbc978-7297-4379-96aa-c32d6eb53d20"}, "__new_primary_file_layer_tsvs|mainmatrix.tsv__": {"id": "01fd6fcd8d297d39", "src": "hda", "uuid": "fa641ce3-a9d6-40d3-aa45-55e2c1bc74bd"}, "__new_primary_file_layer_tsvs|thirdlayer.tsv__": {"id": "ecb83fdf9dcb6c26", "src": "hda", "uuid": "7c8abeb6-9915-4f0a-91db-0620e0c0057b"}}, "copied_from_job_id": null, "output_collections": {"attribute_tsvs": {"src": "hdca", "id": "7100e5847b32f513"}, "layer_tsvs": {"src": "hdca", "id": "1c1c797d10c8d2f2"}}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:16:19", "plugin": "core", "name": "end_epoch", "raw_value": "1725002179.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:16:18", "plugin": "core", "name": "start_epoch", "raw_value": "1725002178.0000000"}, {"title": "Memory Allocated (MB)", "value": "16320", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "16320.0000000"}, {"title": "Cores Allocated", "value": "4", "plugin": "core", "name": "galaxy_slots", "raw_value": "4.0000000"}]}, "status": "success"}}, {"id": "bam_to_sam/2.0.1-0", "has_data": true, "data": {"tool_id": "bam_to_sam", "tool_version": "2.0.1", "test_index": 0, "time_seconds": 34.365830421447754, "inputs": {"input1": {"src": "hda", "id": "7b7320d72f9e293c"}, "header": "-h"}, "job": {"model_class": "Job", "id": "e21ca87e47d02737", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:12:26.661749", "update_time": "2024-08-30T07:12:40.615684", "galaxy_version": "24.1", "external_id": "gxy-vk8rs", "handler": null, "job_runner_name": null, "command_line": "samtools view -o '/galaxy/server/database/objects/1/7/5/dataset_1753b5f2-7084-4d2b-a039-296622de16a4.dat' -h '/galaxy/server/database/objects/b/2/f/dataset_b2f560da-78c4-47f5-b71e-e02829d526e5.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "header": "\"-h\""}, "inputs": {"input1": {"id": "7b7320d72f9e293c", "src": "hda", "uuid": "b2f560da-78c4-47f5-b71e-e02829d526e5"}}, "outputs": {"output1": {"id": "bd6f7f62af7fc97a", "src": "hda", "uuid": "1753b5f2-7084-4d2b-a039-296622de16a4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 07:12:29", "plugin": "core", "name": "end_epoch", "raw_value": "1725001949.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:12:29", "plugin": "core", "name": "start_epoch", "raw_value": "1725001949.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bam_to_sam/2.0.1-1", "has_data": true, "data": {"tool_id": "bam_to_sam", "tool_version": "2.0.1", "test_index": 1, "time_seconds": 11.249733686447144, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "bam_to_sam/2.0.1-2", "has_data": true, "data": {"tool_id": "bam_to_sam", "tool_version": "2.0.1", "test_index": 2, "time_seconds": 32.23485779762268, "inputs": {"input1": {"src": "hda", "id": "0faaa6b568631866"}, "header": ""}, "job": {"model_class": "Job", "id": "092b784731aa0339", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:13:11.578285", "update_time": "2024-08-30T07:13:24.229803", "galaxy_version": "24.1", "external_id": "gxy-nrnp4", "handler": null, "job_runner_name": null, "command_line": "samtools view -o '/galaxy/server/database/objects/1/a/6/dataset_1a6e748d-7293-4e15-b98f-5ad6bb1e1b89.dat' '/galaxy/server/database/objects/2/6/8/dataset_2681c3a9-ecc9-4d01-be83-356f6516651d.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "header": "\"\""}, "inputs": {"input1": {"id": "0faaa6b568631866", "src": "hda", "uuid": "2681c3a9-ecc9-4d01-be83-356f6516651d"}}, "outputs": {"output1": {"id": "49010eaead7e729e", "src": "hda", "uuid": "1a6e748d-7293-4e15-b98f-5ad6bb1e1b89"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 07:13:13", "plugin": "core", "name": "end_epoch", "raw_value": 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"state": "ok", "exit_code": 0, "create_time": "2024-08-30T08:15:48.578051", "update_time": "2024-08-30T08:16:08.616666", "galaxy_version": "24.1", "external_id": "gxy-rb62m", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bcftools convert --output-type 'v' --gensample2vcf '/galaxy/server/database/objects/e/3/d/dataset_e3d7dafa-1b7d-46d2-9b40-35ffafe6800c.dat,/galaxy/server/database/objects/c/2/1/dataset_c21fd1d6-1c99-4aae-825a-684ad4dc4c95.dat' > '/galaxy/server/database/objects/d/f/1/dataset_df1b5ece-5453-40fa-b68f-a14122433cbe.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "convert": "{\"__current_case__\": 2, \"convert_from\": \"gen_sample\", \"input_file\": {\"values\": [{\"id\": 601, \"src\": \"hda\"}]}, \"input_sample\": {\"values\": [{\"id\": 602, \"src\": \"hda\"}]}}"}, "inputs": {"convert|input_sample": {"id": "f87261f049cd4e26", "src": "hda", "uuid": "c21fd1d6-1c99-4aae-825a-684ad4dc4c95"}, "convert|input_file": {"id": "0041a886ca590980", "src": "hda", "uuid": "e3d7dafa-1b7d-46d2-9b40-35ffafe6800c"}}, "outputs": {"output_file": {"id": "cc9e89d83d4c51f9", "src": "hda", "uuid": "df1b5ece-5453-40fa-b68f-a14122433cbe"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of processed rows: \t32\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Number of processed rows: \t32\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 08:15:56", "plugin": "core", "name": "end_epoch", "raw_value": "1725005756.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 08:15:56", "plugin": "core", "name": "start_epoch", "raw_value": "1725005756.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_convert_to_vcf/1.10-1", "has_data": true, "data": {"tool_id": "bcftools_convert_to_vcf", "tool_version": "1.10", "test_index": 1, "time_seconds": 34.32776069641113, "inputs": {"convert|input_file": {"src": "hda", "id": "b76199b6f589c444"}, "convert|input_sample": {"src": "hda", "id": "898de9ae0ab38fd1"}, "convert|convert_from": "hap_sample", "output_type": "v"}, "job": {"model_class": "Job", "id": "4c631faa67f4435b", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T08:16:29.952108", "update_time": "2024-08-30T08:16:43.071554", "galaxy_version": "24.1", "external_id": "gxy-55594", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bcftools convert --output-type 'v' --hapsample2vcf '/galaxy/server/database/objects/c/8/9/dataset_c89ff992-e060-49a6-877b-5c24fa9bc1e9.dat,/galaxy/server/database/objects/c/b/0/dataset_cb0d6adc-71ba-4101-af64-28c1d0fbfbde.dat' > '/galaxy/server/database/objects/c/8/3/dataset_c833d03c-c732-4ca3-bf2d-b448dba97439.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "convert": "{\"__current_case__\": 3, \"convert_from\": \"hap_sample\", \"input_file\": {\"values\": [{\"id\": 604, \"src\": \"hda\"}]}, \"input_sample\": {\"values\": [{\"id\": 605, \"src\": \"hda\"}]}}"}, "inputs": {"convert|input_sample": {"id": "898de9ae0ab38fd1", "src": "hda", "uuid": "cb0d6adc-71ba-4101-af64-28c1d0fbfbde"}, "convert|input_file": {"id": "b76199b6f589c444", "src": "hda", "uuid": "c89ff992-e060-49a6-877b-5c24fa9bc1e9"}}, "outputs": {"output_file": {"id": "642727135ee639b7", "src": "hda", "uuid": "c833d03c-c732-4ca3-bf2d-b448dba97439"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of processed rows: \t35\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Number of processed rows: \t35\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 08:16:32", "plugin": "core", "name": "end_epoch", "raw_value": "1725005792.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 08:16:32", "plugin": "core", "name": "start_epoch", "raw_value": "1725005792.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_convert_to_vcf/1.10-2", "has_data": true, "data": {"tool_id": "bcftools_convert_to_vcf", "tool_version": "1.10", "test_index": 2, "time_seconds": 38.878907918930054, "inputs": {"convert|input_file": {"src": "hda", "id": "68b3704a7abe6a24"}, "convert|input_legend": {"src": "hda", "id": "470a48a6d55d1976"}, "convert|input_sample": {"src": "hda", "id": "29b1a7ae05ddb4b7"}, "convert|convert_from": "hap_legend_sample", "output_type": "v"}, "job": {"model_class": "Job", "id": "8c9132f0c6a1175e", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T08:17:07.958291", "update_time": "2024-08-30T08:17:22.028480", "galaxy_version": "24.1", "external_id": "gxy-z5mw5", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bcftools convert --output-type 'v' --haplegendsample2vcf '/galaxy/server/database/objects/5/f/9/dataset_5f9e01ca-e556-4cd6-b8fb-c79cd8de374a.dat,/galaxy/server/database/objects/9/1/6/dataset_9167239c-8d4f-4ac7-a2cd-c3f19e423614.dat,/galaxy/server/database/objects/5/6/6/dataset_566c20a1-d248-4f50-8f24-44b30d250abe.dat' > '/galaxy/server/database/objects/e/3/f/dataset_e3fbbd9d-6d81-4c0d-ab29-eafcb69f97e0.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "convert": "{\"__current_case__\": 4, \"convert_from\": \"hap_legend_sample\", \"input_file\": {\"values\": [{\"id\": 607, \"src\": \"hda\"}]}, \"input_legend\": {\"values\": [{\"id\": 608, \"src\": \"hda\"}]}, \"input_sample\": {\"values\": [{\"id\": 609, \"src\": \"hda\"}]}}"}, "inputs": {"convert|input_sample": {"id": "29b1a7ae05ddb4b7", "src": "hda", "uuid": "566c20a1-d248-4f50-8f24-44b30d250abe"}, "convert|input_legend": {"id": "470a48a6d55d1976", "src": "hda", "uuid": "9167239c-8d4f-4ac7-a2cd-c3f19e423614"}, "convert|input_file": {"id": "68b3704a7abe6a24", "src": "hda", "uuid": "5f9e01ca-e556-4cd6-b8fb-c79cd8de374a"}}, "outputs": {"output_file": {"id": "51c291131e66f5c6", "src": "hda", "uuid": "e3fbbd9d-6d81-4c0d-ab29-eafcb69f97e0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Number of processed rows: \t35\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Number of processed rows: \t35\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 08:17:10", "plugin": "core", "name": "end_epoch", "raw_value": "1725005830.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 08:17:10", "plugin": "core", "name": "start_epoch", "raw_value": "1725005830.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_convert_to_vcf/1.10-3", "has_data": true, "data": {"tool_id": "bcftools_convert_to_vcf", "tool_version": "1.10", "test_index": 3, "time_seconds": 33.54118514060974, "inputs": {"convert|input_file": {"src": "hda", "id": "60f7b8c3cb713579"}, "convert|reference_source|fasta_ref": {"src": "hda", "id": "328ed2fcf572a677"}, "convert|reference_source|reference_source_selector": "history", "convert|convert_from": "gvcf", "output_type": "v"}, "job": {"model_class": "Job", "id": "46da947090ba3225", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T08:17:42.482356", "update_time": "2024-08-30T08:17:55.649093", "galaxy_version": "24.1", "external_id": "gxy-2ff99", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/7/c/7/dataset_7c772d68-f524-498c-9643-0ff08c7f8725.dat' > input.vcf.gz && bcftools index input.vcf.gz && ln -s '/galaxy/server/database/objects/d/0/6/dataset_d0696dfc-f611-4e1a-9591-ad28b515fabd.dat' ref.fa && samtools faidx ref.fa && bcftools convert --output-type 'v' --fasta-ref ref.fa --gvcf2vcf input.vcf.gz > '/galaxy/server/database/objects/e/5/e/dataset_e5e3ad29-d8a2-4e51-b1c9-00435b175578.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "convert": "{\"__current_case__\": 1, \"convert_from\": \"gvcf\", \"input_file\": {\"values\": [{\"id\": 611, \"src\": \"hda\"}]}, \"reference_source\": {\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 612, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}}"}, "inputs": {"convert|reference_source|fasta_ref": {"id": "328ed2fcf572a677", "src": "hda", "uuid": "d0696dfc-f611-4e1a-9591-ad28b515fabd"}, "convert|input_file": {"id": "60f7b8c3cb713579", "src": "hda", "uuid": "7c772d68-f524-498c-9643-0ff08c7f8725"}}, "outputs": {"output_file": {"id": "8919c3e405fa2c96", "src": "hda", "uuid": "e5e3ad29-d8a2-4e51-b1c9-00435b175578"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 08:17:45", "plugin": "core", "name": "end_epoch", "raw_value": "1725005865.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 08:17:44", "plugin": "core", "name": "start_epoch", "raw_value": "1725005864.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_convert_to_vcf/1.10-4", "has_data": true, "data": {"tool_id": "bcftools_convert_to_vcf", "tool_version": "1.10", "test_index": 4, "status": "skip"}}, {"id": "bcftools_convert_to_vcf/1.10-5", "has_data": true, "data": {"tool_id": "bcftools_convert_to_vcf", "tool_version": "1.10", "test_index": 5, "time_seconds": 34.6780960559845, "inputs": {"convert|input_file": {"src": "hda", "id": "10ec0f17f48d41d2"}, "convert|reference_source|fasta_ref": {"src": "hda", "id": "108f561981dcb2a8"}, "convert|reference_source|reference_source_selector": "history", "convert|samples": "SAMPLE1", "convert|columns": "ID,CHROM,POS,AA", "convert|convert_from": "tsv", "output_type": "v"}, "job": {"model_class": "Job", "id": "ded499747d400639", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_convert_to_vcf/bcftools_convert_to_vcf/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T08:18:16.602385", "update_time": "2024-08-30T08:18:30.225776", "galaxy_version": "24.1", "external_id": "gxy-tgqnf", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; ln -s '/galaxy/server/database/objects/d/6/d/dataset_d6d8c81f-bd19-489e-a346-0ed134c813ed.dat' ref.fa && samtools faidx ref.fa && bcftools convert --output-type 'v' --fasta-ref ref.fa --samples 'SAMPLE1' --columns 'ID,CHROM,POS,AA' --tsv2vcf '/galaxy/server/database/objects/9/2/9/dataset_9295a5b2-cc87-4c33-9267-c2bf0f6e741f.dat' > '/galaxy/server/database/objects/1/d/e/dataset_1de10f4d-28f0-477e-9806-8a9278d4eea1.dat'", "user_email": "tests@fake.org", "command_version": "Version: 1.10.2 (using htslib 1.10.2)", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "output_type": "\"v\"", "convert": "{\"__current_case__\": 0, \"columns\": \"ID,CHROM,POS,AA\", \"convert_from\": \"tsv\", \"input_file\": {\"values\": [{\"id\": 614, \"src\": \"hda\"}]}, \"invert_samples\": false, \"invert_samples_file\": false, \"reference_source\": {\"__current_case__\": 1, \"fasta_ref\": {\"values\": [{\"id\": 615, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}, \"samples\": \"SAMPLE1\", \"samples_file\": null}"}, "inputs": {"convert|reference_source|fasta_ref": {"id": "108f561981dcb2a8", "src": "hda", "uuid": "d6d8c81f-bd19-489e-a346-0ed134c813ed"}, "convert|input_file": {"id": "10ec0f17f48d41d2", "src": "hda", "uuid": "9295a5b2-cc87-4c33-9267-c2bf0f6e741f"}}, "outputs": {"output_file": {"id": "3f8e4fac2e28e358", "src": "hda", "uuid": "1de10f4d-28f0-477e-9806-8a9278d4eea1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Rows total: \t27\nRows skipped: \t0\nMissing GTs: \t1\nHom RR: \t14\nHet RA: \t7\nHom AA: \t5\nHet AA: \t0\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Rows total: \t27\nRows skipped: \t0\nMissing GTs: \t1\nHom RR: \t14\nHet RA: \t7\nHom AA: \t5\nHet AA: \t0\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 08:18:18", "plugin": "core", "name": "end_epoch", "raw_value": "1725005898.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 08:18:17", "plugin": "core", "name": "start_epoch", "raw_value": "1725005897.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "bcftools_convert_to_vcf/1.10-6", "has_data": true, "data": {"tool_id": "bcftools_convert_to_vcf", "tool_version": "1.10", "test_index": 6, "status": "skip"}}, {"id": "bcftools_plugin_fill_an_ac/1.10-0", "has_data": true, "data": {"tool_id": "bcftools_plugin_fill_an_ac", "tool_version": "1.10", "test_index": 0, "time_seconds": 39.2325804233551, "inputs": {"input_file": {"src": "hda", "id": "c484e674ad0997ef"}, "output_type": "v"}, "job": {"model_class": "Job", "id": "ea365538d0103c79", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_plugin_fill_an_ac/bcftools_plugin_fill_an_ac/1.10", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T08:18:51.404467", "update_time": "2024-08-30T08:19:10.749198", "galaxy_version": "24.1", "external_id": "gxy-rfthm", "handler": null, "job_runner_name": null, "command_line": "export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; bgzip -c '/galaxy/server/database/objects/f/2/9/dataset_f29b5932-d44d-4170-b181-91fef5ca53de.dat' > input.vcf.gz && bcftools index input.vcf.gz && bcftools plugin fill-AN-AC --output-type 'v' --threads ${GALAXY_SLOTS:-4} input.vcf.gz > 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"copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, exit_code: None, stderr: .", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join/0.0.3, exit_code: None, stderr: ."], "status": "failure"}}, {"id": "deeptools_plot_coverage/3.3.2.0.0-0", "has_data": true, "data": {"tool_id": "deeptools_plot_coverage", "tool_version": "3.3.2.0.0", "test_index": 0, "time_seconds": 57.20976209640503, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "f8dd7585f070dbe4"}, {"src": "hda", "id": "f8dd7585f070dbe4"}], "advancedOpt|plotTitle": "Test Title from Galaxy", "advancedOpt|showAdvancedOpt": "yes", "outRawCounts": true}, "job": {"model_class": "Job", "id": "7b54e434d98e54d8", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:30:47.057299", "update_time": "2024-08-30T06:31:23.591434", "galaxy_version": "24.1", "external_id": "gxy-csds6", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/f/6/0/dataset_f6098b42-5c07-4c24-b384-bd975ebe8cad.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/6/1/2/metadata_612a1313-973b-40f8-96d4-cbba3f20d1b9.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/f/6/0/dataset_f6098b42-5c07-4c24-b384-bd975ebe8cad.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/6/1/2/metadata_612a1313-973b-40f8-96d4-cbba3f20d1b9.dat' './1.bam.bai' && plotCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --plotFile '/galaxy/server/database/objects/9/5/5/dataset_9552d794-3830-48ec-8459-8a7271ea3f5a.dat' --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --plotFileFormat 'png' --outRawCounts '/galaxy/server/database/objects/4/a/a/dataset_4aa1c99e-9ec9-4634-ab2f-684e89696346.dat' --numberOfSamples '100000' --numberOfSamples 100000 --plotTitle 'Test Title from Galaxy' --minMappingQuality '1' --plotWidth '15.0' --plotHeight '5.0'", "user_email": "tests@fake.org", "command_version": "plotCoverage 3.3.2", "params": {"multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 29, \"src\": \"hda\"}, {\"id\": 29, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}", "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "BED": null, "coverageOpt": "{\"__current_case__\": 0, \"showCoverageOpt\": \"no\"}", "advancedOpt": "{\"__current_case__\": 1, \"blackListFileName\": null, \"centerReads\": false, \"doExtendCustom\": {\"__current_case__\": 0, \"doExtend\": \"no\"}, \"ignoreDuplicates\": false, \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"1\", \"numberOfSamples\": \"100000\", \"plotHeight\": \"5.0\", \"plotTitle\": \"Test Title from Galaxy\", \"plotWidth\": \"15.0\", \"region\": \"\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"showAdvancedOpt\": \"yes\", \"skipZeros\": false}", "outFileFormat": "\"png\"", "outRawCounts": "true", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "dbkey": "\"?\"", "__input_ext": "\"input\""}, "inputs": {"multibam_conditional|bamfiles": {"id": "f8dd7585f070dbe4", "src": "hda", "uuid": "f6098b42-5c07-4c24-b384-bd975ebe8cad"}, "multibam_conditional|bamfiles1": {"id": "f8dd7585f070dbe4", "src": "hda", "uuid": "f6098b42-5c07-4c24-b384-bd975ebe8cad"}, "multibam_conditional|bamfiles2": {"id": "f8dd7585f070dbe4", "src": "hda", "uuid": "f6098b42-5c07-4c24-b384-bd975ebe8cad"}}, "outputs": {"outFileName": {"id": "7b54e434d98e54d8", "src": "hda", "uuid": "9552d794-3830-48ec-8459-8a7271ea3f5a"}, "outFileRawCounts": {"id": "91417bfbdc142bbe", "src": "hda", "uuid": "4aa1c99e-9ec9-4634-ab2f-684e89696346"}, "outFileCoverageMetrics": {"id": "93e9afb013404baf", "src": "hda", "uuid": "64280202-66e6-4fad-bb48-069a26d2da8e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "sample\tmean\tstd\tmin\t25%\t50%\t75%\tmax\nbowtie2 test1.bam\t0.50\t4.10\t0\t0.0\t0.0\t0.0\t35\t\nbowtie2 test1.bam\t0.50\t4.10\t0\t0.0\t0.0\t0.0\t35\t\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "sample\tmean\tstd\tmin\t25%\t50%\t75%\tmax\nbowtie2 test1.bam\t0.50\t4.10\t0\t0.0\t0.0\t0.0\t35\t\nbowtie2 test1.bam\t0.50\t4.10\t0\t0.0\t0.0\t0.0\t35\t\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:31:04", "plugin": "core", "name": "start_epoch", "raw_value": "1724999464.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:31:06", "plugin": "core", "name": "end_epoch", "raw_value": "1724999466.0000000"}, {"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}]}, "status": "success"}}, {"id": "deeptools_plot_coverage/3.3.2.0.0-1", "has_data": true, "data": {"tool_id": "deeptools_plot_coverage", "tool_version": "3.3.2.0.0", "test_index": 1, "time_seconds": 35.33493971824646, "inputs": {"multibam_conditional|bamfiles": [{"src": "hda", "id": "59c964396048ff3a"}, {"src": "hda", "id": "59c964396048ff3a"}], "coverageOpt|thresholds_0|coverageThreshold": "20", "coverageOpt|thresholds_1|coverageThreshold": "10", "coverageOpt|thresholds_2|coverageThreshold": "5", "coverageOpt|thresholds_3|coverageThreshold": "0", "coverageOpt|showCoverageOpt": "yes", "advancedOpt|plotTitle": "Test Title from Galaxy", "advancedOpt|showAdvancedOpt": "yes"}, "job": {"model_class": "Job", "id": "93e9afb013404baf", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:31:43.980709", "update_time": "2024-08-30T06:31:58.945497", "galaxy_version": "24.1", "external_id": "gxy-srfz4", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/a/9/d/dataset_a9d3f4d5-7854-4d9f-a46b-1645ec8be9c1.dat' './0.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/5/a/7/metadata_5a731312-feb6-4d34-bd13-58cf0fdc7bab.dat' './0.bam.bai' && ln -s '/galaxy/server/database/objects/a/9/d/dataset_a9d3f4d5-7854-4d9f-a46b-1645ec8be9c1.dat' './1.bam' && ln -s '/galaxy/server/database/objects/_metadata_files/5/a/7/metadata_5a731312-feb6-4d34-bd13-58cf0fdc7bab.dat' './1.bam.bai' && plotCoverage --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --plotFile '/galaxy/server/database/objects/5/1/7/dataset_517c57d5-216c-4cad-8540-ea560fab91f5.dat' --bamfiles '0.bam' '1.bam' --labels 'bowtie2 test1.bam' 'bowtie2 test1.bam' --plotFileFormat 'png' --outCoverageMetrics '/galaxy/server/database/objects/b/a/0/dataset_ba012fea-98cf-4341-8d05-584312fdbc89.dat' -ct 20 -ct 10 -ct 5 -ct 0 --numberOfSamples '100000' --numberOfSamples 100000 --plotTitle 'Test Title from Galaxy' --minMappingQuality '1' --plotWidth '15.0' --plotHeight '5.0'", "user_email": "tests@fake.org", "command_version": "plotCoverage 3.3.2", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "outRawCounts": "false", "outFileFormat": "\"png\"", "advancedOpt": "{\"__current_case__\": 1, \"blackListFileName\": null, \"centerReads\": false, \"doExtendCustom\": {\"__current_case__\": 0, \"doExtend\": \"no\"}, \"ignoreDuplicates\": false, \"maxFragmentLength\": \"0\", \"minFragmentLength\": \"0\", \"minMappingQuality\": \"1\", \"numberOfSamples\": \"100000\", \"plotHeight\": \"5.0\", \"plotTitle\": \"Test Title from Galaxy\", \"plotWidth\": \"15.0\", \"region\": \"\", \"samFlagExclude\": \"\", \"samFlagInclude\": \"\", \"showAdvancedOpt\": \"yes\", \"skipZeros\": false}", "coverageOpt": "{\"__current_case__\": 1, \"outCoverageMetrics\": false, \"showCoverageOpt\": \"yes\", \"thresholds\": [{\"__index__\": 0, \"coverageThreshold\": \"20\"}, {\"__index__\": 1, \"coverageThreshold\": \"10\"}, {\"__index__\": 2, \"coverageThreshold\": \"5\"}, {\"__index__\": 3, \"coverageThreshold\": \"0\"}]}", "BED": null, "custom_sample_labels_conditional": "{\"__current_case__\": 0, \"custom_labels_select\": \"No\"}", "multibam_conditional": "{\"__current_case__\": 0, \"bamfiles\": {\"values\": [{\"id\": 33, \"src\": \"hda\"}, {\"id\": 33, \"src\": \"hda\"}]}, \"orderMatters\": \"No\"}"}, "inputs": {"multibam_conditional|bamfiles": {"id": "59c964396048ff3a", "src": "hda", "uuid": "a9d3f4d5-7854-4d9f-a46b-1645ec8be9c1"}, "multibam_conditional|bamfiles1": {"id": "59c964396048ff3a", "src": "hda", "uuid": "a9d3f4d5-7854-4d9f-a46b-1645ec8be9c1"}, "multibam_conditional|bamfiles2": {"id": "59c964396048ff3a", "src": "hda", "uuid": "a9d3f4d5-7854-4d9f-a46b-1645ec8be9c1"}}, "outputs": {"outFileName": {"id": "7b9e4b2fc7b1fff8", "src": "hda", "uuid": "517c57d5-216c-4cad-8540-ea560fab91f5"}, "outFileCoverageMetrics": {"id": "962284acfddf59f3", "src": "hda", "uuid": "ba012fea-98cf-4341-8d05-584312fdbc89"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "sample\tmean\tstd\tmin\t25%\t50%\t75%\tmax\nbowtie2 test1.bam\t0.50\t4.10\t0\t0.0\t0.0\t0.0\t35\t\nbowtie2 test1.bam\t0.50\t4.10\t0\t0.0\t0.0\t0.0\t35\t\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "sample\tmean\tstd\tmin\t25%\t50%\t75%\tmax\nbowtie2 test1.bam\t0.50\t4.10\t0\t0.0\t0.0\t0.0\t35\t\nbowtie2 test1.bam\t0.50\t4.10\t0\t0.0\t0.0\t0.0\t35\t\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:31:47", "plugin": "core", "name": "end_epoch", "raw_value": "1724999507.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:31:46", "plugin": "core", "name": "start_epoch", "raw_value": "1724999506.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "flye/2.6-0", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.6", "test_index": 0, "time_seconds": 117.15544581413269, "inputs": {"inputs": {"src": "hda", "id": "4e6f0dd175068b78"}, "mode": "--pacbio-raw", "g": "10000"}, "job": {"model_class": "Job", "id": "459278c878cfe3a2", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:40:16.367323", "update_time": "2024-08-30T06:41:51.828556", "galaxy_version": "24.1", "external_id": "gxy-5wzzm", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/0/f/3/dataset_0f3ece5d-9d70-4d5e-ae7a-bda753aaeedb.dat' ./input_0.fasta && flye --pacbio-raw ./input_0.fasta -o out_dir -g '10000' -t ${GALAXY_SLOTS:-4} -i 1 2>&1", "user_email": "tests@fake.org", "command_version": "2.6-release", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "no_trestle": "false", "meta": "false", "plasmids": "false", "asm": "\"\"", "m": "\"\"", "i": "\"1\"", "g": "\"10000\"", "mode": "\"--pacbio-raw\""}, "inputs": {"inputs": {"id": "4e6f0dd175068b78", "src": "hda", "uuid": "0f3ece5d-9d70-4d5e-ae7a-bda753aaeedb"}, "inputs1": {"id": "4e6f0dd175068b78", "src": "hda", "uuid": "0f3ece5d-9d70-4d5e-ae7a-bda753aaeedb"}}, "outputs": {"consensus": {"id": "e2496e77ca6055d5", "src": "hda", "uuid": "46cbe38e-aeff-4817-83fe-90c6ec9e21a8"}, "assembly_graph": {"id": "da84a85513cca168", "src": "hda", "uuid": "c8f34cd7-5991-4428-b45f-fb6ac51df2c4"}, "assembly_gfa": {"id": "402e33d11f7d82ac", "src": "hda", "uuid": "e087b379-db61-4fa5-8b54-cfd6fa3c3054"}, "assembly_info": {"id": "5495d65c4d343198", "src": "hda", "uuid": "ba859f94-440d-4657-bef8-9c5898e677e8"}, "flye_log": {"id": "1abe3bf7f8dd0c3a", "src": "hda", "uuid": "80c99acf-ad65-49c3-8a72-4796a515569a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[2024-08-30 06:40:23] INFO: Starting Flye 2.6-release\n[2024-08-30 06:40:23] INFO: >>>STAGE: configure\n[2024-08-30 06:40:23] INFO: Configuring run\n[2024-08-30 06:40:23] INFO: Total read length: 1466260\n[2024-08-30 06:40:23] INFO: Input genome size: 10000\n[2024-08-30 06:40:23] INFO: Estimated coverage: 146\n[2024-08-30 06:40:23] INFO: Reads N50/N90: 9054 / 4697\n[2024-08-30 06:40:23] INFO: Minimum overlap set to 5000\n[2024-08-30 06:40:23] INFO: Selected k-mer size: 15\n[2024-08-30 06:40:23] INFO: >>>STAGE: assembly\n[2024-08-30 06:40:23] INFO: Assembling disjointigs\n[2024-08-30 06:40:23] INFO: Reading sequences\n[2024-08-30 06:40:23] INFO: Generating solid k-mer index\n[2024-08-30 06:40:45] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:40:45] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:40:45] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:40:49] INFO: Extending reads\n[2024-08-30 06:40:52] INFO: Overlap-based coverage: 25\n[2024-08-30 06:40:52] INFO: Median overlap divergence: 0.169063\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:40:52] INFO: Assembled 1 disjointigs\n[2024-08-30 06:40:52] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2024-08-30 06:40:52] INFO: >>>STAGE: consensus\n[2024-08-30 06:40:52] INFO: Running Minimap2\n[2024-08-30 06:40:53] INFO: Computing consensus\n[2024-08-30 06:40:54] INFO: Alignment error rate: 0.158711\n[2024-08-30 06:40:54] INFO: >>>STAGE: repeat\n[2024-08-30 06:40:54] INFO: Building and resolving repeat graph\n[2024-08-30 06:40:54] INFO: Reading sequences\n[2024-08-30 06:40:54] INFO: Building repeat graph\n50% 100% \n[2024-08-30 06:41:16] INFO: Median overlap divergence: 0\n[2024-08-30 06:41:16] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:41:38] INFO: Aligned read sequence: 1184568 / 1313105 (0.902112)\n[2024-08-30 06:41:38] INFO: Median overlap divergence: 0.0607255\n[2024-08-30 06:41:38] INFO: Mean edge coverage: 29\n[2024-08-30 06:41:38] INFO: Resolving repeats\n[2024-08-30 06:41:38] INFO: >>>STAGE: trestle\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25aad00000073'\n[2024-08-30 06:41:38] INFO: Simple unbridged repeats: 0\n[2024-08-30 06:41:38] INFO: Resolved: 0\n[2024-08-30 06:41:38] INFO: >>>STAGE: contigger\n[2024-08-30 06:41:38] INFO: Generating contigs\n[2024-08-30 06:41:38] INFO: Reading sequences\n[2024-08-30 06:41:38] INFO: Generated 1 contigs\n[2024-08-30 06:41:38] INFO: Added 0 scaffold connections\n[2024-08-30 06:41:39] INFO: >>>STAGE: polishing\n[2024-08-30 06:41:39] INFO: Polishing genome (1/1)\n[2024-08-30 06:41:39] INFO: Running minimap2\n[2024-08-30 06:41:39] INFO: Separating alignment into bubbles\n[2024-08-30 06:41:40] INFO: Alignment error rate: 0.101562\n[2024-08-30 06:41:40] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25ac700000074'\n[2024-08-30 06:41:41] INFO: >>>STAGE: finalize\n[2024-08-30 06:41:41] INFO: Assembly statistics:\n\n\tTotal length:\t39948\n\tFragments:\t1\n\tFragments N50:\t39948\n\tLargest frg:\t39948\n\tScaffolds:\t0\n\tMean coverage:\t28\n\n[2024-08-30 06:41:41] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/74/working/out_dir/assembly.fasta\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[2024-08-30 06:40:23] INFO: Starting Flye 2.6-release\n[2024-08-30 06:40:23] INFO: >>>STAGE: configure\n[2024-08-30 06:40:23] INFO: Configuring run\n[2024-08-30 06:40:23] INFO: Total read length: 1466260\n[2024-08-30 06:40:23] INFO: Input genome size: 10000\n[2024-08-30 06:40:23] INFO: Estimated coverage: 146\n[2024-08-30 06:40:23] INFO: Reads N50/N90: 9054 / 4697\n[2024-08-30 06:40:23] INFO: Minimum overlap set to 5000\n[2024-08-30 06:40:23] INFO: Selected k-mer size: 15\n[2024-08-30 06:40:23] INFO: >>>STAGE: assembly\n[2024-08-30 06:40:23] INFO: Assembling disjointigs\n[2024-08-30 06:40:23] INFO: Reading sequences\n[2024-08-30 06:40:23] INFO: Generating solid k-mer index\n[2024-08-30 06:40:45] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:40:45] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:40:45] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:40:49] INFO: Extending reads\n[2024-08-30 06:40:52] INFO: Overlap-based coverage: 25\n[2024-08-30 06:40:52] INFO: Median overlap divergence: 0.169063\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:40:52] INFO: Assembled 1 disjointigs\n[2024-08-30 06:40:52] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2024-08-30 06:40:52] INFO: >>>STAGE: consensus\n[2024-08-30 06:40:52] INFO: Running Minimap2\n[2024-08-30 06:40:53] INFO: Computing consensus\n[2024-08-30 06:40:54] INFO: Alignment error rate: 0.158711\n[2024-08-30 06:40:54] INFO: >>>STAGE: repeat\n[2024-08-30 06:40:54] INFO: Building and resolving repeat graph\n[2024-08-30 06:40:54] INFO: Reading sequences\n[2024-08-30 06:40:54] INFO: Building repeat graph\n50% 100% \n[2024-08-30 06:41:16] INFO: Median overlap divergence: 0\n[2024-08-30 06:41:16] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:41:38] INFO: Aligned read sequence: 1184568 / 1313105 (0.902112)\n[2024-08-30 06:41:38] INFO: Median overlap divergence: 0.0607255\n[2024-08-30 06:41:38] INFO: Mean edge coverage: 29\n[2024-08-30 06:41:38] INFO: Resolving repeats\n[2024-08-30 06:41:38] INFO: >>>STAGE: trestle\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25aad00000073'\n[2024-08-30 06:41:38] INFO: Simple unbridged repeats: 0\n[2024-08-30 06:41:38] INFO: Resolved: 0\n[2024-08-30 06:41:38] INFO: >>>STAGE: contigger\n[2024-08-30 06:41:38] INFO: Generating contigs\n[2024-08-30 06:41:38] INFO: Reading sequences\n[2024-08-30 06:41:38] INFO: Generated 1 contigs\n[2024-08-30 06:41:38] INFO: Added 0 scaffold connections\n[2024-08-30 06:41:39] INFO: >>>STAGE: polishing\n[2024-08-30 06:41:39] INFO: Polishing genome (1/1)\n[2024-08-30 06:41:39] INFO: Running minimap2\n[2024-08-30 06:41:39] INFO: Separating alignment into bubbles\n[2024-08-30 06:41:40] INFO: Alignment error rate: 0.101562\n[2024-08-30 06:41:40] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25ac700000074'\n[2024-08-30 06:41:41] INFO: >>>STAGE: finalize\n[2024-08-30 06:41:41] INFO: Assembly statistics:\n\n\tTotal length:\t39948\n\tFragments:\t1\n\tFragments N50:\t39948\n\tLargest frg:\t39948\n\tScaffolds:\t0\n\tMean coverage:\t28\n\n[2024-08-30 06:41:41] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/74/working/out_dir/assembly.fasta\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "78.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:41:41", "plugin": "core", "name": "end_epoch", "raw_value": "1725000101.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:40:23", "plugin": "core", "name": "start_epoch", "raw_value": "1725000023.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "flye/2.6-1", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.6", "test_index": 1, "time_seconds": 111.63512992858887, "inputs": {"inputs": {"src": "hda", "id": "a5af623aa4e7ad53"}, "mode": "--nano-raw", "g": "10000"}, "job": {"model_class": "Job", "id": "60ddc0345154ae3c", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:42:13.345183", "update_time": "2024-08-30T06:43:43.561013", "galaxy_version": "24.1", "external_id": "gxy-vfzgz", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/9/6/4/dataset_96476630-9cbe-4ab6-a118-37223cfb9b95.dat' ./input_0.fasta && flye --nano-raw ./input_0.fasta -o out_dir -g '10000' -t ${GALAXY_SLOTS:-4} -i 1 2>&1", "user_email": "tests@fake.org", "command_version": "2.6-release", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "no_trestle": "false", "meta": "false", "plasmids": "false", "asm": "\"\"", "m": "\"\"", "i": "\"1\"", "g": "\"10000\"", "mode": "\"--nano-raw\""}, "inputs": {"inputs": {"id": "a5af623aa4e7ad53", "src": "hda", "uuid": "96476630-9cbe-4ab6-a118-37223cfb9b95"}, "inputs1": {"id": "a5af623aa4e7ad53", "src": "hda", "uuid": "96476630-9cbe-4ab6-a118-37223cfb9b95"}}, "outputs": {"consensus": {"id": "67476d714b9bb88f", "src": "hda", "uuid": "efb458c5-ac47-4ca8-b7cd-03dc889f90ec"}, "assembly_graph": {"id": "f84bfcca59a27fdd", "src": "hda", "uuid": "5c8d0fed-abc2-4d12-a809-be24dc02cad6"}, "assembly_gfa": {"id": "9db9451af50401c3", "src": "hda", "uuid": "660961b4-a5c2-40f9-af31-72675e975959"}, "assembly_info": {"id": "da1fdfb5c50c2d3e", "src": "hda", "uuid": "36495803-ad24-4945-97d8-a5d37eb92803"}, "flye_log": {"id": "d3f0491e5b846d74", "src": "hda", "uuid": "9b1b4dc1-39e8-45ad-937a-8262d130c190"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[2024-08-30 06:42:15] INFO: Starting Flye 2.6-release\n[2024-08-30 06:42:15] INFO: >>>STAGE: configure\n[2024-08-30 06:42:15] INFO: Configuring run\n[2024-08-30 06:42:15] INFO: Total read length: 1466260\n[2024-08-30 06:42:15] INFO: Input genome size: 10000\n[2024-08-30 06:42:15] INFO: Estimated coverage: 146\n[2024-08-30 06:42:15] INFO: Reads N50/N90: 9054 / 4697\n[2024-08-30 06:42:15] INFO: Minimum overlap set to 5000\n[2024-08-30 06:42:15] INFO: Selected k-mer size: 15\n[2024-08-30 06:42:15] INFO: >>>STAGE: assembly\n[2024-08-30 06:42:15] INFO: Assembling disjointigs\n[2024-08-30 06:42:15] INFO: Reading sequences\n[2024-08-30 06:42:15] INFO: Generating solid k-mer index\n[2024-08-30 06:42:37] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:42:37] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:42:37] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:42:41] INFO: Extending reads\n[2024-08-30 06:42:44] INFO: Overlap-based coverage: 25\n[2024-08-30 06:42:44] INFO: Median overlap divergence: 0.169108\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:42:44] INFO: Assembled 1 disjointigs\n[2024-08-30 06:42:44] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2024-08-30 06:42:44] INFO: >>>STAGE: consensus\n[2024-08-30 06:42:44] INFO: Running Minimap2\n[2024-08-30 06:42:44] INFO: Computing consensus\n[2024-08-30 06:42:45] INFO: Alignment error rate: 0.156815\n[2024-08-30 06:42:45] INFO: >>>STAGE: repeat\n[2024-08-30 06:42:45] INFO: Building and resolving repeat graph\n[2024-08-30 06:42:45] INFO: Reading sequences\n[2024-08-30 06:42:45] INFO: Building repeat graph\n50% 100% \n[2024-08-30 06:43:08] INFO: Median overlap divergence: 0\n[2024-08-30 06:43:08] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:43:30] INFO: Aligned read sequence: 1184563 / 1313105 (0.902108)\n[2024-08-30 06:43:30] INFO: Median overlap divergence: 0.0610287\n[2024-08-30 06:43:30] INFO: Mean edge coverage: 29\n[2024-08-30 06:43:30] INFO: Resolving repeats\n[2024-08-30 06:43:30] INFO: >>>STAGE: trestle\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b1c00000076'\n[2024-08-30 06:43:30] INFO: Simple unbridged repeats: 0\n[2024-08-30 06:43:30] INFO: Resolved: 0\n[2024-08-30 06:43:30] INFO: >>>STAGE: contigger\n[2024-08-30 06:43:30] INFO: Generating contigs\n[2024-08-30 06:43:30] INFO: Reading sequences\n[2024-08-30 06:43:30] INFO: Generated 1 contigs\n[2024-08-30 06:43:30] INFO: Added 0 scaffold connections\n[2024-08-30 06:43:30] INFO: >>>STAGE: polishing\n[2024-08-30 06:43:30] INFO: Polishing genome (1/1)\n[2024-08-30 06:43:30] INFO: Running minimap2\n[2024-08-30 06:43:30] INFO: Separating alignment into bubbles\n[2024-08-30 06:43:32] INFO: Alignment error rate: 0.101979\n[2024-08-30 06:43:32] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b3300000077'\n[2024-08-30 06:43:32] INFO: >>>STAGE: finalize\n[2024-08-30 06:43:32] INFO: Assembly statistics:\n\n\tTotal length:\t40422\n\tFragments:\t1\n\tFragments N50:\t40422\n\tLargest frg:\t40422\n\tScaffolds:\t0\n\tMean coverage:\t27\n\n[2024-08-30 06:43:32] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/76/working/out_dir/assembly.fasta\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[2024-08-30 06:42:15] INFO: Starting Flye 2.6-release\n[2024-08-30 06:42:15] INFO: >>>STAGE: configure\n[2024-08-30 06:42:15] INFO: Configuring run\n[2024-08-30 06:42:15] INFO: Total read length: 1466260\n[2024-08-30 06:42:15] INFO: Input genome size: 10000\n[2024-08-30 06:42:15] INFO: Estimated coverage: 146\n[2024-08-30 06:42:15] INFO: Reads N50/N90: 9054 / 4697\n[2024-08-30 06:42:15] INFO: Minimum overlap set to 5000\n[2024-08-30 06:42:15] INFO: Selected k-mer size: 15\n[2024-08-30 06:42:15] INFO: >>>STAGE: assembly\n[2024-08-30 06:42:15] INFO: Assembling disjointigs\n[2024-08-30 06:42:15] INFO: Reading sequences\n[2024-08-30 06:42:15] INFO: Generating solid k-mer index\n[2024-08-30 06:42:37] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:42:37] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:42:37] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:42:41] INFO: Extending reads\n[2024-08-30 06:42:44] INFO: Overlap-based coverage: 25\n[2024-08-30 06:42:44] INFO: Median overlap divergence: 0.169108\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:42:44] INFO: Assembled 1 disjointigs\n[2024-08-30 06:42:44] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2024-08-30 06:42:44] INFO: >>>STAGE: consensus\n[2024-08-30 06:42:44] INFO: Running Minimap2\n[2024-08-30 06:42:44] INFO: Computing consensus\n[2024-08-30 06:42:45] INFO: Alignment error rate: 0.156815\n[2024-08-30 06:42:45] INFO: >>>STAGE: repeat\n[2024-08-30 06:42:45] INFO: Building and resolving repeat graph\n[2024-08-30 06:42:45] INFO: Reading sequences\n[2024-08-30 06:42:45] INFO: Building repeat graph\n50% 100% \n[2024-08-30 06:43:08] INFO: Median overlap divergence: 0\n[2024-08-30 06:43:08] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:43:30] INFO: Aligned read sequence: 1184563 / 1313105 (0.902108)\n[2024-08-30 06:43:30] INFO: Median overlap divergence: 0.0610287\n[2024-08-30 06:43:30] INFO: Mean edge coverage: 29\n[2024-08-30 06:43:30] INFO: Resolving repeats\n[2024-08-30 06:43:30] INFO: >>>STAGE: trestle\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b1c00000076'\n[2024-08-30 06:43:30] INFO: Simple unbridged repeats: 0\n[2024-08-30 06:43:30] INFO: Resolved: 0\n[2024-08-30 06:43:30] INFO: >>>STAGE: contigger\n[2024-08-30 06:43:30] INFO: Generating contigs\n[2024-08-30 06:43:30] INFO: Reading sequences\n[2024-08-30 06:43:30] INFO: Generated 1 contigs\n[2024-08-30 06:43:30] INFO: Added 0 scaffold connections\n[2024-08-30 06:43:30] INFO: >>>STAGE: polishing\n[2024-08-30 06:43:30] INFO: Polishing genome (1/1)\n[2024-08-30 06:43:30] INFO: Running minimap2\n[2024-08-30 06:43:30] INFO: Separating alignment into bubbles\n[2024-08-30 06:43:32] INFO: Alignment error rate: 0.101979\n[2024-08-30 06:43:32] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b3300000077'\n[2024-08-30 06:43:32] INFO: >>>STAGE: finalize\n[2024-08-30 06:43:32] INFO: Assembly statistics:\n\n\tTotal length:\t40422\n\tFragments:\t1\n\tFragments N50:\t40422\n\tLargest frg:\t40422\n\tScaffolds:\t0\n\tMean coverage:\t27\n\n[2024-08-30 06:43:32] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/76/working/out_dir/assembly.fasta\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "78.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:43:32", "plugin": "core", "name": "end_epoch", "raw_value": "1725000212.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:42:14", "plugin": "core", "name": "start_epoch", "raw_value": "1725000134.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "flye/2.6-2", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.6", "test_index": 2, "time_seconds": 111.81388711929321, "inputs": {"inputs": {"src": "hda", "id": "383e151bb7ab46f4"}, "mode": "--nano-corr", "g": "10000", "i": "2", "asm": "40"}, "job": {"model_class": "Job", "id": "e597c18438e282b4", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:44:04.914332", "update_time": "2024-08-30T06:45:35.595038", "galaxy_version": "24.1", "external_id": "gxy-bjx7z", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/8/5/5/dataset_8559c293-3bde-4ebb-bdef-56cc219c1f79.dat' ./input_0.fasta && flye --nano-corr ./input_0.fasta -o out_dir -g '10000' -t ${GALAXY_SLOTS:-4} -i 2 --asm-coverage '40' 2>&1", "user_email": "tests@fake.org", "command_version": "2.6-release", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "no_trestle": "false", "meta": "false", "plasmids": "false", "asm": "\"40\"", "m": "\"\"", "i": "\"2\"", "g": "\"10000\"", "mode": "\"--nano-corr\""}, "inputs": {"inputs": {"id": "383e151bb7ab46f4", "src": "hda", "uuid": "8559c293-3bde-4ebb-bdef-56cc219c1f79"}, "inputs1": {"id": "383e151bb7ab46f4", "src": "hda", "uuid": "8559c293-3bde-4ebb-bdef-56cc219c1f79"}}, "outputs": {"consensus": {"id": "e2080fb5c7faa815", "src": "hda", "uuid": "12a3924d-dc49-4029-a3d3-47b7476a32b1"}, "assembly_graph": {"id": "edfb9d0cfea2ba20", "src": "hda", "uuid": "b3abe376-d349-422e-8d5d-355b2354637e"}, "assembly_gfa": {"id": "cbc0723085431e77", "src": "hda", "uuid": "5be64a86-3ea5-4bb6-89c8-e97b4b6424da"}, "assembly_info": {"id": "f28bf91daba0409c", "src": "hda", "uuid": "e289a6a6-ebec-490e-b841-820d8612e9c6"}, "flye_log": {"id": "cd3f8a909dc3fb52", "src": "hda", "uuid": "b5a644bf-5117-423d-8876-bb88cb420c75"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[2024-08-30 06:44:07] INFO: Starting Flye 2.6-release\n[2024-08-30 06:44:07] INFO: >>>STAGE: configure\n[2024-08-30 06:44:07] INFO: Configuring run\n[2024-08-30 06:44:07] INFO: Total read length: 1466260\n[2024-08-30 06:44:07] INFO: Input genome size: 10000\n[2024-08-30 06:44:07] INFO: Estimated coverage: 146\n[2024-08-30 06:44:07] INFO: Reads N50/N90: 9054 / 4697\n[2024-08-30 06:44:07] INFO: Minimum overlap set to 5000\n[2024-08-30 06:44:07] INFO: Selected k-mer size: 17\n[2024-08-30 06:44:07] INFO: Using longest 40x reads for contig assembly\n[2024-08-30 06:44:07] INFO: >>>STAGE: assembly\n[2024-08-30 06:44:07] INFO: Assembling disjointigs\n[2024-08-30 06:44:07] INFO: Reading sequences\n[2024-08-30 06:44:07] INFO: Generating solid k-mer index\n[2024-08-30 06:44:29] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:44:29] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:44:29] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:44:33] INFO: Extending reads\n[2024-08-30 06:44:33] INFO: Overlap-based coverage: 3\n[2024-08-30 06:44:33] INFO: Median overlap divergence: 0.173468\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:44:33] INFO: Assembled 1 disjointigs\n[2024-08-30 06:44:33] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2024-08-30 06:44:33] INFO: >>>STAGE: consensus\n[2024-08-30 06:44:33] INFO: Running Minimap2\n[2024-08-30 06:44:33] INFO: Computing consensus\n[2024-08-30 06:44:34] INFO: Alignment error rate: 0.146313\n[2024-08-30 06:44:34] INFO: >>>STAGE: repeat\n[2024-08-30 06:44:34] INFO: Building and resolving repeat graph\n[2024-08-30 06:44:34] INFO: Reading sequences\n[2024-08-30 06:44:34] INFO: Building repeat graph\n50% 100% \n[2024-08-30 06:44:57] INFO: Median overlap divergence: 0\n[2024-08-30 06:44:57] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:45:19] INFO: Aligned read sequence: 1174263 / 1313105 (0.894264)\n[2024-08-30 06:45:19] INFO: Median overlap divergence: 0.0589391\n[2024-08-30 06:45:19] INFO: Mean edge coverage: 29\n[2024-08-30 06:45:19] INFO: Resolving repeats\n[2024-08-30 06:45:19] INFO: >>>STAGE: contigger\n[2024-08-30 06:45:19] INFO: Generating contigs\n[2024-08-30 06:45:19] INFO: Reading sequences\n[2024-08-30 06:45:19] INFO: Generated 1 contigs\n[2024-08-30 06:45:19] INFO: Added 0 scaffold connections\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b8900000079'\n[2024-08-30 06:45:19] INFO: >>>STAGE: polishing\n[2024-08-30 06:45:19] INFO: Polishing genome (1/2)\n[2024-08-30 06:45:19] INFO: Running minimap2\n[2024-08-30 06:45:19] INFO: Separating alignment into bubbles\n[2024-08-30 06:45:20] INFO: Alignment error rate: 0.099017\n[2024-08-30 06:45:20] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b9a0000007a'\n[2024-08-30 06:45:21] INFO: Polishing genome (2/2)\n[2024-08-30 06:45:21] INFO: Running minimap2\n[2024-08-30 06:45:21] INFO: Separating alignment into bubbles\n[2024-08-30 06:45:22] INFO: Alignment error rate: 0.094400\n[2024-08-30 06:45:22] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:45:23] INFO: >>>STAGE: finalize\n[2024-08-30 06:45:23] INFO: Assembly statistics:\n\n\tTotal length:\t40414\n\tFragments:\t1\n\tFragments N50:\t40414\n\tLargest frg:\t40414\n\tScaffolds:\t0\n\tMean coverage:\t27\n\n[2024-08-30 06:45:23] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/78/working/out_dir/assembly.fasta\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b9c0000007c'\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[2024-08-30 06:44:07] INFO: Starting Flye 2.6-release\n[2024-08-30 06:44:07] INFO: >>>STAGE: configure\n[2024-08-30 06:44:07] INFO: Configuring run\n[2024-08-30 06:44:07] INFO: Total read length: 1466260\n[2024-08-30 06:44:07] INFO: Input genome size: 10000\n[2024-08-30 06:44:07] INFO: Estimated coverage: 146\n[2024-08-30 06:44:07] INFO: Reads N50/N90: 9054 / 4697\n[2024-08-30 06:44:07] INFO: Minimum overlap set to 5000\n[2024-08-30 06:44:07] INFO: Selected k-mer size: 17\n[2024-08-30 06:44:07] INFO: Using longest 40x reads for contig assembly\n[2024-08-30 06:44:07] INFO: >>>STAGE: assembly\n[2024-08-30 06:44:07] INFO: Assembling disjointigs\n[2024-08-30 06:44:07] INFO: Reading sequences\n[2024-08-30 06:44:07] INFO: Generating solid k-mer index\n[2024-08-30 06:44:29] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:44:29] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:44:29] INFO: Filling index table\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:44:33] INFO: Extending reads\n[2024-08-30 06:44:33] INFO: Overlap-based coverage: 3\n[2024-08-30 06:44:33] INFO: Median overlap divergence: 0.173468\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:44:33] INFO: Assembled 1 disjointigs\n[2024-08-30 06:44:33] INFO: Generating sequence\n10% 20% 40% 50% 70% 80% 100% \n[2024-08-30 06:44:33] INFO: >>>STAGE: consensus\n[2024-08-30 06:44:33] INFO: Running Minimap2\n[2024-08-30 06:44:33] INFO: Computing consensus\n[2024-08-30 06:44:34] INFO: Alignment error rate: 0.146313\n[2024-08-30 06:44:34] INFO: >>>STAGE: repeat\n[2024-08-30 06:44:34] INFO: Building and resolving repeat graph\n[2024-08-30 06:44:34] INFO: Reading sequences\n[2024-08-30 06:44:34] INFO: Building repeat graph\n50% 100% \n[2024-08-30 06:44:57] INFO: Median overlap divergence: 0\n[2024-08-30 06:44:57] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:45:19] INFO: Aligned read sequence: 1174263 / 1313105 (0.894264)\n[2024-08-30 06:45:19] INFO: Median overlap divergence: 0.0589391\n[2024-08-30 06:45:19] INFO: Mean edge coverage: 29\n[2024-08-30 06:45:19] INFO: Resolving repeats\n[2024-08-30 06:45:19] INFO: >>>STAGE: contigger\n[2024-08-30 06:45:19] INFO: Generating contigs\n[2024-08-30 06:45:19] INFO: Reading sequences\n[2024-08-30 06:45:19] INFO: Generated 1 contigs\n[2024-08-30 06:45:19] INFO: Added 0 scaffold connections\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b8900000079'\n[2024-08-30 06:45:19] INFO: >>>STAGE: polishing\n[2024-08-30 06:45:19] INFO: Polishing genome (1/2)\n[2024-08-30 06:45:19] INFO: Running minimap2\n[2024-08-30 06:45:19] INFO: Separating alignment into bubbles\n[2024-08-30 06:45:20] INFO: Alignment error rate: 0.099017\n[2024-08-30 06:45:20] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b9a0000007a'\n[2024-08-30 06:45:21] INFO: Polishing genome (2/2)\n[2024-08-30 06:45:21] INFO: Running minimap2\n[2024-08-30 06:45:21] INFO: Separating alignment into bubbles\n[2024-08-30 06:45:22] INFO: Alignment error rate: 0.094400\n[2024-08-30 06:45:22] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:45:23] INFO: >>>STAGE: finalize\n[2024-08-30 06:45:23] INFO: Assembly statistics:\n\n\tTotal length:\t40414\n\tFragments:\t1\n\tFragments N50:\t40414\n\tLargest frg:\t40414\n\tScaffolds:\t0\n\tMean coverage:\t27\n\n[2024-08-30 06:45:23] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/78/working/out_dir/assembly.fasta\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b9c0000007c'\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "76.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:45:23", "plugin": "core", "name": "end_epoch", "raw_value": "1725000323.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:44:07", "plugin": "core", "name": "start_epoch", "raw_value": "1725000247.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "flye/2.6-3", "has_data": true, "data": {"tool_id": "flye", "tool_version": "2.6", "test_index": 3, "time_seconds": 113.85081005096436, "inputs": {"inputs": {"src": "hda", "id": "bd78b872588b7227"}, "mode": "--pacbio-raw", "g": "10000", "i": "1", "plasmids": true, "meta": true}, "job": {"model_class": "Job", "id": "3925f521cb40181f", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/flye/flye/2.6", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:45:57.611167", "update_time": "2024-08-30T06:47:29.250950", "galaxy_version": "24.1", "external_id": "gxy-6rkz8", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/b/7/1/dataset_b7172779-11b5-4bfb-b4f6-6de27462070d.dat' ./input_0.fasta && flye --pacbio-raw ./input_0.fasta -o out_dir -g '10000' -t ${GALAXY_SLOTS:-4} -i 1 --plasmids --meta 2>&1", "user_email": "tests@fake.org", "command_version": "2.6-release", "params": {"__input_ext": "\"fasta\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "no_trestle": "false", "meta": "true", "plasmids": "true", "asm": "\"\"", "m": "\"\"", "i": "\"1\"", "g": "\"10000\"", "mode": "\"--pacbio-raw\""}, "inputs": {"inputs": {"id": "bd78b872588b7227", "src": "hda", "uuid": "b7172779-11b5-4bfb-b4f6-6de27462070d"}, "inputs1": {"id": "bd78b872588b7227", "src": "hda", "uuid": "b7172779-11b5-4bfb-b4f6-6de27462070d"}}, "outputs": {"consensus": {"id": "ef03759c02239840", "src": "hda", "uuid": "9aff4b70-60d4-47d9-b580-9e6eab7872f1"}, "assembly_graph": {"id": "d0d4815ee1ebd1e5", "src": "hda", "uuid": "cda2a2ce-1e90-42bb-8f52-8e86da7b73cf"}, "assembly_gfa": {"id": "23f58efe1a283f81", "src": "hda", "uuid": "3fd7791e-aab5-41bc-8694-aab4a8e2f9d9"}, "assembly_info": {"id": "af714289f2a12cab", "src": "hda", "uuid": "0bdb2fb5-47a0-4787-8800-da83c7f4b95f"}, "flye_log": {"id": "f4f71fb0965fcf05", "src": "hda", "uuid": "98d3bce7-2c2d-4e22-ad2c-4fef2c69fb88"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "[2024-08-30 06:46:00] INFO: Starting Flye 2.6-release\n[2024-08-30 06:46:00] INFO: >>>STAGE: configure\n[2024-08-30 06:46:00] INFO: Configuring run\n[2024-08-30 06:46:00] INFO: Total read length: 1466260\n[2024-08-30 06:46:00] INFO: Input genome size: 10000\n[2024-08-30 06:46:00] INFO: Estimated coverage: 146\n[2024-08-30 06:46:00] INFO: Reads N50/N90: 9054 / 4697\n[2024-08-30 06:46:00] INFO: Minimum overlap set to 5000\n[2024-08-30 06:46:00] INFO: Selected k-mer size: 15\n[2024-08-30 06:46:00] INFO: >>>STAGE: assembly\n[2024-08-30 06:46:00] INFO: Assembling disjointigs\n[2024-08-30 06:46:00] INFO: Reading sequences\n[2024-08-30 06:46:00] INFO: Generating solid k-mer index\n[2024-08-30 06:46:22] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:46:22] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:46:22] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:46:22] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:46:26] INFO: Extending reads\n[2024-08-30 06:46:28] INFO: Overlap-based coverage: 24\n[2024-08-30 06:46:28] INFO: Median overlap divergence: 0.184492\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:46:29] INFO: Assembled 1 disjointigs\n[2024-08-30 06:46:29] INFO: Generating sequence\n10% 20% 30% 40% 50% 60% 70% 80% 100% \n[2024-08-30 06:46:29] INFO: >>>STAGE: consensus\n[2024-08-30 06:46:29] INFO: Running Minimap2\n[2024-08-30 06:46:29] INFO: Computing consensus\n[2024-08-30 06:46:30] INFO: Alignment error rate: 0.182990\n[2024-08-30 06:46:30] INFO: >>>STAGE: repeat\n[2024-08-30 06:46:30] INFO: Building and resolving repeat graph\n[2024-08-30 06:46:30] INFO: Reading sequences\n[2024-08-30 06:46:30] INFO: Building repeat graph\n50% 100% \n[2024-08-30 06:46:53] INFO: Median overlap divergence: 0\n[2024-08-30 06:46:53] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:47:15] INFO: Aligned read sequence: 1158758 / 1313105 (0.882456)\n[2024-08-30 06:47:15] INFO: Median overlap divergence: 0.0639983\n[2024-08-30 06:47:15] INFO: Mean edge coverage: 32\n[2024-08-30 06:47:15] INFO: Resolving repeats\n[2024-08-30 06:47:15] INFO: >>>STAGE: plasmids\n[2024-08-30 06:47:15] INFO: Recovering short unassembled sequences\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25bef0000007e'\n[2024-08-30 06:47:15] INFO: Added 0 extra contigs\n[2024-08-30 06:47:15] INFO: >>>STAGE: contigger\n[2024-08-30 06:47:15] INFO: Generating contigs\n[2024-08-30 06:47:15] INFO: Reading sequences\n[2024-08-30 06:47:15] INFO: Generated 1 contigs\n[2024-08-30 06:47:15] INFO: Added 0 scaffold connections\n[2024-08-30 06:47:15] INFO: >>>STAGE: polishing\n[2024-08-30 06:47:15] INFO: Polishing genome (1/1)\n[2024-08-30 06:47:15] INFO: Running minimap2\n[2024-08-30 06:47:16] INFO: Separating alignment into bubbles\n[2024-08-30 06:47:17] INFO: Alignment error rate: 0.115118\n[2024-08-30 06:47:17] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25bff0000007f'\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25c0b00000080'\n[2024-08-30 06:47:18] INFO: >>>STAGE: finalize\n[2024-08-30 06:47:18] INFO: Assembly statistics:\n\n\tTotal length:\t35687\n\tFragments:\t1\n\tFragments N50:\t35687\n\tLargest frg:\t35687\n\tScaffolds:\t0\n\tMean coverage:\t35\n\n[2024-08-30 06:47:18] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/80/working/out_dir/assembly.fasta\n", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "[2024-08-30 06:46:00] INFO: Starting Flye 2.6-release\n[2024-08-30 06:46:00] INFO: >>>STAGE: configure\n[2024-08-30 06:46:00] INFO: Configuring run\n[2024-08-30 06:46:00] INFO: Total read length: 1466260\n[2024-08-30 06:46:00] INFO: Input genome size: 10000\n[2024-08-30 06:46:00] INFO: Estimated coverage: 146\n[2024-08-30 06:46:00] INFO: Reads N50/N90: 9054 / 4697\n[2024-08-30 06:46:00] INFO: Minimum overlap set to 5000\n[2024-08-30 06:46:00] INFO: Selected k-mer size: 15\n[2024-08-30 06:46:00] INFO: >>>STAGE: assembly\n[2024-08-30 06:46:00] INFO: Assembling disjointigs\n[2024-08-30 06:46:00] INFO: Reading sequences\n[2024-08-30 06:46:00] INFO: Generating solid k-mer index\n[2024-08-30 06:46:22] INFO: Counting k-mers (1/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:46:22] INFO: Counting k-mers (2/2):\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:46:22] INFO: Filling index table (1/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:46:22] INFO: Filling index table (2/2)\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:46:26] INFO: Extending reads\n[2024-08-30 06:46:28] INFO: Overlap-based coverage: 24\n[2024-08-30 06:46:28] INFO: Median overlap divergence: 0.184492\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:46:29] INFO: Assembled 1 disjointigs\n[2024-08-30 06:46:29] INFO: Generating sequence\n10% 20% 30% 40% 50% 60% 70% 80% 100% \n[2024-08-30 06:46:29] INFO: >>>STAGE: consensus\n[2024-08-30 06:46:29] INFO: Running Minimap2\n[2024-08-30 06:46:29] INFO: Computing consensus\n[2024-08-30 06:46:30] INFO: Alignment error rate: 0.182990\n[2024-08-30 06:46:30] INFO: >>>STAGE: repeat\n[2024-08-30 06:46:30] INFO: Building and resolving repeat graph\n[2024-08-30 06:46:30] INFO: Reading sequences\n[2024-08-30 06:46:30] INFO: Building repeat graph\n50% 100% \n[2024-08-30 06:46:53] INFO: Median overlap divergence: 0\n[2024-08-30 06:46:53] INFO: Aligning reads to the graph\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \n[2024-08-30 06:47:15] INFO: Aligned read sequence: 1158758 / 1313105 (0.882456)\n[2024-08-30 06:47:15] INFO: Median overlap divergence: 0.0639983\n[2024-08-30 06:47:15] INFO: Mean edge coverage: 32\n[2024-08-30 06:47:15] INFO: Resolving repeats\n[2024-08-30 06:47:15] INFO: >>>STAGE: plasmids\n[2024-08-30 06:47:15] INFO: Recovering short unassembled sequences\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25bef0000007e'\n[2024-08-30 06:47:15] INFO: Added 0 extra contigs\n[2024-08-30 06:47:15] INFO: >>>STAGE: contigger\n[2024-08-30 06:47:15] INFO: Generating contigs\n[2024-08-30 06:47:15] INFO: Reading sequences\n[2024-08-30 06:47:15] INFO: Generated 1 contigs\n[2024-08-30 06:47:15] INFO: Added 0 scaffold connections\n[2024-08-30 06:47:15] INFO: >>>STAGE: polishing\n[2024-08-30 06:47:15] INFO: Polishing genome (1/1)\n[2024-08-30 06:47:15] INFO: Running minimap2\n[2024-08-30 06:47:16] INFO: Separating alignment into bubbles\n[2024-08-30 06:47:17] INFO: Alignment error rate: 0.115118\n[2024-08-30 06:47:17] INFO: Correcting bubbles\n0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% \nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25bff0000007f'\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 297, in _bootstrap\n self.run()\n File \"/usr/local/lib/python3.7/multiprocessing/process.py\", line 99, in run\n self._target(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 577, in _run_server\n server.serve_forever()\n File \"/usr/local/lib/python3.7/multiprocessing/managers.py\", line 173, in serve_forever\n sys.exit(0)\nSystemExit: 0\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 265, in _run_finalizers\n finalizer()\n File \"/usr/local/lib/python3.7/multiprocessing/util.py\", line 189, in __call__\n res = self._callback(*self._args, **self._kwargs)\n File \"/usr/local/lib/python3.7/shutil.py\", line 491, in rmtree\n _rmtree_safe_fd(fd, path, onerror)\n File \"/usr/local/lib/python3.7/shutil.py\", line 449, in _rmtree_safe_fd\n onerror(os.unlink, fullname, sys.exc_info())\n File \"/usr/local/lib/python3.7/shutil.py\", line 447, in _rmtree_safe_fd\n os.unlink(entry.name, dir_fd=topfd)\nOSError: [Errno 16] Device or resource busy: '.nfs0000000000b25c0b00000080'\n[2024-08-30 06:47:18] INFO: >>>STAGE: finalize\n[2024-08-30 06:47:18] INFO: Assembly statistics:\n\n\tTotal length:\t35687\n\tFragments:\t1\n\tFragments N50:\t35687\n\tLargest frg:\t35687\n\tScaffolds:\t0\n\tMean coverage:\t35\n\n[2024-08-30 06:47:18] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/80/working/out_dir/assembly.fasta\n", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 minute", "plugin": "core", "name": "runtime_seconds", "raw_value": "79.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:47:18", "plugin": "core", "name": "end_epoch", "raw_value": "1725000438.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:45:59", "plugin": "core", "name": "start_epoch", "raw_value": "1725000359.0000000"}, {"title": "Memory Allocated (MB)", "value": "51539", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "51539.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-0", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 0, "time_seconds": 12.279859781265259, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "hisat2/2.2.1+galaxy1-0", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 0, "time_seconds": 38.52446365356445, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "047992ce100c3a7a"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "3d5304c4d2ced23e"}, "library|input_2": {"src": "hda", "id": "5d65279e7ef66f7a"}, "library|type": "paired", "adv|reporting_options|reporting_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "01547d2d72cffcb2", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:59:06.863649", "update_time": "2024-08-30T06:59:20.261991", "galaxy_version": "24.1", "external_id": "gxy-h89d6", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/c/f/f/dataset_cff1d753-c2f5-408a-b37f-f34850cd7080.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/3/b/5/dataset_3b50cd25-9d64-42b4-a28d-740a66606c79.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/3/2/7/dataset_327990df-d53a-4972-8beb-962057918f83.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/7/5/a/dataset_75a2c5ec-d51d-4ddf-9109-0c65d1ef3560.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 1, \"max_primary\": \"\", \"reporting_options_selector\": \"advanced\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 176, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 177, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 175, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "047992ce100c3a7a", "src": "hda", "uuid": "cff1d753-c2f5-408a-b37f-f34850cd7080"}, "library|input_1": {"id": "3d5304c4d2ced23e", "src": "hda", "uuid": "3b50cd25-9d64-42b4-a28d-740a66606c79"}, "library|input_2": {"id": "5d65279e7ef66f7a", "src": "hda", "uuid": "327990df-d53a-4972-8beb-962057918f83"}}, "outputs": {"output_alignments": {"id": "b7c5dfe00a988157", "src": "hda", "uuid": "75a2c5ec-d51d-4ddf-9109-0c65d1ef3560"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n bucket 1: 10%\n bucket 2: 10%\n bucket 1: 20%\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n bucket 1: 30%\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n bucket 2: 20%\n Entering block accumulator loop for bucket 3:\n Reserving size (126) for bucket 5\n bucket 2: 30%\nGetting block 7 of 60\n bucket 2: 40%\n bucket 1: 40%\n Calculating Z arrays for bucket 5\n bucket 2: 50%\n bucket 1: 50%\n bucket 3: 10%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 5:\n bucket 1: 60%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 4:\n bucket 2: 60%\n bucket 3: 20%\n Reserving size (126) for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 1: 70%\n bucket 2: 70%\n bucket 3: 30%\n bucket 5: 10%\n Calculating Z arrays for bucket 7\n bucket 4: 10%\n bucket 1: 80%\n Calculating Z arrays for bucket 8\n bucket 2: 80%\n bucket 5: 20%\n bucket 4: 20%\n bucket 2: 90%\n Entering block accumulator loop for bucket 7:\n bucket 5: 30%\n bucket 4: 30%\n bucket 1: 90%\n bucket 5: 40%\n Calculating Z arrays for bucket 6\n bucket 7: 10%\n bucket 5: 50%\n bucket 4: 40%\n Entering block accumulator loop for bucket 8:\n bucket 5: 60%\n bucket 2: 100%\n bucket 1: 100%\n bucket 7: 20%\n bucket 4: 50%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 3: 40%\n bucket 7: 30%\n bucket 8: 10%\n Entering block accumulator loop for bucket 6:\n bucket 3: 50%\n bucket 4: 60%\n bucket 5: 70%\n bucket 8: 20%\n bucket 3: 60%\n bucket 7: 40%\n bucket 5: 80%\n bucket 6: 10%\n bucket 4: 70%\n Sorting block of length 84 for bucket 2\n bucket 5: 90%\n (Using difference cover)\n bucket 6: 20%\n bucket 4: 80%\n bucket 5: 100%\n bucket 3: 70%\n bucket 7: 50%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 4: 90%\n bucket 3: 80%\n bucket 7: 60%\n bucket 6: 30%\n bucket 3: 90%\n bucket 4: 100%\n bucket 7: 70%\n bucket 8: 30%\n bucket 6: 40%\n bucket 3: 100%\n bucket 7: 80%\n bucket 6: 50%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Sorting block of length 68 for bucket 4\n bucket 6: 60%\n (Using difference cover)\n bucket 8: 40%\n bucket 7: 90%\n bucket 6: 70%\n bucket 8: 50%\n bucket 6: 80%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n bucket 8: 60%\n bucket 6: 90%\n bucket 6: 100%\n bucket 8: 70%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 70%\n bucket 9: 80%\nGetting block 11 of 60\n bucket 9: 90%\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n Entering block accumulator loop for bucket 11:\n bucket 10: 40%\n bucket 10: 50%\n bucket 11: 10%\n bucket 10: 60%\n bucket 11: 20%\n bucket 10: 70%\n bucket 11: 30%\n bucket 10: 80%\n bucket 11: 40%\n bucket 10: 90%\n bucket 11: 50%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n Entering block accumulator loop for bucket 15:\n bucket 14: 20%\n bucket 15: 10%\n bucket 14: 30%\n bucket 15: 20%\n bucket 14: 40%\n bucket 15: 30%\n bucket 14: 50%\n bucket 15: 40%\n bucket 14: 60%\n bucket 15: 50%\n bucket 14: 70%\n bucket 15: 60%\n bucket 14: 80%\n bucket 15: 70%\n bucket 14: 90%\n bucket 15: 80%\n bucket 14: 100%\n bucket 15: 90%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 16 of 60\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 16: 10%\n bucket 17: 20%\n bucket 16: 20%\n bucket 17: 30%\n bucket 16: 30%\n bucket 16: 40%\n bucket 17: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 17: 50%\n bucket 16: 70%\n bucket 17: 60%\n bucket 16: 80%\n bucket 17: 70%\n bucket 16: 90%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 80%\n bucket 18: 90%\n Entering block accumulator loop for bucket 19:\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n Sorting block time: 00:00:00\n bucket 19: 90%\nReturning block of 123 for bucket 18\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 30%\n bucket 20: 40%\n Entering block accumulator loop for bucket 21:\n bucket 20: 50%\n bucket 21: 10%\n bucket 20: 60%\n bucket 21: 20%\n bucket 20: 70%\n bucket 21: 30%\n bucket 20: 80%\n bucket 21: 40%\n bucket 21: 50%\n bucket 20: 90%\n bucket 21: 60%\n bucket 20: 100%\n bucket 21: 70%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 10%\n bucket 22: 20%\n Entering block accumulator loop for bucket 23:\n bucket 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n bucket 23: 20%\n bucket 22: 50%\n bucket 23: 30%\n bucket 22: 60%\n bucket 23: 40%\n bucket 22: 70%\n bucket 22: 80%\n bucket 23: 50%\n bucket 22: 90%\n bucket 23: 60%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\nGetting block 25 of 60\n bucket 24: 40%\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 50%\n bucket 24: 60%\n Entering block accumulator loop for bucket 25:\n bucket 24: 70%\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 24: 80%\n bucket 25: 40%\n bucket 24: 90%\n bucket 25: 50%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 29:\n bucket 30: 10%\n bucket 30: 20%\n bucket 29: 10%\n Entering block accumulator loop for bucket 31:\n bucket 30: 30%\n bucket 29: 20%\n bucket 30: 40%\n bucket 31: 10%\n bucket 29: 30%\n bucket 30: 50%\n bucket 31: 20%\n bucket 30: 60%\n bucket 29: 40%\n bucket 31: 30%\n bucket 30: 70%\n bucket 29: 50%\n bucket 30: 80%\n bucket 31: 40%\n bucket 29: 60%\n bucket 30: 90%\n bucket 31: 50%\n bucket 30: 100%\n bucket 29: 70%\n bucket 31: 60%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 29: 80%\n bucket 31: 70%\n bucket 29: 90%\n bucket 31: 80%\n bucket 31: 90%\n bucket 29: 100%\n bucket 31: 100%\n Sorting block of length 51 for bucket 29\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Entering block accumulator loop for bucket 32:\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 10%\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 30%\n bucket 33: 10%\n bucket 32: 40%\n bucket 33: 20%\n bucket 32: 50%\n bucket 33: 30%\n bucket 32: 60%\n bucket 33: 40%\n bucket 32: 70%\n bucket 33: 50%\n bucket 33: 60%\n bucket 32: 80%\n bucket 33: 70%\n bucket 33: 80%\n bucket 32: 90%\n bucket 33: 90%\n bucket 32: 100%\n bucket 33: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 35:\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 34: 20%\n bucket 35: 40%\n bucket 34: 30%\n bucket 35: 50%\n bucket 34: 40%\n bucket 35: 60%\n bucket 34: 50%\n bucket 35: 70%\n bucket 34: 60%\n bucket 35: 80%\n bucket 34: 70%\n bucket 35: 90%\n bucket 34: 80%\n bucket 35: 100%\n bucket 34: 90%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 38: 10%\n bucket 39: 20%\n bucket 38: 20%\n bucket 39: 30%\n bucket 38: 30%\n bucket 39: 40%\n bucket 38: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 38: 50%\n bucket 39: 70%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 39: 80%\n bucket 38: 90%\n bucket 39: 90%\n bucket 38: 100%\n bucket 39: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 40 of 60\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 40:\n bucket 41: 10%\n bucket 40: 10%\n bucket 41: 20%\n bucket 40: 20%\n bucket 41: 30%\n bucket 40: 30%\n bucket 41: 40%\n bucket 40: 40%\n bucket 41: 50%\n bucket 40: 50%\n bucket 41: 60%\n bucket 40: 60%\n bucket 41: 70%\n bucket 40: 70%\n bucket 41: 80%\n bucket 40: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 20%\n bucket 42: 30%\n Entering block accumulator loop for bucket 43:\n bucket 42: 40%\n bucket 43: 10%\n bucket 42: 50%\n bucket 43: 20%\n bucket 42: 60%\n bucket 43: 30%\n bucket 42: 70%\n bucket 43: 40%\n bucket 42: 80%\n bucket 43: 50%\n bucket 42: 90%\n bucket 43: 60%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 60\n Entering block accumulator loop for bucket 46:\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 10%\n bucket 46: 20%\n Entering block accumulator loop for bucket 47:\n bucket 46: 30%\n bucket 46: 40%\n bucket 47: 10%\n bucket 46: 50%\n bucket 47: 20%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 48:\n bucket 49: 10%\n bucket 48: 10%\n bucket 49: 20%\n bucket 48: 20%\n bucket 48: 30%\n bucket 49: 30%\n bucket 48: 40%\n bucket 49: 40%\n bucket 48: 50%\n bucket 49: 50%\n bucket 48: 60%\n bucket 49: 60%\n bucket 48: 70%\n bucket 49: 70%\n bucket 48: 80%\n bucket 49: 80%\n bucket 48: 90%\n bucket 49: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n Entering block accumulator loop for bucket 51:\n bucket 50: 20%\n bucket 51: 10%\n bucket 50: 30%\n bucket 51: 20%\n bucket 50: 40%\n bucket 51: 30%\n bucket 50: 50%\n bucket 51: 40%\n bucket 50: 60%\n bucket 51: 50%\n bucket 50: 70%\n bucket 51: 60%\n bucket 50: 80%\n bucket 51: 70%\n bucket 50: 90%\n bucket 51: 80%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Entering block accumulator loop for bucket 52:\n Calculating Z arrays for bucket 53\n bucket 52: 10%\n Entering block accumulator loop for bucket 53:\n bucket 52: 20%\n bucket 53: 10%\n bucket 52: 30%\n bucket 53: 20%\n bucket 52: 40%\n bucket 53: 30%\n bucket 53: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 53: 50%\n bucket 52: 90%\n bucket 53: 60%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 54:\n Entering block accumulator loop for bucket 55:\n bucket 54: 10%\n bucket 55: 10%\n bucket 54: 20%\n bucket 55: 20%\n bucket 54: 30%\n bucket 55: 30%\n bucket 54: 40%\n bucket 55: 40%\n bucket 54: 50%\n bucket 55: 50%\n bucket 54: 60%\n bucket 55: 60%\n bucket 54: 70%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 54: 80%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n bucket 54: 90%\n (Using difference cover)\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\nGetting block 58 of 60\n Entering block accumulator loop for bucket 57:\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 10%\n bucket 57: 20%\n Entering block accumulator loop for bucket 58:\nGetting block 59 of 60\n bucket 57: 30%\n bucket 58: 10%\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n bucket 57: 40%\n bucket 58: 20%\n bucket 57: 50%\n bucket 58: 30%\n Entering block accumulator loop for bucket 59:\n bucket 57: 60%\n bucket 58: 40%\n bucket 57: 70%\n bucket 59: 10%\n bucket 57: 80%\n bucket 58: 50%\n bucket 57: 90%\n bucket 59: 20%\n bucket 58: 60%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n bucket 58: 70%\n (Using difference cover)\n bucket 59: 30%\n bucket 58: 80%\n bucket 59: 40%\n bucket 58: 90%\n bucket 59: 50%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n bucket 1: 10%\n bucket 2: 10%\n bucket 1: 20%\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n bucket 1: 30%\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n bucket 2: 20%\n Entering block accumulator loop for bucket 3:\n Reserving size (126) for bucket 5\n bucket 2: 30%\nGetting block 7 of 60\n bucket 2: 40%\n bucket 1: 40%\n Calculating Z arrays for bucket 5\n bucket 2: 50%\n bucket 1: 50%\n bucket 3: 10%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 5:\n bucket 1: 60%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 4:\n bucket 2: 60%\n bucket 3: 20%\n Reserving size (126) for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 1: 70%\n bucket 2: 70%\n bucket 3: 30%\n bucket 5: 10%\n Calculating Z arrays for bucket 7\n bucket 4: 10%\n bucket 1: 80%\n Calculating Z arrays for bucket 8\n bucket 2: 80%\n bucket 5: 20%\n bucket 4: 20%\n bucket 2: 90%\n Entering block accumulator loop for bucket 7:\n bucket 5: 30%\n bucket 4: 30%\n bucket 1: 90%\n bucket 5: 40%\n Calculating Z arrays for bucket 6\n bucket 7: 10%\n bucket 5: 50%\n bucket 4: 40%\n Entering block accumulator loop for bucket 8:\n bucket 5: 60%\n bucket 2: 100%\n bucket 1: 100%\n bucket 7: 20%\n bucket 4: 50%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 3: 40%\n bucket 7: 30%\n bucket 8: 10%\n Entering block accumulator loop for bucket 6:\n bucket 3: 50%\n bucket 4: 60%\n bucket 5: 70%\n bucket 8: 20%\n bucket 3: 60%\n bucket 7: 40%\n bucket 5: 80%\n bucket 6: 10%\n bucket 4: 70%\n Sorting block of length 84 for bucket 2\n bucket 5: 90%\n (Using difference cover)\n bucket 6: 20%\n bucket 4: 80%\n bucket 5: 100%\n bucket 3: 70%\n bucket 7: 50%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 4: 90%\n bucket 3: 80%\n bucket 7: 60%\n bucket 6: 30%\n bucket 3: 90%\n bucket 4: 100%\n bucket 7: 70%\n bucket 8: 30%\n bucket 6: 40%\n bucket 3: 100%\n bucket 7: 80%\n bucket 6: 50%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Sorting block of length 68 for bucket 4\n bucket 6: 60%\n (Using difference cover)\n bucket 8: 40%\n bucket 7: 90%\n bucket 6: 70%\n bucket 8: 50%\n bucket 6: 80%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n bucket 8: 60%\n bucket 6: 90%\n bucket 6: 100%\n bucket 8: 70%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 70%\n bucket 9: 80%\nGetting block 11 of 60\n bucket 9: 90%\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n Entering block accumulator loop for bucket 11:\n bucket 10: 40%\n bucket 10: 50%\n bucket 11: 10%\n bucket 10: 60%\n bucket 11: 20%\n bucket 10: 70%\n bucket 11: 30%\n bucket 10: 80%\n bucket 11: 40%\n bucket 10: 90%\n bucket 11: 50%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n Entering block accumulator loop for bucket 15:\n bucket 14: 20%\n bucket 15: 10%\n bucket 14: 30%\n bucket 15: 20%\n bucket 14: 40%\n bucket 15: 30%\n bucket 14: 50%\n bucket 15: 40%\n bucket 14: 60%\n bucket 15: 50%\n bucket 14: 70%\n bucket 15: 60%\n bucket 14: 80%\n bucket 15: 70%\n bucket 14: 90%\n bucket 15: 80%\n bucket 14: 100%\n bucket 15: 90%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 16 of 60\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 16: 10%\n bucket 17: 20%\n bucket 16: 20%\n bucket 17: 30%\n bucket 16: 30%\n bucket 16: 40%\n bucket 17: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 17: 50%\n bucket 16: 70%\n bucket 17: 60%\n bucket 16: 80%\n bucket 17: 70%\n bucket 16: 90%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 80%\n bucket 18: 90%\n Entering block accumulator loop for bucket 19:\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n Sorting block time: 00:00:00\n bucket 19: 90%\nReturning block of 123 for bucket 18\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 30%\n bucket 20: 40%\n Entering block accumulator loop for bucket 21:\n bucket 20: 50%\n bucket 21: 10%\n bucket 20: 60%\n bucket 21: 20%\n bucket 20: 70%\n bucket 21: 30%\n bucket 20: 80%\n bucket 21: 40%\n bucket 21: 50%\n bucket 20: 90%\n bucket 21: 60%\n bucket 20: 100%\n bucket 21: 70%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 10%\n bucket 22: 20%\n Entering block accumulator loop for bucket 23:\n bucket 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n bucket 23: 20%\n bucket 22: 50%\n bucket 23: 30%\n bucket 22: 60%\n bucket 23: 40%\n bucket 22: 70%\n bucket 22: 80%\n bucket 23: 50%\n bucket 22: 90%\n bucket 23: 60%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\nGetting block 25 of 60\n bucket 24: 40%\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 50%\n bucket 24: 60%\n Entering block accumulator loop for bucket 25:\n bucket 24: 70%\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 24: 80%\n bucket 25: 40%\n bucket 24: 90%\n bucket 25: 50%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 29:\n bucket 30: 10%\n bucket 30: 20%\n bucket 29: 10%\n Entering block accumulator loop for bucket 31:\n bucket 30: 30%\n bucket 29: 20%\n bucket 30: 40%\n bucket 31: 10%\n bucket 29: 30%\n bucket 30: 50%\n bucket 31: 20%\n bucket 30: 60%\n bucket 29: 40%\n bucket 31: 30%\n bucket 30: 70%\n bucket 29: 50%\n bucket 30: 80%\n bucket 31: 40%\n bucket 29: 60%\n bucket 30: 90%\n bucket 31: 50%\n bucket 30: 100%\n bucket 29: 70%\n bucket 31: 60%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 29: 80%\n bucket 31: 70%\n bucket 29: 90%\n bucket 31: 80%\n bucket 31: 90%\n bucket 29: 100%\n bucket 31: 100%\n Sorting block of length 51 for bucket 29\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Entering block accumulator loop for bucket 32:\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 10%\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 30%\n bucket 33: 10%\n bucket 32: 40%\n bucket 33: 20%\n bucket 32: 50%\n bucket 33: 30%\n bucket 32: 60%\n bucket 33: 40%\n bucket 32: 70%\n bucket 33: 50%\n bucket 33: 60%\n bucket 32: 80%\n bucket 33: 70%\n bucket 33: 80%\n bucket 32: 90%\n bucket 33: 90%\n bucket 32: 100%\n bucket 33: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 35:\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 34: 20%\n bucket 35: 40%\n bucket 34: 30%\n bucket 35: 50%\n bucket 34: 40%\n bucket 35: 60%\n bucket 34: 50%\n bucket 35: 70%\n bucket 34: 60%\n bucket 35: 80%\n bucket 34: 70%\n bucket 35: 90%\n bucket 34: 80%\n bucket 35: 100%\n bucket 34: 90%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 38: 10%\n bucket 39: 20%\n bucket 38: 20%\n bucket 39: 30%\n bucket 38: 30%\n bucket 39: 40%\n bucket 38: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 38: 50%\n bucket 39: 70%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 39: 80%\n bucket 38: 90%\n bucket 39: 90%\n bucket 38: 100%\n bucket 39: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 40 of 60\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 40:\n bucket 41: 10%\n bucket 40: 10%\n bucket 41: 20%\n bucket 40: 20%\n bucket 41: 30%\n bucket 40: 30%\n bucket 41: 40%\n bucket 40: 40%\n bucket 41: 50%\n bucket 40: 50%\n bucket 41: 60%\n bucket 40: 60%\n bucket 41: 70%\n bucket 40: 70%\n bucket 41: 80%\n bucket 40: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 20%\n bucket 42: 30%\n Entering block accumulator loop for bucket 43:\n bucket 42: 40%\n bucket 43: 10%\n bucket 42: 50%\n bucket 43: 20%\n bucket 42: 60%\n bucket 43: 30%\n bucket 42: 70%\n bucket 43: 40%\n bucket 42: 80%\n bucket 43: 50%\n bucket 42: 90%\n bucket 43: 60%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 60\n Entering block accumulator loop for bucket 46:\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 10%\n bucket 46: 20%\n Entering block accumulator loop for bucket 47:\n bucket 46: 30%\n bucket 46: 40%\n bucket 47: 10%\n bucket 46: 50%\n bucket 47: 20%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 48:\n bucket 49: 10%\n bucket 48: 10%\n bucket 49: 20%\n bucket 48: 20%\n bucket 48: 30%\n bucket 49: 30%\n bucket 48: 40%\n bucket 49: 40%\n bucket 48: 50%\n bucket 49: 50%\n bucket 48: 60%\n bucket 49: 60%\n bucket 48: 70%\n bucket 49: 70%\n bucket 48: 80%\n bucket 49: 80%\n bucket 48: 90%\n bucket 49: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n Entering block accumulator loop for bucket 51:\n bucket 50: 20%\n bucket 51: 10%\n bucket 50: 30%\n bucket 51: 20%\n bucket 50: 40%\n bucket 51: 30%\n bucket 50: 50%\n bucket 51: 40%\n bucket 50: 60%\n bucket 51: 50%\n bucket 50: 70%\n bucket 51: 60%\n bucket 50: 80%\n bucket 51: 70%\n bucket 50: 90%\n bucket 51: 80%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Entering block accumulator loop for bucket 52:\n Calculating Z arrays for bucket 53\n bucket 52: 10%\n Entering block accumulator loop for bucket 53:\n bucket 52: 20%\n bucket 53: 10%\n bucket 52: 30%\n bucket 53: 20%\n bucket 52: 40%\n bucket 53: 30%\n bucket 53: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 53: 50%\n bucket 52: 90%\n bucket 53: 60%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 54:\n Entering block accumulator loop for bucket 55:\n bucket 54: 10%\n bucket 55: 10%\n bucket 54: 20%\n bucket 55: 20%\n bucket 54: 30%\n bucket 55: 30%\n bucket 54: 40%\n bucket 55: 40%\n bucket 54: 50%\n bucket 55: 50%\n bucket 54: 60%\n bucket 55: 60%\n bucket 54: 70%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 54: 80%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n bucket 54: 90%\n (Using difference cover)\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\nGetting block 58 of 60\n Entering block accumulator loop for bucket 57:\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 10%\n bucket 57: 20%\n Entering block accumulator loop for bucket 58:\nGetting block 59 of 60\n bucket 57: 30%\n bucket 58: 10%\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n bucket 57: 40%\n bucket 58: 20%\n bucket 57: 50%\n bucket 58: 30%\n Entering block accumulator loop for bucket 59:\n bucket 57: 60%\n bucket 58: 40%\n bucket 57: 70%\n bucket 59: 10%\n bucket 57: 80%\n bucket 58: 50%\n bucket 57: 90%\n bucket 59: 20%\n bucket 58: 60%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n bucket 58: 70%\n (Using difference cover)\n bucket 59: 30%\n bucket 58: 80%\n bucket 59: 40%\n bucket 58: 90%\n bucket 59: 50%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:59:08", "plugin": "core", "name": "end_epoch", "raw_value": "1725001148.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:59:08", "plugin": "core", "name": "start_epoch", "raw_value": "1725001148.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-1", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 1, "time_seconds": 39.2322940826416, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "fe260f14d51542d3"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "375e718d538c5a3b"}, "library|input_2": {"src": "hda", "id": "96ac5aa6b750add6"}, "library|type": "paired"}, "job": {"model_class": "Job", "id": "edfb9d0cfea2ba20", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-08-30T06:51:14.463932", "update_time": "2024-08-30T06:51:28.344770", "galaxy_version": "24.1", "external_id": "gxy-d4fv8", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/e/6/c/dataset_e6c6903b-b451-422e-ad48-3ddd5467e448.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/8/7/f/dataset_87f76930-c2d2-47eb-bd5b-cc95f566edb4.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/1/7/6/dataset_1769e135-20e6-4d81-884c-f5ed7b68bedf.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/d/1/9/dataset_d192bf07-81d7-403a-bcdd-7d131622b82a.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 121, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 122, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 120, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "fe260f14d51542d3", "src": "hda", "uuid": "e6c6903b-b451-422e-ad48-3ddd5467e448"}, "library|input_1": {"id": "375e718d538c5a3b", "src": "hda", "uuid": "87f76930-c2d2-47eb-bd5b-cc95f566edb4"}, "library|input_2": {"id": "96ac5aa6b750add6", "src": "hda", "uuid": "1769e135-20e6-4d81-884c-f5ed7b68bedf"}}, "outputs": {"output_alignments": {"id": "ffde76bc567fd181", "src": "hda", "uuid": "d192bf07-81d7-403a-bcdd-7d131622b82a"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n bucket 1: 20%\nGetting block 3 of 60\n bucket 1: 30%\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\nGetting block 4 of 60\n Calculating Z arrays for bucket 3\n bucket 1: 40%\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n bucket 1: 50%\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 4\n bucket 1: 60%\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 3:\n bucket 1: 70%\nGetting block 6 of 60\n bucket 2: 10%\n Entering block accumulator loop for bucket 5:\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 3: 10%\n Reserving size (126) for bucket 6\n bucket 1: 80%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 1: 90%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 7\n bucket 2: 20%\n Entering block accumulator loop for bucket 4:\n bucket 3: 20%\n bucket 2: 30%\n Entering block accumulator loop for bucket 7:\n Entering block accumulator loop for bucket 6:\n bucket 4: 10%\n bucket 1: 100%\n Calculating Z arrays for bucket 8\n bucket 7: 10%\n Sorting block of length 42 for bucket 1\n bucket 4: 20%\n bucket 6: 10%\n bucket 7: 20%\n bucket 2: 40%\n bucket 4: 30%\n bucket 6: 20%\n bucket 2: 50%\n Entering block accumulator loop for bucket 8:\n (Using difference cover)\n bucket 6: 30%\n bucket 2: 60%\n bucket 7: 30%\n bucket 4: 40%\n bucket 3: 30%\n bucket 7: 40%\n bucket 6: 40%\n bucket 5: 10%\n bucket 2: 70%\n bucket 8: 10%\n bucket 3: 40%\n bucket 6: 50%\n bucket 5: 20%\n bucket 2: 80%\n bucket 4: 50%\n bucket 3: 50%\n bucket 6: 60%\n bucket 2: 90%\n bucket 8: 20%\n bucket 5: 30%\n bucket 2: 100%\n bucket 3: 60%\n bucket 8: 30%\n bucket 6: 70%\n bucket 7: 50%\n bucket 5: 40%\n bucket 4: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 8: 40%\n Sorting block time: 00:00:00\n bucket 5: 50%\n bucket 3: 70%\n bucket 6: 80%\n bucket 4: 70%\n bucket 7: 60%\n bucket 5: 60%\n bucket 8: 50%\n bucket 4: 80%\n bucket 7: 70%\n bucket 6: 90%\n bucket 5: 70%\n bucket 4: 90%\n bucket 8: 60%\nReturning block of 43 for bucket 1\n bucket 7: 80%\n bucket 8: 70%\n bucket 3: 80%\n bucket 6: 100%\n bucket 4: 100%\n bucket 7: 90%\n bucket 8: 80%\n bucket 5: 80%\n bucket 3: 90%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 3: 100%\n bucket 5: 90%\n bucket 8: 90%\n bucket 5: 100%\n Sorting block of length 106 for bucket 3\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\n Sorting block of length 68 for bucket 4\n bucket 8: 100%\nReturning block of 85 for bucket 2\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 9: 50%\n bucket 10: 50%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 60%\n bucket 9: 60%\n bucket 10: 70%\n bucket 9: 70%\n Entering block accumulator loop for bucket 11:\n bucket 9: 80%\n bucket 10: 80%\n bucket 11: 10%\n bucket 9: 90%\n bucket 10: 90%\n bucket 11: 20%\n bucket 9: 100%\n bucket 10: 100%\n bucket 11: 30%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block of length 124 for bucket 9\n bucket 11: 40%\n bucket 11: 50%\n (Using difference cover)\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 12 of 60\n Reserving size (126) for bucket 12\nGetting block 14 of 60\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Entering block accumulator loop for bucket 12:\n Calculating Z arrays for bucket 13\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 12: 10%\n Entering block accumulator loop for bucket 13:\n bucket 12: 20%\n bucket 13: 10%\n bucket 12: 30%\n Entering block accumulator loop for bucket 14:\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 12: 60%\n bucket 13: 50%\n bucket 14: 20%\n bucket 13: 60%\n bucket 12: 70%\n bucket 14: 30%\n bucket 13: 70%\n bucket 12: 80%\n bucket 14: 40%\n bucket 13: 80%\n bucket 12: 90%\n bucket 13: 90%\n bucket 14: 50%\n bucket 12: 100%\n bucket 13: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 14: 60%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Entering block accumulator loop for bucket 15:\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 15: 10%\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 20%\n bucket 15: 30%\n Entering block accumulator loop for bucket 17:\n bucket 15: 40%\n bucket 17: 10%\n bucket 15: 50%\n Entering block accumulator loop for bucket 16:\n bucket 17: 20%\n bucket 15: 60%\n bucket 16: 10%\n bucket 15: 70%\n bucket 17: 30%\n bucket 16: 20%\n bucket 15: 80%\n bucket 17: 40%\n bucket 16: 30%\n bucket 15: 90%\n bucket 17: 50%\n bucket 16: 40%\n bucket 15: 100%\n bucket 17: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 50%\n bucket 17: 70%\n bucket 16: 60%\n bucket 17: 80%\n bucket 16: 70%\n bucket 17: 90%\n bucket 16: 80%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n bucket 19: 70%\n bucket 20: 50%\n bucket 19: 80%\n bucket 20: 60%\n bucket 19: 90%\n bucket 20: 70%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 22:\n bucket 21: 10%\n bucket 22: 10%\n bucket 21: 20%\n bucket 22: 20%\n bucket 21: 30%\n bucket 22: 30%\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 22: 50%\n bucket 21: 60%\n bucket 22: 60%\n bucket 21: 70%\n bucket 22: 70%\n bucket 21: 80%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n bucket 22: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\nGetting block 24 of 60\n bucket 23: 20%\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 23: 30%\n Entering block accumulator loop for bucket 24:\n bucket 23: 40%\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 23: 50%\n bucket 24: 20%\n bucket 25: 10%\n bucket 23: 60%\n bucket 24: 30%\n bucket 23: 70%\n bucket 24: 40%\n bucket 25: 20%\n bucket 23: 80%\n bucket 24: 50%\n bucket 23: 90%\n bucket 24: 60%\n bucket 25: 30%\n bucket 23: 100%\n bucket 24: 70%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 25: 40%\n bucket 24: 80%\n bucket 25: 50%\n bucket 24: 90%\n bucket 25: 60%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 26: 10%\n bucket 27: 20%\n bucket 26: 20%\n bucket 27: 30%\n bucket 26: 30%\n bucket 27: 40%\n bucket 26: 40%\n bucket 27: 50%\n bucket 26: 50%\n bucket 27: 60%\n bucket 26: 60%\n bucket 27: 70%\n bucket 26: 70%\n bucket 27: 80%\n bucket 26: 80%\n bucket 27: 90%\n bucket 26: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 30:\n bucket 29: 10%\n bucket 30: 10%\n bucket 29: 20%\n bucket 30: 20%\n bucket 30: 30%\n bucket 29: 30%\n bucket 30: 40%\n bucket 29: 40%\n bucket 30: 50%\n bucket 29: 50%\n bucket 30: 60%\n bucket 29: 60%\n bucket 30: 70%\n bucket 29: 70%\n bucket 30: 80%\n bucket 29: 80%\n bucket 30: 90%\n bucket 29: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 10%\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 30%\n bucket 33: 10%\n bucket 32: 40%\n bucket 33: 20%\n bucket 32: 50%\n bucket 33: 30%\n bucket 32: 60%\n bucket 33: 40%\n bucket 32: 70%\n bucket 33: 50%\n bucket 32: 80%\n bucket 33: 60%\n bucket 32: 90%\n bucket 33: 70%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 60%\n bucket 34: 70%\n Entering block accumulator loop for bucket 35:\n bucket 34: 80%\n bucket 35: 10%\n bucket 34: 90%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 20%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 30%\n Entering block accumulator loop for bucket 36:\n bucket 35: 40%\n bucket 36: 10%\n bucket 35: 50%\n bucket 36: 20%\n bucket 35: 60%\n bucket 36: 30%\n bucket 35: 70%\n bucket 36: 40%\n bucket 35: 80%\n bucket 36: 50%\n bucket 35: 90%\n bucket 36: 60%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 70%\n bucket 36: 80%\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n Entering block accumulator loop for bucket 38:\n bucket 37: 20%\n bucket 38: 10%\n bucket 37: 30%\n bucket 38: 20%\n bucket 37: 40%\n bucket 38: 30%\n bucket 37: 50%\n bucket 38: 40%\n bucket 37: 60%\n bucket 38: 50%\n bucket 37: 70%\n bucket 38: 60%\n bucket 37: 80%\n bucket 38: 70%\n bucket 37: 90%\n bucket 38: 80%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 39: 30%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n bucket 39: 40%\n bucket 39: 50%\n Entering block accumulator loop for bucket 40:\n bucket 39: 60%\n bucket 40: 10%\n bucket 39: 70%\n bucket 40: 20%\n bucket 39: 80%\n bucket 40: 30%\n bucket 39: 90%\n bucket 40: 40%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\nGetting block 41 of 60\n bucket 40: 90%\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n Sorting block time: 00:00:00\n bucket 41: 20%\nReturning block of 126 for bucket 39\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 80%\n bucket 42: 90%\n Entering block accumulator loop for bucket 43:\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 50%\n Entering block accumulator loop for bucket 45:\n bucket 44: 60%\n bucket 45: 10%\n bucket 44: 70%\n bucket 45: 20%\n bucket 44: 80%\n bucket 45: 30%\n bucket 44: 90%\n bucket 44: 100%\n bucket 45: 40%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Entering block accumulator loop for bucket 47:\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n Entering block accumulator loop for bucket 48:\n bucket 47: 20%\n bucket 48: 10%\n bucket 47: 30%\n bucket 48: 20%\n bucket 47: 40%\n bucket 48: 30%\n bucket 47: 50%\n bucket 48: 40%\n bucket 47: 60%\n bucket 48: 50%\n bucket 47: 70%\n bucket 48: 60%\n bucket 47: 80%\n bucket 48: 70%\nGetting block 49 of 60\n bucket 48: 80%\n bucket 47: 90%\n Reserving size (126) for bucket 49\n bucket 48: 90%\n Calculating Z arrays for bucket 49\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n bucket 50: 30%\n Calculating Z arrays for bucket 51\n bucket 50: 40%\n Entering block accumulator loop for bucket 51:\n bucket 50: 50%\n bucket 51: 10%\n bucket 50: 60%\n bucket 51: 20%\n bucket 50: 70%\n bucket 51: 30%\n bucket 50: 80%\n bucket 51: 40%\n bucket 50: 90%\n bucket 51: 50%\n bucket 50: 100%\n bucket 51: 60%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\nGetting block 53 of 60\n bucket 52: 10%\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 20%\n bucket 52: 30%\n Entering block accumulator loop for bucket 53:\n bucket 52: 40%\n bucket 52: 50%\n bucket 53: 10%\n bucket 52: 60%\n bucket 53: 20%\n bucket 52: 70%\n bucket 53: 30%\n bucket 52: 80%\n bucket 53: 40%\n bucket 53: 50%\n bucket 52: 90%\n bucket 53: 60%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\nGetting block 56 of 60\n bucket 55: 30%\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 55: 40%\n Entering block accumulator loop for bucket 56:\n bucket 55: 50%\n Entering block accumulator loop for bucket 57:\n bucket 56: 10%\n bucket 55: 60%\n bucket 57: 10%\n bucket 56: 20%\n bucket 55: 70%\n bucket 57: 20%\n bucket 55: 80%\n bucket 56: 30%\n bucket 55: 90%\n bucket 57: 30%\n bucket 56: 40%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 57: 40%\n bucket 56: 50%\n bucket 57: 50%\n bucket 56: 60%\n bucket 57: 60%\n bucket 56: 70%\n bucket 57: 70%\n bucket 56: 80%\n bucket 57: 80%\n bucket 56: 90%\n bucket 57: 90%\n bucket 56: 100%\n bucket 57: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n Sorting block time: 00:00:00\n bucket 59: 60%\nReturning block of 114 for bucket 58\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": null, "job_stderr": null, "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n bucket 1: 20%\nGetting block 3 of 60\n bucket 1: 30%\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\nGetting block 4 of 60\n Calculating Z arrays for bucket 3\n bucket 1: 40%\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n bucket 1: 50%\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 4\n bucket 1: 60%\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 3:\n bucket 1: 70%\nGetting block 6 of 60\n bucket 2: 10%\n Entering block accumulator loop for bucket 5:\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 3: 10%\n Reserving size (126) for bucket 6\n bucket 1: 80%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 1: 90%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 7\n bucket 2: 20%\n Entering block accumulator loop for bucket 4:\n bucket 3: 20%\n bucket 2: 30%\n Entering block accumulator loop for bucket 7:\n Entering block accumulator loop for bucket 6:\n bucket 4: 10%\n bucket 1: 100%\n Calculating Z arrays for bucket 8\n bucket 7: 10%\n Sorting block of length 42 for bucket 1\n bucket 4: 20%\n bucket 6: 10%\n bucket 7: 20%\n bucket 2: 40%\n bucket 4: 30%\n bucket 6: 20%\n bucket 2: 50%\n Entering block accumulator loop for bucket 8:\n (Using difference cover)\n bucket 6: 30%\n bucket 2: 60%\n bucket 7: 30%\n bucket 4: 40%\n bucket 3: 30%\n bucket 7: 40%\n bucket 6: 40%\n bucket 5: 10%\n bucket 2: 70%\n bucket 8: 10%\n bucket 3: 40%\n bucket 6: 50%\n bucket 5: 20%\n bucket 2: 80%\n bucket 4: 50%\n bucket 3: 50%\n bucket 6: 60%\n bucket 2: 90%\n bucket 8: 20%\n bucket 5: 30%\n bucket 2: 100%\n bucket 3: 60%\n bucket 8: 30%\n bucket 6: 70%\n bucket 7: 50%\n bucket 5: 40%\n bucket 4: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 8: 40%\n Sorting block time: 00:00:00\n bucket 5: 50%\n bucket 3: 70%\n bucket 6: 80%\n bucket 4: 70%\n bucket 7: 60%\n bucket 5: 60%\n bucket 8: 50%\n bucket 4: 80%\n bucket 7: 70%\n bucket 6: 90%\n bucket 5: 70%\n bucket 4: 90%\n bucket 8: 60%\nReturning block of 43 for bucket 1\n bucket 7: 80%\n bucket 8: 70%\n bucket 3: 80%\n bucket 6: 100%\n bucket 4: 100%\n bucket 7: 90%\n bucket 8: 80%\n bucket 5: 80%\n bucket 3: 90%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 3: 100%\n bucket 5: 90%\n bucket 8: 90%\n bucket 5: 100%\n Sorting block of length 106 for bucket 3\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\n Sorting block of length 68 for bucket 4\n bucket 8: 100%\nReturning block of 85 for bucket 2\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 9: 50%\n bucket 10: 50%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 60%\n bucket 9: 60%\n bucket 10: 70%\n bucket 9: 70%\n Entering block accumulator loop for bucket 11:\n bucket 9: 80%\n bucket 10: 80%\n bucket 11: 10%\n bucket 9: 90%\n bucket 10: 90%\n bucket 11: 20%\n bucket 9: 100%\n bucket 10: 100%\n bucket 11: 30%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block of length 124 for bucket 9\n bucket 11: 40%\n bucket 11: 50%\n (Using difference cover)\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 12 of 60\n Reserving size (126) for bucket 12\nGetting block 14 of 60\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Entering block accumulator loop for bucket 12:\n Calculating Z arrays for bucket 13\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 12: 10%\n Entering block accumulator loop for bucket 13:\n bucket 12: 20%\n bucket 13: 10%\n bucket 12: 30%\n Entering block accumulator loop for bucket 14:\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 12: 60%\n bucket 13: 50%\n bucket 14: 20%\n bucket 13: 60%\n bucket 12: 70%\n bucket 14: 30%\n bucket 13: 70%\n bucket 12: 80%\n bucket 14: 40%\n bucket 13: 80%\n bucket 12: 90%\n bucket 13: 90%\n bucket 14: 50%\n bucket 12: 100%\n bucket 13: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 14: 60%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Entering block accumulator loop for bucket 15:\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 15: 10%\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 20%\n bucket 15: 30%\n Entering block accumulator loop for bucket 17:\n bucket 15: 40%\n bucket 17: 10%\n bucket 15: 50%\n Entering block accumulator loop for bucket 16:\n bucket 17: 20%\n bucket 15: 60%\n bucket 16: 10%\n bucket 15: 70%\n bucket 17: 30%\n bucket 16: 20%\n bucket 15: 80%\n bucket 17: 40%\n bucket 16: 30%\n bucket 15: 90%\n bucket 17: 50%\n bucket 16: 40%\n bucket 15: 100%\n bucket 17: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 50%\n bucket 17: 70%\n bucket 16: 60%\n bucket 17: 80%\n bucket 16: 70%\n bucket 17: 90%\n bucket 16: 80%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n bucket 19: 70%\n bucket 20: 50%\n bucket 19: 80%\n bucket 20: 60%\n bucket 19: 90%\n bucket 20: 70%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 22:\n bucket 21: 10%\n bucket 22: 10%\n bucket 21: 20%\n bucket 22: 20%\n bucket 21: 30%\n bucket 22: 30%\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 22: 50%\n bucket 21: 60%\n bucket 22: 60%\n bucket 21: 70%\n bucket 22: 70%\n bucket 21: 80%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n bucket 22: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\nGetting block 24 of 60\n bucket 23: 20%\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 23: 30%\n Entering block accumulator loop for bucket 24:\n bucket 23: 40%\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 23: 50%\n bucket 24: 20%\n bucket 25: 10%\n bucket 23: 60%\n bucket 24: 30%\n bucket 23: 70%\n bucket 24: 40%\n bucket 25: 20%\n bucket 23: 80%\n bucket 24: 50%\n bucket 23: 90%\n bucket 24: 60%\n bucket 25: 30%\n bucket 23: 100%\n bucket 24: 70%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 25: 40%\n bucket 24: 80%\n bucket 25: 50%\n bucket 24: 90%\n bucket 25: 60%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 26: 10%\n bucket 27: 20%\n bucket 26: 20%\n bucket 27: 30%\n bucket 26: 30%\n bucket 27: 40%\n bucket 26: 40%\n bucket 27: 50%\n bucket 26: 50%\n bucket 27: 60%\n bucket 26: 60%\n bucket 27: 70%\n bucket 26: 70%\n bucket 27: 80%\n bucket 26: 80%\n bucket 27: 90%\n bucket 26: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 30:\n bucket 29: 10%\n bucket 30: 10%\n bucket 29: 20%\n bucket 30: 20%\n bucket 30: 30%\n bucket 29: 30%\n bucket 30: 40%\n bucket 29: 40%\n bucket 30: 50%\n bucket 29: 50%\n bucket 30: 60%\n bucket 29: 60%\n bucket 30: 70%\n bucket 29: 70%\n bucket 30: 80%\n bucket 29: 80%\n bucket 30: 90%\n bucket 29: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 10%\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 30%\n bucket 33: 10%\n bucket 32: 40%\n bucket 33: 20%\n bucket 32: 50%\n bucket 33: 30%\n bucket 32: 60%\n bucket 33: 40%\n bucket 32: 70%\n bucket 33: 50%\n bucket 32: 80%\n bucket 33: 60%\n bucket 32: 90%\n bucket 33: 70%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 60%\n bucket 34: 70%\n Entering block accumulator loop for bucket 35:\n bucket 34: 80%\n bucket 35: 10%\n bucket 34: 90%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 20%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 30%\n Entering block accumulator loop for bucket 36:\n bucket 35: 40%\n bucket 36: 10%\n bucket 35: 50%\n bucket 36: 20%\n bucket 35: 60%\n bucket 36: 30%\n bucket 35: 70%\n bucket 36: 40%\n bucket 35: 80%\n bucket 36: 50%\n bucket 35: 90%\n bucket 36: 60%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 70%\n bucket 36: 80%\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n Entering block accumulator loop for bucket 38:\n bucket 37: 20%\n bucket 38: 10%\n bucket 37: 30%\n bucket 38: 20%\n bucket 37: 40%\n bucket 38: 30%\n bucket 37: 50%\n bucket 38: 40%\n bucket 37: 60%\n bucket 38: 50%\n bucket 37: 70%\n bucket 38: 60%\n bucket 37: 80%\n bucket 38: 70%\n bucket 37: 90%\n bucket 38: 80%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 39: 30%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n bucket 39: 40%\n bucket 39: 50%\n Entering block accumulator loop for bucket 40:\n bucket 39: 60%\n bucket 40: 10%\n bucket 39: 70%\n bucket 40: 20%\n bucket 39: 80%\n bucket 40: 30%\n bucket 39: 90%\n bucket 40: 40%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\nGetting block 41 of 60\n bucket 40: 90%\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n Sorting block time: 00:00:00\n bucket 41: 20%\nReturning block of 126 for bucket 39\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 80%\n bucket 42: 90%\n Entering block accumulator loop for bucket 43:\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 50%\n Entering block accumulator loop for bucket 45:\n bucket 44: 60%\n bucket 45: 10%\n bucket 44: 70%\n bucket 45: 20%\n bucket 44: 80%\n bucket 45: 30%\n bucket 44: 90%\n bucket 44: 100%\n bucket 45: 40%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Entering block accumulator loop for bucket 47:\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n Entering block accumulator loop for bucket 48:\n bucket 47: 20%\n bucket 48: 10%\n bucket 47: 30%\n bucket 48: 20%\n bucket 47: 40%\n bucket 48: 30%\n bucket 47: 50%\n bucket 48: 40%\n bucket 47: 60%\n bucket 48: 50%\n bucket 47: 70%\n bucket 48: 60%\n bucket 47: 80%\n bucket 48: 70%\nGetting block 49 of 60\n bucket 48: 80%\n bucket 47: 90%\n Reserving size (126) for bucket 49\n bucket 48: 90%\n Calculating Z arrays for bucket 49\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n bucket 50: 30%\n Calculating Z arrays for bucket 51\n bucket 50: 40%\n Entering block accumulator loop for bucket 51:\n bucket 50: 50%\n bucket 51: 10%\n bucket 50: 60%\n bucket 51: 20%\n bucket 50: 70%\n bucket 51: 30%\n bucket 50: 80%\n bucket 51: 40%\n bucket 50: 90%\n bucket 51: 50%\n bucket 50: 100%\n bucket 51: 60%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\nGetting block 53 of 60\n bucket 52: 10%\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 20%\n bucket 52: 30%\n Entering block accumulator loop for bucket 53:\n bucket 52: 40%\n bucket 52: 50%\n bucket 53: 10%\n bucket 52: 60%\n bucket 53: 20%\n bucket 52: 70%\n bucket 53: 30%\n bucket 52: 80%\n bucket 53: 40%\n bucket 53: 50%\n bucket 52: 90%\n bucket 53: 60%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\nGetting block 56 of 60\n bucket 55: 30%\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 55: 40%\n Entering block accumulator loop for bucket 56:\n bucket 55: 50%\n Entering block accumulator loop for bucket 57:\n bucket 56: 10%\n bucket 55: 60%\n bucket 57: 10%\n bucket 56: 20%\n bucket 55: 70%\n bucket 57: 20%\n bucket 55: 80%\n bucket 56: 30%\n bucket 55: 90%\n bucket 57: 30%\n bucket 56: 40%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 57: 40%\n bucket 56: 50%\n bucket 57: 50%\n bucket 56: 60%\n bucket 57: 60%\n bucket 56: 70%\n bucket 57: 70%\n bucket 56: 80%\n bucket 57: 80%\n bucket 56: 90%\n bucket 57: 90%\n bucket 56: 100%\n bucket 57: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n Sorting block time: 00:00:00\n bucket 59: 60%\nReturning block of 114 for bucket 58\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, exit_code: None, stderr: Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, exit_code: None, stderr: Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n."], "status": "failure"}}, {"id": "hisat2/2.2.1+galaxy1-1", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 1, "time_seconds": 37.89061784744263, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "a33a2dd288cb5184"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "157c9d88c71a1af3"}, "library|input_2": {"src": "hda", "id": "228918233c8d6930"}, "library|type": "paired"}, "job": {"model_class": "Job", "id": "289fd1d4cda0dfe4", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:59:44.743472", "update_time": "2024-08-30T06:59:58.257651", "galaxy_version": "24.1", "external_id": "gxy-658wx", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/7/c/b/dataset_7cb22dc5-5865-477a-9b79-8f86eacf4113.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/0/2/b/dataset_02b7a97f-be6b-4cea-b2ee-056c60a81ca1.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/2/7/a/dataset_27a7ccec-7b4c-4c99-9fa6-2ac955d3f54c.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/c/c/b/dataset_ccb5b504-6696-4be4-ad08-59bfcfd4458e.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 180, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 181, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 179, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "a33a2dd288cb5184", "src": "hda", "uuid": "7cb22dc5-5865-477a-9b79-8f86eacf4113"}, "library|input_1": {"id": "157c9d88c71a1af3", "src": "hda", "uuid": "02b7a97f-be6b-4cea-b2ee-056c60a81ca1"}, "library|input_2": {"id": "228918233c8d6930", "src": "hda", "uuid": "27a7ccec-7b4c-4c99-9fa6-2ac955d3f54c"}}, "outputs": {"output_alignments": {"id": "9566e093fecc270e", "src": "hda", "uuid": "ccb5b504-6696-4be4-ad08-59bfcfd4458e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 1\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\nGetting block 4 of 60\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 3\n bucket 2: 10%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 1: 10%\n bucket 2: 20%\n Reserving size (126) for bucket 4\n bucket 2: 30%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 4\n bucket 2: 40%\n bucket 1: 20%\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 6:\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 6: 10%\n Entering block accumulator loop for bucket 4:\n bucket 1: 30%\n bucket 2: 50%\nGetting block 8 of 60\n bucket 2: 60%\n bucket 4: 10%\n Calculating Z arrays for bucket 5\n bucket 2: 70%\n bucket 4: 20%\n bucket 2: 80%\n bucket 3: 10%\n bucket 2: 90%\n bucket 1: 40%\n bucket 6: 20%\n bucket 2: 100%\n bucket 3: 20%\n bucket 6: 30%\n Entering block accumulator loop for bucket 5:\n Sorting block of length 84 for bucket 2\n bucket 6: 40%\n (Using difference cover)\n bucket 3: 30%\n bucket 1: 50%\n bucket 4: 30%\n bucket 6: 50%\n bucket 1: 60%\nGetting block 7 of 60\n bucket 3: 40%\n bucket 1: 70%\n Reserving size (126) for bucket 8\n bucket 6: 60%\n bucket 4: 40%\n Reserving size (126) for bucket 7\n bucket 3: 50%\n Sorting block time: 00:00:00\n Calculating Z arrays for bucket 8\n Calculating Z arrays for bucket 7\nReturning block of 85 for bucket 2\n bucket 6: 70%\n bucket 1: 80%\n bucket 6: 80%\n bucket 3: 60%\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 7:\n bucket 5: 10%\n bucket 4: 50%\n bucket 6: 90%\n bucket 3: 70%\n bucket 7: 10%\n bucket 4: 60%\n bucket 6: 100%\n bucket 1: 90%\n bucket 4: 70%\n bucket 3: 80%\n Sorting block of length 90 for bucket 6\n bucket 4: 80%\n (Using difference cover)\n bucket 8: 10%\n bucket 7: 20%\n bucket 5: 20%\n bucket 4: 90%\n bucket 7: 30%\n bucket 5: 30%\n bucket 4: 100%\n bucket 1: 100%\n bucket 3: 90%\n bucket 5: 40%\n Sorting block of length 42 for bucket 1\n bucket 7: 40%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 5: 50%\n bucket 3: 100%\n bucket 7: 50%\n bucket 5: 60%\n bucket 8: 20%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n (Using difference cover)\n bucket 5: 70%\n bucket 7: 60%\n bucket 8: 30%\n bucket 5: 80%\n bucket 7: 70%\n bucket 8: 40%\n bucket 5: 90%\n bucket 7: 80%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 50%\n bucket 7: 90%\n bucket 8: 60%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n bucket 8: 70%\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n bucket 9: 20%\n Calculating Z arrays for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n bucket 9: 30%\n Entering block accumulator loop for bucket 10:\n Calculating Z arrays for bucket 11\n bucket 9: 40%\n bucket 10: 10%\n bucket 9: 50%\n bucket 10: 20%\n bucket 9: 60%\n bucket 10: 30%\n Entering block accumulator loop for bucket 11:\n bucket 9: 70%\n bucket 10: 40%\n bucket 11: 10%\n bucket 9: 80%\n bucket 11: 20%\n bucket 10: 50%\n bucket 9: 90%\n bucket 10: 60%\n bucket 11: 30%\n bucket 9: 100%\n bucket 10: 70%\n bucket 11: 40%\n Sorting block of length 124 for bucket 9\n bucket 10: 80%\n (Using difference cover)\n bucket 11: 50%\n bucket 10: 90%\n bucket 11: 60%\n bucket 10: 100%\n bucket 11: 70%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nReturning block of 83 for bucket 12\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 40%\n bucket 14: 50%\n Entering block accumulator loop for bucket 15:\n bucket 14: 60%\n bucket 15: 10%\n bucket 14: 70%\n bucket 15: 20%\n bucket 14: 80%\n bucket 15: 30%\n bucket 14: 90%\n bucket 15: 40%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 70%\n bucket 18: 80%\n Entering block accumulator loop for bucket 19:\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 10%\n bucket 20: 20%\n Entering block accumulator loop for bucket 21:\n bucket 20: 30%\n bucket 21: 10%\n bucket 20: 40%\n bucket 21: 20%\n bucket 20: 50%\n bucket 21: 30%\n bucket 20: 60%\n bucket 21: 40%\n bucket 20: 70%\n bucket 21: 50%\n bucket 20: 80%\n bucket 21: 60%\n bucket 20: 90%\n bucket 21: 70%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n bucket 21: 80%\n (Using difference cover)\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n bucket 23: 20%\n bucket 22: 50%\n bucket 23: 30%\n bucket 22: 60%\n bucket 23: 40%\n bucket 22: 70%\n bucket 23: 50%\n bucket 22: 80%\n bucket 23: 60%\n bucket 22: 90%\n bucket 23: 70%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n Entering block accumulator loop for bucket 26:\n bucket 25: 20%\n bucket 26: 10%\n bucket 25: 30%\n bucket 26: 20%\n bucket 25: 40%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 25: 50%\n bucket 26: 60%\n bucket 25: 60%\n bucket 26: 70%\n bucket 25: 70%\n bucket 26: 80%\n bucket 25: 80%\n bucket 26: 90%\n bucket 25: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n bucket 25: 100%\n (Using difference cover)\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 27: 10%\n bucket 28: 20%\n bucket 27: 20%\n bucket 28: 30%\n bucket 27: 30%\n bucket 28: 40%\n bucket 27: 40%\n bucket 28: 50%\n bucket 27: 50%\n bucket 28: 60%\n bucket 27: 60%\n bucket 28: 70%\n bucket 27: 70%\n bucket 28: 80%\n bucket 27: 80%\n bucket 28: 90%\n bucket 27: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 31:\n Entering block accumulator loop for bucket 30:\n bucket 31: 10%\n bucket 30: 10%\n bucket 31: 20%\n bucket 30: 20%\n bucket 31: 30%\n bucket 30: 30%\n bucket 31: 40%\n bucket 30: 40%\n bucket 31: 50%\n bucket 30: 50%\n bucket 31: 60%\n bucket 30: 60%\n bucket 31: 70%\n bucket 30: 70%\n bucket 31: 80%\n bucket 30: 80%\n bucket 31: 90%\n bucket 30: 90%\n bucket 31: 100%\n bucket 30: 100%\n Sorting block of length 110 for bucket 31\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Entering block accumulator loop for bucket 32:\n Reserving size (126) for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 32: 10%\n Calculating Z arrays for bucket 33\n bucket 32: 20%\n Entering block accumulator loop for bucket 34:\n bucket 32: 30%\n Entering block accumulator loop for bucket 33:\n bucket 34: 10%\n bucket 32: 40%\n bucket 33: 10%\n bucket 32: 50%\n bucket 34: 20%\n bucket 33: 20%\n bucket 32: 60%\n bucket 34: 30%\n bucket 32: 70%\n bucket 33: 30%\n bucket 32: 80%\n bucket 34: 40%\n bucket 33: 40%\n bucket 32: 90%\n bucket 32: 100%\n bucket 34: 50%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 50%\n bucket 34: 60%\n bucket 33: 60%\n bucket 34: 70%\n bucket 33: 70%\n bucket 34: 80%\n bucket 33: 80%\n bucket 34: 90%\n bucket 33: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\nGetting block 36 of 60\n Entering block accumulator loop for bucket 35:\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 10%\n Entering block accumulator loop for bucket 36:\n bucket 35: 20%\n bucket 36: 10%\n bucket 35: 30%\n bucket 36: 20%\n bucket 35: 40%\n bucket 36: 30%\n bucket 36: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 36: 50%\n bucket 35: 70%\n bucket 36: 60%\n bucket 36: 70%\n bucket 35: 80%\n bucket 36: 80%\n bucket 36: 90%\n bucket 35: 90%\n bucket 36: 100%\n bucket 35: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 37:\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 39:\n bucket 37: 10%\n bucket 39: 10%\n Entering block accumulator loop for bucket 38:\n bucket 37: 20%\n bucket 39: 20%\n bucket 38: 10%\n bucket 37: 30%\n bucket 39: 30%\n bucket 38: 20%\n bucket 39: 40%\n bucket 37: 40%\n bucket 39: 50%\n bucket 38: 30%\n bucket 37: 50%\n bucket 39: 60%\n bucket 38: 40%\n bucket 39: 70%\n bucket 37: 60%\n bucket 38: 50%\n bucket 39: 80%\n bucket 37: 70%\n bucket 38: 60%\n bucket 39: 90%\n bucket 37: 80%\n bucket 38: 70%\n bucket 37: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 38: 80%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 10%\n bucket 40: 20%\n Entering block accumulator loop for bucket 41:\n bucket 40: 30%\n bucket 41: 10%\n bucket 40: 40%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 40: 50%\n bucket 41: 80%\n bucket 40: 60%\n bucket 41: 90%\n bucket 40: 70%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\nGetting block 45 of 60\n Calculating Z arrays for bucket 44\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 44:\n bucket 45: 10%\n bucket 44: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 44: 20%\n bucket 45: 40%\n bucket 45: 50%\n bucket 44: 30%\n bucket 45: 60%\n bucket 45: 70%\n bucket 44: 40%\n bucket 45: 80%\n bucket 45: 90%\n bucket 44: 50%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 46:\n Calculating Z arrays for bucket 47\n bucket 48: 10%\n bucket 46: 10%\n bucket 48: 20%\n bucket 46: 20%\n Entering block accumulator loop for bucket 47:\n bucket 48: 30%\n bucket 46: 30%\n bucket 48: 40%\n bucket 46: 40%\n bucket 47: 10%\n bucket 48: 50%\n bucket 46: 50%\n bucket 47: 20%\n bucket 48: 60%\n bucket 46: 60%\n bucket 47: 30%\n bucket 48: 70%\n bucket 46: 70%\n bucket 47: 40%\n bucket 46: 80%\n bucket 48: 80%\n bucket 46: 90%\n bucket 48: 90%\n bucket 47: 50%\n bucket 46: 100%\n bucket 48: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 49:\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 49: 10%\n Entering block accumulator loop for bucket 50:\n bucket 49: 20%\n Entering block accumulator loop for bucket 51:\n bucket 49: 30%\n bucket 50: 10%\n bucket 51: 10%\n bucket 49: 40%\n bucket 49: 50%\n bucket 51: 20%\n bucket 50: 20%\n bucket 49: 60%\n bucket 49: 70%\n bucket 51: 30%\n bucket 50: 30%\n bucket 49: 80%\n bucket 49: 90%\n bucket 51: 40%\n bucket 50: 40%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 51: 50%\n bucket 50: 50%\n bucket 51: 60%\n bucket 50: 60%\n bucket 51: 70%\n bucket 50: 70%\n bucket 51: 80%\n bucket 50: 80%\n bucket 51: 90%\n bucket 50: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 52 of 60\n Reserving size (126) for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 52\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 52: 10%\n bucket 53: 10%\n bucket 52: 20%\n bucket 53: 20%\n bucket 52: 30%\n bucket 53: 30%\n bucket 52: 40%\n bucket 52: 50%\n bucket 53: 40%\n bucket 52: 60%\n bucket 53: 50%\n bucket 52: 70%\n bucket 52: 80%\n bucket 53: 60%\n bucket 52: 90%\n bucket 53: 70%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 30%\n bucket 54: 40%\n Entering block accumulator loop for bucket 55:\n bucket 54: 50%\n bucket 54: 60%\n bucket 55: 10%\n bucket 54: 70%\n bucket 55: 20%\n bucket 54: 80%\n bucket 55: 30%\n bucket 54: 90%\n bucket 55: 40%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n bucket 55: 50%\n bucket 55: 60%\n (Using difference cover)\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\nGetting block 58 of 60\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 50%\n Entering block accumulator loop for bucket 59:\n bucket 57: 60%\n Entering block accumulator loop for bucket 58:\n bucket 57: 70%\n bucket 59: 10%\n bucket 57: 80%\n bucket 59: 20%\n bucket 58: 10%\n bucket 57: 90%\n bucket 59: 30%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 20%\n bucket 59: 40%\n bucket 59: 50%\n bucket 58: 30%\n bucket 59: 60%\n bucket 59: 70%\n bucket 58: 40%\n bucket 59: 80%\n bucket 58: 50%\n bucket 59: 90%\n bucket 59: 100%\n bucket 58: 60%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 58: 70%\n bucket 58: 80%\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 1\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\nGetting block 4 of 60\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 3\n bucket 2: 10%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 1: 10%\n bucket 2: 20%\n Reserving size (126) for bucket 4\n bucket 2: 30%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 4\n bucket 2: 40%\n bucket 1: 20%\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 6:\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 6: 10%\n Entering block accumulator loop for bucket 4:\n bucket 1: 30%\n bucket 2: 50%\nGetting block 8 of 60\n bucket 2: 60%\n bucket 4: 10%\n Calculating Z arrays for bucket 5\n bucket 2: 70%\n bucket 4: 20%\n bucket 2: 80%\n bucket 3: 10%\n bucket 2: 90%\n bucket 1: 40%\n bucket 6: 20%\n bucket 2: 100%\n bucket 3: 20%\n bucket 6: 30%\n Entering block accumulator loop for bucket 5:\n Sorting block of length 84 for bucket 2\n bucket 6: 40%\n (Using difference cover)\n bucket 3: 30%\n bucket 1: 50%\n bucket 4: 30%\n bucket 6: 50%\n bucket 1: 60%\nGetting block 7 of 60\n bucket 3: 40%\n bucket 1: 70%\n Reserving size (126) for bucket 8\n bucket 6: 60%\n bucket 4: 40%\n Reserving size (126) for bucket 7\n bucket 3: 50%\n Sorting block time: 00:00:00\n Calculating Z arrays for bucket 8\n Calculating Z arrays for bucket 7\nReturning block of 85 for bucket 2\n bucket 6: 70%\n bucket 1: 80%\n bucket 6: 80%\n bucket 3: 60%\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 7:\n bucket 5: 10%\n bucket 4: 50%\n bucket 6: 90%\n bucket 3: 70%\n bucket 7: 10%\n bucket 4: 60%\n bucket 6: 100%\n bucket 1: 90%\n bucket 4: 70%\n bucket 3: 80%\n Sorting block of length 90 for bucket 6\n bucket 4: 80%\n (Using difference cover)\n bucket 8: 10%\n bucket 7: 20%\n bucket 5: 20%\n bucket 4: 90%\n bucket 7: 30%\n bucket 5: 30%\n bucket 4: 100%\n bucket 1: 100%\n bucket 3: 90%\n bucket 5: 40%\n Sorting block of length 42 for bucket 1\n bucket 7: 40%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 5: 50%\n bucket 3: 100%\n bucket 7: 50%\n bucket 5: 60%\n bucket 8: 20%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n (Using difference cover)\n bucket 5: 70%\n bucket 7: 60%\n bucket 8: 30%\n bucket 5: 80%\n bucket 7: 70%\n bucket 8: 40%\n bucket 5: 90%\n bucket 7: 80%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 50%\n bucket 7: 90%\n bucket 8: 60%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n bucket 8: 70%\n (Using difference cover)\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n bucket 9: 20%\n Calculating Z arrays for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n bucket 9: 30%\n Entering block accumulator loop for bucket 10:\n Calculating Z arrays for bucket 11\n bucket 9: 40%\n bucket 10: 10%\n bucket 9: 50%\n bucket 10: 20%\n bucket 9: 60%\n bucket 10: 30%\n Entering block accumulator loop for bucket 11:\n bucket 9: 70%\n bucket 10: 40%\n bucket 11: 10%\n bucket 9: 80%\n bucket 11: 20%\n bucket 10: 50%\n bucket 9: 90%\n bucket 10: 60%\n bucket 11: 30%\n bucket 9: 100%\n bucket 10: 70%\n bucket 11: 40%\n Sorting block of length 124 for bucket 9\n bucket 10: 80%\n (Using difference cover)\n bucket 11: 50%\n bucket 10: 90%\n bucket 11: 60%\n bucket 10: 100%\n bucket 11: 70%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nReturning block of 83 for bucket 12\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 40%\n bucket 14: 50%\n Entering block accumulator loop for bucket 15:\n bucket 14: 60%\n bucket 15: 10%\n bucket 14: 70%\n bucket 15: 20%\n bucket 14: 80%\n bucket 15: 30%\n bucket 14: 90%\n bucket 15: 40%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 70%\n bucket 18: 80%\n Entering block accumulator loop for bucket 19:\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 10%\n bucket 20: 20%\n Entering block accumulator loop for bucket 21:\n bucket 20: 30%\n bucket 21: 10%\n bucket 20: 40%\n bucket 21: 20%\n bucket 20: 50%\n bucket 21: 30%\n bucket 20: 60%\n bucket 21: 40%\n bucket 20: 70%\n bucket 21: 50%\n bucket 20: 80%\n bucket 21: 60%\n bucket 20: 90%\n bucket 21: 70%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n bucket 21: 80%\n (Using difference cover)\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n bucket 23: 20%\n bucket 22: 50%\n bucket 23: 30%\n bucket 22: 60%\n bucket 23: 40%\n bucket 22: 70%\n bucket 23: 50%\n bucket 22: 80%\n bucket 23: 60%\n bucket 22: 90%\n bucket 23: 70%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n Entering block accumulator loop for bucket 26:\n bucket 25: 20%\n bucket 26: 10%\n bucket 25: 30%\n bucket 26: 20%\n bucket 25: 40%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 25: 50%\n bucket 26: 60%\n bucket 25: 60%\n bucket 26: 70%\n bucket 25: 70%\n bucket 26: 80%\n bucket 25: 80%\n bucket 26: 90%\n bucket 25: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n bucket 25: 100%\n (Using difference cover)\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 27: 10%\n bucket 28: 20%\n bucket 27: 20%\n bucket 28: 30%\n bucket 27: 30%\n bucket 28: 40%\n bucket 27: 40%\n bucket 28: 50%\n bucket 27: 50%\n bucket 28: 60%\n bucket 27: 60%\n bucket 28: 70%\n bucket 27: 70%\n bucket 28: 80%\n bucket 27: 80%\n bucket 28: 90%\n bucket 27: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 31:\n Entering block accumulator loop for bucket 30:\n bucket 31: 10%\n bucket 30: 10%\n bucket 31: 20%\n bucket 30: 20%\n bucket 31: 30%\n bucket 30: 30%\n bucket 31: 40%\n bucket 30: 40%\n bucket 31: 50%\n bucket 30: 50%\n bucket 31: 60%\n bucket 30: 60%\n bucket 31: 70%\n bucket 30: 70%\n bucket 31: 80%\n bucket 30: 80%\n bucket 31: 90%\n bucket 30: 90%\n bucket 31: 100%\n bucket 30: 100%\n Sorting block of length 110 for bucket 31\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Entering block accumulator loop for bucket 32:\n Reserving size (126) for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 32: 10%\n Calculating Z arrays for bucket 33\n bucket 32: 20%\n Entering block accumulator loop for bucket 34:\n bucket 32: 30%\n Entering block accumulator loop for bucket 33:\n bucket 34: 10%\n bucket 32: 40%\n bucket 33: 10%\n bucket 32: 50%\n bucket 34: 20%\n bucket 33: 20%\n bucket 32: 60%\n bucket 34: 30%\n bucket 32: 70%\n bucket 33: 30%\n bucket 32: 80%\n bucket 34: 40%\n bucket 33: 40%\n bucket 32: 90%\n bucket 32: 100%\n bucket 34: 50%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 50%\n bucket 34: 60%\n bucket 33: 60%\n bucket 34: 70%\n bucket 33: 70%\n bucket 34: 80%\n bucket 33: 80%\n bucket 34: 90%\n bucket 33: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\nGetting block 36 of 60\n Entering block accumulator loop for bucket 35:\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 10%\n Entering block accumulator loop for bucket 36:\n bucket 35: 20%\n bucket 36: 10%\n bucket 35: 30%\n bucket 36: 20%\n bucket 35: 40%\n bucket 36: 30%\n bucket 36: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 36: 50%\n bucket 35: 70%\n bucket 36: 60%\n bucket 36: 70%\n bucket 35: 80%\n bucket 36: 80%\n bucket 36: 90%\n bucket 35: 90%\n bucket 36: 100%\n bucket 35: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 37:\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 39:\n bucket 37: 10%\n bucket 39: 10%\n Entering block accumulator loop for bucket 38:\n bucket 37: 20%\n bucket 39: 20%\n bucket 38: 10%\n bucket 37: 30%\n bucket 39: 30%\n bucket 38: 20%\n bucket 39: 40%\n bucket 37: 40%\n bucket 39: 50%\n bucket 38: 30%\n bucket 37: 50%\n bucket 39: 60%\n bucket 38: 40%\n bucket 39: 70%\n bucket 37: 60%\n bucket 38: 50%\n bucket 39: 80%\n bucket 37: 70%\n bucket 38: 60%\n bucket 39: 90%\n bucket 37: 80%\n bucket 38: 70%\n bucket 37: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 38: 80%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 10%\n bucket 40: 20%\n Entering block accumulator loop for bucket 41:\n bucket 40: 30%\n bucket 41: 10%\n bucket 40: 40%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 40: 50%\n bucket 41: 80%\n bucket 40: 60%\n bucket 41: 90%\n bucket 40: 70%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\nGetting block 45 of 60\n Calculating Z arrays for bucket 44\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 44:\n bucket 45: 10%\n bucket 44: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 44: 20%\n bucket 45: 40%\n bucket 45: 50%\n bucket 44: 30%\n bucket 45: 60%\n bucket 45: 70%\n bucket 44: 40%\n bucket 45: 80%\n bucket 45: 90%\n bucket 44: 50%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 46:\n Calculating Z arrays for bucket 47\n bucket 48: 10%\n bucket 46: 10%\n bucket 48: 20%\n bucket 46: 20%\n Entering block accumulator loop for bucket 47:\n bucket 48: 30%\n bucket 46: 30%\n bucket 48: 40%\n bucket 46: 40%\n bucket 47: 10%\n bucket 48: 50%\n bucket 46: 50%\n bucket 47: 20%\n bucket 48: 60%\n bucket 46: 60%\n bucket 47: 30%\n bucket 48: 70%\n bucket 46: 70%\n bucket 47: 40%\n bucket 46: 80%\n bucket 48: 80%\n bucket 46: 90%\n bucket 48: 90%\n bucket 47: 50%\n bucket 46: 100%\n bucket 48: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 49:\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 49: 10%\n Entering block accumulator loop for bucket 50:\n bucket 49: 20%\n Entering block accumulator loop for bucket 51:\n bucket 49: 30%\n bucket 50: 10%\n bucket 51: 10%\n bucket 49: 40%\n bucket 49: 50%\n bucket 51: 20%\n bucket 50: 20%\n bucket 49: 60%\n bucket 49: 70%\n bucket 51: 30%\n bucket 50: 30%\n bucket 49: 80%\n bucket 49: 90%\n bucket 51: 40%\n bucket 50: 40%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 51: 50%\n bucket 50: 50%\n bucket 51: 60%\n bucket 50: 60%\n bucket 51: 70%\n bucket 50: 70%\n bucket 51: 80%\n bucket 50: 80%\n bucket 51: 90%\n bucket 50: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 52 of 60\n Reserving size (126) for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 52\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 52: 10%\n bucket 53: 10%\n bucket 52: 20%\n bucket 53: 20%\n bucket 52: 30%\n bucket 53: 30%\n bucket 52: 40%\n bucket 52: 50%\n bucket 53: 40%\n bucket 52: 60%\n bucket 53: 50%\n bucket 52: 70%\n bucket 52: 80%\n bucket 53: 60%\n bucket 52: 90%\n bucket 53: 70%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 30%\n bucket 54: 40%\n Entering block accumulator loop for bucket 55:\n bucket 54: 50%\n bucket 54: 60%\n bucket 55: 10%\n bucket 54: 70%\n bucket 55: 20%\n bucket 54: 80%\n bucket 55: 30%\n bucket 54: 90%\n bucket 55: 40%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n bucket 55: 50%\n bucket 55: 60%\n (Using difference cover)\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\nGetting block 58 of 60\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 50%\n Entering block accumulator loop for bucket 59:\n bucket 57: 60%\n Entering block accumulator loop for bucket 58:\n bucket 57: 70%\n bucket 59: 10%\n bucket 57: 80%\n bucket 59: 20%\n bucket 58: 10%\n bucket 57: 90%\n bucket 59: 30%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 20%\n bucket 59: 40%\n bucket 59: 50%\n bucket 58: 30%\n bucket 59: 60%\n bucket 59: 70%\n bucket 58: 40%\n bucket 59: 80%\n bucket 58: 50%\n bucket 59: 90%\n bucket 59: 100%\n bucket 58: 60%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 58: 70%\n bucket 58: 80%\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:59:46", "plugin": "core", "name": "end_epoch", "raw_value": "1725001186.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:59:46", "plugin": "core", "name": "start_epoch", "raw_value": "1725001186.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-10", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 10, "time_seconds": 33.59005689620972, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "80bad9b07eac38c4"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "6f4071d2a7067ec3"}, "library|rna_strandness": "R", "library|type": "single", "sum|new_summary": true, "sum|summary_file": true}, "job": {"model_class": "Job", "id": "58faae816ea8ef23", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:55:45.727760", "update_time": "2024-08-30T06:55:59.001609", "galaxy_version": "24.1", "external_id": "gxy-628gd", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/1/7/b/dataset_17b5f161-c250-4d01-a05e-8b990caf2fb2.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/9/3/a/dataset_93afa377-b0ad-421e-aae4-73e5ac2aa3c2.dat' input_f.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -U 'input_f.fastq' --rna-strandness R --new-summary --summary-file summary.txt | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/c/a/7/dataset_ca77a1c3-61ec-4e7c-8821-e9aca71b7f38.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": true, \"summary_file\": true}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 155, \"src\": \"hda\"}]}, \"rna_strandness\": \"R\", \"type\": \"single\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 154, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "80bad9b07eac38c4", "src": "hda", "uuid": "17b5f161-c250-4d01-a05e-8b990caf2fb2"}, "library|input_1": {"id": "6f4071d2a7067ec3", "src": "hda", "uuid": "93afa377-b0ad-421e-aae4-73e5ac2aa3c2"}}, "outputs": {"output_alignments": {"id": "568deb7e518268f5", "src": "hda", "uuid": "ca77a1c3-61ec-4e7c-8821-e9aca71b7f38"}, "summary_file": {"id": "d03992d555bd8aff", "src": "hda", "uuid": "61320aeb-3d05-44fe-8ea2-ca0ea3f7b1a5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 2\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 4\nGetting block 3 of 60\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\nGetting block 5 of 60\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 4:\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 4: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 3:\nGetting block 6 of 60\n bucket 2: 10%\n Reserving size (126) for bucket 6\n bucket 3: 10%\n bucket 4: 20%\n bucket 3: 20%\n bucket 2: 20%\n bucket 1: 30%\n Reserving size (126) for bucket 5\n bucket 4: 30%\n bucket 1: 40%\n Calculating Z arrays for bucket 7\n bucket 3: 30%\n bucket 1: 50%\n bucket 4: 40%\n Calculating Z arrays for bucket 6\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Entering block accumulator loop for bucket 7:\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 8\n bucket 4: 50%\n bucket 2: 30%\n bucket 3: 40%\n bucket 1: 60%\n bucket 4: 60%\n bucket 3: 50%\n bucket 1: 70%\n Entering block accumulator loop for bucket 6:\n bucket 3: 60%\n bucket 1: 80%\n bucket 4: 70%\n bucket 3: 70%\n bucket 2: 40%\n bucket 4: 80%\n bucket 1: 90%\n bucket 7: 10%\n bucket 3: 80%\n bucket 1: 100%\n bucket 6: 10%\n bucket 2: 50%\n bucket 7: 20%\n bucket 4: 90%\n bucket 3: 90%\n bucket 2: 60%\n Entering block accumulator loop for bucket 8:\n bucket 6: 20%\n Sorting block of length 42 for bucket 1\n bucket 2: 70%\n bucket 8: 10%\n bucket 7: 30%\n bucket 2: 80%\n bucket 8: 20%\n bucket 3: 100%\n bucket 7: 40%\n Entering block accumulator loop for bucket 5:\n bucket 7: 50%\n bucket 6: 30%\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 30%\n bucket 7: 60%\n bucket 2: 90%\n bucket 4: 100%\n bucket 6: 40%\n bucket 5: 10%\n bucket 8: 40%\n Sorting block of length 68 for bucket 4\n bucket 5: 20%\n bucket 8: 50%\n bucket 7: 70%\n bucket 5: 30%\n (Using difference cover)\n bucket 6: 50%\n bucket 2: 100%\n bucket 7: 80%\n bucket 8: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 7: 90%\n bucket 6: 60%\n bucket 8: 70%\n bucket 5: 40%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 50%\n bucket 6: 70%\n bucket 8: 80%\n bucket 5: 60%\n bucket 6: 80%\n bucket 8: 90%\n bucket 5: 70%\n bucket 6: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n bucket 5: 80%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Entering block accumulator loop for bucket 9:\n Calculating Z arrays for bucket 10\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 10: 50%\n bucket 9: 50%\n bucket 10: 60%\n bucket 9: 60%\n bucket 10: 70%\n bucket 9: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 9: 80%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 12:\n bucket 11: 10%\n bucket 11: 20%\n Entering block accumulator loop for bucket 13:\n bucket 12: 10%\n bucket 13: 10%\n bucket 11: 30%\n bucket 12: 20%\n bucket 13: 20%\n bucket 11: 40%\n bucket 12: 30%\n bucket 13: 30%\n bucket 11: 50%\n bucket 12: 40%\n bucket 13: 40%\n bucket 11: 60%\n bucket 12: 50%\n bucket 13: 50%\n bucket 11: 70%\n bucket 12: 60%\n bucket 11: 80%\n bucket 13: 60%\n bucket 12: 70%\n bucket 11: 90%\n bucket 13: 70%\n bucket 12: 80%\n bucket 11: 100%\n bucket 13: 80%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 12: 90%\n bucket 13: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\nGetting block 17 of 60\n bucket 16: 80%\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 90%\n Entering block accumulator loop for bucket 17:\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Entering block accumulator loop for bucket 19:\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n bucket 20: 50%\n bucket 19: 70%\n bucket 20: 60%\n bucket 19: 80%\n bucket 20: 70%\n bucket 19: 90%\n bucket 20: 80%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 21:\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 21: 10%\n Entering block accumulator loop for bucket 23:\n bucket 21: 20%\n bucket 22: 10%\n bucket 21: 30%\n bucket 22: 20%\n bucket 21: 40%\n bucket 23: 10%\n bucket 22: 30%\n bucket 21: 50%\n bucket 23: 20%\n bucket 22: 40%\n bucket 21: 60%\n bucket 22: 50%\n bucket 23: 30%\n bucket 21: 70%\n bucket 22: 60%\n bucket 23: 40%\n bucket 21: 80%\n bucket 22: 70%\n bucket 23: 50%\n bucket 22: 80%\n bucket 23: 60%\n bucket 22: 90%\n bucket 23: 70%\n bucket 21: 90%\n bucket 22: 100%\n bucket 23: 80%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 21: 100%\n bucket 23: 90%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 24:\n bucket 25: 10%\n bucket 24: 10%\n bucket 25: 20%\n bucket 24: 20%\n bucket 25: 30%\n bucket 24: 30%\n bucket 25: 40%\n bucket 24: 40%\n bucket 25: 50%\n bucket 24: 50%\n bucket 25: 60%\n bucket 24: 60%\n bucket 25: 70%\n bucket 24: 70%\n bucket 25: 80%\n bucket 24: 80%\n bucket 25: 90%\n bucket 24: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 26\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\n bucket 27: 20%\n bucket 26: 30%\n bucket 27: 30%\n bucket 26: 40%\n bucket 27: 40%\n bucket 26: 50%\n bucket 27: 50%\n bucket 26: 60%\n bucket 27: 60%\n bucket 26: 70%\n bucket 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 26: 90%\n bucket 27: 90%\n bucket 26: 100%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 30%\n bucket 28: 40%\n Entering block accumulator loop for bucket 29:\n bucket 28: 50%\n bucket 28: 60%\n bucket 29: 10%\n bucket 28: 70%\n bucket 29: 20%\n bucket 28: 80%\n bucket 29: 30%\n bucket 28: 90%\n bucket 29: 40%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n Entering block accumulator loop for bucket 31:\n bucket 30: 70%\n bucket 30: 80%\n bucket 31: 10%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\n bucket 32: 40%\n bucket 32: 50%\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 60%\n bucket 32: 70%\n Entering block accumulator loop for bucket 33:\n bucket 32: 80%\n bucket 32: 90%\n bucket 33: 10%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n Entering block accumulator loop for bucket 35:\n bucket 34: 10%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 34: 20%\n bucket 35: 10%\n Entering block accumulator loop for bucket 36:\n bucket 35: 20%\n bucket 34: 30%\n bucket 36: 10%\n bucket 35: 30%\n bucket 34: 40%\n bucket 36: 20%\n bucket 35: 40%\n bucket 36: 30%\n bucket 36: 40%\n bucket 35: 50%\n bucket 36: 50%\n bucket 35: 60%\n bucket 36: 60%\n bucket 34: 50%\n bucket 35: 70%\n bucket 36: 70%\n bucket 34: 60%\n bucket 35: 80%\n bucket 36: 80%\n bucket 34: 70%\n bucket 35: 90%\n bucket 36: 90%\n bucket 34: 80%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 100%\n bucket 34: 90%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 40%\n bucket 38: 50%\n Entering block accumulator loop for bucket 39:\n bucket 38: 60%\n bucket 38: 70%\n bucket 39: 10%\n bucket 38: 80%\n bucket 38: 90%\n bucket 39: 20%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block time: 00:00:00\n Sorting block of length 125 for bucket 39\n (Using difference cover)\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n Entering block accumulator loop for bucket 41:\n bucket 40: 20%\n bucket 41: 10%\n bucket 40: 30%\n bucket 41: 20%\n bucket 40: 40%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 40: 60%\n bucket 41: 50%\n bucket 40: 70%\n bucket 41: 60%\n bucket 40: 80%\n bucket 41: 70%\n bucket 40: 90%\n bucket 41: 80%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 43: 20%\n bucket 44: 10%\n bucket 43: 30%\n bucket 44: 20%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 43: 90%\n bucket 44: 80%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n bucket 44: 90%\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n Entering block accumulator loop for bucket 46:\n bucket 45: 20%\n bucket 46: 10%\n bucket 45: 30%\n bucket 46: 20%\n bucket 45: 40%\n bucket 46: 30%\n bucket 45: 50%\n bucket 46: 40%\n bucket 45: 60%\n bucket 46: 50%\n bucket 45: 70%\n bucket 46: 60%\n bucket 45: 80%\n bucket 45: 90%\n bucket 46: 70%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Entering block accumulator loop for bucket 47:\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n Entering block accumulator loop for bucket 48:\n bucket 47: 20%\n bucket 48: 10%\n bucket 47: 30%\n bucket 48: 20%\n bucket 47: 40%\n bucket 48: 30%\n bucket 48: 40%\n bucket 47: 50%\n bucket 48: 50%\n bucket 47: 60%\n bucket 48: 60%\n bucket 47: 70%\n bucket 48: 70%\n bucket 47: 80%\n bucket 48: 80%\n bucket 47: 90%\n bucket 48: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 49: 30%\n bucket 49: 40%\n bucket 50: 10%\nGetting block 51 of 60\n bucket 50: 20%\n bucket 49: 50%\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 30%\n bucket 49: 60%\n bucket 50: 40%\n bucket 49: 70%\n Entering block accumulator loop for bucket 51:\n bucket 50: 50%\n bucket 49: 80%\n bucket 51: 10%\n bucket 50: 60%\n bucket 49: 90%\n bucket 51: 20%\n bucket 50: 70%\n bucket 49: 100%\n bucket 51: 30%\n bucket 50: 80%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 51: 40%\n bucket 50: 90%\n bucket 51: 50%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n Entering block accumulator loop for bucket 54:\n bucket 53: 40%\n bucket 53: 50%\n bucket 54: 10%\nGetting block 55 of 60\n bucket 53: 60%\n bucket 54: 20%\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 53: 70%\n bucket 54: 30%\n bucket 54: 40%\n bucket 53: 80%\n Entering block accumulator loop for bucket 55:\n bucket 54: 50%\n bucket 53: 90%\n bucket 54: 60%\n bucket 53: 100%\n bucket 54: 70%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 55: 10%\n bucket 54: 80%\n bucket 55: 20%\n bucket 54: 90%\n bucket 54: 100%\n bucket 55: 30%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 57:\n Entering block accumulator loop for bucket 56:\n bucket 57: 10%\n bucket 56: 10%\n bucket 57: 20%\n bucket 56: 20%\n bucket 57: 30%\n bucket 56: 30%\n bucket 57: 40%\n bucket 56: 40%\n bucket 57: 50%\n bucket 56: 50%\n bucket 57: 60%\n bucket 56: 60%\n bucket 57: 70%\n bucket 56: 70%\n bucket 57: 80%\n bucket 56: 80%\n bucket 57: 90%\n bucket 56: 90%\n bucket 57: 100%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n bucket 58: 50%\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n bucket 58: 60%\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 58: 70%\n bucket 59: 20%\n bucket 60: 20%\n bucket 58: 80%\n bucket 60: 30%\n bucket 59: 30%\n bucket 58: 90%\n bucket 60: 40%\n bucket 59: 40%\n bucket 58: 100%\n bucket 60: 50%\n Sorting block of length 113 for bucket 58\n bucket 59: 50%\n (Using difference cover)\n bucket 60: 60%\n bucket 59: 60%\n bucket 60: 70%\n bucket 59: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n bucket 59: 100%\n (Using difference cover)\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\nHISAT2 summary stats:\n\tTotal reads: 10\n\t\tAligned 0 time: 0 (0.00%)\n\t\tAligned 1 time: 10 (100.00%)\n\t\tAligned >1 times: 0 (0.00%)\n\tOverall alignment rate: 100.00%\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 2\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 4\nGetting block 3 of 60\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\nGetting block 5 of 60\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 4:\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 4: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 3:\nGetting block 6 of 60\n bucket 2: 10%\n Reserving size (126) for bucket 6\n bucket 3: 10%\n bucket 4: 20%\n bucket 3: 20%\n bucket 2: 20%\n bucket 1: 30%\n Reserving size (126) for bucket 5\n bucket 4: 30%\n bucket 1: 40%\n Calculating Z arrays for bucket 7\n bucket 3: 30%\n bucket 1: 50%\n bucket 4: 40%\n Calculating Z arrays for bucket 6\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Entering block accumulator loop for bucket 7:\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 8\n bucket 4: 50%\n bucket 2: 30%\n bucket 3: 40%\n bucket 1: 60%\n bucket 4: 60%\n bucket 3: 50%\n bucket 1: 70%\n Entering block accumulator loop for bucket 6:\n bucket 3: 60%\n bucket 1: 80%\n bucket 4: 70%\n bucket 3: 70%\n bucket 2: 40%\n bucket 4: 80%\n bucket 1: 90%\n bucket 7: 10%\n bucket 3: 80%\n bucket 1: 100%\n bucket 6: 10%\n bucket 2: 50%\n bucket 7: 20%\n bucket 4: 90%\n bucket 3: 90%\n bucket 2: 60%\n Entering block accumulator loop for bucket 8:\n bucket 6: 20%\n Sorting block of length 42 for bucket 1\n bucket 2: 70%\n bucket 8: 10%\n bucket 7: 30%\n bucket 2: 80%\n bucket 8: 20%\n bucket 3: 100%\n bucket 7: 40%\n Entering block accumulator loop for bucket 5:\n bucket 7: 50%\n bucket 6: 30%\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 30%\n bucket 7: 60%\n bucket 2: 90%\n bucket 4: 100%\n bucket 6: 40%\n bucket 5: 10%\n bucket 8: 40%\n Sorting block of length 68 for bucket 4\n bucket 5: 20%\n bucket 8: 50%\n bucket 7: 70%\n bucket 5: 30%\n (Using difference cover)\n bucket 6: 50%\n bucket 2: 100%\n bucket 7: 80%\n bucket 8: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 7: 90%\n bucket 6: 60%\n bucket 8: 70%\n bucket 5: 40%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 50%\n bucket 6: 70%\n bucket 8: 80%\n bucket 5: 60%\n bucket 6: 80%\n bucket 8: 90%\n bucket 5: 70%\n bucket 6: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n bucket 5: 80%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Entering block accumulator loop for bucket 9:\n Calculating Z arrays for bucket 10\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 10: 30%\n bucket 9: 40%\n bucket 10: 40%\n bucket 10: 50%\n bucket 9: 50%\n bucket 10: 60%\n bucket 9: 60%\n bucket 10: 70%\n bucket 9: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 9: 80%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 12:\n bucket 11: 10%\n bucket 11: 20%\n Entering block accumulator loop for bucket 13:\n bucket 12: 10%\n bucket 13: 10%\n bucket 11: 30%\n bucket 12: 20%\n bucket 13: 20%\n bucket 11: 40%\n bucket 12: 30%\n bucket 13: 30%\n bucket 11: 50%\n bucket 12: 40%\n bucket 13: 40%\n bucket 11: 60%\n bucket 12: 50%\n bucket 13: 50%\n bucket 11: 70%\n bucket 12: 60%\n bucket 11: 80%\n bucket 13: 60%\n bucket 12: 70%\n bucket 11: 90%\n bucket 13: 70%\n bucket 12: 80%\n bucket 11: 100%\n bucket 13: 80%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 12: 90%\n bucket 13: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\nGetting block 17 of 60\n bucket 16: 80%\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 90%\n Entering block accumulator loop for bucket 17:\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Entering block accumulator loop for bucket 19:\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n bucket 20: 50%\n bucket 19: 70%\n bucket 20: 60%\n bucket 19: 80%\n bucket 20: 70%\n bucket 19: 90%\n bucket 20: 80%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 21:\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 21: 10%\n Entering block accumulator loop for bucket 23:\n bucket 21: 20%\n bucket 22: 10%\n bucket 21: 30%\n bucket 22: 20%\n bucket 21: 40%\n bucket 23: 10%\n bucket 22: 30%\n bucket 21: 50%\n bucket 23: 20%\n bucket 22: 40%\n bucket 21: 60%\n bucket 22: 50%\n bucket 23: 30%\n bucket 21: 70%\n bucket 22: 60%\n bucket 23: 40%\n bucket 21: 80%\n bucket 22: 70%\n bucket 23: 50%\n bucket 22: 80%\n bucket 23: 60%\n bucket 22: 90%\n bucket 23: 70%\n bucket 21: 90%\n bucket 22: 100%\n bucket 23: 80%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 21: 100%\n bucket 23: 90%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 24:\n bucket 25: 10%\n bucket 24: 10%\n bucket 25: 20%\n bucket 24: 20%\n bucket 25: 30%\n bucket 24: 30%\n bucket 25: 40%\n bucket 24: 40%\n bucket 25: 50%\n bucket 24: 50%\n bucket 25: 60%\n bucket 24: 60%\n bucket 25: 70%\n bucket 24: 70%\n bucket 25: 80%\n bucket 24: 80%\n bucket 25: 90%\n bucket 24: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 26\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\n bucket 27: 20%\n bucket 26: 30%\n bucket 27: 30%\n bucket 26: 40%\n bucket 27: 40%\n bucket 26: 50%\n bucket 27: 50%\n bucket 26: 60%\n bucket 27: 60%\n bucket 26: 70%\n bucket 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 26: 90%\n bucket 27: 90%\n bucket 26: 100%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 30%\n bucket 28: 40%\n Entering block accumulator loop for bucket 29:\n bucket 28: 50%\n bucket 28: 60%\n bucket 29: 10%\n bucket 28: 70%\n bucket 29: 20%\n bucket 28: 80%\n bucket 29: 30%\n bucket 28: 90%\n bucket 29: 40%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n Entering block accumulator loop for bucket 31:\n bucket 30: 70%\n bucket 30: 80%\n bucket 31: 10%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\n bucket 32: 40%\n bucket 32: 50%\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 60%\n bucket 32: 70%\n Entering block accumulator loop for bucket 33:\n bucket 32: 80%\n bucket 32: 90%\n bucket 33: 10%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n Entering block accumulator loop for bucket 35:\n bucket 34: 10%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 34: 20%\n bucket 35: 10%\n Entering block accumulator loop for bucket 36:\n bucket 35: 20%\n bucket 34: 30%\n bucket 36: 10%\n bucket 35: 30%\n bucket 34: 40%\n bucket 36: 20%\n bucket 35: 40%\n bucket 36: 30%\n bucket 36: 40%\n bucket 35: 50%\n bucket 36: 50%\n bucket 35: 60%\n bucket 36: 60%\n bucket 34: 50%\n bucket 35: 70%\n bucket 36: 70%\n bucket 34: 60%\n bucket 35: 80%\n bucket 36: 80%\n bucket 34: 70%\n bucket 35: 90%\n bucket 36: 90%\n bucket 34: 80%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 100%\n bucket 34: 90%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 40%\n bucket 38: 50%\n Entering block accumulator loop for bucket 39:\n bucket 38: 60%\n bucket 38: 70%\n bucket 39: 10%\n bucket 38: 80%\n bucket 38: 90%\n bucket 39: 20%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block time: 00:00:00\n Sorting block of length 125 for bucket 39\n (Using difference cover)\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n Entering block accumulator loop for bucket 41:\n bucket 40: 20%\n bucket 41: 10%\n bucket 40: 30%\n bucket 41: 20%\n bucket 40: 40%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 40: 60%\n bucket 41: 50%\n bucket 40: 70%\n bucket 41: 60%\n bucket 40: 80%\n bucket 41: 70%\n bucket 40: 90%\n bucket 41: 80%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 43: 20%\n bucket 44: 10%\n bucket 43: 30%\n bucket 44: 20%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 43: 90%\n bucket 44: 80%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n bucket 44: 90%\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n Entering block accumulator loop for bucket 46:\n bucket 45: 20%\n bucket 46: 10%\n bucket 45: 30%\n bucket 46: 20%\n bucket 45: 40%\n bucket 46: 30%\n bucket 45: 50%\n bucket 46: 40%\n bucket 45: 60%\n bucket 46: 50%\n bucket 45: 70%\n bucket 46: 60%\n bucket 45: 80%\n bucket 45: 90%\n bucket 46: 70%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Entering block accumulator loop for bucket 47:\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n Entering block accumulator loop for bucket 48:\n bucket 47: 20%\n bucket 48: 10%\n bucket 47: 30%\n bucket 48: 20%\n bucket 47: 40%\n bucket 48: 30%\n bucket 48: 40%\n bucket 47: 50%\n bucket 48: 50%\n bucket 47: 60%\n bucket 48: 60%\n bucket 47: 70%\n bucket 48: 70%\n bucket 47: 80%\n bucket 48: 80%\n bucket 47: 90%\n bucket 48: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 49: 30%\n bucket 49: 40%\n bucket 50: 10%\nGetting block 51 of 60\n bucket 50: 20%\n bucket 49: 50%\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 30%\n bucket 49: 60%\n bucket 50: 40%\n bucket 49: 70%\n Entering block accumulator loop for bucket 51:\n bucket 50: 50%\n bucket 49: 80%\n bucket 51: 10%\n bucket 50: 60%\n bucket 49: 90%\n bucket 51: 20%\n bucket 50: 70%\n bucket 49: 100%\n bucket 51: 30%\n bucket 50: 80%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 51: 40%\n bucket 50: 90%\n bucket 51: 50%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n Entering block accumulator loop for bucket 54:\n bucket 53: 40%\n bucket 53: 50%\n bucket 54: 10%\nGetting block 55 of 60\n bucket 53: 60%\n bucket 54: 20%\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 53: 70%\n bucket 54: 30%\n bucket 54: 40%\n bucket 53: 80%\n Entering block accumulator loop for bucket 55:\n bucket 54: 50%\n bucket 53: 90%\n bucket 54: 60%\n bucket 53: 100%\n bucket 54: 70%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 55: 10%\n bucket 54: 80%\n bucket 55: 20%\n bucket 54: 90%\n bucket 54: 100%\n bucket 55: 30%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 57:\n Entering block accumulator loop for bucket 56:\n bucket 57: 10%\n bucket 56: 10%\n bucket 57: 20%\n bucket 56: 20%\n bucket 57: 30%\n bucket 56: 30%\n bucket 57: 40%\n bucket 56: 40%\n bucket 57: 50%\n bucket 56: 50%\n bucket 57: 60%\n bucket 56: 60%\n bucket 57: 70%\n bucket 56: 70%\n bucket 57: 80%\n bucket 56: 80%\n bucket 57: 90%\n bucket 56: 90%\n bucket 57: 100%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n bucket 58: 50%\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n bucket 58: 60%\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 58: 70%\n bucket 59: 20%\n bucket 60: 20%\n bucket 58: 80%\n bucket 60: 30%\n bucket 59: 30%\n bucket 58: 90%\n bucket 60: 40%\n bucket 59: 40%\n bucket 58: 100%\n bucket 60: 50%\n Sorting block of length 113 for bucket 58\n bucket 59: 50%\n (Using difference cover)\n bucket 60: 60%\n bucket 59: 60%\n bucket 60: 70%\n bucket 59: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n bucket 59: 100%\n (Using difference cover)\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\nHISAT2 summary stats:\n\tTotal reads: 10\n\t\tAligned 0 time: 0 (0.00%)\n\t\tAligned 1 time: 10 (100.00%)\n\t\tAligned >1 times: 0 (0.00%)\n\tOverall alignment rate: 100.00%\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:55:48", "plugin": "core", "name": "end_epoch", "raw_value": "1725000948.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:55:47", "plugin": "core", "name": "start_epoch", "raw_value": "1725000947.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-10", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 10, "time_seconds": 11.5907883644104, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "hisat2/2.2.1+galaxy1-11", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 11, "time_seconds": 11.904400110244751, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "hisat2/2.2.1+galaxy1-11", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 11, "time_seconds": 34.24563789367676, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "40b3459611ff938b"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "f617c33c17a88152"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "9566e093fecc270e", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:04:44.091037", "update_time": "2024-08-30T07:04:57.435189", "galaxy_version": "24.1", "external_id": "gxy-7phrf", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/b/a/8/dataset_ba886707-32c8-4d65-a8dd-c93a7f9afa37.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/3/b/e/dataset_3be931ac-e411-4993-bb5c-bd38887753a8.dat' > input_f.fastq && seqtk seq -2 '/galaxy/server/database/objects/3/b/e/dataset_3be931ac-e411-4993-bb5c-bd38887753a8.dat' > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/7/9/f/dataset_79f5ec90-b698-4e18-b972-c5b2f1d20879.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 217, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 216, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "40b3459611ff938b", "src": "hda", "uuid": "ba886707-32c8-4d65-a8dd-c93a7f9afa37"}, "library|input_1": {"id": "f617c33c17a88152", "src": "hda", "uuid": "3be931ac-e411-4993-bb5c-bd38887753a8"}}, "outputs": {"output_alignments": {"id": "cf7d34e0a64dec07", "src": "hda", "uuid": "79f5ec90-b698-4e18-b972-c5b2f1d20879"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n bucket 1: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n bucket 1: 40%\n bucket 2: 10%\n bucket 1: 50%\n bucket 2: 20%\n bucket 1: 60%\nGetting block 3 of 60\n bucket 1: 70%\n Reserving size (126) for bucket 3\n bucket 1: 80%\n bucket 2: 30%\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n bucket 1: 90%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\n bucket 2: 40%\nGetting block 5 of 60\n bucket 3: 10%\n bucket 2: 50%\n Entering block accumulator loop for bucket 4:\n bucket 1: 100%\n Reserving size (126) for bucket 5\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Calculating Z arrays for bucket 5\nGetting block 6 of 60\n Sorting block time: 00:00:00\nGetting block 7 of 60\n Reserving size (126) for bucket 7\nReturning block of 43 for bucket 1\n Entering block accumulator loop for bucket 5:\n bucket 4: 10%\n bucket 3: 20%\n bucket 2: 60%\nGetting block 8 of 60\n bucket 2: 70%\n bucket 4: 20%\n Reserving size (126) for bucket 8\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 7\n bucket 3: 30%\n bucket 5: 10%\n Calculating Z arrays for bucket 6\n bucket 3: 40%\n bucket 4: 30%\n bucket 5: 20%\n bucket 3: 50%\n bucket 4: 40%\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 6:\n bucket 4: 50%\n bucket 5: 30%\n bucket 2: 80%\n bucket 4: 60%\n bucket 5: 40%\n bucket 3: 60%\n bucket 4: 70%\n bucket 2: 90%\n bucket 6: 10%\n bucket 4: 80%\n bucket 5: 50%\n bucket 2: 100%\n bucket 6: 20%\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 7:\n bucket 4: 90%\n Sorting block of length 84 for bucket 2\n bucket 3: 70%\n bucket 8: 10%\n bucket 3: 80%\n (Using difference cover)\n bucket 5: 60%\n bucket 6: 30%\n bucket 8: 20%\n bucket 4: 100%\n bucket 3: 90%\n bucket 5: 70%\n bucket 7: 10%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 8: 30%\n bucket 5: 80%\n bucket 6: 40%\n bucket 8: 40%\n bucket 5: 90%\n bucket 7: 20%\n bucket 6: 50%\n bucket 8: 50%\n bucket 5: 100%\n bucket 6: 60%\n bucket 3: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 60%\n bucket 6: 70%\n bucket 7: 30%\n Sorting block of length 106 for bucket 3\n bucket 6: 80%\n (Using difference cover)\n bucket 7: 40%\n bucket 8: 70%\n bucket 6: 90%\n bucket 7: 50%\n bucket 8: 80%\n bucket 6: 100%\n bucket 7: 60%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 90%\n bucket 7: 70%\n bucket 8: 100%\n bucket 7: 80%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 9: 60%\n bucket 10: 70%\n bucket 9: 70%\n bucket 10: 80%\n bucket 9: 80%\n bucket 10: 90%\n bucket 9: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n Entering block accumulator loop for bucket 11:\n bucket 12: 20%\n bucket 11: 10%\n bucket 12: 30%\n bucket 11: 20%\n bucket 12: 40%\n bucket 11: 30%\n bucket 12: 50%\n bucket 11: 40%\n bucket 12: 60%\n bucket 11: 50%\n bucket 12: 70%\n bucket 11: 60%\n bucket 12: 80%\n bucket 11: 70%\n bucket 12: 90%\n bucket 11: 80%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n Entering block accumulator loop for bucket 14:\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 14: 60%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 70%\n bucket 15: 80%\n Entering block accumulator loop for bucket 16:\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 60%\n Entering block accumulator loop for bucket 18:\n bucket 17: 70%\n bucket 18: 10%\n bucket 17: 80%\n bucket 17: 90%\n bucket 18: 20%\n bucket 17: 100%\n bucket 18: 30%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n Sorting block time: 00:00:00\n bucket 18: 100%\nReturning block of 40 for bucket 17\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 50%\n bucket 20: 60%\n Entering block accumulator loop for bucket 21:\n bucket 20: 70%\n bucket 21: 10%\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n bucket 20: 80%\n Calculating Z arrays for bucket 22\n bucket 21: 20%\n bucket 20: 90%\n bucket 21: 30%\n Entering block accumulator loop for bucket 22:\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 40%\n bucket 22: 10%\n bucket 21: 50%\n bucket 22: 20%\n bucket 21: 60%\n bucket 22: 30%\n bucket 21: 70%\n bucket 22: 40%\n bucket 21: 80%\n bucket 22: 50%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 60%\n bucket 22: 70%\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 50%\n bucket 23: 60%\n Entering block accumulator loop for bucket 24:\n bucket 23: 70%\n bucket 24: 10%\n bucket 23: 80%\n bucket 24: 20%\n bucket 23: 90%\n bucket 24: 30%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 26:\n bucket 25: 10%\n bucket 26: 10%\n bucket 25: 20%\n bucket 26: 20%\n bucket 25: 30%\n bucket 26: 30%\n bucket 25: 40%\n bucket 26: 40%\n bucket 25: 50%\n bucket 26: 50%\n bucket 25: 60%\n bucket 26: 60%\n bucket 25: 70%\n bucket 26: 70%\n bucket 25: 80%\n bucket 26: 80%\n bucket 25: 90%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\nGetting block 28 of 60\n bucket 27: 20%\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 30%\n bucket 27: 40%\n Entering block accumulator loop for bucket 28:\n bucket 27: 50%\n bucket 27: 60%\n bucket 28: 10%\n bucket 27: 70%\n bucket 27: 80%\n bucket 28: 20%\n bucket 27: 90%\n bucket 28: 30%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 30: 10%\n bucket 29: 30%\n bucket 30: 20%\n bucket 29: 40%\n bucket 30: 30%\n bucket 29: 50%\n bucket 30: 40%\n bucket 30: 50%\n bucket 29: 60%\n bucket 30: 60%\n bucket 29: 70%\n bucket 30: 70%\n bucket 29: 80%\n bucket 30: 80%\n bucket 29: 90%\n bucket 30: 90%\n bucket 29: 100%\n bucket 30: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 10%\n bucket 31: 20%\n Entering block accumulator loop for bucket 32:\n bucket 31: 30%\n bucket 31: 40%\n bucket 32: 10%\n bucket 31: 50%\n bucket 32: 20%\n bucket 31: 60%\n bucket 32: 30%\n bucket 31: 70%\n bucket 32: 40%\n bucket 31: 80%\n bucket 32: 50%\n bucket 31: 90%\n bucket 32: 60%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 10%\n bucket 33: 20%\n Entering block accumulator loop for bucket 34:\n bucket 33: 30%\n bucket 34: 10%\n bucket 33: 40%\n bucket 34: 20%\n bucket 33: 50%\n bucket 34: 30%\n bucket 33: 60%\n bucket 34: 40%\n bucket 33: 70%\n bucket 34: 50%\n bucket 33: 80%\n bucket 34: 60%\n bucket 33: 90%\n bucket 34: 70%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 60%\n Entering block accumulator loop for bucket 36:\n bucket 35: 70%\n bucket 36: 10%\n bucket 35: 80%\n bucket 36: 20%\n bucket 35: 90%\n bucket 36: 30%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n bucket 36: 40%\n (Using difference cover)\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 40%\n bucket 37: 50%\n Entering block accumulator loop for bucket 38:\n bucket 37: 60%\n bucket 38: 10%\n bucket 37: 70%\n bucket 38: 20%\n bucket 38: 30%\n bucket 37: 80%\n bucket 38: 40%\n bucket 37: 90%\n bucket 38: 50%\n bucket 38: 60%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n bucket 38: 70%\n bucket 38: 80%\n (Using difference cover)\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n bucket 39: 20%\n Calculating Z arrays for bucket 40\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n Entering block accumulator loop for bucket 40:\n bucket 39: 60%\n bucket 39: 70%\n bucket 40: 10%\n bucket 39: 80%\n bucket 40: 20%\n bucket 39: 90%\n bucket 39: 100%\n bucket 40: 30%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 30%\n bucket 42: 40%\n Entering block accumulator loop for bucket 43:\n bucket 42: 50%\n bucket 43: 10%\n bucket 42: 60%\n bucket 43: 20%\n bucket 42: 70%\n bucket 43: 30%\n bucket 42: 80%\n bucket 43: 40%\n bucket 42: 90%\n bucket 43: 50%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 80%\n bucket 44: 90%\n Entering block accumulator loop for bucket 45:\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n Entering block accumulator loop for bucket 46:\n bucket 45: 40%\n bucket 45: 50%\n bucket 46: 10%\n bucket 45: 60%\n bucket 46: 20%\n bucket 45: 70%\n bucket 46: 30%\n Sorting block time: 00:00:00\n bucket 45: 80%\nReturning block of 67 for bucket 44\n bucket 45: 90%\n bucket 46: 40%\n bucket 45: 100%\n bucket 46: 50%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 48: 10%\n bucket 47: 20%\n bucket 48: 20%\n bucket 47: 30%\n bucket 48: 30%\n bucket 47: 40%\n bucket 48: 40%\n bucket 47: 50%\n bucket 48: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 48: 60%\n bucket 47: 80%\n bucket 48: 70%\n bucket 47: 90%\n bucket 47: 100%\n bucket 48: 80%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 40%\n bucket 49: 50%\n Entering block accumulator loop for bucket 50:\n bucket 49: 60%\n bucket 50: 10%\n bucket 49: 70%\n bucket 50: 20%\n bucket 49: 80%\n bucket 50: 30%\n bucket 50: 40%\n bucket 49: 90%\n bucket 50: 50%\n bucket 49: 100%\n bucket 50: 60%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\n bucket 52: 40%\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Entering block accumulator loop for bucket 53:\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 10%\n bucket 53: 20%\n Entering block accumulator loop for bucket 54:\n bucket 53: 30%\n bucket 54: 10%\n bucket 53: 40%\n bucket 54: 20%\n bucket 53: 50%\n bucket 54: 30%\n bucket 53: 60%\n bucket 54: 40%\n bucket 53: 70%\n bucket 54: 50%\n bucket 53: 80%\n bucket 54: 60%\n bucket 53: 90%\n bucket 54: 70%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n Entering block accumulator loop for bucket 56:\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 10%\n bucket 55: 20%\n Entering block accumulator loop for bucket 57:\n bucket 56: 20%\n bucket 55: 30%\n bucket 57: 10%\n bucket 56: 30%\n bucket 57: 20%\n bucket 55: 40%\n bucket 57: 30%\n bucket 56: 40%\n bucket 55: 50%\n bucket 57: 40%\n bucket 56: 50%\n bucket 57: 50%\n bucket 55: 60%\n bucket 56: 60%\n bucket 57: 60%\n bucket 55: 70%\n bucket 56: 70%\n bucket 57: 70%\n bucket 55: 80%\n bucket 56: 80%\n bucket 57: 80%\n bucket 55: 90%\n bucket 56: 90%\n bucket 57: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n bucket 57: 100%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\nGetting block 59 of 60\n Calculating Z arrays for bucket 58\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 58:\n Entering block accumulator loop for bucket 59:\n bucket 58: 10%\n bucket 59: 10%\n bucket 58: 20%\n bucket 59: 20%\n bucket 58: 30%\n bucket 59: 30%\n bucket 58: 40%\n bucket 59: 40%\n bucket 59: 50%\n bucket 58: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 58: 60%\n bucket 59: 80%\n bucket 58: 70%\n bucket 59: 90%\n bucket 59: 100%\n bucket 58: 80%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\n bucket 1: 10%\n bucket 1: 20%\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n bucket 1: 40%\n bucket 2: 10%\n bucket 1: 50%\n bucket 2: 20%\n bucket 1: 60%\nGetting block 3 of 60\n bucket 1: 70%\n Reserving size (126) for bucket 3\n bucket 1: 80%\n bucket 2: 30%\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n bucket 1: 90%\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 3:\n bucket 2: 40%\nGetting block 5 of 60\n bucket 3: 10%\n bucket 2: 50%\n Entering block accumulator loop for bucket 4:\n bucket 1: 100%\n Reserving size (126) for bucket 5\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Calculating Z arrays for bucket 5\nGetting block 6 of 60\n Sorting block time: 00:00:00\nGetting block 7 of 60\n Reserving size (126) for bucket 7\nReturning block of 43 for bucket 1\n Entering block accumulator loop for bucket 5:\n bucket 4: 10%\n bucket 3: 20%\n bucket 2: 60%\nGetting block 8 of 60\n bucket 2: 70%\n bucket 4: 20%\n Reserving size (126) for bucket 8\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 7\n bucket 3: 30%\n bucket 5: 10%\n Calculating Z arrays for bucket 6\n bucket 3: 40%\n bucket 4: 30%\n bucket 5: 20%\n bucket 3: 50%\n bucket 4: 40%\n Calculating Z arrays for bucket 8\n Entering block accumulator loop for bucket 6:\n bucket 4: 50%\n bucket 5: 30%\n bucket 2: 80%\n bucket 4: 60%\n bucket 5: 40%\n bucket 3: 60%\n bucket 4: 70%\n bucket 2: 90%\n bucket 6: 10%\n bucket 4: 80%\n bucket 5: 50%\n bucket 2: 100%\n bucket 6: 20%\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 7:\n bucket 4: 90%\n Sorting block of length 84 for bucket 2\n bucket 3: 70%\n bucket 8: 10%\n bucket 3: 80%\n (Using difference cover)\n bucket 5: 60%\n bucket 6: 30%\n bucket 8: 20%\n bucket 4: 100%\n bucket 3: 90%\n bucket 5: 70%\n bucket 7: 10%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 8: 30%\n bucket 5: 80%\n bucket 6: 40%\n bucket 8: 40%\n bucket 5: 90%\n bucket 7: 20%\n bucket 6: 50%\n bucket 8: 50%\n bucket 5: 100%\n bucket 6: 60%\n bucket 3: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 60%\n bucket 6: 70%\n bucket 7: 30%\n Sorting block of length 106 for bucket 3\n bucket 6: 80%\n (Using difference cover)\n bucket 7: 40%\n bucket 8: 70%\n bucket 6: 90%\n bucket 7: 50%\n bucket 8: 80%\n bucket 6: 100%\n bucket 7: 60%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 90%\n bucket 7: 70%\n bucket 8: 100%\n bucket 7: 80%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 9: 60%\n bucket 10: 70%\n bucket 9: 70%\n bucket 10: 80%\n bucket 9: 80%\n bucket 10: 90%\n bucket 9: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n Entering block accumulator loop for bucket 11:\n bucket 12: 20%\n bucket 11: 10%\n bucket 12: 30%\n bucket 11: 20%\n bucket 12: 40%\n bucket 11: 30%\n bucket 12: 50%\n bucket 11: 40%\n bucket 12: 60%\n bucket 11: 50%\n bucket 12: 70%\n bucket 11: 60%\n bucket 12: 80%\n bucket 11: 70%\n bucket 12: 90%\n bucket 11: 80%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n Entering block accumulator loop for bucket 14:\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 14: 60%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 70%\n bucket 15: 80%\n Entering block accumulator loop for bucket 16:\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 60%\n Entering block accumulator loop for bucket 18:\n bucket 17: 70%\n bucket 18: 10%\n bucket 17: 80%\n bucket 17: 90%\n bucket 18: 20%\n bucket 17: 100%\n bucket 18: 30%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n Sorting block time: 00:00:00\n bucket 18: 100%\nReturning block of 40 for bucket 17\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 50%\n bucket 20: 60%\n Entering block accumulator loop for bucket 21:\n bucket 20: 70%\n bucket 21: 10%\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n bucket 20: 80%\n Calculating Z arrays for bucket 22\n bucket 21: 20%\n bucket 20: 90%\n bucket 21: 30%\n Entering block accumulator loop for bucket 22:\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 40%\n bucket 22: 10%\n bucket 21: 50%\n bucket 22: 20%\n bucket 21: 60%\n bucket 22: 30%\n bucket 21: 70%\n bucket 22: 40%\n bucket 21: 80%\n bucket 22: 50%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 60%\n bucket 22: 70%\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 50%\n bucket 23: 60%\n Entering block accumulator loop for bucket 24:\n bucket 23: 70%\n bucket 24: 10%\n bucket 23: 80%\n bucket 24: 20%\n bucket 23: 90%\n bucket 24: 30%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 26:\n bucket 25: 10%\n bucket 26: 10%\n bucket 25: 20%\n bucket 26: 20%\n bucket 25: 30%\n bucket 26: 30%\n bucket 25: 40%\n bucket 26: 40%\n bucket 25: 50%\n bucket 26: 50%\n bucket 25: 60%\n bucket 26: 60%\n bucket 25: 70%\n bucket 26: 70%\n bucket 25: 80%\n bucket 26: 80%\n bucket 25: 90%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\nGetting block 28 of 60\n bucket 27: 20%\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 30%\n bucket 27: 40%\n Entering block accumulator loop for bucket 28:\n bucket 27: 50%\n bucket 27: 60%\n bucket 28: 10%\n bucket 27: 70%\n bucket 27: 80%\n bucket 28: 20%\n bucket 27: 90%\n bucket 28: 30%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 30: 10%\n bucket 29: 30%\n bucket 30: 20%\n bucket 29: 40%\n bucket 30: 30%\n bucket 29: 50%\n bucket 30: 40%\n bucket 30: 50%\n bucket 29: 60%\n bucket 30: 60%\n bucket 29: 70%\n bucket 30: 70%\n bucket 29: 80%\n bucket 30: 80%\n bucket 29: 90%\n bucket 30: 90%\n bucket 29: 100%\n bucket 30: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 10%\n bucket 31: 20%\n Entering block accumulator loop for bucket 32:\n bucket 31: 30%\n bucket 31: 40%\n bucket 32: 10%\n bucket 31: 50%\n bucket 32: 20%\n bucket 31: 60%\n bucket 32: 30%\n bucket 31: 70%\n bucket 32: 40%\n bucket 31: 80%\n bucket 32: 50%\n bucket 31: 90%\n bucket 32: 60%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 10%\n bucket 33: 20%\n Entering block accumulator loop for bucket 34:\n bucket 33: 30%\n bucket 34: 10%\n bucket 33: 40%\n bucket 34: 20%\n bucket 33: 50%\n bucket 34: 30%\n bucket 33: 60%\n bucket 34: 40%\n bucket 33: 70%\n bucket 34: 50%\n bucket 33: 80%\n bucket 34: 60%\n bucket 33: 90%\n bucket 34: 70%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 60%\n Entering block accumulator loop for bucket 36:\n bucket 35: 70%\n bucket 36: 10%\n bucket 35: 80%\n bucket 36: 20%\n bucket 35: 90%\n bucket 36: 30%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n bucket 36: 40%\n (Using difference cover)\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 40%\n bucket 37: 50%\n Entering block accumulator loop for bucket 38:\n bucket 37: 60%\n bucket 38: 10%\n bucket 37: 70%\n bucket 38: 20%\n bucket 38: 30%\n bucket 37: 80%\n bucket 38: 40%\n bucket 37: 90%\n bucket 38: 50%\n bucket 38: 60%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n bucket 38: 70%\n bucket 38: 80%\n (Using difference cover)\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n bucket 39: 20%\n Calculating Z arrays for bucket 40\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n Entering block accumulator loop for bucket 40:\n bucket 39: 60%\n bucket 39: 70%\n bucket 40: 10%\n bucket 39: 80%\n bucket 40: 20%\n bucket 39: 90%\n bucket 39: 100%\n bucket 40: 30%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 30%\n bucket 42: 40%\n Entering block accumulator loop for bucket 43:\n bucket 42: 50%\n bucket 43: 10%\n bucket 42: 60%\n bucket 43: 20%\n bucket 42: 70%\n bucket 43: 30%\n bucket 42: 80%\n bucket 43: 40%\n bucket 42: 90%\n bucket 43: 50%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 80%\n bucket 44: 90%\n Entering block accumulator loop for bucket 45:\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n Entering block accumulator loop for bucket 46:\n bucket 45: 40%\n bucket 45: 50%\n bucket 46: 10%\n bucket 45: 60%\n bucket 46: 20%\n bucket 45: 70%\n bucket 46: 30%\n Sorting block time: 00:00:00\n bucket 45: 80%\nReturning block of 67 for bucket 44\n bucket 45: 90%\n bucket 46: 40%\n bucket 45: 100%\n bucket 46: 50%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 48: 10%\n bucket 47: 20%\n bucket 48: 20%\n bucket 47: 30%\n bucket 48: 30%\n bucket 47: 40%\n bucket 48: 40%\n bucket 47: 50%\n bucket 48: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 48: 60%\n bucket 47: 80%\n bucket 48: 70%\n bucket 47: 90%\n bucket 47: 100%\n bucket 48: 80%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 40%\n bucket 49: 50%\n Entering block accumulator loop for bucket 50:\n bucket 49: 60%\n bucket 50: 10%\n bucket 49: 70%\n bucket 50: 20%\n bucket 49: 80%\n bucket 50: 30%\n bucket 50: 40%\n bucket 49: 90%\n bucket 50: 50%\n bucket 49: 100%\n bucket 50: 60%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\n bucket 52: 40%\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Entering block accumulator loop for bucket 53:\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 10%\n bucket 53: 20%\n Entering block accumulator loop for bucket 54:\n bucket 53: 30%\n bucket 54: 10%\n bucket 53: 40%\n bucket 54: 20%\n bucket 53: 50%\n bucket 54: 30%\n bucket 53: 60%\n bucket 54: 40%\n bucket 53: 70%\n bucket 54: 50%\n bucket 53: 80%\n bucket 54: 60%\n bucket 53: 90%\n bucket 54: 70%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n Entering block accumulator loop for bucket 56:\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 10%\n bucket 55: 20%\n Entering block accumulator loop for bucket 57:\n bucket 56: 20%\n bucket 55: 30%\n bucket 57: 10%\n bucket 56: 30%\n bucket 57: 20%\n bucket 55: 40%\n bucket 57: 30%\n bucket 56: 40%\n bucket 55: 50%\n bucket 57: 40%\n bucket 56: 50%\n bucket 57: 50%\n bucket 55: 60%\n bucket 56: 60%\n bucket 57: 60%\n bucket 55: 70%\n bucket 56: 70%\n bucket 57: 70%\n bucket 55: 80%\n bucket 56: 80%\n bucket 57: 80%\n bucket 55: 90%\n bucket 56: 90%\n bucket 57: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n bucket 57: 100%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\nGetting block 59 of 60\n Calculating Z arrays for bucket 58\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 58:\n Entering block accumulator loop for bucket 59:\n bucket 58: 10%\n bucket 59: 10%\n bucket 58: 20%\n bucket 59: 20%\n bucket 58: 30%\n bucket 59: 30%\n bucket 58: 40%\n bucket 59: 40%\n bucket 59: 50%\n bucket 58: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 58: 60%\n bucket 59: 80%\n bucket 58: 70%\n bucket 59: 90%\n bucket 59: 100%\n bucket 58: 80%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:04:46", "plugin": "core", "name": "end_epoch", "raw_value": "1725001486.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:04:45", "plugin": "core", "name": "start_epoch", "raw_value": "1725001485.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-12", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 12, "time_seconds": 34.26149010658264, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "4eea5e6094bb2d99"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "fb4c3b841421ac3f"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "b4ac6a1c72b1396c", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:56:32.015151", "update_time": "2024-08-30T06:56:45.397539", "galaxy_version": "24.1", "external_id": "gxy-hqbbq", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/3/3/6/dataset_336d2a7c-0e89-4fd3-a981-57c752e6f2cb.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && bzcat '/galaxy/server/database/objects/f/7/e/dataset_f7e417f0-7a9d-435c-a1ad-12caad6d6451.dat' | seqtk seq -1 /dev/stdin > input_f.fastq && bzcat '/galaxy/server/database/objects/f/7/e/dataset_f7e417f0-7a9d-435c-a1ad-12caad6d6451.dat' | seqtk seq -2 /dev/stdin > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/0/9/8/dataset_098d4ebd-3fe3-466f-9f25-064fc3126c04.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 161, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 160, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "4eea5e6094bb2d99", "src": "hda", "uuid": "336d2a7c-0e89-4fd3-a981-57c752e6f2cb"}, "library|input_1": {"id": "fb4c3b841421ac3f", "src": "hda", "uuid": "f7e417f0-7a9d-435c-a1ad-12caad6d6451"}}, "outputs": {"output_alignments": {"id": "d25e41c024255004", "src": "hda", "uuid": "098d4ebd-3fe3-466f-9f25-064fc3126c04"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n bucket 2: 10%\n bucket 1: 20%\nGetting block 4 of 60\n Entering block accumulator loop for bucket 3:\n bucket 1: 30%\n bucket 3: 10%\n Reserving size (126) for bucket 4\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 1: 40%\n bucket 2: 20%\nGetting block 5 of 60\n Calculating Z arrays for bucket 6\n bucket 1: 50%\n bucket 3: 20%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 2: 30%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 7:\n bucket 1: 60%\n bucket 2: 40%\n Calculating Z arrays for bucket 5\n bucket 3: 30%\n bucket 1: 70%\n bucket 2: 50%\n bucket 4: 10%\n Entering block accumulator loop for bucket 5:\n bucket 2: 60%\n bucket 7: 10%\n bucket 5: 10%\n bucket 4: 20%\n bucket 5: 20%\n bucket 6: 10%\n Calculating Z arrays for bucket 8\n bucket 1: 80%\n bucket 5: 30%\n bucket 6: 20%\n bucket 4: 30%\n bucket 1: 90%\n bucket 6: 30%\n bucket 2: 70%\n bucket 3: 40%\n bucket 4: 40%\n bucket 7: 20%\n bucket 3: 50%\n Entering block accumulator loop for bucket 8:\n bucket 3: 60%\n bucket 1: 100%\n bucket 2: 80%\n Sorting block of length 42 for bucket 1\n bucket 3: 70%\n bucket 8: 10%\n (Using difference cover)\n bucket 2: 90%\n bucket 8: 20%\n bucket 5: 40%\n bucket 3: 80%\n bucket 2: 100%\n bucket 4: 50%\n bucket 8: 30%\n bucket 7: 30%\n bucket 6: 40%\n bucket 3: 90%\n bucket 5: 50%\n bucket 8: 40%\n bucket 5: 60%\n bucket 3: 100%\n bucket 7: 40%\n bucket 5: 70%\n Sorting block of length 84 for bucket 2\n bucket 5: 80%\n bucket 8: 50%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 7: 50%\n bucket 4: 60%\n (Using difference cover)\n bucket 6: 50%\n bucket 5: 90%\n bucket 7: 60%\n bucket 8: 60%\n bucket 6: 60%\n bucket 4: 70%\n bucket 5: 100%\n bucket 7: 70%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 70%\n bucket 7: 80%\n bucket 6: 70%\n bucket 8: 80%\n bucket 7: 90%\n bucket 4: 80%\n bucket 6: 80%\n bucket 7: 100%\n bucket 4: 90%\n Sorting block of length 75 for bucket 7\n bucket 6: 90%\n bucket 4: 100%\n bucket 6: 100%\n (Using difference cover)\n Sorting block of length 68 for bucket 4\n bucket 8: 90%\n (Using difference cover)\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\nGetting block 11 of 60\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n Entering block accumulator loop for bucket 11:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 11: 10%\n bucket 10: 20%\n bucket 9: 40%\n bucket 11: 20%\n bucket 10: 30%\n bucket 9: 50%\n bucket 11: 30%\n bucket 10: 40%\n bucket 11: 40%\n bucket 9: 60%\n bucket 10: 50%\n bucket 11: 50%\n bucket 9: 70%\n bucket 10: 60%\n bucket 11: 60%\n bucket 9: 80%\n bucket 10: 70%\n bucket 11: 70%\n bucket 9: 90%\n bucket 10: 80%\n bucket 11: 80%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n bucket 11: 90%\n (Using difference cover)\n bucket 10: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n bucket 12: 10%\n Calculating Z arrays for bucket 13\n bucket 12: 20%\n bucket 12: 30%\n Entering block accumulator loop for bucket 13:\n bucket 12: 40%\n bucket 12: 50%\n bucket 13: 10%\n bucket 12: 60%\n bucket 13: 20%\n bucket 12: 70%\n bucket 13: 30%\n bucket 12: 80%\n bucket 13: 40%\n bucket 12: 90%\n bucket 13: 50%\n bucket 12: 100%\n bucket 13: 60%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 30%\nGetting block 18 of 60\n bucket 16: 40%\n Entering block accumulator loop for bucket 17:\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 16: 50%\n bucket 17: 10%\n bucket 16: 60%\n Entering block accumulator loop for bucket 18:\n bucket 17: 20%\n bucket 16: 70%\n bucket 18: 10%\n bucket 17: 30%\n bucket 16: 80%\n bucket 18: 20%\n bucket 17: 40%\n bucket 16: 90%\n bucket 18: 30%\n bucket 17: 50%\n bucket 16: 100%\n bucket 18: 40%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 60%\n bucket 18: 50%\n bucket 17: 70%\n bucket 18: 60%\n bucket 17: 80%\n bucket 18: 70%\n bucket 17: 90%\n bucket 18: 80%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 20:\n bucket 21: 10%\n bucket 20: 10%\n bucket 21: 20%\n bucket 20: 20%\n bucket 21: 30%\n bucket 20: 30%\n bucket 21: 40%\n bucket 20: 40%\n bucket 21: 50%\n bucket 20: 50%\n bucket 21: 60%\n bucket 20: 60%\n bucket 21: 70%\n bucket 20: 70%\n bucket 21: 80%\n bucket 20: 80%\n bucket 21: 90%\n bucket 20: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n bucket 20: 100%\n (Using difference cover)\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 70%\n bucket 22: 80%\n Entering block accumulator loop for bucket 23:\n bucket 22: 90%\n bucket 23: 10%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n (Using difference cover)\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\n bucket 27: 20%\n bucket 26: 30%\n bucket 27: 30%\n bucket 26: 40%\n bucket 27: 40%\n bucket 26: 50%\n bucket 27: 50%\n bucket 26: 60%\n bucket 27: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 27: 70%\n bucket 26: 90%\n bucket 27: 80%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Entering block accumulator loop for bucket 28:\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 10%\n bucket 28: 20%\n Entering block accumulator loop for bucket 29:\n bucket 28: 30%\n bucket 28: 40%\n bucket 29: 10%\n bucket 28: 50%\n bucket 28: 60%\n bucket 29: 20%\n bucket 28: 70%\n bucket 29: 30%\n bucket 28: 80%\n bucket 29: 40%\n bucket 28: 90%\n bucket 29: 50%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n Sorting block time: 00:00:00\n bucket 29: 100%\nReturning block of 107 for bucket 28\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Entering block accumulator loop for bucket 30:\nGetting block 32 of 60\n bucket 30: 10%\n Calculating Z arrays for bucket 31\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 30: 20%\n Entering block accumulator loop for bucket 31:\n bucket 30: 30%\n Entering block accumulator loop for bucket 32:\n bucket 30: 40%\n bucket 31: 10%\n bucket 30: 50%\n bucket 32: 10%\n bucket 30: 60%\n bucket 31: 20%\n bucket 32: 20%\n bucket 30: 70%\n bucket 31: 30%\n bucket 32: 30%\n bucket 31: 40%\n bucket 30: 80%\n bucket 32: 40%\n bucket 31: 50%\n bucket 32: 50%\n bucket 31: 60%\n bucket 32: 60%\n bucket 31: 70%\n bucket 32: 70%\n bucket 31: 80%\n bucket 30: 90%\n bucket 31: 90%\n bucket 32: 80%\n bucket 30: 100%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 33 of 60\n Reserving size (126) for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 34:\n Entering block accumulator loop for bucket 33:\n bucket 34: 10%\n bucket 33: 10%\n bucket 34: 20%\n bucket 33: 20%\n bucket 34: 30%\n bucket 33: 30%\n bucket 34: 40%\nGetting block 35 of 60\n bucket 34: 50%\n bucket 33: 40%\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 33: 50%\n bucket 34: 60%\n bucket 33: 60%\n bucket 34: 70%\n bucket 33: 70%\n Entering block accumulator loop for bucket 35:\n bucket 34: 80%\n bucket 33: 80%\n bucket 35: 10%\n bucket 33: 90%\n bucket 34: 90%\n bucket 33: 100%\n bucket 34: 100%\n bucket 35: 20%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n bucket 36: 20%\n bucket 36: 30%\n Calculating Z arrays for bucket 37\n bucket 36: 40%\n bucket 36: 50%\n Entering block accumulator loop for bucket 37:\n bucket 36: 60%\n bucket 37: 10%\n bucket 36: 70%\n bucket 37: 20%\n bucket 36: 80%\n bucket 37: 30%\n bucket 36: 90%\n bucket 37: 40%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Entering block accumulator loop for bucket 38:\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n Entering block accumulator loop for bucket 39:\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 38: 40%\n bucket 39: 20%\n bucket 38: 50%\n bucket 39: 30%\n bucket 38: 60%\n bucket 39: 40%\n bucket 38: 70%\n bucket 39: 50%\n bucket 38: 80%\n bucket 38: 90%\n bucket 39: 60%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n Entering block accumulator loop for bucket 41:\n bucket 40: 20%\n bucket 41: 10%\n bucket 40: 30%\n bucket 41: 20%\n bucket 40: 40%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 40: 60%\n bucket 41: 50%\n bucket 40: 70%\n bucket 41: 60%\n bucket 40: 80%\n bucket 41: 70%\n bucket 40: 90%\n bucket 41: 80%\n bucket 40: 100%\n bucket 41: 90%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n Entering block accumulator loop for bucket 43:\n bucket 42: 80%\n bucket 42: 90%\n bucket 43: 10%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n bucket 44: 10%\n Calculating Z arrays for bucket 45\n bucket 44: 20%\n bucket 44: 30%\n Entering block accumulator loop for bucket 45:\n bucket 44: 40%\n bucket 45: 10%\n bucket 44: 50%\n bucket 45: 20%\n bucket 44: 60%\n bucket 45: 30%\n bucket 44: 70%\n bucket 45: 40%\n bucket 44: 80%\n bucket 45: 50%\n bucket 44: 90%\n bucket 45: 60%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 46:\n Entering block accumulator loop for bucket 47:\n bucket 46: 10%\n bucket 47: 10%\n bucket 46: 20%\n bucket 47: 20%\n bucket 46: 30%\n bucket 47: 30%\n bucket 46: 40%\n bucket 47: 40%\n bucket 46: 50%\n bucket 47: 50%\n bucket 46: 60%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 46: 70%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 60\n Entering block accumulator loop for bucket 48:\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 48: 10%\n bucket 48: 20%\n Entering block accumulator loop for bucket 49:\n bucket 48: 30%\n bucket 48: 40%\n bucket 49: 10%\n bucket 48: 50%\n bucket 49: 20%\n bucket 48: 60%\n bucket 49: 30%\n bucket 48: 70%\n bucket 49: 40%\n bucket 48: 80%\n bucket 49: 50%\n bucket 49: 60%\n bucket 48: 90%\n bucket 49: 70%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\nGetting block 52 of 60\nGetting block 53 of 60\n Reserving size (126) for bucket 52\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Calculating Z arrays for bucket 52\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 51:\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 51: 10%\n bucket 53: 10%\n bucket 51: 20%\n bucket 52: 10%\n bucket 53: 20%\n bucket 51: 30%\n bucket 52: 20%\n bucket 51: 40%\n bucket 53: 30%\n bucket 52: 30%\n bucket 51: 50%\n bucket 53: 40%\n bucket 52: 40%\n bucket 51: 60%\n bucket 53: 50%\n bucket 52: 50%\n bucket 53: 60%\n bucket 51: 70%\n bucket 52: 60%\n bucket 53: 70%\n bucket 51: 80%\n bucket 52: 70%\n bucket 51: 90%\n bucket 53: 80%\n bucket 52: 80%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 53: 90%\n bucket 52: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 54:\n Entering block accumulator loop for bucket 55:\n bucket 54: 10%\n bucket 55: 10%\n bucket 54: 20%\n bucket 55: 20%\n bucket 54: 30%\n bucket 55: 30%\n bucket 54: 40%\n bucket 55: 40%\n bucket 54: 50%\n bucket 55: 50%\n bucket 54: 60%\n bucket 55: 60%\n bucket 55: 70%\n bucket 54: 70%\n bucket 55: 80%\n bucket 54: 80%\n bucket 55: 90%\n bucket 54: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 60%\n bucket 56: 70%\n Entering block accumulator loop for bucket 57:\n bucket 56: 80%\n bucket 56: 90%\n bucket 57: 10%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 58: 70%\n bucket 59: 10%\n bucket 59: 20%\n bucket 58: 80%\n bucket 59: 30%\n bucket 58: 90%\n bucket 59: 40%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n bucket 2: 10%\n bucket 1: 20%\nGetting block 4 of 60\n Entering block accumulator loop for bucket 3:\n bucket 1: 30%\n bucket 3: 10%\n Reserving size (126) for bucket 4\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 1: 40%\n bucket 2: 20%\nGetting block 5 of 60\n Calculating Z arrays for bucket 6\n bucket 1: 50%\n bucket 3: 20%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 2: 30%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 7:\n bucket 1: 60%\n bucket 2: 40%\n Calculating Z arrays for bucket 5\n bucket 3: 30%\n bucket 1: 70%\n bucket 2: 50%\n bucket 4: 10%\n Entering block accumulator loop for bucket 5:\n bucket 2: 60%\n bucket 7: 10%\n bucket 5: 10%\n bucket 4: 20%\n bucket 5: 20%\n bucket 6: 10%\n Calculating Z arrays for bucket 8\n bucket 1: 80%\n bucket 5: 30%\n bucket 6: 20%\n bucket 4: 30%\n bucket 1: 90%\n bucket 6: 30%\n bucket 2: 70%\n bucket 3: 40%\n bucket 4: 40%\n bucket 7: 20%\n bucket 3: 50%\n Entering block accumulator loop for bucket 8:\n bucket 3: 60%\n bucket 1: 100%\n bucket 2: 80%\n Sorting block of length 42 for bucket 1\n bucket 3: 70%\n bucket 8: 10%\n (Using difference cover)\n bucket 2: 90%\n bucket 8: 20%\n bucket 5: 40%\n bucket 3: 80%\n bucket 2: 100%\n bucket 4: 50%\n bucket 8: 30%\n bucket 7: 30%\n bucket 6: 40%\n bucket 3: 90%\n bucket 5: 50%\n bucket 8: 40%\n bucket 5: 60%\n bucket 3: 100%\n bucket 7: 40%\n bucket 5: 70%\n Sorting block of length 84 for bucket 2\n bucket 5: 80%\n bucket 8: 50%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 7: 50%\n bucket 4: 60%\n (Using difference cover)\n bucket 6: 50%\n bucket 5: 90%\n bucket 7: 60%\n bucket 8: 60%\n bucket 6: 60%\n bucket 4: 70%\n bucket 5: 100%\n bucket 7: 70%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 70%\n bucket 7: 80%\n bucket 6: 70%\n bucket 8: 80%\n bucket 7: 90%\n bucket 4: 80%\n bucket 6: 80%\n bucket 7: 100%\n bucket 4: 90%\n Sorting block of length 75 for bucket 7\n bucket 6: 90%\n bucket 4: 100%\n bucket 6: 100%\n (Using difference cover)\n Sorting block of length 68 for bucket 4\n bucket 8: 90%\n (Using difference cover)\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\nGetting block 11 of 60\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n Entering block accumulator loop for bucket 11:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 11: 10%\n bucket 10: 20%\n bucket 9: 40%\n bucket 11: 20%\n bucket 10: 30%\n bucket 9: 50%\n bucket 11: 30%\n bucket 10: 40%\n bucket 11: 40%\n bucket 9: 60%\n bucket 10: 50%\n bucket 11: 50%\n bucket 9: 70%\n bucket 10: 60%\n bucket 11: 60%\n bucket 9: 80%\n bucket 10: 70%\n bucket 11: 70%\n bucket 9: 90%\n bucket 10: 80%\n bucket 11: 80%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n bucket 11: 90%\n (Using difference cover)\n bucket 10: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n bucket 12: 10%\n Calculating Z arrays for bucket 13\n bucket 12: 20%\n bucket 12: 30%\n Entering block accumulator loop for bucket 13:\n bucket 12: 40%\n bucket 12: 50%\n bucket 13: 10%\n bucket 12: 60%\n bucket 13: 20%\n bucket 12: 70%\n bucket 13: 30%\n bucket 12: 80%\n bucket 13: 40%\n bucket 12: 90%\n bucket 13: 50%\n bucket 12: 100%\n bucket 13: 60%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 30%\nGetting block 18 of 60\n bucket 16: 40%\n Entering block accumulator loop for bucket 17:\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 16: 50%\n bucket 17: 10%\n bucket 16: 60%\n Entering block accumulator loop for bucket 18:\n bucket 17: 20%\n bucket 16: 70%\n bucket 18: 10%\n bucket 17: 30%\n bucket 16: 80%\n bucket 18: 20%\n bucket 17: 40%\n bucket 16: 90%\n bucket 18: 30%\n bucket 17: 50%\n bucket 16: 100%\n bucket 18: 40%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 60%\n bucket 18: 50%\n bucket 17: 70%\n bucket 18: 60%\n bucket 17: 80%\n bucket 18: 70%\n bucket 17: 90%\n bucket 18: 80%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 20:\n bucket 21: 10%\n bucket 20: 10%\n bucket 21: 20%\n bucket 20: 20%\n bucket 21: 30%\n bucket 20: 30%\n bucket 21: 40%\n bucket 20: 40%\n bucket 21: 50%\n bucket 20: 50%\n bucket 21: 60%\n bucket 20: 60%\n bucket 21: 70%\n bucket 20: 70%\n bucket 21: 80%\n bucket 20: 80%\n bucket 21: 90%\n bucket 20: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n bucket 20: 100%\n (Using difference cover)\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 70%\n bucket 22: 80%\n Entering block accumulator loop for bucket 23:\n bucket 22: 90%\n bucket 23: 10%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n (Using difference cover)\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\n bucket 27: 20%\n bucket 26: 30%\n bucket 27: 30%\n bucket 26: 40%\n bucket 27: 40%\n bucket 26: 50%\n bucket 27: 50%\n bucket 26: 60%\n bucket 27: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 27: 70%\n bucket 26: 90%\n bucket 27: 80%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Entering block accumulator loop for bucket 28:\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 10%\n bucket 28: 20%\n Entering block accumulator loop for bucket 29:\n bucket 28: 30%\n bucket 28: 40%\n bucket 29: 10%\n bucket 28: 50%\n bucket 28: 60%\n bucket 29: 20%\n bucket 28: 70%\n bucket 29: 30%\n bucket 28: 80%\n bucket 29: 40%\n bucket 28: 90%\n bucket 29: 50%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n Sorting block time: 00:00:00\n bucket 29: 100%\nReturning block of 107 for bucket 28\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Entering block accumulator loop for bucket 30:\nGetting block 32 of 60\n bucket 30: 10%\n Calculating Z arrays for bucket 31\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 30: 20%\n Entering block accumulator loop for bucket 31:\n bucket 30: 30%\n Entering block accumulator loop for bucket 32:\n bucket 30: 40%\n bucket 31: 10%\n bucket 30: 50%\n bucket 32: 10%\n bucket 30: 60%\n bucket 31: 20%\n bucket 32: 20%\n bucket 30: 70%\n bucket 31: 30%\n bucket 32: 30%\n bucket 31: 40%\n bucket 30: 80%\n bucket 32: 40%\n bucket 31: 50%\n bucket 32: 50%\n bucket 31: 60%\n bucket 32: 60%\n bucket 31: 70%\n bucket 32: 70%\n bucket 31: 80%\n bucket 30: 90%\n bucket 31: 90%\n bucket 32: 80%\n bucket 30: 100%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 33 of 60\n Reserving size (126) for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 34:\n Entering block accumulator loop for bucket 33:\n bucket 34: 10%\n bucket 33: 10%\n bucket 34: 20%\n bucket 33: 20%\n bucket 34: 30%\n bucket 33: 30%\n bucket 34: 40%\nGetting block 35 of 60\n bucket 34: 50%\n bucket 33: 40%\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 33: 50%\n bucket 34: 60%\n bucket 33: 60%\n bucket 34: 70%\n bucket 33: 70%\n Entering block accumulator loop for bucket 35:\n bucket 34: 80%\n bucket 33: 80%\n bucket 35: 10%\n bucket 33: 90%\n bucket 34: 90%\n bucket 33: 100%\n bucket 34: 100%\n bucket 35: 20%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n bucket 36: 20%\n bucket 36: 30%\n Calculating Z arrays for bucket 37\n bucket 36: 40%\n bucket 36: 50%\n Entering block accumulator loop for bucket 37:\n bucket 36: 60%\n bucket 37: 10%\n bucket 36: 70%\n bucket 37: 20%\n bucket 36: 80%\n bucket 37: 30%\n bucket 36: 90%\n bucket 37: 40%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Entering block accumulator loop for bucket 38:\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n Entering block accumulator loop for bucket 39:\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 38: 40%\n bucket 39: 20%\n bucket 38: 50%\n bucket 39: 30%\n bucket 38: 60%\n bucket 39: 40%\n bucket 38: 70%\n bucket 39: 50%\n bucket 38: 80%\n bucket 38: 90%\n bucket 39: 60%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n Entering block accumulator loop for bucket 41:\n bucket 40: 20%\n bucket 41: 10%\n bucket 40: 30%\n bucket 41: 20%\n bucket 40: 40%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 40: 60%\n bucket 41: 50%\n bucket 40: 70%\n bucket 41: 60%\n bucket 40: 80%\n bucket 41: 70%\n bucket 40: 90%\n bucket 41: 80%\n bucket 40: 100%\n bucket 41: 90%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n Entering block accumulator loop for bucket 43:\n bucket 42: 80%\n bucket 42: 90%\n bucket 43: 10%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n bucket 44: 10%\n Calculating Z arrays for bucket 45\n bucket 44: 20%\n bucket 44: 30%\n Entering block accumulator loop for bucket 45:\n bucket 44: 40%\n bucket 45: 10%\n bucket 44: 50%\n bucket 45: 20%\n bucket 44: 60%\n bucket 45: 30%\n bucket 44: 70%\n bucket 45: 40%\n bucket 44: 80%\n bucket 45: 50%\n bucket 44: 90%\n bucket 45: 60%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 46:\n Entering block accumulator loop for bucket 47:\n bucket 46: 10%\n bucket 47: 10%\n bucket 46: 20%\n bucket 47: 20%\n bucket 46: 30%\n bucket 47: 30%\n bucket 46: 40%\n bucket 47: 40%\n bucket 46: 50%\n bucket 47: 50%\n bucket 46: 60%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 46: 70%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 60\n Entering block accumulator loop for bucket 48:\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 48: 10%\n bucket 48: 20%\n Entering block accumulator loop for bucket 49:\n bucket 48: 30%\n bucket 48: 40%\n bucket 49: 10%\n bucket 48: 50%\n bucket 49: 20%\n bucket 48: 60%\n bucket 49: 30%\n bucket 48: 70%\n bucket 49: 40%\n bucket 48: 80%\n bucket 49: 50%\n bucket 49: 60%\n bucket 48: 90%\n bucket 49: 70%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\nGetting block 52 of 60\nGetting block 53 of 60\n Reserving size (126) for bucket 52\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Calculating Z arrays for bucket 52\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 51:\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 51: 10%\n bucket 53: 10%\n bucket 51: 20%\n bucket 52: 10%\n bucket 53: 20%\n bucket 51: 30%\n bucket 52: 20%\n bucket 51: 40%\n bucket 53: 30%\n bucket 52: 30%\n bucket 51: 50%\n bucket 53: 40%\n bucket 52: 40%\n bucket 51: 60%\n bucket 53: 50%\n bucket 52: 50%\n bucket 53: 60%\n bucket 51: 70%\n bucket 52: 60%\n bucket 53: 70%\n bucket 51: 80%\n bucket 52: 70%\n bucket 51: 90%\n bucket 53: 80%\n bucket 52: 80%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 53: 90%\n bucket 52: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 54:\n Entering block accumulator loop for bucket 55:\n bucket 54: 10%\n bucket 55: 10%\n bucket 54: 20%\n bucket 55: 20%\n bucket 54: 30%\n bucket 55: 30%\n bucket 54: 40%\n bucket 55: 40%\n bucket 54: 50%\n bucket 55: 50%\n bucket 54: 60%\n bucket 55: 60%\n bucket 55: 70%\n bucket 54: 70%\n bucket 55: 80%\n bucket 54: 80%\n bucket 55: 90%\n bucket 54: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 60%\n bucket 56: 70%\n Entering block accumulator loop for bucket 57:\n bucket 56: 80%\n bucket 56: 90%\n bucket 57: 10%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 58: 70%\n bucket 59: 10%\n bucket 59: 20%\n bucket 58: 80%\n bucket 59: 30%\n bucket 58: 90%\n bucket 59: 40%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:56:34", "plugin": "core", "name": "end_epoch", "raw_value": "1725000994.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:56:34", "plugin": "core", "name": "start_epoch", "raw_value": "1725000994.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-12", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 12, "time_seconds": 35.869327545166016, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "4fac0398c2d03772"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "581b53313248a836"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "e70b5c7d6296e58d", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:05:18.609164", "update_time": "2024-08-30T07:05:33.420100", "galaxy_version": "24.1", "external_id": "gxy-7cwxx", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/f/5/b/dataset_f5b7dc43-3553-4ff3-b17b-0a5fa8403bac.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && bzcat '/galaxy/server/database/objects/1/e/c/dataset_1ec11458-a18f-49bb-b01f-682ec881806e.dat' | seqtk seq -1 /dev/stdin > input_f.fastq && bzcat '/galaxy/server/database/objects/1/e/c/dataset_1ec11458-a18f-49bb-b01f-682ec881806e.dat' | seqtk seq -2 /dev/stdin > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/e/3/6/dataset_e36e0a42-678c-4b3d-a223-2a23290445be.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 220, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 219, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "4fac0398c2d03772", "src": "hda", "uuid": "f5b7dc43-3553-4ff3-b17b-0a5fa8403bac"}, "library|input_1": {"id": "581b53313248a836", "src": "hda", "uuid": "1ec11458-a18f-49bb-b01f-682ec881806e"}}, "outputs": {"output_alignments": {"id": "8533352dd2d460a0", "src": "hda", "uuid": "e36e0a42-678c-4b3d-a223-2a23290445be"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n bucket 1: 10%\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 4\nGetting block 6 of 60\n Entering block accumulator loop for bucket 4:\n Reserving size (126) for bucket 6\n bucket 1: 20%\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 2: 10%\n Calculating Z arrays for bucket 5\n bucket 1: 30%\n bucket 2: 20%\n bucket 4: 10%\n Entering block accumulator loop for bucket 3:\n bucket 1: 40%\n Calculating Z arrays for bucket 6\n bucket 2: 30%\n bucket 4: 20%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 1: 50%\n bucket 4: 30%\n Calculating Z arrays for bucket 7\n bucket 2: 40%\n bucket 4: 40%\n Entering block accumulator loop for bucket 6:\n bucket 2: 50%\n Entering block accumulator loop for bucket 7:\nGetting block 8 of 60\n Entering block accumulator loop for bucket 5:\n bucket 4: 50%\n bucket 7: 10%\n bucket 2: 60%\n bucket 1: 60%\n bucket 7: 20%\n Reserving size (126) for bucket 8\n bucket 5: 10%\n bucket 3: 10%\n bucket 1: 70%\n bucket 2: 70%\n bucket 4: 60%\n bucket 1: 80%\n bucket 5: 20%\n bucket 7: 30%\n Calculating Z arrays for bucket 8\n bucket 4: 70%\n bucket 7: 40%\n bucket 1: 90%\n bucket 2: 80%\n bucket 4: 80%\n bucket 6: 10%\n bucket 5: 30%\n bucket 2: 90%\n bucket 3: 20%\n bucket 6: 20%\n bucket 2: 100%\n bucket 4: 90%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 6: 30%\n bucket 7: 50%\n bucket 3: 30%\n bucket 4: 100%\n bucket 6: 40%\n bucket 3: 40%\n Sorting block of length 68 for bucket 4\n bucket 7: 60%\n (Using difference cover)\n bucket 3: 50%\n bucket 7: 70%\n Entering block accumulator loop for bucket 8:\n bucket 3: 60%\n bucket 5: 40%\n bucket 7: 80%\n bucket 8: 10%\n bucket 3: 70%\n bucket 1: 100%\n bucket 5: 50%\n bucket 7: 90%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 5: 60%\n bucket 8: 20%\n bucket 3: 80%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 70%\n bucket 6: 50%\n bucket 8: 30%\n bucket 5: 80%\n bucket 3: 90%\n bucket 8: 40%\n bucket 6: 60%\n bucket 5: 90%\n bucket 8: 50%\n bucket 3: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 6: 70%\n bucket 5: 100%\n bucket 8: 60%\n bucket 6: 80%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 70%\n bucket 6: 90%\n bucket 8: 80%\n bucket 8: 90%\n bucket 6: 100%\n bucket 8: 100%\n Sorting block of length 90 for bucket 6\n Sorting block time: 00:00:00\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n (Using difference cover)\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Entering block accumulator loop for bucket 9:\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n Entering block accumulator loop for bucket 10:\n bucket 9: 40%\n bucket 10: 10%\n bucket 9: 50%\n bucket 10: 20%\n bucket 9: 60%\n bucket 10: 30%\n bucket 9: 70%\n bucket 10: 40%\n bucket 9: 80%\n bucket 10: 50%\n bucket 9: 90%\n bucket 10: 60%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n bucket 10: 70%\n (Using difference cover)\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Entering block accumulator loop for bucket 11:\n Sorting block time: 00:00:00\n bucket 11: 10%\nReturning block of 90 for bucket 10\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n bucket 12: 80%\n Entering block accumulator loop for bucket 13:\n bucket 12: 90%\nGetting block 14 of 60\n bucket 12: 100%\n Reserving size (126) for bucket 14\n bucket 13: 10%\n Sorting block of length 82 for bucket 12\n Calculating Z arrays for bucket 14\n (Using difference cover)\n bucket 13: 20%\n bucket 13: 30%\n Entering block accumulator loop for bucket 14:\n bucket 13: 40%\n bucket 14: 10%\n bucket 13: 50%\n bucket 14: 20%\n bucket 13: 60%\n bucket 14: 30%\n bucket 13: 70%\n bucket 14: 40%\n bucket 13: 80%\n bucket 14: 50%\n bucket 13: 90%\n bucket 14: 60%\n bucket 13: 100%\n bucket 14: 70%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 15: 40%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 15: 50%\n bucket 16: 50%\n bucket 15: 60%\n bucket 16: 60%\n bucket 15: 70%\n bucket 16: 70%\n bucket 15: 80%\n bucket 16: 80%\n bucket 15: 90%\n bucket 16: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\nGetting block 17 of 60\n bucket 16: 100%\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n Entering block accumulator loop for bucket 19:\n bucket 18: 20%\n bucket 18: 30%\n bucket 19: 10%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 19: 50%\n bucket 18: 80%\n bucket 19: 60%\n bucket 18: 90%\n bucket 19: 70%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n Entering block accumulator loop for bucket 21:\n bucket 20: 20%\n bucket 21: 10%\n bucket 20: 30%\n bucket 21: 20%\n bucket 20: 40%\n bucket 21: 30%\n bucket 20: 50%\n bucket 21: 40%\n bucket 20: 60%\n bucket 21: 50%\n bucket 20: 70%\n bucket 21: 60%\n bucket 20: 80%\n bucket 21: 70%\n bucket 20: 90%\n bucket 21: 80%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Entering block accumulator loop for bucket 22:\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 22: 50%\n bucket 23: 40%\n bucket 22: 60%\n bucket 23: 50%\n bucket 22: 70%\n bucket 23: 60%\n bucket 22: 80%\n bucket 23: 70%\n bucket 22: 90%\n bucket 23: 80%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\nGetting block 25 of 60\n bucket 24: 70%\n Reserving size (126) for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n bucket 24: 80%\n Calculating Z arrays for bucket 25\n bucket 24: 90%\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 25:\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 26: 10%\n bucket 25: 10%\n bucket 26: 20%\n bucket 25: 20%\n bucket 26: 30%\n bucket 25: 30%\n bucket 26: 40%\n bucket 25: 40%\n bucket 26: 50%\n bucket 25: 50%\n bucket 26: 60%\n bucket 25: 60%\n bucket 26: 70%\n bucket 25: 70%\n bucket 26: 80%\n bucket 25: 80%\n bucket 26: 90%\n bucket 25: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 70%\n Entering block accumulator loop for bucket 29:\n bucket 28: 80%\n bucket 28: 90%\n bucket 29: 10%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 40%\n Calculating Z arrays for bucket 31\n bucket 30: 50%\n bucket 30: 60%\n Entering block accumulator loop for bucket 31:\n bucket 30: 70%\n bucket 31: 10%\n bucket 30: 80%\n bucket 31: 20%\n bucket 30: 90%\n bucket 31: 30%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\n bucket 32: 40%\nGetting block 33 of 60\n bucket 32: 50%\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Calculating Z arrays for bucket 34\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n Entering block accumulator loop for bucket 34:\n bucket 32: 90%\n Entering block accumulator loop for bucket 33:\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 34: 10%\n bucket 33: 10%\n bucket 34: 20%\n bucket 33: 20%\n bucket 34: 30%\n bucket 33: 30%\n bucket 34: 40%\n bucket 33: 40%\n bucket 34: 50%\n bucket 33: 50%\n bucket 34: 60%\n bucket 33: 60%\n bucket 33: 70%\n bucket 34: 70%\n bucket 33: 80%\n Sorting block time: 00:00:00\n bucket 33: 90%\nReturning block of 126 for bucket 32\n bucket 34: 80%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 36:\n Entering block accumulator loop for bucket 37:\n bucket 36: 10%\n bucket 37: 10%\n bucket 36: 20%\n bucket 37: 20%\n bucket 36: 30%\n bucket 37: 30%\n bucket 36: 40%\n bucket 37: 40%\n bucket 36: 50%\n bucket 37: 50%\n bucket 36: 60%\n bucket 37: 60%\n bucket 36: 70%\n bucket 37: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 37: 80%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Entering block accumulator loop for bucket 38:\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n Entering block accumulator loop for bucket 39:\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 39: 20%\n bucket 38: 40%\n bucket 39: 30%\n bucket 38: 50%\n bucket 39: 40%\n bucket 38: 60%\n bucket 39: 50%\n bucket 38: 70%\n bucket 39: 60%\n bucket 38: 80%\n bucket 39: 70%\n bucket 38: 90%\n bucket 39: 80%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\n bucket 41: 20%\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 41: 50%\n bucket 40: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n bucket 41: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n bucket 42: 20%\n Calculating Z arrays for bucket 43\n bucket 42: 30%\n Entering block accumulator loop for bucket 43:\n bucket 42: 40%\n bucket 43: 10%\n bucket 42: 50%\n bucket 43: 20%\n bucket 43: 30%\n bucket 42: 60%\n bucket 42: 70%\n bucket 43: 40%\n bucket 43: 50%\n bucket 42: 80%\n bucket 43: 60%\n bucket 42: 90%\n bucket 43: 70%\n bucket 43: 80%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 44:\n bucket 45: 10%\n bucket 44: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 44: 20%\n bucket 45: 40%\n bucket 45: 50%\n bucket 44: 30%\n bucket 45: 60%\n bucket 44: 40%\n bucket 45: 70%\n bucket 44: 50%\n bucket 45: 80%\n bucket 44: 60%\n bucket 45: 90%\n bucket 44: 70%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n bucket 44: 80%\n bucket 44: 90%\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n Entering block accumulator loop for bucket 47:\n bucket 46: 20%\n bucket 47: 10%\n bucket 46: 30%\n bucket 47: 20%\n bucket 46: 40%\n bucket 47: 30%\n bucket 46: 50%\n bucket 47: 40%\n bucket 46: 60%\n bucket 46: 70%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 46: 80%\n bucket 46: 90%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 49: 30%\n bucket 50: 20%\n bucket 49: 40%\n bucket 50: 30%\n bucket 49: 50%\n bucket 50: 40%\n bucket 49: 60%\n Sorting block time: 00:00:00\n bucket 50: 50%\nReturning block of 114 for bucket 48\n bucket 49: 70%\n bucket 50: 60%\n bucket 50: 70%\n bucket 49: 80%\n bucket 50: 80%\n bucket 49: 90%\n bucket 50: 90%\n bucket 49: 100%\n bucket 50: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 40%\n bucket 51: 50%\n Entering block accumulator loop for bucket 52:\n bucket 51: 60%\n bucket 52: 10%\n bucket 51: 70%\n bucket 52: 20%\n bucket 51: 80%\n bucket 52: 30%\n bucket 51: 90%\n bucket 52: 40%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 70%\n bucket 54: 80%\n Entering block accumulator loop for bucket 55:\n bucket 54: 90%\n bucket 55: 10%\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 54: 100%\n bucket 55: 20%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Entering block accumulator loop for bucket 56:\n bucket 55: 30%\n bucket 56: 10%\n bucket 55: 40%\n bucket 56: 20%\n bucket 56: 30%\n bucket 55: 50%\n bucket 56: 40%\n bucket 55: 60%\n bucket 56: 50%\n bucket 55: 70%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Sorting block time: 00:00:00\n bucket 55: 80%\n Entering block accumulator loop for bucket 57:\nReturning block of 65 for bucket 54\n bucket 56: 60%\n bucket 55: 90%\n bucket 57: 10%\n bucket 56: 70%\n bucket 55: 100%\n bucket 57: 20%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 80%\n bucket 57: 30%\n bucket 56: 90%\n bucket 57: 40%\n bucket 56: 100%\n bucket 57: 50%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 59: 10%\n bucket 60: 20%\n bucket 59: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 59: 30%\n bucket 60: 50%\n bucket 59: 40%\n bucket 60: 60%\n bucket 60: 70%\n bucket 59: 50%\n bucket 60: 80%\n bucket 59: 60%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n bucket 1: 10%\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 4\nGetting block 6 of 60\n Entering block accumulator loop for bucket 4:\n Reserving size (126) for bucket 6\n bucket 1: 20%\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 2: 10%\n Calculating Z arrays for bucket 5\n bucket 1: 30%\n bucket 2: 20%\n bucket 4: 10%\n Entering block accumulator loop for bucket 3:\n bucket 1: 40%\n Calculating Z arrays for bucket 6\n bucket 2: 30%\n bucket 4: 20%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 1: 50%\n bucket 4: 30%\n Calculating Z arrays for bucket 7\n bucket 2: 40%\n bucket 4: 40%\n Entering block accumulator loop for bucket 6:\n bucket 2: 50%\n Entering block accumulator loop for bucket 7:\nGetting block 8 of 60\n Entering block accumulator loop for bucket 5:\n bucket 4: 50%\n bucket 7: 10%\n bucket 2: 60%\n bucket 1: 60%\n bucket 7: 20%\n Reserving size (126) for bucket 8\n bucket 5: 10%\n bucket 3: 10%\n bucket 1: 70%\n bucket 2: 70%\n bucket 4: 60%\n bucket 1: 80%\n bucket 5: 20%\n bucket 7: 30%\n Calculating Z arrays for bucket 8\n bucket 4: 70%\n bucket 7: 40%\n bucket 1: 90%\n bucket 2: 80%\n bucket 4: 80%\n bucket 6: 10%\n bucket 5: 30%\n bucket 2: 90%\n bucket 3: 20%\n bucket 6: 20%\n bucket 2: 100%\n bucket 4: 90%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 6: 30%\n bucket 7: 50%\n bucket 3: 30%\n bucket 4: 100%\n bucket 6: 40%\n bucket 3: 40%\n Sorting block of length 68 for bucket 4\n bucket 7: 60%\n (Using difference cover)\n bucket 3: 50%\n bucket 7: 70%\n Entering block accumulator loop for bucket 8:\n bucket 3: 60%\n bucket 5: 40%\n bucket 7: 80%\n bucket 8: 10%\n bucket 3: 70%\n bucket 1: 100%\n bucket 5: 50%\n bucket 7: 90%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 5: 60%\n bucket 8: 20%\n bucket 3: 80%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 70%\n bucket 6: 50%\n bucket 8: 30%\n bucket 5: 80%\n bucket 3: 90%\n bucket 8: 40%\n bucket 6: 60%\n bucket 5: 90%\n bucket 8: 50%\n bucket 3: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 6: 70%\n bucket 5: 100%\n bucket 8: 60%\n bucket 6: 80%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 70%\n bucket 6: 90%\n bucket 8: 80%\n bucket 8: 90%\n bucket 6: 100%\n bucket 8: 100%\n Sorting block of length 90 for bucket 6\n Sorting block time: 00:00:00\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n (Using difference cover)\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Entering block accumulator loop for bucket 9:\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n Entering block accumulator loop for bucket 10:\n bucket 9: 40%\n bucket 10: 10%\n bucket 9: 50%\n bucket 10: 20%\n bucket 9: 60%\n bucket 10: 30%\n bucket 9: 70%\n bucket 10: 40%\n bucket 9: 80%\n bucket 10: 50%\n bucket 9: 90%\n bucket 10: 60%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n bucket 10: 70%\n (Using difference cover)\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Entering block accumulator loop for bucket 11:\n Sorting block time: 00:00:00\n bucket 11: 10%\nReturning block of 90 for bucket 10\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n bucket 12: 80%\n Entering block accumulator loop for bucket 13:\n bucket 12: 90%\nGetting block 14 of 60\n bucket 12: 100%\n Reserving size (126) for bucket 14\n bucket 13: 10%\n Sorting block of length 82 for bucket 12\n Calculating Z arrays for bucket 14\n (Using difference cover)\n bucket 13: 20%\n bucket 13: 30%\n Entering block accumulator loop for bucket 14:\n bucket 13: 40%\n bucket 14: 10%\n bucket 13: 50%\n bucket 14: 20%\n bucket 13: 60%\n bucket 14: 30%\n bucket 13: 70%\n bucket 14: 40%\n bucket 13: 80%\n bucket 14: 50%\n bucket 13: 90%\n bucket 14: 60%\n bucket 13: 100%\n bucket 14: 70%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n Entering block accumulator loop for bucket 16:\n bucket 15: 10%\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 15: 40%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 15: 50%\n bucket 16: 50%\n bucket 15: 60%\n bucket 16: 60%\n bucket 15: 70%\n bucket 16: 70%\n bucket 15: 80%\n bucket 16: 80%\n bucket 15: 90%\n bucket 16: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\nGetting block 17 of 60\n bucket 16: 100%\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n Entering block accumulator loop for bucket 19:\n bucket 18: 20%\n bucket 18: 30%\n bucket 19: 10%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 19: 50%\n bucket 18: 80%\n bucket 19: 60%\n bucket 18: 90%\n bucket 19: 70%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n Entering block accumulator loop for bucket 21:\n bucket 20: 20%\n bucket 21: 10%\n bucket 20: 30%\n bucket 21: 20%\n bucket 20: 40%\n bucket 21: 30%\n bucket 20: 50%\n bucket 21: 40%\n bucket 20: 60%\n bucket 21: 50%\n bucket 20: 70%\n bucket 21: 60%\n bucket 20: 80%\n bucket 21: 70%\n bucket 20: 90%\n bucket 21: 80%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Entering block accumulator loop for bucket 22:\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 22: 50%\n bucket 23: 40%\n bucket 22: 60%\n bucket 23: 50%\n bucket 22: 70%\n bucket 23: 60%\n bucket 22: 80%\n bucket 23: 70%\n bucket 22: 90%\n bucket 23: 80%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\nGetting block 25 of 60\n bucket 24: 70%\n Reserving size (126) for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n bucket 24: 80%\n Calculating Z arrays for bucket 25\n bucket 24: 90%\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 25:\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 26: 10%\n bucket 25: 10%\n bucket 26: 20%\n bucket 25: 20%\n bucket 26: 30%\n bucket 25: 30%\n bucket 26: 40%\n bucket 25: 40%\n bucket 26: 50%\n bucket 25: 50%\n bucket 26: 60%\n bucket 25: 60%\n bucket 26: 70%\n bucket 25: 70%\n bucket 26: 80%\n bucket 25: 80%\n bucket 26: 90%\n bucket 25: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 70%\n Entering block accumulator loop for bucket 29:\n bucket 28: 80%\n bucket 28: 90%\n bucket 29: 10%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 40%\n Calculating Z arrays for bucket 31\n bucket 30: 50%\n bucket 30: 60%\n Entering block accumulator loop for bucket 31:\n bucket 30: 70%\n bucket 31: 10%\n bucket 30: 80%\n bucket 31: 20%\n bucket 30: 90%\n bucket 31: 30%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\n bucket 32: 40%\nGetting block 33 of 60\n bucket 32: 50%\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Calculating Z arrays for bucket 34\n bucket 32: 60%\n bucket 32: 70%\n bucket 32: 80%\n Entering block accumulator loop for bucket 34:\n bucket 32: 90%\n Entering block accumulator loop for bucket 33:\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 34: 10%\n bucket 33: 10%\n bucket 34: 20%\n bucket 33: 20%\n bucket 34: 30%\n bucket 33: 30%\n bucket 34: 40%\n bucket 33: 40%\n bucket 34: 50%\n bucket 33: 50%\n bucket 34: 60%\n bucket 33: 60%\n bucket 33: 70%\n bucket 34: 70%\n bucket 33: 80%\n Sorting block time: 00:00:00\n bucket 33: 90%\nReturning block of 126 for bucket 32\n bucket 34: 80%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 36:\n Entering block accumulator loop for bucket 37:\n bucket 36: 10%\n bucket 37: 10%\n bucket 36: 20%\n bucket 37: 20%\n bucket 36: 30%\n bucket 37: 30%\n bucket 36: 40%\n bucket 37: 40%\n bucket 36: 50%\n bucket 37: 50%\n bucket 36: 60%\n bucket 37: 60%\n bucket 36: 70%\n bucket 37: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 37: 80%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Entering block accumulator loop for bucket 38:\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n Entering block accumulator loop for bucket 39:\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 39: 20%\n bucket 38: 40%\n bucket 39: 30%\n bucket 38: 50%\n bucket 39: 40%\n bucket 38: 60%\n bucket 39: 50%\n bucket 38: 70%\n bucket 39: 60%\n bucket 38: 80%\n bucket 39: 70%\n bucket 38: 90%\n bucket 39: 80%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\n bucket 41: 20%\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 41: 50%\n bucket 40: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n bucket 41: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n bucket 42: 20%\n Calculating Z arrays for bucket 43\n bucket 42: 30%\n Entering block accumulator loop for bucket 43:\n bucket 42: 40%\n bucket 43: 10%\n bucket 42: 50%\n bucket 43: 20%\n bucket 43: 30%\n bucket 42: 60%\n bucket 42: 70%\n bucket 43: 40%\n bucket 43: 50%\n bucket 42: 80%\n bucket 43: 60%\n bucket 42: 90%\n bucket 43: 70%\n bucket 43: 80%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 44:\n bucket 45: 10%\n bucket 44: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 44: 20%\n bucket 45: 40%\n bucket 45: 50%\n bucket 44: 30%\n bucket 45: 60%\n bucket 44: 40%\n bucket 45: 70%\n bucket 44: 50%\n bucket 45: 80%\n bucket 44: 60%\n bucket 45: 90%\n bucket 44: 70%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n bucket 44: 80%\n bucket 44: 90%\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n Entering block accumulator loop for bucket 47:\n bucket 46: 20%\n bucket 47: 10%\n bucket 46: 30%\n bucket 47: 20%\n bucket 46: 40%\n bucket 47: 30%\n bucket 46: 50%\n bucket 47: 40%\n bucket 46: 60%\n bucket 46: 70%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 46: 80%\n bucket 46: 90%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 49: 30%\n bucket 50: 20%\n bucket 49: 40%\n bucket 50: 30%\n bucket 49: 50%\n bucket 50: 40%\n bucket 49: 60%\n Sorting block time: 00:00:00\n bucket 50: 50%\nReturning block of 114 for bucket 48\n bucket 49: 70%\n bucket 50: 60%\n bucket 50: 70%\n bucket 49: 80%\n bucket 50: 80%\n bucket 49: 90%\n bucket 50: 90%\n bucket 49: 100%\n bucket 50: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 40%\n bucket 51: 50%\n Entering block accumulator loop for bucket 52:\n bucket 51: 60%\n bucket 52: 10%\n bucket 51: 70%\n bucket 52: 20%\n bucket 51: 80%\n bucket 52: 30%\n bucket 51: 90%\n bucket 52: 40%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 70%\n bucket 54: 80%\n Entering block accumulator loop for bucket 55:\n bucket 54: 90%\n bucket 55: 10%\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 54: 100%\n bucket 55: 20%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Entering block accumulator loop for bucket 56:\n bucket 55: 30%\n bucket 56: 10%\n bucket 55: 40%\n bucket 56: 20%\n bucket 56: 30%\n bucket 55: 50%\n bucket 56: 40%\n bucket 55: 60%\n bucket 56: 50%\n bucket 55: 70%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Sorting block time: 00:00:00\n bucket 55: 80%\n Entering block accumulator loop for bucket 57:\nReturning block of 65 for bucket 54\n bucket 56: 60%\n bucket 55: 90%\n bucket 57: 10%\n bucket 56: 70%\n bucket 55: 100%\n bucket 57: 20%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 80%\n bucket 57: 30%\n bucket 56: 90%\n bucket 57: 40%\n bucket 56: 100%\n bucket 57: 50%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 59: 10%\n bucket 60: 20%\n bucket 59: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 59: 30%\n bucket 60: 50%\n bucket 59: 40%\n bucket 60: 60%\n bucket 60: 70%\n bucket 59: 50%\n bucket 60: 80%\n bucket 59: 60%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:05:21", "plugin": "core", "name": "end_epoch", "raw_value": "1725001521.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:05:20", "plugin": "core", "name": "start_epoch", "raw_value": "1725001520.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-13", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 13, "time_seconds": 34.859352588653564, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "dab93d21ece8822d"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "d9ce919af34d5dda"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "13df7a486c8004eb", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:57:06.296297", "update_time": "2024-08-30T06:57:20.152929", "galaxy_version": "24.1", "external_id": "gxy-5zpdt", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/7/8/2/dataset_782af619-28dc-4c60-bbcb-62e49118942f.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/3/c/4/dataset_3c454e27-6e0c-49d7-9c57-289d5e469fc8.dat' > input_f.fastq && seqtk seq -2 '/galaxy/server/database/objects/3/c/4/dataset_3c454e27-6e0c-49d7-9c57-289d5e469fc8.dat' > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/9/6/8/dataset_96814f2c-fe2d-4e6f-9b2f-5179f256a642.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 164, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 163, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "dab93d21ece8822d", "src": "hda", "uuid": "782af619-28dc-4c60-bbcb-62e49118942f"}, "library|input_1": {"id": "d9ce919af34d5dda", "src": "hda", "uuid": "3c454e27-6e0c-49d7-9c57-289d5e469fc8"}}, "outputs": {"output_alignments": {"id": "74698d208f06f7f8", "src": "hda", "uuid": "96814f2c-fe2d-4e6f-9b2f-5179f256a642"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 1:\nGetting block 4 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n bucket 1: 20%\n Reserving size (126) for bucket 4\n bucket 1: 30%\n Calculating Z arrays for bucket 4\n bucket 1: 40%\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 2:\n bucket 1: 50%\n Entering block accumulator loop for bucket 4:\n bucket 1: 60%\n bucket 2: 10%\n bucket 3: 10%\n bucket 1: 70%\n bucket 2: 20%\n bucket 3: 20%\n bucket 1: 80%\nGetting block 5 of 60\n bucket 1: 90%\n bucket 3: 30%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 3: 40%\n bucket 2: 30%\n bucket 1: 100%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 4: 10%\n bucket 3: 50%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 2: 40%\n Calculating Z arrays for bucket 7\n bucket 2: 50%\n Calculating Z arrays for bucket 8\n bucket 4: 20%\n Reserving size (126) for bucket 5\n bucket 4: 30%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 3: 60%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 5\n bucket 4: 40%\n bucket 2: 60%\n bucket 4: 50%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 6: 10%\n bucket 3: 70%\n Entering block accumulator loop for bucket 5:\n bucket 3: 80%\n bucket 2: 70%\n bucket 6: 20%\n Sorting block time: 00:00:00\n bucket 5: 10%\n Entering block accumulator loop for bucket 8:\n bucket 6: 30%\n bucket 5: 20%\n bucket 4: 60%\n bucket 7: 10%\n bucket 2: 80%\n bucket 4: 70%\n bucket 8: 10%\n bucket 4: 80%\n bucket 7: 20%\n bucket 5: 30%\n bucket 4: 90%\n bucket 3: 90%\n bucket 2: 90%\n bucket 8: 20%\n bucket 4: 100%\n bucket 7: 30%\n bucket 5: 40%\nReturning block of 43 for bucket 1\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 5: 50%\n bucket 7: 40%\n bucket 2: 100%\n bucket 6: 40%\n bucket 3: 100%\n bucket 7: 50%\n bucket 5: 60%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 6: 50%\n bucket 8: 30%\n Sorting block of length 84 for bucket 2\n bucket 7: 60%\n bucket 8: 40%\n bucket 7: 70%\n bucket 6: 60%\n (Using difference cover)\n bucket 7: 80%\n bucket 5: 70%\n bucket 6: 70%\n bucket 8: 50%\n bucket 7: 90%\n bucket 6: 80%\n bucket 8: 60%\n bucket 5: 80%\n bucket 7: 100%\n bucket 6: 90%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 90%\n bucket 6: 100%\n bucket 8: 70%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 80%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 70%\n bucket 9: 80%\n Entering block accumulator loop for bucket 10:\n bucket 9: 90%\n bucket 10: 10%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\nGetting block 12 of 60\n bucket 11: 40%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n bucket 11: 50%\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 60%\n Entering block accumulator loop for bucket 13:\n bucket 11: 70%\n Entering block accumulator loop for bucket 12:\n bucket 13: 10%\n bucket 11: 80%\n bucket 12: 10%\n bucket 13: 20%\n bucket 12: 20%\n bucket 11: 90%\n bucket 13: 30%\n bucket 12: 30%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n bucket 12: 40%\n bucket 13: 40%\n bucket 12: 50%\n (Using difference cover)\n bucket 13: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 13: 60%\n bucket 12: 80%\n bucket 12: 90%\n bucket 13: 70%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 70%\n Entering block accumulator loop for bucket 15:\n bucket 14: 80%\n bucket 15: 10%\n bucket 14: 90%\n bucket 15: 20%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 70%\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 17:\n bucket 16: 80%\n bucket 17: 10%\n Entering block accumulator loop for bucket 18:\n bucket 16: 90%\n bucket 17: 20%\n bucket 18: 10%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n bucket 18: 20%\n bucket 17: 30%\n (Using difference cover)\n bucket 18: 30%\n bucket 17: 40%\n bucket 18: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 18: 50%\n bucket 17: 70%\n bucket 18: 60%\n bucket 17: 80%\n bucket 18: 70%\n bucket 17: 90%\n bucket 18: 80%\n bucket 18: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Entering block accumulator loop for bucket 19:\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n bucket 20: 50%\n bucket 19: 70%\n bucket 20: 60%\n bucket 19: 80%\n bucket 20: 70%\n bucket 20: 80%\n bucket 19: 90%\n bucket 20: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n bucket 22: 10%\n Calculating Z arrays for bucket 23\n bucket 22: 20%\n bucket 22: 30%\n Entering block accumulator loop for bucket 23:\n bucket 22: 40%\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n bucket 23: 10%\n bucket 22: 50%\n bucket 22: 60%\n bucket 23: 20%\n bucket 22: 70%\n bucket 23: 30%\n bucket 22: 80%\n bucket 23: 40%\n bucket 22: 90%\n bucket 23: 50%\n bucket 23: 60%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 40%\n bucket 24: 50%\n Entering block accumulator loop for bucket 25:\n bucket 24: 60%\n bucket 25: 10%\n bucket 24: 70%\n bucket 24: 80%\n bucket 25: 20%\n bucket 24: 90%\n bucket 25: 30%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Entering block accumulator loop for bucket 26:\n Calculating Z arrays for bucket 27\n bucket 26: 10%\n Entering block accumulator loop for bucket 27:\n bucket 26: 20%\n bucket 27: 10%\n bucket 26: 30%\n bucket 27: 20%\n bucket 26: 40%\n bucket 27: 30%\n bucket 26: 50%\n bucket 27: 40%\n bucket 26: 60%\n bucket 27: 50%\n bucket 26: 70%\n bucket 27: 60%\n bucket 26: 80%\n bucket 27: 70%\n bucket 26: 90%\n bucket 27: 80%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Entering block accumulator loop for bucket 28:\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 10%\n Entering block accumulator loop for bucket 29:\n bucket 28: 20%\n bucket 29: 10%\n bucket 28: 30%\n bucket 29: 20%\n bucket 28: 40%\n bucket 29: 30%\n bucket 28: 50%\n bucket 29: 40%\n bucket 28: 60%\n bucket 29: 50%\n bucket 28: 70%\n bucket 29: 60%\n bucket 28: 80%\n bucket 29: 70%\n bucket 28: 90%\n bucket 29: 80%\n bucket 28: 100%\n bucket 29: 90%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 31:\n bucket 30: 10%\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 10%\n bucket 30: 20%\n bucket 31: 20%\n Entering block accumulator loop for bucket 32:\n bucket 30: 30%\n bucket 31: 30%\n bucket 32: 10%\n bucket 30: 40%\n bucket 31: 40%\n bucket 32: 20%\n bucket 30: 50%\n bucket 31: 50%\n bucket 32: 30%\n bucket 30: 60%\n bucket 32: 40%\n bucket 31: 60%\n bucket 32: 50%\n bucket 30: 70%\n bucket 31: 70%\n bucket 32: 60%\n bucket 30: 80%\n bucket 31: 80%\n bucket 32: 70%\n bucket 30: 90%\n bucket 32: 80%\n bucket 31: 90%\n bucket 30: 100%\n bucket 32: 90%\n bucket 31: 100%\n Sorting block of length 124 for bucket 30\n Sorting block of length 110 for bucket 31\n bucket 32: 100%\n (Using difference cover)\n (Using difference cover)\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\nGetting block 35 of 60\n bucket 34: 30%\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 40%\n bucket 34: 50%\n Entering block accumulator loop for bucket 35:\n bucket 34: 60%\n bucket 34: 70%\n bucket 35: 10%\n bucket 34: 80%\n bucket 35: 20%\n bucket 34: 90%\n bucket 35: 30%\n bucket 34: 100%\n bucket 35: 40%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 39:\n bucket 38: 10%\n bucket 39: 10%\n bucket 38: 20%\n bucket 39: 20%\n bucket 38: 30%\n bucket 39: 30%\n bucket 38: 40%\n bucket 39: 40%\n bucket 38: 50%\n bucket 39: 50%\n bucket 38: 60%\n bucket 39: 60%\n bucket 38: 70%\n bucket 39: 70%\n bucket 38: 80%\n bucket 39: 80%\n bucket 38: 90%\n bucket 39: 90%\n bucket 39: 100%\n bucket 38: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Entering block accumulator loop for bucket 40:\n Calculating Z arrays for bucket 41\n bucket 40: 10%\n Entering block accumulator loop for bucket 41:\n bucket 40: 20%\n bucket 41: 10%\n bucket 40: 30%\n bucket 41: 20%\n bucket 40: 40%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 40: 60%\n bucket 41: 50%\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n bucket 41: 60%\n bucket 40: 70%\n Calculating Z arrays for bucket 42\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n Entering block accumulator loop for bucket 42:\n bucket 41: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block time: 00:00:00\n Sorting block of length 119 for bucket 42\n (Using difference cover)\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 43: 20%\n bucket 44: 10%\n bucket 43: 30%\n bucket 44: 20%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 43: 90%\n bucket 44: 80%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n bucket 49: 20%\n bucket 50: 10%\n bucket 49: 30%\n Entering block accumulator loop for bucket 51:\nGetting block 52 of 60\n bucket 50: 20%\n bucket 49: 40%\n bucket 51: 10%\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 49: 50%\n bucket 51: 20%\n bucket 49: 60%\n bucket 51: 30%\n Entering block accumulator loop for bucket 52:\n bucket 49: 70%\n bucket 51: 40%\n bucket 52: 10%\n bucket 49: 80%\n bucket 51: 50%\n bucket 52: 20%\n bucket 50: 30%\n bucket 49: 90%\n bucket 51: 60%\n bucket 52: 30%\n bucket 50: 40%\n bucket 51: 70%\n bucket 52: 40%\n bucket 49: 100%\n bucket 51: 80%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 50%\n bucket 51: 90%\n bucket 52: 50%\n bucket 51: 100%\n bucket 52: 60%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 50: 60%\n bucket 52: 70%\n bucket 50: 70%\n bucket 52: 80%\n bucket 50: 80%\n bucket 52: 90%\n bucket 50: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 53: 20%\n Entering block accumulator loop for bucket 54:\n bucket 53: 30%\n bucket 54: 10%\n bucket 53: 40%\n bucket 54: 20%\n bucket 53: 50%\n bucket 54: 30%\n bucket 53: 60%\n bucket 54: 40%\n bucket 53: 70%\n bucket 54: 50%\n Entering block accumulator loop for bucket 55:\n bucket 53: 80%\n bucket 54: 60%\n bucket 55: 10%\n bucket 53: 90%\n bucket 54: 70%\n bucket 55: 20%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 80%\n bucket 55: 30%\n bucket 54: 90%\n bucket 55: 40%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n Entering block accumulator loop for bucket 57:\n bucket 56: 20%\n bucket 57: 10%\n bucket 56: 30%\n bucket 57: 20%\n bucket 56: 40%\n bucket 57: 30%\n bucket 56: 50%\n bucket 57: 40%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 57: 50%\n bucket 56: 90%\n bucket 57: 60%\n bucket 56: 100%\n bucket 57: 70%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n Entering block accumulator loop for bucket 59:\n bucket 58: 20%\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 58: 30%\n bucket 59: 10%\n Entering block accumulator loop for bucket 60:\n bucket 58: 40%\n bucket 60: 10%\n bucket 59: 20%\n bucket 58: 50%\n bucket 60: 20%\n bucket 59: 30%\n bucket 58: 60%\n bucket 60: 30%\n bucket 59: 40%\n bucket 58: 70%\n bucket 60: 40%\n bucket 59: 50%\n bucket 58: 80%\n bucket 60: 50%\n bucket 59: 60%\n bucket 58: 90%\n bucket 60: 60%\n bucket 59: 70%\n bucket 58: 100%\n bucket 60: 70%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 80%\n bucket 60: 80%\n bucket 59: 90%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 1:\nGetting block 4 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n bucket 1: 20%\n Reserving size (126) for bucket 4\n bucket 1: 30%\n Calculating Z arrays for bucket 4\n bucket 1: 40%\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 2:\n bucket 1: 50%\n Entering block accumulator loop for bucket 4:\n bucket 1: 60%\n bucket 2: 10%\n bucket 3: 10%\n bucket 1: 70%\n bucket 2: 20%\n bucket 3: 20%\n bucket 1: 80%\nGetting block 5 of 60\n bucket 1: 90%\n bucket 3: 30%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 3: 40%\n bucket 2: 30%\n bucket 1: 100%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 4: 10%\n bucket 3: 50%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 2: 40%\n Calculating Z arrays for bucket 7\n bucket 2: 50%\n Calculating Z arrays for bucket 8\n bucket 4: 20%\n Reserving size (126) for bucket 5\n bucket 4: 30%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 3: 60%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 5\n bucket 4: 40%\n bucket 2: 60%\n bucket 4: 50%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 6: 10%\n bucket 3: 70%\n Entering block accumulator loop for bucket 5:\n bucket 3: 80%\n bucket 2: 70%\n bucket 6: 20%\n Sorting block time: 00:00:00\n bucket 5: 10%\n Entering block accumulator loop for bucket 8:\n bucket 6: 30%\n bucket 5: 20%\n bucket 4: 60%\n bucket 7: 10%\n bucket 2: 80%\n bucket 4: 70%\n bucket 8: 10%\n bucket 4: 80%\n bucket 7: 20%\n bucket 5: 30%\n bucket 4: 90%\n bucket 3: 90%\n bucket 2: 90%\n bucket 8: 20%\n bucket 4: 100%\n bucket 7: 30%\n bucket 5: 40%\nReturning block of 43 for bucket 1\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 5: 50%\n bucket 7: 40%\n bucket 2: 100%\n bucket 6: 40%\n bucket 3: 100%\n bucket 7: 50%\n bucket 5: 60%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 6: 50%\n bucket 8: 30%\n Sorting block of length 84 for bucket 2\n bucket 7: 60%\n bucket 8: 40%\n bucket 7: 70%\n bucket 6: 60%\n (Using difference cover)\n bucket 7: 80%\n bucket 5: 70%\n bucket 6: 70%\n bucket 8: 50%\n bucket 7: 90%\n bucket 6: 80%\n bucket 8: 60%\n bucket 5: 80%\n bucket 7: 100%\n bucket 6: 90%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 90%\n bucket 6: 100%\n bucket 8: 70%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 8: 80%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 70%\n bucket 9: 80%\n Entering block accumulator loop for bucket 10:\n bucket 9: 90%\n bucket 10: 10%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\nGetting block 12 of 60\n bucket 11: 40%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n bucket 11: 50%\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 60%\n Entering block accumulator loop for bucket 13:\n bucket 11: 70%\n Entering block accumulator loop for bucket 12:\n bucket 13: 10%\n bucket 11: 80%\n bucket 12: 10%\n bucket 13: 20%\n bucket 12: 20%\n bucket 11: 90%\n bucket 13: 30%\n bucket 12: 30%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n bucket 12: 40%\n bucket 13: 40%\n bucket 12: 50%\n (Using difference cover)\n bucket 13: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 13: 60%\n bucket 12: 80%\n bucket 12: 90%\n bucket 13: 70%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 70%\n Entering block accumulator loop for bucket 15:\n bucket 14: 80%\n bucket 15: 10%\n bucket 14: 90%\n bucket 15: 20%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 70%\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 17:\n bucket 16: 80%\n bucket 17: 10%\n Entering block accumulator loop for bucket 18:\n bucket 16: 90%\n bucket 17: 20%\n bucket 18: 10%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n bucket 18: 20%\n bucket 17: 30%\n (Using difference cover)\n bucket 18: 30%\n bucket 17: 40%\n bucket 18: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 18: 50%\n bucket 17: 70%\n bucket 18: 60%\n bucket 17: 80%\n bucket 18: 70%\n bucket 17: 90%\n bucket 18: 80%\n bucket 18: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Entering block accumulator loop for bucket 19:\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 20: 30%\n bucket 19: 50%\n bucket 20: 40%\n bucket 19: 60%\n bucket 20: 50%\n bucket 19: 70%\n bucket 20: 60%\n bucket 19: 80%\n bucket 20: 70%\n bucket 20: 80%\n bucket 19: 90%\n bucket 20: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n bucket 22: 10%\n Calculating Z arrays for bucket 23\n bucket 22: 20%\n bucket 22: 30%\n Entering block accumulator loop for bucket 23:\n bucket 22: 40%\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n bucket 23: 10%\n bucket 22: 50%\n bucket 22: 60%\n bucket 23: 20%\n bucket 22: 70%\n bucket 23: 30%\n bucket 22: 80%\n bucket 23: 40%\n bucket 22: 90%\n bucket 23: 50%\n bucket 23: 60%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 40%\n bucket 24: 50%\n Entering block accumulator loop for bucket 25:\n bucket 24: 60%\n bucket 25: 10%\n bucket 24: 70%\n bucket 24: 80%\n bucket 25: 20%\n bucket 24: 90%\n bucket 25: 30%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Entering block accumulator loop for bucket 26:\n Calculating Z arrays for bucket 27\n bucket 26: 10%\n Entering block accumulator loop for bucket 27:\n bucket 26: 20%\n bucket 27: 10%\n bucket 26: 30%\n bucket 27: 20%\n bucket 26: 40%\n bucket 27: 30%\n bucket 26: 50%\n bucket 27: 40%\n bucket 26: 60%\n bucket 27: 50%\n bucket 26: 70%\n bucket 27: 60%\n bucket 26: 80%\n bucket 27: 70%\n bucket 26: 90%\n bucket 27: 80%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Entering block accumulator loop for bucket 28:\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 10%\n Entering block accumulator loop for bucket 29:\n bucket 28: 20%\n bucket 29: 10%\n bucket 28: 30%\n bucket 29: 20%\n bucket 28: 40%\n bucket 29: 30%\n bucket 28: 50%\n bucket 29: 40%\n bucket 28: 60%\n bucket 29: 50%\n bucket 28: 70%\n bucket 29: 60%\n bucket 28: 80%\n bucket 29: 70%\n bucket 28: 90%\n bucket 29: 80%\n bucket 28: 100%\n bucket 29: 90%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 31:\n bucket 30: 10%\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 10%\n bucket 30: 20%\n bucket 31: 20%\n Entering block accumulator loop for bucket 32:\n bucket 30: 30%\n bucket 31: 30%\n bucket 32: 10%\n bucket 30: 40%\n bucket 31: 40%\n bucket 32: 20%\n bucket 30: 50%\n bucket 31: 50%\n bucket 32: 30%\n bucket 30: 60%\n bucket 32: 40%\n bucket 31: 60%\n bucket 32: 50%\n bucket 30: 70%\n bucket 31: 70%\n bucket 32: 60%\n bucket 30: 80%\n bucket 31: 80%\n bucket 32: 70%\n bucket 30: 90%\n bucket 32: 80%\n bucket 31: 90%\n bucket 30: 100%\n bucket 32: 90%\n bucket 31: 100%\n Sorting block of length 124 for bucket 30\n Sorting block of length 110 for bucket 31\n bucket 32: 100%\n (Using difference cover)\n (Using difference cover)\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\nGetting block 35 of 60\n bucket 34: 30%\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 40%\n bucket 34: 50%\n Entering block accumulator loop for bucket 35:\n bucket 34: 60%\n bucket 34: 70%\n bucket 35: 10%\n bucket 34: 80%\n bucket 35: 20%\n bucket 34: 90%\n bucket 35: 30%\n bucket 34: 100%\n bucket 35: 40%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 39:\n bucket 38: 10%\n bucket 39: 10%\n bucket 38: 20%\n bucket 39: 20%\n bucket 38: 30%\n bucket 39: 30%\n bucket 38: 40%\n bucket 39: 40%\n bucket 38: 50%\n bucket 39: 50%\n bucket 38: 60%\n bucket 39: 60%\n bucket 38: 70%\n bucket 39: 70%\n bucket 38: 80%\n bucket 39: 80%\n bucket 38: 90%\n bucket 39: 90%\n bucket 39: 100%\n bucket 38: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Entering block accumulator loop for bucket 40:\n Calculating Z arrays for bucket 41\n bucket 40: 10%\n Entering block accumulator loop for bucket 41:\n bucket 40: 20%\n bucket 41: 10%\n bucket 40: 30%\n bucket 41: 20%\n bucket 40: 40%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 40: 60%\n bucket 41: 50%\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n bucket 41: 60%\n bucket 40: 70%\n Calculating Z arrays for bucket 42\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n Entering block accumulator loop for bucket 42:\n bucket 41: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block time: 00:00:00\n Sorting block of length 119 for bucket 42\n (Using difference cover)\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 43: 20%\n bucket 44: 10%\n bucket 43: 30%\n bucket 44: 20%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 43: 90%\n bucket 44: 80%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n bucket 49: 20%\n bucket 50: 10%\n bucket 49: 30%\n Entering block accumulator loop for bucket 51:\nGetting block 52 of 60\n bucket 50: 20%\n bucket 49: 40%\n bucket 51: 10%\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 49: 50%\n bucket 51: 20%\n bucket 49: 60%\n bucket 51: 30%\n Entering block accumulator loop for bucket 52:\n bucket 49: 70%\n bucket 51: 40%\n bucket 52: 10%\n bucket 49: 80%\n bucket 51: 50%\n bucket 52: 20%\n bucket 50: 30%\n bucket 49: 90%\n bucket 51: 60%\n bucket 52: 30%\n bucket 50: 40%\n bucket 51: 70%\n bucket 52: 40%\n bucket 49: 100%\n bucket 51: 80%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 50%\n bucket 51: 90%\n bucket 52: 50%\n bucket 51: 100%\n bucket 52: 60%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 50: 60%\n bucket 52: 70%\n bucket 50: 70%\n bucket 52: 80%\n bucket 50: 80%\n bucket 52: 90%\n bucket 50: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 53: 20%\n Entering block accumulator loop for bucket 54:\n bucket 53: 30%\n bucket 54: 10%\n bucket 53: 40%\n bucket 54: 20%\n bucket 53: 50%\n bucket 54: 30%\n bucket 53: 60%\n bucket 54: 40%\n bucket 53: 70%\n bucket 54: 50%\n Entering block accumulator loop for bucket 55:\n bucket 53: 80%\n bucket 54: 60%\n bucket 55: 10%\n bucket 53: 90%\n bucket 54: 70%\n bucket 55: 20%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 80%\n bucket 55: 30%\n bucket 54: 90%\n bucket 55: 40%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n Entering block accumulator loop for bucket 57:\n bucket 56: 20%\n bucket 57: 10%\n bucket 56: 30%\n bucket 57: 20%\n bucket 56: 40%\n bucket 57: 30%\n bucket 56: 50%\n bucket 57: 40%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 57: 50%\n bucket 56: 90%\n bucket 57: 60%\n bucket 56: 100%\n bucket 57: 70%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n Entering block accumulator loop for bucket 59:\n bucket 58: 20%\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 58: 30%\n bucket 59: 10%\n Entering block accumulator loop for bucket 60:\n bucket 58: 40%\n bucket 60: 10%\n bucket 59: 20%\n bucket 58: 50%\n bucket 60: 20%\n bucket 59: 30%\n bucket 58: 60%\n bucket 60: 30%\n bucket 59: 40%\n bucket 58: 70%\n bucket 60: 40%\n bucket 59: 50%\n bucket 58: 80%\n bucket 60: 50%\n bucket 59: 60%\n bucket 58: 90%\n bucket 60: 60%\n bucket 59: 70%\n bucket 58: 100%\n bucket 60: 70%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 80%\n bucket 60: 80%\n bucket 59: 90%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:57:08", "plugin": "core", "name": "end_epoch", "raw_value": "1725001028.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:57:07", "plugin": "core", "name": "start_epoch", "raw_value": "1725001027.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-13", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 13, "time_seconds": 25.918893337249756, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "99f189e7e8c10e7f"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "8956761243b33003"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "9cd2ea9e0fa020ae", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:05:53.505379", "update_time": "2024-08-30T07:05:59.658893", "galaxy_version": "24.1", "external_id": "gxy-fm7pt", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/5/2/d/dataset_52d2be35-52cf-4590-a306-85aba8da3c7b.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/7/b/4/dataset_7b47d477-51c8-4336-8843-1baefab9f8c3.dat' > input_f.fastq && seqtk seq -2 '/galaxy/server/database/objects/7/b/4/dataset_7b47d477-51c8-4336-8843-1baefab9f8c3.dat' > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/d/5/4/dataset_d54d3050-5220-4f35-9a58-b3a92d1aa263.dat'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 223, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 222, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "99f189e7e8c10e7f", "src": "hda", "uuid": "52d2be35-52cf-4590-a306-85aba8da3c7b"}, "library|input_1": {"id": "8956761243b33003", "src": "hda", "uuid": "7b47d477-51c8-4336-8843-1baefab9f8c3"}}, "outputs": {"output_alignments": {"id": "3cb1bb014a0d8afa", "src": "hda", "uuid": "d54d3050-5220-4f35-9a58-b3a92d1aa263"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 20%\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n bucket 2: 10%\n Calculating Z arrays for bucket 4\n bucket 1: 30%\n Entering block accumulator loop for bucket 3:\n bucket 1: 40%\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 1: 50%\n bucket 3: 10%\n bucket 2: 20%\n bucket 1: 60%\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 5\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 3: 20%\n bucket 1: 70%\n bucket 2: 30%\nGetting block 7 of 60\n Calculating Z arrays for bucket 6\n bucket 5: 10%\n bucket 1: 80%\n bucket 3: 30%\n bucket 2: 40%\n bucket 1: 90%\n bucket 4: 10%\n bucket 2: 50%\nGetting block 8 of 60\n bucket 4: 20%\n bucket 5: 20%\n Reserving size (126) for bucket 8\n bucket 1: 100%\n bucket 4: 30%\n Reserving size (126) for bucket 7\n bucket 2: 60%\n bucket 4: 40%\n bucket 5: 30%\n Calculating Z arrays for bucket 7\n bucket 2: 70%\n bucket 3: 40%\n Calculating Z arrays for bucket 8\n bucket 4: 50%\n bucket 2: 80%\n bucket 5: 40%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Entering block accumulator loop for bucket 7:\n bucket 2: 90%\n bucket 5: 50%\n bucket 3: 50%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 8:\n bucket 2: 100%\n bucket 7: 10%\n bucket 4: 60%\n bucket 5: 60%\n bucket 3: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 7: 20%\n bucket 6: 10%\n bucket 8: 10%\n bucket 5: 70%\n bucket 3: 70%\n bucket 4: 70%\n bucket 6: 20%\n bucket 7: 30%\n bucket 8: 20%\n bucket 5: 80%\n bucket 4: 80%\n bucket 6: 30%\n bucket 7: 40%\n bucket 4: 90%\n bucket 8: 30%\n bucket 3: 80%\n bucket 6: 40%\n bucket 7: 50%\n bucket 4: 100%\n bucket 5: 90%\n bucket 8: 40%\n bucket 3: 90%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 7: 60%\n bucket 8: 50%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 3: 100%\n bucket 6: 50%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 7: 70%\n bucket 6: 60%\n bucket 8: 60%\n bucket 7: 80%\n bucket 6: 70%\n bucket 8: 70%\n bucket 7: 90%\n Sorting block time: 00:00:00\n bucket 6: 80%\n bucket 7: 100%\n bucket 8: 80%\nReturning block of 43 for bucket 1\n Sorting block of length 75 for bucket 7\n bucket 8: 90%\n bucket 6: 90%\n bucket 8: 100%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\nGetting block 11 of 60\n bucket 9: 60%\n bucket 10: 40%\n Reserving size (126) for bucket 11\n bucket 10: 50%\n Calculating Z arrays for bucket 11\n bucket 9: 70%\n bucket 10: 60%\n bucket 9: 80%\n bucket 10: 70%\n Entering block accumulator loop for bucket 11:\n bucket 9: 90%\n bucket 10: 80%\n bucket 11: 10%\n bucket 9: 100%\n bucket 10: 90%\n Sorting block of length 124 for bucket 9\n bucket 11: 20%\n (Using difference cover)\n bucket 10: 100%\n bucket 11: 30%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n bucket 12: 20%\n Entering block accumulator loop for bucket 13:\n bucket 12: 30%\n bucket 13: 10%\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 40%\n bucket 12: 70%\n bucket 13: 50%\n Entering block accumulator loop for bucket 14:\n bucket 12: 80%\n bucket 13: 60%\n bucket 14: 10%\n bucket 12: 90%\n bucket 13: 70%\n bucket 14: 20%\n bucket 12: 100%\n bucket 13: 80%\n bucket 14: 30%\n Sorting block of length 82 for bucket 12\n bucket 13: 90%\n (Using difference cover)\n bucket 14: 40%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 30%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n bucket 15: 40%\n bucket 16: 10%\n Entering block accumulator loop for bucket 17:\n bucket 15: 50%\n bucket 16: 20%\n bucket 17: 10%\n bucket 15: 60%\n bucket 16: 30%\n bucket 17: 20%\n bucket 16: 40%\n bucket 17: 30%\n bucket 15: 70%\n bucket 16: 50%\n bucket 17: 40%\n bucket 16: 60%\n bucket 15: 80%\n bucket 17: 50%\n bucket 16: 70%\n bucket 15: 90%\n bucket 17: 60%\n bucket 16: 80%\n bucket 15: 100%\n bucket 17: 70%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 90%\n bucket 17: 80%\n bucket 16: 100%\n bucket 17: 90%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 20%\n Entering block accumulator loop for bucket 19:\n bucket 18: 30%\n bucket 19: 10%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 19: 50%\n bucket 19: 60%\n bucket 18: 80%\n bucket 19: 70%\n bucket 18: 90%\n bucket 19: 80%\n bucket 18: 100%\n bucket 19: 90%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\nGetting block 22 of 60\n bucket 20: 10%\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n Entering block accumulator loop for bucket 22:\n bucket 20: 50%\n Entering block accumulator loop for bucket 21:\n bucket 22: 10%\n bucket 20: 60%\n bucket 21: 10%\n bucket 20: 70%\n bucket 22: 20%\n bucket 20: 80%\n bucket 21: 20%\n bucket 22: 30%\n bucket 20: 90%\n bucket 21: 30%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 22: 50%\n bucket 21: 60%\n bucket 22: 60%\n bucket 21: 70%\n bucket 22: 70%\n bucket 21: 80%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 24: 10%\n bucket 23: 30%\n bucket 24: 20%\n bucket 23: 40%\n bucket 24: 30%\n bucket 23: 50%\n bucket 24: 40%\n bucket 23: 60%\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 26\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 27:\n bucket 25: 10%\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 25: 20%\n bucket 26: 10%\n bucket 27: 20%\n bucket 25: 30%\n bucket 26: 20%\n bucket 27: 30%\n bucket 25: 40%\n bucket 27: 40%\n bucket 26: 30%\n bucket 25: 50%\n bucket 27: 50%\n bucket 26: 40%\n bucket 27: 60%\n bucket 25: 60%\n bucket 27: 70%\n bucket 26: 50%\n bucket 25: 70%\n bucket 27: 80%\n bucket 26: 60%\n bucket 25: 80%\n bucket 26: 70%\n bucket 27: 90%\n bucket 25: 90%\n bucket 26: 80%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\nGetting block 29 of 60\n bucket 28: 100%\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 30%\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 30: 40%\n bucket 30: 50%\n bucket 31: 10%\n bucket 30: 60%\n bucket 31: 20%\n bucket 30: 70%\n bucket 30: 80%\n bucket 31: 30%\n bucket 30: 90%\n bucket 31: 40%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n Entering block accumulator loop for bucket 33:\n bucket 32: 20%\n bucket 33: 10%\n bucket 32: 30%\n bucket 33: 20%\n bucket 32: 40%\n bucket 33: 30%\n bucket 32: 50%\n bucket 33: 40%\n bucket 32: 60%\n bucket 33: 50%\n bucket 32: 70%\n bucket 33: 60%\n bucket 32: 80%\n bucket 33: 70%\n bucket 32: 90%\n bucket 33: 80%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n bucket 35: 10%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 35: 30%\n bucket 34: 50%\n bucket 35: 40%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\nGetting block 36 of 60\n bucket 34: 90%\n bucket 35: 70%\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 34: 100%\n bucket 35: 80%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n Entering block accumulator loop for bucket 36:\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Entering block accumulator loop for bucket 38:\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n bucket 38: 20%\n Entering block accumulator loop for bucket 39:\n bucket 38: 30%\n bucket 39: 10%\n bucket 38: 40%\n bucket 39: 20%\n bucket 38: 50%\n bucket 39: 30%\n bucket 38: 60%\n bucket 39: 40%\n bucket 38: 70%\n bucket 38: 80%\n bucket 39: 50%\n bucket 38: 90%\n bucket 39: 60%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\n bucket 41: 20%\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 41: 50%\n bucket 40: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n bucket 41: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\nGetting block 43 of 60\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 60%\n bucket 42: 70%\n Entering block accumulator loop for bucket 44:\n bucket 42: 80%\n Entering block accumulator loop for bucket 43:\n bucket 42: 90%\n bucket 44: 10%\n bucket 42: 100%\n bucket 43: 10%\n Sorting block of length 119 for bucket 42\n bucket 44: 20%\n (Using difference cover)\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 44: 80%\n bucket 43: 90%\n bucket 44: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n Entering block accumulator loop for bucket 46:\n bucket 45: 20%\n bucket 45: 30%\n bucket 46: 10%\n bucket 45: 40%\n bucket 46: 20%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 46: 40%\n bucket 45: 70%\n bucket 46: 50%\n bucket 45: 80%\n bucket 46: 60%\n bucket 45: 90%\n bucket 46: 70%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n bucket 46: 80%\n bucket 46: 90%\n (Using difference cover)\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n Entering block accumulator loop for bucket 50:\n bucket 49: 50%\n bucket 49: 60%\n bucket 50: 10%\n bucket 49: 70%\n bucket 50: 20%\n bucket 49: 80%\n bucket 50: 30%\n bucket 49: 90%\n bucket 50: 40%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n bucket 51: 20%\n Entering block accumulator loop for bucket 52:\n bucket 51: 30%\n bucket 52: 10%\n bucket 51: 40%\n bucket 52: 20%\n bucket 52: 30%\n bucket 51: 50%\n bucket 52: 40%\n bucket 52: 50%\n bucket 51: 60%\n bucket 52: 60%\n bucket 51: 70%\n bucket 52: 70%\n bucket 51: 80%\n bucket 52: 80%\n bucket 52: 90%\n bucket 51: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n Entering block accumulator loop for bucket 54:\n bucket 53: 20%\n bucket 54: 10%\n bucket 53: 30%\n bucket 54: 20%\n bucket 53: 40%\n bucket 54: 30%\n bucket 53: 50%\n bucket 54: 40%\n bucket 53: 60%\n bucket 54: 50%\n bucket 53: 70%\n bucket 54: 60%\n bucket 54: 70%\n bucket 53: 80%\n bucket 54: 80%\n bucket 53: 90%\n bucket 54: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 56:\n bucket 55: 10%\n bucket 56: 10%\n bucket 55: 20%\n bucket 56: 20%\n bucket 55: 30%\n bucket 56: 30%\n bucket 55: 40%\n bucket 56: 40%\n bucket 55: 50%\n bucket 56: 50%\n bucket 55: 60%\n bucket 56: 60%\n bucket 55: 70%\n bucket 56: 70%\n bucket 55: 80%\n bucket 56: 80%\n bucket 55: 90%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n Entering block accumulator loop for bucket 58:\n bucket 57: 20%\n bucket 57: 30%\n bucket 58: 10%\n bucket 57: 40%\n bucket 57: 50%\n bucket 58: 20%\n bucket 57: 60%\n bucket 58: 30%\n bucket 57: 70%\n bucket 58: 40%\n bucket 57: 80%\n bucket 58: 50%\n bucket 57: 90%\n bucket 57: 100%\n bucket 58: 60%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 59: 20%\n bucket 60: 20%\n bucket 59: 30%\n bucket 60: 30%\n bucket 59: 40%\n bucket 60: 40%\n bucket 59: 50%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n bucket 59: 100%\n (Using difference cover)\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": null, "job_stderr": null, "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 20%\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n bucket 2: 10%\n Calculating Z arrays for bucket 4\n bucket 1: 30%\n Entering block accumulator loop for bucket 3:\n bucket 1: 40%\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 1: 50%\n bucket 3: 10%\n bucket 2: 20%\n bucket 1: 60%\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 5\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 3: 20%\n bucket 1: 70%\n bucket 2: 30%\nGetting block 7 of 60\n Calculating Z arrays for bucket 6\n bucket 5: 10%\n bucket 1: 80%\n bucket 3: 30%\n bucket 2: 40%\n bucket 1: 90%\n bucket 4: 10%\n bucket 2: 50%\nGetting block 8 of 60\n bucket 4: 20%\n bucket 5: 20%\n Reserving size (126) for bucket 8\n bucket 1: 100%\n bucket 4: 30%\n Reserving size (126) for bucket 7\n bucket 2: 60%\n bucket 4: 40%\n bucket 5: 30%\n Calculating Z arrays for bucket 7\n bucket 2: 70%\n bucket 3: 40%\n Calculating Z arrays for bucket 8\n bucket 4: 50%\n bucket 2: 80%\n bucket 5: 40%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Entering block accumulator loop for bucket 7:\n bucket 2: 90%\n bucket 5: 50%\n bucket 3: 50%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 8:\n bucket 2: 100%\n bucket 7: 10%\n bucket 4: 60%\n bucket 5: 60%\n bucket 3: 60%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 7: 20%\n bucket 6: 10%\n bucket 8: 10%\n bucket 5: 70%\n bucket 3: 70%\n bucket 4: 70%\n bucket 6: 20%\n bucket 7: 30%\n bucket 8: 20%\n bucket 5: 80%\n bucket 4: 80%\n bucket 6: 30%\n bucket 7: 40%\n bucket 4: 90%\n bucket 8: 30%\n bucket 3: 80%\n bucket 6: 40%\n bucket 7: 50%\n bucket 4: 100%\n bucket 5: 90%\n bucket 8: 40%\n bucket 3: 90%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 7: 60%\n bucket 8: 50%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 3: 100%\n bucket 6: 50%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 7: 70%\n bucket 6: 60%\n bucket 8: 60%\n bucket 7: 80%\n bucket 6: 70%\n bucket 8: 70%\n bucket 7: 90%\n Sorting block time: 00:00:00\n bucket 6: 80%\n bucket 7: 100%\n bucket 8: 80%\nReturning block of 43 for bucket 1\n Sorting block of length 75 for bucket 7\n bucket 8: 90%\n bucket 6: 90%\n bucket 8: 100%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\nGetting block 11 of 60\n bucket 9: 60%\n bucket 10: 40%\n Reserving size (126) for bucket 11\n bucket 10: 50%\n Calculating Z arrays for bucket 11\n bucket 9: 70%\n bucket 10: 60%\n bucket 9: 80%\n bucket 10: 70%\n Entering block accumulator loop for bucket 11:\n bucket 9: 90%\n bucket 10: 80%\n bucket 11: 10%\n bucket 9: 100%\n bucket 10: 90%\n Sorting block of length 124 for bucket 9\n bucket 11: 20%\n (Using difference cover)\n bucket 10: 100%\n bucket 11: 30%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n bucket 12: 20%\n Entering block accumulator loop for bucket 13:\n bucket 12: 30%\n bucket 13: 10%\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 40%\n bucket 12: 70%\n bucket 13: 50%\n Entering block accumulator loop for bucket 14:\n bucket 12: 80%\n bucket 13: 60%\n bucket 14: 10%\n bucket 12: 90%\n bucket 13: 70%\n bucket 14: 20%\n bucket 12: 100%\n bucket 13: 80%\n bucket 14: 30%\n Sorting block of length 82 for bucket 12\n bucket 13: 90%\n (Using difference cover)\n bucket 14: 40%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 30%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 16:\n bucket 15: 40%\n bucket 16: 10%\n Entering block accumulator loop for bucket 17:\n bucket 15: 50%\n bucket 16: 20%\n bucket 17: 10%\n bucket 15: 60%\n bucket 16: 30%\n bucket 17: 20%\n bucket 16: 40%\n bucket 17: 30%\n bucket 15: 70%\n bucket 16: 50%\n bucket 17: 40%\n bucket 16: 60%\n bucket 15: 80%\n bucket 17: 50%\n bucket 16: 70%\n bucket 15: 90%\n bucket 17: 60%\n bucket 16: 80%\n bucket 15: 100%\n bucket 17: 70%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 90%\n bucket 17: 80%\n bucket 16: 100%\n bucket 17: 90%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 20%\n Entering block accumulator loop for bucket 19:\n bucket 18: 30%\n bucket 19: 10%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 19: 50%\n bucket 19: 60%\n bucket 18: 80%\n bucket 19: 70%\n bucket 18: 90%\n bucket 19: 80%\n bucket 18: 100%\n bucket 19: 90%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\nGetting block 22 of 60\n bucket 20: 10%\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n Entering block accumulator loop for bucket 22:\n bucket 20: 50%\n Entering block accumulator loop for bucket 21:\n bucket 22: 10%\n bucket 20: 60%\n bucket 21: 10%\n bucket 20: 70%\n bucket 22: 20%\n bucket 20: 80%\n bucket 21: 20%\n bucket 22: 30%\n bucket 20: 90%\n bucket 21: 30%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 22: 50%\n bucket 21: 60%\n bucket 22: 60%\n bucket 21: 70%\n bucket 22: 70%\n bucket 21: 80%\n bucket 22: 80%\n bucket 21: 90%\n bucket 22: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 24: 10%\n bucket 23: 30%\n bucket 24: 20%\n bucket 23: 40%\n bucket 24: 30%\n bucket 23: 50%\n bucket 24: 40%\n bucket 23: 60%\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 26\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 25:\n Entering block accumulator loop for bucket 27:\n bucket 25: 10%\n Entering block accumulator loop for bucket 26:\n bucket 27: 10%\n bucket 25: 20%\n bucket 26: 10%\n bucket 27: 20%\n bucket 25: 30%\n bucket 26: 20%\n bucket 27: 30%\n bucket 25: 40%\n bucket 27: 40%\n bucket 26: 30%\n bucket 25: 50%\n bucket 27: 50%\n bucket 26: 40%\n bucket 27: 60%\n bucket 25: 60%\n bucket 27: 70%\n bucket 26: 50%\n bucket 25: 70%\n bucket 27: 80%\n bucket 26: 60%\n bucket 25: 80%\n bucket 26: 70%\n bucket 27: 90%\n bucket 25: 90%\n bucket 26: 80%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\nGetting block 29 of 60\n bucket 28: 100%\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 30%\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 30: 40%\n bucket 30: 50%\n bucket 31: 10%\n bucket 30: 60%\n bucket 31: 20%\n bucket 30: 70%\n bucket 30: 80%\n bucket 31: 30%\n bucket 30: 90%\n bucket 31: 40%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n Entering block accumulator loop for bucket 33:\n bucket 32: 20%\n bucket 33: 10%\n bucket 32: 30%\n bucket 33: 20%\n bucket 32: 40%\n bucket 33: 30%\n bucket 32: 50%\n bucket 33: 40%\n bucket 32: 60%\n bucket 33: 50%\n bucket 32: 70%\n bucket 33: 60%\n bucket 32: 80%\n bucket 33: 70%\n bucket 32: 90%\n bucket 33: 80%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n bucket 35: 10%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 35: 30%\n bucket 34: 50%\n bucket 35: 40%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\nGetting block 36 of 60\n bucket 34: 90%\n bucket 35: 70%\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 34: 100%\n bucket 35: 80%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n Entering block accumulator loop for bucket 36:\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Entering block accumulator loop for bucket 38:\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 10%\n bucket 38: 20%\n Entering block accumulator loop for bucket 39:\n bucket 38: 30%\n bucket 39: 10%\n bucket 38: 40%\n bucket 39: 20%\n bucket 38: 50%\n bucket 39: 30%\n bucket 38: 60%\n bucket 39: 40%\n bucket 38: 70%\n bucket 38: 80%\n bucket 39: 50%\n bucket 38: 90%\n bucket 39: 60%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\n bucket 41: 20%\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 41: 50%\n bucket 40: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n bucket 41: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\nGetting block 43 of 60\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 60%\n bucket 42: 70%\n Entering block accumulator loop for bucket 44:\n bucket 42: 80%\n Entering block accumulator loop for bucket 43:\n bucket 42: 90%\n bucket 44: 10%\n bucket 42: 100%\n bucket 43: 10%\n Sorting block of length 119 for bucket 42\n bucket 44: 20%\n (Using difference cover)\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 44: 30%\n bucket 43: 50%\n bucket 44: 40%\n bucket 43: 60%\n bucket 44: 50%\n bucket 43: 70%\n bucket 44: 60%\n bucket 43: 80%\n bucket 44: 70%\n bucket 44: 80%\n bucket 43: 90%\n bucket 44: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n Entering block accumulator loop for bucket 46:\n bucket 45: 20%\n bucket 45: 30%\n bucket 46: 10%\n bucket 45: 40%\n bucket 46: 20%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 46: 40%\n bucket 45: 70%\n bucket 46: 50%\n bucket 45: 80%\n bucket 46: 60%\n bucket 45: 90%\n bucket 46: 70%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n bucket 46: 80%\n bucket 46: 90%\n (Using difference cover)\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n Entering block accumulator loop for bucket 50:\n bucket 49: 50%\n bucket 49: 60%\n bucket 50: 10%\n bucket 49: 70%\n bucket 50: 20%\n bucket 49: 80%\n bucket 50: 30%\n bucket 49: 90%\n bucket 50: 40%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 10%\n bucket 51: 20%\n Entering block accumulator loop for bucket 52:\n bucket 51: 30%\n bucket 52: 10%\n bucket 51: 40%\n bucket 52: 20%\n bucket 52: 30%\n bucket 51: 50%\n bucket 52: 40%\n bucket 52: 50%\n bucket 51: 60%\n bucket 52: 60%\n bucket 51: 70%\n bucket 52: 70%\n bucket 51: 80%\n bucket 52: 80%\n bucket 52: 90%\n bucket 51: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n Entering block accumulator loop for bucket 54:\n bucket 53: 20%\n bucket 54: 10%\n bucket 53: 30%\n bucket 54: 20%\n bucket 53: 40%\n bucket 54: 30%\n bucket 53: 50%\n bucket 54: 40%\n bucket 53: 60%\n bucket 54: 50%\n bucket 53: 70%\n bucket 54: 60%\n bucket 54: 70%\n bucket 53: 80%\n bucket 54: 80%\n bucket 53: 90%\n bucket 54: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 56:\n bucket 55: 10%\n bucket 56: 10%\n bucket 55: 20%\n bucket 56: 20%\n bucket 55: 30%\n bucket 56: 30%\n bucket 55: 40%\n bucket 56: 40%\n bucket 55: 50%\n bucket 56: 50%\n bucket 55: 60%\n bucket 56: 60%\n bucket 55: 70%\n bucket 56: 70%\n bucket 55: 80%\n bucket 56: 80%\n bucket 55: 90%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n Entering block accumulator loop for bucket 58:\n bucket 57: 20%\n bucket 57: 30%\n bucket 58: 10%\n bucket 57: 40%\n bucket 57: 50%\n bucket 58: 20%\n bucket 57: 60%\n bucket 58: 30%\n bucket 57: 70%\n bucket 58: 40%\n bucket 57: 80%\n bucket 58: 50%\n bucket 57: 90%\n bucket 57: 100%\n bucket 58: 60%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 59: 20%\n bucket 60: 20%\n bucket 59: 30%\n bucket 60: 30%\n bucket 59: 40%\n bucket 60: 40%\n bucket 59: 50%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n bucket 59: 100%\n (Using difference cover)\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, exit_code: None, stderr: Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1, exit_code: None, stderr: Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n."], "status": "failure"}}, {"id": "hisat2/2.2.1+galaxy1-14", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 14, "time_seconds": 33.35663938522339, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "e52d23b342e23023"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "43cae05b4679de4d"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "74ce2bf6b3b2a9b0", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:57:40.315371", "update_time": "2024-08-30T06:57:53.641458", "galaxy_version": "24.1", "external_id": "gxy-2vlzh", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/3/5/d/dataset_35dfd3b8-926f-4cd4-81cc-1b566ce92d90.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/b/a/6/dataset_ba6afe30-d3f2-4308-8e16-1fbe422a9783.dat' > input_f.fasta && seqtk seq -2 '/galaxy/server/database/objects/b/a/6/dataset_ba6afe30-d3f2-4308-8e16-1fbe422a9783.dat' > input_r.fasta && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -f -1 input_f.fasta -2 input_r.fasta | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/a/2/1/dataset_a218d5f9-85d0-48ee-9c16-b7f6941d0efe.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 167, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 166, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "e52d23b342e23023", "src": "hda", "uuid": "35dfd3b8-926f-4cd4-81cc-1b566ce92d90"}, "library|input_1": {"id": "43cae05b4679de4d", "src": "hda", "uuid": "ba6afe30-d3f2-4308-8e16-1fbe422a9783"}}, "outputs": {"output_alignments": {"id": "129ba610e1226a78", "src": "hda", "uuid": "a218d5f9-85d0-48ee-9c16-b7f6941d0efe"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 3 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 2:\nGetting block 5 of 60\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 3\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 5\n bucket 2: 10%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 3:\n bucket 2: 20%\n Calculating Z arrays for bucket 6\nGetting block 8 of 60\n Reserving size (126) for bucket 8\nGetting block 7 of 60\n Entering block accumulator loop for bucket 6:\n bucket 2: 30%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 5:\n bucket 6: 10%\n Calculating Z arrays for bucket 8\n bucket 3: 10%\n bucket 6: 20%\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 4:\n bucket 2: 40%\n bucket 8: 10%\n bucket 1: 10%\n bucket 4: 10%\n bucket 2: 50%\n bucket 6: 30%\n bucket 3: 20%\n bucket 8: 20%\n bucket 1: 20%\n bucket 4: 20%\n Calculating Z arrays for bucket 7\n bucket 6: 40%\n bucket 1: 30%\n bucket 2: 60%\n bucket 5: 10%\n Entering block accumulator loop for bucket 7:\n bucket 6: 50%\n bucket 1: 40%\n bucket 3: 30%\n bucket 6: 60%\n bucket 8: 30%\n bucket 5: 20%\n bucket 6: 70%\n bucket 3: 40%\n bucket 2: 70%\n bucket 4: 30%\n bucket 6: 80%\n bucket 1: 50%\n bucket 2: 80%\n bucket 3: 50%\n bucket 4: 40%\n bucket 1: 60%\n bucket 6: 90%\n bucket 2: 90%\n bucket 3: 60%\n bucket 6: 100%\n bucket 7: 10%\n bucket 2: 100%\n bucket 5: 30%\n bucket 3: 70%\n bucket 8: 40%\n bucket 1: 70%\n bucket 4: 50%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 7: 20%\n bucket 3: 80%\n bucket 1: 80%\n bucket 8: 50%\n bucket 4: 60%\n bucket 8: 60%\n bucket 1: 90%\n bucket 8: 70%\n bucket 5: 40%\n bucket 8: 80%\n bucket 4: 70%\n bucket 1: 100%\n bucket 8: 90%\n bucket 5: 50%\n bucket 4: 80%\n bucket 7: 30%\n bucket 8: 100%\n bucket 3: 90%\n bucket 7: 40%\n bucket 4: 90%\n Sorting block of length 42 for bucket 1\n bucket 7: 50%\n (Using difference cover)\n bucket 3: 100%\n bucket 4: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 5: 60%\n bucket 7: 60%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n bucket 7: 70%\n bucket 5: 70%\n (Using difference cover)\n bucket 7: 80%\n bucket 5: 80%\n bucket 7: 90%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\n Entering block accumulator loop for bucket 10:\nReturning block of 125 for bucket 9\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 12:\n bucket 11: 10%\n bucket 12: 10%\n bucket 11: 20%\n bucket 12: 20%\n bucket 11: 30%\n bucket 12: 30%\n bucket 11: 40%\n bucket 12: 40%\n bucket 11: 50%\n bucket 12: 50%\n bucket 11: 60%\n bucket 12: 60%\n bucket 11: 70%\n bucket 12: 70%\n bucket 11: 80%\n bucket 12: 80%\n bucket 11: 90%\n bucket 12: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Entering block accumulator loop for bucket 13:\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 13: 10%\n Entering block accumulator loop for bucket 14:\n bucket 13: 20%\n bucket 14: 10%\n Entering block accumulator loop for bucket 15:\n bucket 14: 20%\n bucket 13: 30%\n bucket 14: 30%\n bucket 15: 10%\n bucket 13: 40%\n bucket 14: 40%\n bucket 15: 20%\n bucket 14: 50%\n bucket 13: 50%\n bucket 15: 30%\n bucket 14: 60%\n bucket 13: 60%\n bucket 14: 70%\n bucket 15: 40%\n bucket 13: 70%\n bucket 14: 80%\n bucket 15: 50%\n bucket 14: 90%\n bucket 13: 80%\n bucket 15: 60%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 13: 90%\n bucket 15: 70%\n bucket 13: 100%\n bucket 15: 80%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\nGetting block 17 of 60\nGetting block 18 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n Entering block accumulator loop for bucket 17:\n bucket 18: 10%\n bucket 17: 10%\n bucket 18: 20%\n bucket 17: 20%\n bucket 17: 30%\n Sorting block time: 00:00:00\n bucket 17: 40%\nReturning block of 101 for bucket 16\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n Entering block accumulator loop for bucket 20:\n bucket 19: 60%\n bucket 19: 70%\n bucket 20: 10%\n bucket 19: 80%\n bucket 20: 20%\n bucket 19: 90%\n bucket 19: 100%\n bucket 20: 30%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Entering block accumulator loop for bucket 21:\n Calculating Z arrays for bucket 22\n bucket 21: 10%\n Entering block accumulator loop for bucket 22:\n bucket 21: 20%\n bucket 22: 10%\n bucket 21: 30%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 20%\n bucket 21: 40%\n bucket 22: 30%\n Entering block accumulator loop for bucket 23:\n bucket 21: 50%\n bucket 22: 40%\n bucket 23: 10%\n bucket 21: 60%\n bucket 22: 50%\n bucket 23: 20%\n bucket 21: 70%\n bucket 22: 60%\n bucket 23: 30%\n bucket 21: 80%\n bucket 22: 70%\n bucket 23: 40%\n bucket 21: 90%\n bucket 22: 80%\n bucket 23: 50%\n bucket 21: 100%\n bucket 22: 90%\n Sorting block of length 54 for bucket 21\n bucket 23: 60%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 70%\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 20%\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 24: 30%\n bucket 25: 20%\n bucket 24: 40%\n bucket 25: 30%\n bucket 25: 40%\n bucket 24: 50%\n bucket 25: 50%\n bucket 24: 60%\n bucket 25: 60%\n bucket 25: 70%\n bucket 24: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 24: 80%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n bucket 26: 90%\n Calculating Z arrays for bucket 27\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\nGetting block 30 of 60\n bucket 29: 60%\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 70%\n Entering block accumulator loop for bucket 30:\n bucket 29: 80%\n bucket 30: 10%\n bucket 29: 90%\n bucket 30: 20%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 33:\n Entering block accumulator loop for bucket 32:\n bucket 33: 10%\n bucket 32: 10%\n bucket 33: 20%\n bucket 32: 20%\n bucket 33: 30%\n bucket 32: 30%\n bucket 33: 40%\n bucket 32: 40%\n bucket 33: 50%\n bucket 32: 50%\n bucket 33: 60%\n bucket 32: 60%\n bucket 33: 70%\n bucket 32: 70%\n bucket 33: 80%\n bucket 32: 80%\n bucket 33: 90%\n bucket 32: 90%\n bucket 33: 100%\n bucket 32: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n Entering block accumulator loop for bucket 35:\n bucket 34: 60%\n bucket 34: 70%\n bucket 35: 10%\n bucket 34: 80%\n bucket 35: 20%\n bucket 34: 90%\n bucket 35: 30%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n bucket 36: 20%\n Calculating Z arrays for bucket 37\n bucket 36: 30%\n bucket 36: 40%\n Entering block accumulator loop for bucket 37:\n bucket 36: 50%\n bucket 36: 60%\n bucket 37: 10%\n bucket 36: 70%\n bucket 37: 20%\n bucket 36: 80%\n bucket 37: 30%\n bucket 36: 90%\n bucket 37: 40%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n bucket 37: 50%\n (Using difference cover)\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 39:\n bucket 38: 10%\n bucket 39: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 39: 20%\n bucket 38: 40%\n bucket 38: 50%\n bucket 39: 30%\n bucket 38: 60%\n bucket 39: 40%\n bucket 38: 70%\n bucket 39: 50%\n bucket 38: 80%\n bucket 39: 60%\n bucket 38: 90%\n bucket 39: 70%\n bucket 38: 100%\n bucket 39: 80%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\n bucket 41: 20%\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 41: 50%\n bucket 40: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n bucket 41: 90%\n bucket 40: 100%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 43:\n Entering block accumulator loop for bucket 42:\n bucket 43: 10%\n bucket 42: 10%\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n bucket 43: 20%\n bucket 42: 20%\n bucket 43: 30%\n Entering block accumulator loop for bucket 44:\n bucket 42: 30%\n bucket 43: 40%\n bucket 44: 10%\n bucket 42: 40%\n bucket 43: 50%\n bucket 44: 20%\n bucket 42: 50%\n bucket 43: 60%\n bucket 44: 30%\n bucket 42: 60%\n bucket 43: 70%\n bucket 44: 40%\n bucket 42: 70%\n bucket 43: 80%\n bucket 44: 50%\n bucket 43: 90%\n bucket 42: 80%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 60%\n bucket 42: 90%\n bucket 44: 70%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n bucket 45: 20%\n Entering block accumulator loop for bucket 46:\n bucket 45: 30%\n bucket 46: 10%\n bucket 45: 40%\n bucket 46: 20%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 46: 40%\n bucket 45: 70%\n bucket 46: 50%\n bucket 45: 80%\n bucket 46: 60%\n bucket 45: 90%\n bucket 46: 70%\n bucket 45: 100%\n bucket 46: 80%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n Entering block accumulator loop for bucket 49:\n bucket 48: 20%\n bucket 49: 10%\n bucket 48: 30%\n bucket 49: 20%\n bucket 48: 40%\n bucket 49: 30%\n bucket 48: 50%\n bucket 49: 40%\n bucket 48: 60%\n bucket 49: 50%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n bucket 49: 60%\n Calculating Z arrays for bucket 50\n bucket 48: 70%\n bucket 49: 70%\n bucket 49: 80%\n Entering block accumulator loop for bucket 50:\n bucket 48: 80%\n bucket 49: 90%\n bucket 50: 10%\n bucket 48: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 20%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n Entering block accumulator loop for bucket 52:\n bucket 51: 80%\n bucket 52: 10%\n bucket 51: 90%\n bucket 52: 20%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 30%\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 20%\n bucket 53: 30%\n Entering block accumulator loop for bucket 54:\n bucket 53: 40%\n bucket 54: 10%\n bucket 53: 50%\n bucket 54: 20%\n bucket 53: 60%\n bucket 54: 30%\n bucket 53: 70%\n bucket 54: 40%\n bucket 53: 80%\n bucket 54: 50%\n bucket 53: 90%\n bucket 54: 60%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\nGetting block 56 of 60\n bucket 55: 60%\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 70%\n bucket 55: 80%\n Entering block accumulator loop for bucket 56:\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 50%\n bucket 57: 60%\n Entering block accumulator loop for bucket 58:\n bucket 57: 70%\n bucket 58: 10%\n bucket 57: 80%\n bucket 58: 20%\n bucket 57: 90%\n bucket 58: 30%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Entering block accumulator loop for bucket 59:\n Calculating Z arrays for bucket 60\n bucket 59: 10%\n Entering block accumulator loop for bucket 60:\n bucket 59: 20%\n bucket 60: 10%\n bucket 59: 30%\n bucket 60: 20%\n bucket 60: 30%\n bucket 59: 40%\n bucket 60: 40%\n bucket 59: 50%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 59: 80%\n bucket 60: 80%\n bucket 59: 90%\n bucket 60: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 3 (30.00%) aligned concordantly 0 times\n 7 (70.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 3 (50.00%) aligned 0 times\n 3 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n85.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 3 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 2:\nGetting block 5 of 60\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 3\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 5\n bucket 2: 10%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 3:\n bucket 2: 20%\n Calculating Z arrays for bucket 6\nGetting block 8 of 60\n Reserving size (126) for bucket 8\nGetting block 7 of 60\n Entering block accumulator loop for bucket 6:\n bucket 2: 30%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 5:\n bucket 6: 10%\n Calculating Z arrays for bucket 8\n bucket 3: 10%\n bucket 6: 20%\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 8:\n Entering block accumulator loop for bucket 4:\n bucket 2: 40%\n bucket 8: 10%\n bucket 1: 10%\n bucket 4: 10%\n bucket 2: 50%\n bucket 6: 30%\n bucket 3: 20%\n bucket 8: 20%\n bucket 1: 20%\n bucket 4: 20%\n Calculating Z arrays for bucket 7\n bucket 6: 40%\n bucket 1: 30%\n bucket 2: 60%\n bucket 5: 10%\n Entering block accumulator loop for bucket 7:\n bucket 6: 50%\n bucket 1: 40%\n bucket 3: 30%\n bucket 6: 60%\n bucket 8: 30%\n bucket 5: 20%\n bucket 6: 70%\n bucket 3: 40%\n bucket 2: 70%\n bucket 4: 30%\n bucket 6: 80%\n bucket 1: 50%\n bucket 2: 80%\n bucket 3: 50%\n bucket 4: 40%\n bucket 1: 60%\n bucket 6: 90%\n bucket 2: 90%\n bucket 3: 60%\n bucket 6: 100%\n bucket 7: 10%\n bucket 2: 100%\n bucket 5: 30%\n bucket 3: 70%\n bucket 8: 40%\n bucket 1: 70%\n bucket 4: 50%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 7: 20%\n bucket 3: 80%\n bucket 1: 80%\n bucket 8: 50%\n bucket 4: 60%\n bucket 8: 60%\n bucket 1: 90%\n bucket 8: 70%\n bucket 5: 40%\n bucket 8: 80%\n bucket 4: 70%\n bucket 1: 100%\n bucket 8: 90%\n bucket 5: 50%\n bucket 4: 80%\n bucket 7: 30%\n bucket 8: 100%\n bucket 3: 90%\n bucket 7: 40%\n bucket 4: 90%\n Sorting block of length 42 for bucket 1\n bucket 7: 50%\n (Using difference cover)\n bucket 3: 100%\n bucket 4: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 5: 60%\n bucket 7: 60%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n bucket 7: 70%\n bucket 5: 70%\n (Using difference cover)\n bucket 7: 80%\n bucket 5: 80%\n bucket 7: 90%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\n Entering block accumulator loop for bucket 10:\nReturning block of 125 for bucket 9\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n Entering block accumulator loop for bucket 12:\n bucket 11: 10%\n bucket 12: 10%\n bucket 11: 20%\n bucket 12: 20%\n bucket 11: 30%\n bucket 12: 30%\n bucket 11: 40%\n bucket 12: 40%\n bucket 11: 50%\n bucket 12: 50%\n bucket 11: 60%\n bucket 12: 60%\n bucket 11: 70%\n bucket 12: 70%\n bucket 11: 80%\n bucket 12: 80%\n bucket 11: 90%\n bucket 12: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Entering block accumulator loop for bucket 13:\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 13: 10%\n Entering block accumulator loop for bucket 14:\n bucket 13: 20%\n bucket 14: 10%\n Entering block accumulator loop for bucket 15:\n bucket 14: 20%\n bucket 13: 30%\n bucket 14: 30%\n bucket 15: 10%\n bucket 13: 40%\n bucket 14: 40%\n bucket 15: 20%\n bucket 14: 50%\n bucket 13: 50%\n bucket 15: 30%\n bucket 14: 60%\n bucket 13: 60%\n bucket 14: 70%\n bucket 15: 40%\n bucket 13: 70%\n bucket 14: 80%\n bucket 15: 50%\n bucket 14: 90%\n bucket 13: 80%\n bucket 15: 60%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 13: 90%\n bucket 15: 70%\n bucket 13: 100%\n bucket 15: 80%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\nGetting block 17 of 60\nGetting block 18 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n Entering block accumulator loop for bucket 17:\n bucket 18: 10%\n bucket 17: 10%\n bucket 18: 20%\n bucket 17: 20%\n bucket 17: 30%\n Sorting block time: 00:00:00\n bucket 17: 40%\nReturning block of 101 for bucket 16\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n Entering block accumulator loop for bucket 20:\n bucket 19: 60%\n bucket 19: 70%\n bucket 20: 10%\n bucket 19: 80%\n bucket 20: 20%\n bucket 19: 90%\n bucket 19: 100%\n bucket 20: 30%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Entering block accumulator loop for bucket 21:\n Calculating Z arrays for bucket 22\n bucket 21: 10%\n Entering block accumulator loop for bucket 22:\n bucket 21: 20%\n bucket 22: 10%\n bucket 21: 30%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 20%\n bucket 21: 40%\n bucket 22: 30%\n Entering block accumulator loop for bucket 23:\n bucket 21: 50%\n bucket 22: 40%\n bucket 23: 10%\n bucket 21: 60%\n bucket 22: 50%\n bucket 23: 20%\n bucket 21: 70%\n bucket 22: 60%\n bucket 23: 30%\n bucket 21: 80%\n bucket 22: 70%\n bucket 23: 40%\n bucket 21: 90%\n bucket 22: 80%\n bucket 23: 50%\n bucket 21: 100%\n bucket 22: 90%\n Sorting block of length 54 for bucket 21\n bucket 23: 60%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 70%\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 20%\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 24: 30%\n bucket 25: 20%\n bucket 24: 40%\n bucket 25: 30%\n bucket 25: 40%\n bucket 24: 50%\n bucket 25: 50%\n bucket 24: 60%\n bucket 25: 60%\n bucket 25: 70%\n bucket 24: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 24: 80%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n bucket 26: 90%\n Calculating Z arrays for bucket 27\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\nGetting block 30 of 60\n bucket 29: 60%\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 70%\n Entering block accumulator loop for bucket 30:\n bucket 29: 80%\n bucket 30: 10%\n bucket 29: 90%\n bucket 30: 20%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 33:\n Entering block accumulator loop for bucket 32:\n bucket 33: 10%\n bucket 32: 10%\n bucket 33: 20%\n bucket 32: 20%\n bucket 33: 30%\n bucket 32: 30%\n bucket 33: 40%\n bucket 32: 40%\n bucket 33: 50%\n bucket 32: 50%\n bucket 33: 60%\n bucket 32: 60%\n bucket 33: 70%\n bucket 32: 70%\n bucket 33: 80%\n bucket 32: 80%\n bucket 33: 90%\n bucket 32: 90%\n bucket 33: 100%\n bucket 32: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n Entering block accumulator loop for bucket 35:\n bucket 34: 60%\n bucket 34: 70%\n bucket 35: 10%\n bucket 34: 80%\n bucket 35: 20%\n bucket 34: 90%\n bucket 35: 30%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n bucket 36: 20%\n Calculating Z arrays for bucket 37\n bucket 36: 30%\n bucket 36: 40%\n Entering block accumulator loop for bucket 37:\n bucket 36: 50%\n bucket 36: 60%\n bucket 37: 10%\n bucket 36: 70%\n bucket 37: 20%\n bucket 36: 80%\n bucket 37: 30%\n bucket 36: 90%\n bucket 37: 40%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n bucket 37: 50%\n (Using difference cover)\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n Entering block accumulator loop for bucket 39:\n bucket 38: 10%\n bucket 39: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 39: 20%\n bucket 38: 40%\n bucket 38: 50%\n bucket 39: 30%\n bucket 38: 60%\n bucket 39: 40%\n bucket 38: 70%\n bucket 39: 50%\n bucket 38: 80%\n bucket 39: 60%\n bucket 38: 90%\n bucket 39: 70%\n bucket 38: 100%\n bucket 39: 80%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\n bucket 41: 20%\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 41: 50%\n bucket 40: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 40: 90%\n bucket 41: 90%\n bucket 40: 100%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 43:\n Entering block accumulator loop for bucket 42:\n bucket 43: 10%\n bucket 42: 10%\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n bucket 43: 20%\n bucket 42: 20%\n bucket 43: 30%\n Entering block accumulator loop for bucket 44:\n bucket 42: 30%\n bucket 43: 40%\n bucket 44: 10%\n bucket 42: 40%\n bucket 43: 50%\n bucket 44: 20%\n bucket 42: 50%\n bucket 43: 60%\n bucket 44: 30%\n bucket 42: 60%\n bucket 43: 70%\n bucket 44: 40%\n bucket 42: 70%\n bucket 43: 80%\n bucket 44: 50%\n bucket 43: 90%\n bucket 42: 80%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 60%\n bucket 42: 90%\n bucket 44: 70%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n bucket 45: 20%\n Entering block accumulator loop for bucket 46:\n bucket 45: 30%\n bucket 46: 10%\n bucket 45: 40%\n bucket 46: 20%\n bucket 45: 50%\n bucket 46: 30%\n bucket 45: 60%\n bucket 46: 40%\n bucket 45: 70%\n bucket 46: 50%\n bucket 45: 80%\n bucket 46: 60%\n bucket 45: 90%\n bucket 46: 70%\n bucket 45: 100%\n bucket 46: 80%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n Entering block accumulator loop for bucket 49:\n bucket 48: 20%\n bucket 49: 10%\n bucket 48: 30%\n bucket 49: 20%\n bucket 48: 40%\n bucket 49: 30%\n bucket 48: 50%\n bucket 49: 40%\n bucket 48: 60%\n bucket 49: 50%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n bucket 49: 60%\n Calculating Z arrays for bucket 50\n bucket 48: 70%\n bucket 49: 70%\n bucket 49: 80%\n Entering block accumulator loop for bucket 50:\n bucket 48: 80%\n bucket 49: 90%\n bucket 50: 10%\n bucket 48: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 20%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n Entering block accumulator loop for bucket 52:\n bucket 51: 80%\n bucket 52: 10%\n bucket 51: 90%\n bucket 52: 20%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 30%\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 20%\n bucket 53: 30%\n Entering block accumulator loop for bucket 54:\n bucket 53: 40%\n bucket 54: 10%\n bucket 53: 50%\n bucket 54: 20%\n bucket 53: 60%\n bucket 54: 30%\n bucket 53: 70%\n bucket 54: 40%\n bucket 53: 80%\n bucket 54: 50%\n bucket 53: 90%\n bucket 54: 60%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\nGetting block 56 of 60\n bucket 55: 60%\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 70%\n bucket 55: 80%\n Entering block accumulator loop for bucket 56:\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 50%\n bucket 57: 60%\n Entering block accumulator loop for bucket 58:\n bucket 57: 70%\n bucket 58: 10%\n bucket 57: 80%\n bucket 58: 20%\n bucket 57: 90%\n bucket 58: 30%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Entering block accumulator loop for bucket 59:\n Calculating Z arrays for bucket 60\n bucket 59: 10%\n Entering block accumulator loop for bucket 60:\n bucket 59: 20%\n bucket 60: 10%\n bucket 59: 30%\n bucket 60: 20%\n bucket 60: 30%\n bucket 59: 40%\n bucket 60: 40%\n bucket 59: 50%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 59: 80%\n bucket 60: 80%\n bucket 59: 90%\n bucket 60: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 3 (30.00%) aligned concordantly 0 times\n 7 (70.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 3 (50.00%) aligned 0 times\n 3 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n85.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:57:42", "plugin": "core", "name": "end_epoch", "raw_value": "1725001062.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:57:42", "plugin": "core", "name": "start_epoch", "raw_value": "1725001062.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-14", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 14, "time_seconds": 34.777429819107056, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "5a36e3f3b94568a8"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "d46d1e7994f19126"}, "library|type": "paired_interleaved"}, "job": {"model_class": "Job", "id": "1f2589c0628914d3", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:06:20.727900", "update_time": "2024-08-30T07:06:34.180590", "galaxy_version": "24.1", "external_id": "gxy-84crx", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/0/c/6/dataset_0c6d0aa2-635a-4f2e-be2e-3e3bcbcd693c.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/9/7/f/dataset_97f11fd1-010d-4603-a6be-04e21b4995a0.dat' > input_f.fasta && seqtk seq -2 '/galaxy/server/database/objects/9/7/f/dataset_97f11fd1-010d-4603-a6be-04e21b4995a0.dat' > input_r.fasta && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -f -1 input_f.fasta -2 input_r.fasta | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/6/4/b/dataset_64bdbb1f-cba0-417a-bf5e-7ac784cc53f3.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 226, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 225, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "5a36e3f3b94568a8", "src": "hda", "uuid": "0c6d0aa2-635a-4f2e-be2e-3e3bcbcd693c"}, "library|input_1": {"id": "d46d1e7994f19126", "src": "hda", "uuid": "97f11fd1-010d-4603-a6be-04e21b4995a0"}}, "outputs": {"output_alignments": {"id": "e21ca87e47d02737", "src": "hda", "uuid": "64bdbb1f-cba0-417a-bf5e-7ac784cc53f3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\nGetting block 4 of 60\n bucket 2: 10%\n bucket 1: 10%\n Reserving size (126) for bucket 3\n bucket 1: 20%\n bucket 2: 20%\n Calculating Z arrays for bucket 3\nGetting block 5 of 60\n Reserving size (126) for bucket 5\nGetting block 6 of 60\n Reserving size (126) for bucket 4\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 6\n bucket 2: 30%\nGetting block 7 of 60\nGetting block 8 of 60\n Entering block accumulator loop for bucket 6:\n Reserving size (126) for bucket 7\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 3:\n bucket 1: 30%\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 5:\n bucket 2: 40%\n bucket 1: 40%\n Calculating Z arrays for bucket 7\n bucket 5: 10%\n bucket 1: 50%\n bucket 2: 50%\n bucket 4: 10%\n bucket 3: 10%\n bucket 1: 60%\n Entering block accumulator loop for bucket 7:\n bucket 2: 60%\n bucket 3: 20%\n bucket 6: 10%\n bucket 4: 20%\n bucket 1: 70%\n Reserving size (126) for bucket 8\n bucket 1: 80%\n bucket 5: 20%\n bucket 3: 30%\n bucket 6: 20%\n Calculating Z arrays for bucket 8\n bucket 7: 10%\n bucket 1: 90%\n bucket 2: 70%\n bucket 4: 30%\n bucket 7: 20%\n bucket 5: 30%\n bucket 2: 80%\n bucket 3: 40%\n bucket 4: 40%\n bucket 7: 30%\n bucket 6: 30%\n bucket 3: 50%\n bucket 5: 40%\n bucket 6: 40%\n bucket 1: 100%\n bucket 2: 90%\n bucket 7: 40%\n bucket 5: 50%\n Entering block accumulator loop for bucket 8:\n bucket 7: 50%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 4: 50%\n bucket 7: 60%\n bucket 6: 50%\n bucket 4: 60%\n bucket 8: 10%\n bucket 2: 100%\n bucket 5: 60%\n bucket 7: 70%\n bucket 3: 60%\n bucket 5: 70%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 6: 60%\n bucket 5: 80%\n bucket 3: 70%\n bucket 7: 80%\n bucket 4: 70%\n bucket 5: 90%\n bucket 3: 80%\n bucket 4: 80%\n bucket 8: 20%\n bucket 7: 90%\n bucket 4: 90%\n bucket 5: 100%\n bucket 3: 90%\n bucket 4: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 100%\n bucket 8: 30%\n bucket 3: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 6: 70%\n bucket 8: 40%\n bucket 6: 80%\n bucket 8: 50%\n bucket 6: 90%\n bucket 8: 60%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\nGetting block 12 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 11:\n bucket 12: 10%\n bucket 11: 10%\n bucket 12: 20%\n bucket 11: 20%\n bucket 12: 30%\n bucket 11: 30%\n bucket 12: 40%\n bucket 11: 40%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n bucket 12: 50%\n Calculating Z arrays for bucket 13\n bucket 11: 50%\n bucket 12: 60%\n bucket 11: 60%\n bucket 12: 70%\n bucket 11: 70%\n Entering block accumulator loop for bucket 13:\n bucket 12: 80%\n bucket 11: 80%\n bucket 13: 10%\n bucket 12: 90%\n bucket 11: 90%\n bucket 13: 20%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 30%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n bucket 14: 40%\n Calculating Z arrays for bucket 15\n bucket 14: 50%\n bucket 14: 60%\n Entering block accumulator loop for bucket 15:\n bucket 14: 70%\n bucket 15: 10%\n bucket 14: 80%\n bucket 15: 20%\n bucket 14: 90%\n bucket 15: 30%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 40%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 50%\n bucket 15: 60%\n Entering block accumulator loop for bucket 16:\n bucket 15: 70%\n Sorting block time: 00:00:00\n bucket 16: 10%\nReturning block of 83 for bucket 14\n bucket 15: 80%\n bucket 16: 20%\n bucket 15: 90%\n bucket 16: 30%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\nGetting block 20 of 60\n Entering block accumulator loop for bucket 19:\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 19: 40%\n bucket 20: 20%\n bucket 19: 50%\n Sorting block time: 00:00:00\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nReturning block of 123 for bucket 18\n bucket 19: 60%\n bucket 20: 30%\n bucket 19: 70%\n bucket 20: 40%\n Entering block accumulator loop for bucket 21:\n bucket 19: 80%\n bucket 20: 50%\n bucket 19: 90%\n bucket 21: 10%\n bucket 20: 60%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n bucket 20: 70%\n bucket 21: 20%\n (Using difference cover)\n bucket 20: 80%\n bucket 21: 30%\n bucket 20: 90%\n bucket 21: 40%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 80%\n bucket 22: 90%\n Entering block accumulator loop for bucket 23:\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 60%\n bucket 23: 70%\n Entering block accumulator loop for bucket 24:\n bucket 23: 80%\n bucket 24: 10%\n bucket 23: 90%\n bucket 24: 20%\n Sorting block time: 00:00:00\n bucket 23: 100%\n bucket 24: 30%\nReturning block of 81 for bucket 22\n bucket 24: 40%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n Sorting block time: 00:00:00\n bucket 26: 60%\nReturning block of 67 for bucket 25\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 60%\n bucket 27: 70%\n Entering block accumulator loop for bucket 28:\n bucket 27: 80%\n bucket 27: 90%\n bucket 28: 10%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 20%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 30%\n bucket 28: 40%\n Entering block accumulator loop for bucket 29:\n bucket 28: 50%\n bucket 28: 60%\n bucket 29: 10%\n bucket 28: 70%\n bucket 28: 80%\n bucket 29: 20%\n bucket 28: 90%\n Sorting block time: 00:00:00\n bucket 29: 30%\nReturning block of 120 for bucket 27\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 80%\n Calculating Z arrays for bucket 31\n bucket 30: 90%\n Entering block accumulator loop for bucket 31:\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n bucket 32: 10%\n Calculating Z arrays for bucket 33\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 30%\n bucket 32: 40%\n bucket 33: 10%\n bucket 32: 50%\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n bucket 32: 60%\n bucket 33: 20%\n Calculating Z arrays for bucket 34\n bucket 32: 70%\n bucket 33: 30%\n Entering block accumulator loop for bucket 34:\n bucket 33: 40%\n bucket 32: 80%\n bucket 34: 10%\n bucket 32: 90%\n bucket 33: 50%\n bucket 34: 20%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 60%\n bucket 34: 30%\n bucket 33: 70%\n bucket 34: 40%\n bucket 33: 80%\n bucket 34: 50%\n bucket 33: 90%\n bucket 34: 60%\n bucket 33: 100%\n bucket 34: 70%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Entering block accumulator loop for bucket 35:\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Entering block accumulator loop for bucket 36:\n Reserving size (126) for bucket 37\n bucket 35: 10%\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n bucket 35: 20%\n bucket 36: 20%\n Entering block accumulator loop for bucket 37:\n bucket 35: 30%\n bucket 36: 30%\n bucket 35: 40%\n bucket 36: 40%\n bucket 37: 10%\n bucket 35: 50%\n bucket 36: 50%\n bucket 37: 20%\n bucket 36: 60%\n bucket 35: 60%\n bucket 37: 30%\n bucket 36: 70%\n bucket 37: 40%\n bucket 36: 80%\n bucket 35: 70%\n bucket 37: 50%\n bucket 36: 90%\n bucket 37: 60%\n bucket 35: 80%\n bucket 36: 100%\n bucket 37: 70%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 35: 90%\n bucket 37: 80%\n bucket 35: 100%\n bucket 37: 90%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n bucket 39: 60%\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\nGetting block 42 of 60\n bucket 41: 20%\n Reserving size (126) for bucket 42\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 40: 60%\n Calculating Z arrays for bucket 42\n bucket 40: 70%\n bucket 41: 50%\n bucket 40: 80%\n Entering block accumulator loop for bucket 42:\n bucket 41: 60%\n bucket 40: 90%\n bucket 41: 70%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 42: 10%\n bucket 41: 80%\n bucket 42: 20%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Entering block accumulator loop for bucket 43:\n Calculating Z arrays for bucket 44\n bucket 43: 10%\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 43: 20%\n Entering block accumulator loop for bucket 44:\n bucket 43: 30%\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 44: 10%\n bucket 43: 40%\n Entering block accumulator loop for bucket 45:\nGetting block 47 of 60\n bucket 43: 50%\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 46:\n bucket 43: 60%\n bucket 45: 10%\n bucket 46: 10%\n Entering block accumulator loop for bucket 47:\n bucket 43: 70%\n bucket 45: 20%\n bucket 46: 20%\n bucket 44: 20%\n bucket 47: 10%\n bucket 46: 30%\n bucket 43: 80%\n bucket 44: 30%\n bucket 46: 40%\n bucket 47: 20%\n bucket 43: 90%\n bucket 45: 30%\n bucket 44: 40%\n bucket 47: 30%\n bucket 46: 50%\n bucket 43: 100%\n bucket 44: 50%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 46: 60%\n bucket 45: 40%\n bucket 44: 60%\n bucket 46: 70%\n bucket 47: 40%\n bucket 44: 70%\n bucket 45: 50%\n bucket 46: 80%\n bucket 44: 80%\n bucket 47: 50%\n bucket 46: 90%\n bucket 45: 60%\n bucket 44: 90%\n bucket 47: 60%\n bucket 46: 100%\n bucket 45: 70%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 44: 100%\n bucket 47: 70%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 80%\n bucket 47: 80%\n Sorting block time: 00:00:00\n bucket 45: 90%\nReturning block of 122 for bucket 43\n bucket 47: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n Entering block accumulator loop for bucket 49:\n bucket 48: 20%\n bucket 49: 10%\n bucket 48: 30%\n bucket 49: 20%\n bucket 48: 40%\n bucket 49: 30%\n bucket 48: 50%\n bucket 49: 40%\n bucket 48: 60%\n bucket 49: 50%\n bucket 48: 70%\n bucket 49: 60%\n bucket 48: 80%\n bucket 49: 70%\n bucket 48: 90%\n bucket 49: 80%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n Entering block accumulator loop for bucket 51:\n bucket 50: 20%\n bucket 51: 10%\n bucket 50: 30%\n bucket 51: 20%\n bucket 50: 40%\n bucket 51: 30%\n bucket 50: 50%\n bucket 50: 60%\n bucket 51: 40%\n bucket 50: 70%\n bucket 51: 50%\n bucket 50: 80%\n bucket 51: 60%\n bucket 50: 90%\n bucket 51: 70%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n Entering block accumulator loop for bucket 53:\n bucket 52: 20%\n bucket 53: 10%\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 20%\n bucket 52: 30%\n bucket 53: 30%\n bucket 52: 40%\n Entering block accumulator loop for bucket 54:\n bucket 53: 40%\n bucket 52: 50%\n bucket 54: 10%\n bucket 53: 50%\n bucket 54: 20%\n bucket 53: 60%\n bucket 52: 60%\n bucket 54: 30%\n bucket 53: 70%\n bucket 52: 70%\n bucket 54: 40%\n bucket 53: 80%\n bucket 52: 80%\n bucket 54: 50%\n bucket 53: 90%\n bucket 52: 90%\n bucket 54: 60%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 70%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n Entering block accumulator loop for bucket 57:\n bucket 56: 20%\n bucket 57: 10%\n bucket 56: 30%\n bucket 57: 20%\n bucket 56: 40%\n bucket 57: 30%\n bucket 56: 50%\n bucket 57: 40%\n bucket 56: 60%\n bucket 57: 50%\n bucket 56: 70%\n bucket 57: 60%\n bucket 56: 80%\n bucket 57: 70%\n bucket 56: 90%\n bucket 57: 80%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Entering block accumulator loop for bucket 58:\n Calculating Z arrays for bucket 59\n bucket 58: 10%\n Entering block accumulator loop for bucket 59:\n bucket 58: 20%\n bucket 58: 30%\n bucket 59: 10%\n bucket 58: 40%\n bucket 59: 20%\n bucket 58: 50%\n bucket 58: 60%\n bucket 59: 30%\n bucket 58: 70%\n bucket 59: 40%\n bucket 58: 80%\n bucket 59: 50%\n bucket 58: 90%\n bucket 59: 60%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 3 (30.00%) aligned concordantly 0 times\n 7 (70.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 3 (50.00%) aligned 0 times\n 3 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n85.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\nGetting block 4 of 60\n bucket 2: 10%\n bucket 1: 10%\n Reserving size (126) for bucket 3\n bucket 1: 20%\n bucket 2: 20%\n Calculating Z arrays for bucket 3\nGetting block 5 of 60\n Reserving size (126) for bucket 5\nGetting block 6 of 60\n Reserving size (126) for bucket 4\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 6\n bucket 2: 30%\nGetting block 7 of 60\nGetting block 8 of 60\n Entering block accumulator loop for bucket 6:\n Reserving size (126) for bucket 7\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 3:\n bucket 1: 30%\n Entering block accumulator loop for bucket 4:\n Entering block accumulator loop for bucket 5:\n bucket 2: 40%\n bucket 1: 40%\n Calculating Z arrays for bucket 7\n bucket 5: 10%\n bucket 1: 50%\n bucket 2: 50%\n bucket 4: 10%\n bucket 3: 10%\n bucket 1: 60%\n Entering block accumulator loop for bucket 7:\n bucket 2: 60%\n bucket 3: 20%\n bucket 6: 10%\n bucket 4: 20%\n bucket 1: 70%\n Reserving size (126) for bucket 8\n bucket 1: 80%\n bucket 5: 20%\n bucket 3: 30%\n bucket 6: 20%\n Calculating Z arrays for bucket 8\n bucket 7: 10%\n bucket 1: 90%\n bucket 2: 70%\n bucket 4: 30%\n bucket 7: 20%\n bucket 5: 30%\n bucket 2: 80%\n bucket 3: 40%\n bucket 4: 40%\n bucket 7: 30%\n bucket 6: 30%\n bucket 3: 50%\n bucket 5: 40%\n bucket 6: 40%\n bucket 1: 100%\n bucket 2: 90%\n bucket 7: 40%\n bucket 5: 50%\n Entering block accumulator loop for bucket 8:\n bucket 7: 50%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 4: 50%\n bucket 7: 60%\n bucket 6: 50%\n bucket 4: 60%\n bucket 8: 10%\n bucket 2: 100%\n bucket 5: 60%\n bucket 7: 70%\n bucket 3: 60%\n bucket 5: 70%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 6: 60%\n bucket 5: 80%\n bucket 3: 70%\n bucket 7: 80%\n bucket 4: 70%\n bucket 5: 90%\n bucket 3: 80%\n bucket 4: 80%\n bucket 8: 20%\n bucket 7: 90%\n bucket 4: 90%\n bucket 5: 100%\n bucket 3: 90%\n bucket 4: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 100%\n bucket 8: 30%\n bucket 3: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 6: 70%\n bucket 8: 40%\n bucket 6: 80%\n bucket 8: 50%\n bucket 6: 90%\n bucket 8: 60%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\nGetting block 12 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 11:\n bucket 12: 10%\n bucket 11: 10%\n bucket 12: 20%\n bucket 11: 20%\n bucket 12: 30%\n bucket 11: 30%\n bucket 12: 40%\n bucket 11: 40%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n bucket 12: 50%\n Calculating Z arrays for bucket 13\n bucket 11: 50%\n bucket 12: 60%\n bucket 11: 60%\n bucket 12: 70%\n bucket 11: 70%\n Entering block accumulator loop for bucket 13:\n bucket 12: 80%\n bucket 11: 80%\n bucket 13: 10%\n bucket 12: 90%\n bucket 11: 90%\n bucket 13: 20%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 30%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n bucket 14: 40%\n Calculating Z arrays for bucket 15\n bucket 14: 50%\n bucket 14: 60%\n Entering block accumulator loop for bucket 15:\n bucket 14: 70%\n bucket 15: 10%\n bucket 14: 80%\n bucket 15: 20%\n bucket 14: 90%\n bucket 15: 30%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 40%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 50%\n bucket 15: 60%\n Entering block accumulator loop for bucket 16:\n bucket 15: 70%\n Sorting block time: 00:00:00\n bucket 16: 10%\nReturning block of 83 for bucket 14\n bucket 15: 80%\n bucket 16: 20%\n bucket 15: 90%\n bucket 16: 30%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\nGetting block 20 of 60\n Entering block accumulator loop for bucket 19:\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n bucket 20: 10%\n bucket 19: 30%\n bucket 19: 40%\n bucket 20: 20%\n bucket 19: 50%\n Sorting block time: 00:00:00\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nReturning block of 123 for bucket 18\n bucket 19: 60%\n bucket 20: 30%\n bucket 19: 70%\n bucket 20: 40%\n Entering block accumulator loop for bucket 21:\n bucket 19: 80%\n bucket 20: 50%\n bucket 19: 90%\n bucket 21: 10%\n bucket 20: 60%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n bucket 20: 70%\n bucket 21: 20%\n (Using difference cover)\n bucket 20: 80%\n bucket 21: 30%\n bucket 20: 90%\n bucket 21: 40%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 80%\n bucket 22: 90%\n Entering block accumulator loop for bucket 23:\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 60%\n bucket 23: 70%\n Entering block accumulator loop for bucket 24:\n bucket 23: 80%\n bucket 24: 10%\n bucket 23: 90%\n bucket 24: 20%\n Sorting block time: 00:00:00\n bucket 23: 100%\n bucket 24: 30%\nReturning block of 81 for bucket 22\n bucket 24: 40%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 50%\n bucket 24: 60%\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n Sorting block time: 00:00:00\n bucket 26: 60%\nReturning block of 67 for bucket 25\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 60%\n bucket 27: 70%\n Entering block accumulator loop for bucket 28:\n bucket 27: 80%\n bucket 27: 90%\n bucket 28: 10%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 20%\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 30%\n bucket 28: 40%\n Entering block accumulator loop for bucket 29:\n bucket 28: 50%\n bucket 28: 60%\n bucket 29: 10%\n bucket 28: 70%\n bucket 28: 80%\n bucket 29: 20%\n bucket 28: 90%\n Sorting block time: 00:00:00\n bucket 29: 30%\nReturning block of 120 for bucket 27\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 80%\n Calculating Z arrays for bucket 31\n bucket 30: 90%\n Entering block accumulator loop for bucket 31:\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n bucket 32: 10%\n Calculating Z arrays for bucket 33\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 32: 30%\n bucket 32: 40%\n bucket 33: 10%\n bucket 32: 50%\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n bucket 32: 60%\n bucket 33: 20%\n Calculating Z arrays for bucket 34\n bucket 32: 70%\n bucket 33: 30%\n Entering block accumulator loop for bucket 34:\n bucket 33: 40%\n bucket 32: 80%\n bucket 34: 10%\n bucket 32: 90%\n bucket 33: 50%\n bucket 34: 20%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 60%\n bucket 34: 30%\n bucket 33: 70%\n bucket 34: 40%\n bucket 33: 80%\n bucket 34: 50%\n bucket 33: 90%\n bucket 34: 60%\n bucket 33: 100%\n bucket 34: 70%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Entering block accumulator loop for bucket 35:\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Entering block accumulator loop for bucket 36:\n Reserving size (126) for bucket 37\n bucket 35: 10%\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n bucket 35: 20%\n bucket 36: 20%\n Entering block accumulator loop for bucket 37:\n bucket 35: 30%\n bucket 36: 30%\n bucket 35: 40%\n bucket 36: 40%\n bucket 37: 10%\n bucket 35: 50%\n bucket 36: 50%\n bucket 37: 20%\n bucket 36: 60%\n bucket 35: 60%\n bucket 37: 30%\n bucket 36: 70%\n bucket 37: 40%\n bucket 36: 80%\n bucket 35: 70%\n bucket 37: 50%\n bucket 36: 90%\n bucket 37: 60%\n bucket 35: 80%\n bucket 36: 100%\n bucket 37: 70%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 35: 90%\n bucket 37: 80%\n bucket 35: 100%\n bucket 37: 90%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n bucket 39: 60%\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 41:\n bucket 40: 10%\n bucket 41: 10%\n bucket 40: 20%\nGetting block 42 of 60\n bucket 41: 20%\n Reserving size (126) for bucket 42\n bucket 40: 30%\n bucket 41: 30%\n bucket 40: 40%\n bucket 41: 40%\n bucket 40: 50%\n bucket 40: 60%\n Calculating Z arrays for bucket 42\n bucket 40: 70%\n bucket 41: 50%\n bucket 40: 80%\n Entering block accumulator loop for bucket 42:\n bucket 41: 60%\n bucket 40: 90%\n bucket 41: 70%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 42: 10%\n bucket 41: 80%\n bucket 42: 20%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Entering block accumulator loop for bucket 43:\n Calculating Z arrays for bucket 44\n bucket 43: 10%\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 43: 20%\n Entering block accumulator loop for bucket 44:\n bucket 43: 30%\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 44: 10%\n bucket 43: 40%\n Entering block accumulator loop for bucket 45:\nGetting block 47 of 60\n bucket 43: 50%\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 46:\n bucket 43: 60%\n bucket 45: 10%\n bucket 46: 10%\n Entering block accumulator loop for bucket 47:\n bucket 43: 70%\n bucket 45: 20%\n bucket 46: 20%\n bucket 44: 20%\n bucket 47: 10%\n bucket 46: 30%\n bucket 43: 80%\n bucket 44: 30%\n bucket 46: 40%\n bucket 47: 20%\n bucket 43: 90%\n bucket 45: 30%\n bucket 44: 40%\n bucket 47: 30%\n bucket 46: 50%\n bucket 43: 100%\n bucket 44: 50%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 46: 60%\n bucket 45: 40%\n bucket 44: 60%\n bucket 46: 70%\n bucket 47: 40%\n bucket 44: 70%\n bucket 45: 50%\n bucket 46: 80%\n bucket 44: 80%\n bucket 47: 50%\n bucket 46: 90%\n bucket 45: 60%\n bucket 44: 90%\n bucket 47: 60%\n bucket 46: 100%\n bucket 45: 70%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 44: 100%\n bucket 47: 70%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 80%\n bucket 47: 80%\n Sorting block time: 00:00:00\n bucket 45: 90%\nReturning block of 122 for bucket 43\n bucket 47: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n Entering block accumulator loop for bucket 49:\n bucket 48: 20%\n bucket 49: 10%\n bucket 48: 30%\n bucket 49: 20%\n bucket 48: 40%\n bucket 49: 30%\n bucket 48: 50%\n bucket 49: 40%\n bucket 48: 60%\n bucket 49: 50%\n bucket 48: 70%\n bucket 49: 60%\n bucket 48: 80%\n bucket 49: 70%\n bucket 48: 90%\n bucket 49: 80%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n Entering block accumulator loop for bucket 51:\n bucket 50: 20%\n bucket 51: 10%\n bucket 50: 30%\n bucket 51: 20%\n bucket 50: 40%\n bucket 51: 30%\n bucket 50: 50%\n bucket 50: 60%\n bucket 51: 40%\n bucket 50: 70%\n bucket 51: 50%\n bucket 50: 80%\n bucket 51: 60%\n bucket 50: 90%\n bucket 51: 70%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n Entering block accumulator loop for bucket 53:\n bucket 52: 20%\n bucket 53: 10%\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 20%\n bucket 52: 30%\n bucket 53: 30%\n bucket 52: 40%\n Entering block accumulator loop for bucket 54:\n bucket 53: 40%\n bucket 52: 50%\n bucket 54: 10%\n bucket 53: 50%\n bucket 54: 20%\n bucket 53: 60%\n bucket 52: 60%\n bucket 54: 30%\n bucket 53: 70%\n bucket 52: 70%\n bucket 54: 40%\n bucket 53: 80%\n bucket 52: 80%\n bucket 54: 50%\n bucket 53: 90%\n bucket 52: 90%\n bucket 54: 60%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 70%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n Entering block accumulator loop for bucket 57:\n bucket 56: 20%\n bucket 57: 10%\n bucket 56: 30%\n bucket 57: 20%\n bucket 56: 40%\n bucket 57: 30%\n bucket 56: 50%\n bucket 57: 40%\n bucket 56: 60%\n bucket 57: 50%\n bucket 56: 70%\n bucket 57: 60%\n bucket 56: 80%\n bucket 57: 70%\n bucket 56: 90%\n bucket 57: 80%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Entering block accumulator loop for bucket 58:\n Calculating Z arrays for bucket 59\n bucket 58: 10%\n Entering block accumulator loop for bucket 59:\n bucket 58: 20%\n bucket 58: 30%\n bucket 59: 10%\n bucket 58: 40%\n bucket 59: 20%\n bucket 58: 50%\n bucket 58: 60%\n bucket 59: 30%\n bucket 58: 70%\n bucket 59: 40%\n bucket 58: 80%\n bucket 59: 50%\n bucket 58: 90%\n bucket 59: 60%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 3 (30.00%) aligned concordantly 0 times\n 7 (70.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 3 (50.00%) aligned 0 times\n 3 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n85.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 07:06:22", "plugin": "core", "name": "end_epoch", "raw_value": "1725001582.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:06:22", "plugin": "core", "name": "start_epoch", "raw_value": "1725001582.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-15", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 15, "time_seconds": 35.07818913459778, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "3b6b6ae24dc1e01e"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "d10b5b587df398f0"}, "library|rna_strandness": "R", "library|type": "single", "adv|spliced_options|novel_splicesite_outfile": true, "adv|spliced_options|spliced_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "53b0e16a29081cba", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:58:15.009388", "update_time": "2024-08-30T06:58:28.282464", "galaxy_version": "24.1", "external_id": "gxy-96vvh", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/e/4/a/dataset_e4a17b59-aac1-4359-bda7-076b79391e94.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/7/7/8/dataset_7780016b-fd47-4e6f-9f59-ffa81c2d6e0a.dat' input_f.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -U 'input_f.fastq' --rna-strandness R --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000 --novel-splicesite-outfile '/galaxy/server/database/objects/4/4/e/dataset_44e44186-2dbe-4b64-b665-3175ecf4ff40.dat' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/7/4/8/dataset_748c7afc-c0f0-4e33-bb32-b7af4bcca94a.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 1, \"canonical_penalty\": \"0\", \"coefficient\": \"1.0\", \"constant_term\": \"-8.0\", \"function_type\": \"G\", \"known_splice_gtf\": null, \"max_intron\": \"500000\", \"min_intron\": \"20\", \"nc_coefficient\": \"1.0\", \"nc_constant_term\": \"-8.0\", \"nc_function_type\": \"G\", \"no_spliced_alignment_options\": {\"__current_case__\": 1, \"no_spliced_alignment\": \"\"}, \"noncanonical_penalty\": \"12\", \"notmplen\": false, \"novel_splicesite_outfile\": true, \"spliced_options_selector\": \"advanced\", \"tma\": \"\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 170, \"src\": \"hda\"}]}, \"rna_strandness\": \"R\", \"type\": \"single\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 169, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "3b6b6ae24dc1e01e", "src": "hda", "uuid": "e4a17b59-aac1-4359-bda7-076b79391e94"}, "library|input_1": {"id": "d10b5b587df398f0", "src": "hda", "uuid": "7780016b-fd47-4e6f-9f59-ffa81c2d6e0a"}}, "outputs": {"output_alignments": {"id": "041f9fd4e1fe68f3", "src": "hda", "uuid": "748c7afc-c0f0-4e33-bb32-b7af4bcca94a"}, "novel_splicesite_output": {"id": "bb76b6cd4d4a3d5b", "src": "hda", "uuid": "44e44186-2dbe-4b64-b665-3175ecf4ff40"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 3\n bucket 1: 10%\nGetting block 5 of 60\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 4:\nGetting block 7 of 60\n Calculating Z arrays for bucket 2\n bucket 1: 20%\n bucket 3: 10%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Reserving size (126) for bucket 5\n Entering block accumulator loop for bucket 2:\nGetting block 8 of 60\n Calculating Z arrays for bucket 5\n bucket 3: 20%\n Reserving size (126) for bucket 8\n bucket 3: 30%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 5:\n Calculating Z arrays for bucket 8\n Calculating Z arrays for bucket 6\n bucket 1: 30%\n bucket 4: 10%\n bucket 3: 40%\n bucket 5: 10%\n Entering block accumulator loop for bucket 8:\n Calculating Z arrays for bucket 7\n bucket 3: 50%\n bucket 2: 10%\n Entering block accumulator loop for bucket 6:\n bucket 4: 20%\n bucket 5: 20%\n bucket 1: 40%\n bucket 2: 20%\n bucket 8: 10%\n bucket 4: 30%\n Entering block accumulator loop for bucket 7:\n bucket 6: 10%\n bucket 5: 30%\n bucket 3: 60%\n bucket 8: 20%\n bucket 2: 30%\n bucket 4: 40%\n bucket 5: 40%\n bucket 1: 50%\n bucket 8: 30%\n bucket 2: 40%\n bucket 4: 50%\n bucket 5: 50%\n bucket 6: 20%\n bucket 8: 40%\n bucket 5: 60%\n bucket 3: 70%\n bucket 1: 60%\n bucket 7: 10%\n bucket 6: 30%\n bucket 8: 50%\n bucket 2: 50%\n bucket 3: 80%\n bucket 5: 70%\n bucket 4: 60%\n bucket 7: 20%\n bucket 1: 70%\n bucket 3: 90%\n bucket 6: 40%\n bucket 4: 70%\n bucket 5: 80%\n bucket 8: 60%\n bucket 3: 100%\n bucket 4: 80%\n bucket 1: 80%\n bucket 2: 60%\n bucket 6: 50%\n bucket 5: 90%\n bucket 7: 30%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 70%\n bucket 1: 90%\n bucket 6: 60%\n bucket 4: 90%\n bucket 2: 70%\n bucket 5: 100%\n bucket 7: 40%\n bucket 1: 100%\n bucket 4: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 70%\n bucket 8: 80%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block of length 42 for bucket 1\n bucket 2: 80%\n bucket 8: 90%\n bucket 2: 90%\n bucket 8: 100%\n bucket 6: 80%\n Sorting block of length 94 for bucket 8\n bucket 2: 100%\n (Using difference cover)\n bucket 6: 90%\n (Using difference cover)\n bucket 7: 50%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n bucket 7: 60%\n (Using difference cover)\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\nGetting block 9 of 60\nGetting block 10 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\n Entering block accumulator loop for bucket 11:\n bucket 9: 60%\n bucket 10: 40%\n bucket 9: 70%\n bucket 11: 10%\n bucket 9: 80%\n bucket 10: 50%\n bucket 11: 20%\n bucket 10: 60%\n bucket 11: 30%\n bucket 9: 90%\n bucket 11: 40%\n bucket 10: 70%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n bucket 11: 50%\n (Using difference cover)\n bucket 10: 80%\n bucket 11: 60%\n bucket 10: 90%\n bucket 10: 100%\n bucket 11: 70%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\nGetting block 13 of 60\n bucket 12: 80%\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\n bucket 12: 90%\n bucket 13: 10%\n bucket 12: 100%\n Entering block accumulator loop for bucket 14:\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 20%\n bucket 14: 10%\n bucket 13: 30%\n bucket 14: 20%\n bucket 13: 40%\n bucket 14: 30%\n bucket 14: 40%\n bucket 13: 50%\n bucket 14: 50%\n bucket 13: 60%\n bucket 14: 60%\n bucket 13: 70%\n bucket 14: 70%\n bucket 13: 80%\n bucket 14: 80%\n bucket 13: 90%\n bucket 14: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 30%\n bucket 15: 40%\n Entering block accumulator loop for bucket 16:\n bucket 15: 50%\n bucket 16: 10%\n bucket 15: 60%\n bucket 16: 20%\n bucket 15: 70%\n bucket 16: 30%\n bucket 15: 80%\n bucket 16: 40%\n bucket 15: 90%\n bucket 16: 50%\n bucket 15: 100%\n bucket 16: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n bucket 17: 50%\n Calculating Z arrays for bucket 18\n bucket 17: 60%\n bucket 17: 70%\n Entering block accumulator loop for bucket 18:\n bucket 17: 80%\n bucket 18: 10%\n bucket 17: 90%\n bucket 18: 20%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 23:\n bucket 22: 10%\n bucket 21: 10%\n bucket 23: 10%\n bucket 22: 20%\n bucket 21: 20%\n bucket 23: 20%\n bucket 21: 30%\n bucket 22: 30%\n bucket 23: 30%\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 23: 40%\n bucket 22: 50%\n bucket 21: 60%\n bucket 23: 50%\n bucket 21: 70%\n bucket 22: 60%\n bucket 23: 60%\n bucket 21: 80%\n bucket 22: 70%\n bucket 23: 70%\n bucket 21: 90%\n bucket 22: 80%\n bucket 23: 80%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 90%\n bucket 23: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 70%\n bucket 24: 80%\n Entering block accumulator loop for bucket 25:\n bucket 24: 90%\n bucket 25: 10%\n bucket 25: 20%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\nGetting block 27 of 60\n bucket 26: 90%\n Reserving size (126) for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 26: 100%\n Calculating Z arrays for bucket 27\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Entering block accumulator loop for bucket 28:\n Entering block accumulator loop for bucket 27:\n bucket 28: 10%\n bucket 27: 10%\n bucket 28: 20%\n bucket 27: 20%\n bucket 28: 30%\n bucket 27: 30%\n bucket 28: 40%\n bucket 27: 40%\n bucket 28: 50%\n bucket 27: 50%\n bucket 28: 60%\n bucket 27: 60%\n bucket 28: 70%\n bucket 27: 70%\n bucket 28: 80%\n bucket 27: 80%\n bucket 28: 90%\n bucket 27: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\nGetting block 30 of 60\n bucket 29: 60%\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 70%\n bucket 29: 80%\n Entering block accumulator loop for bucket 30:\n bucket 29: 90%\n bucket 30: 10%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 31: 30%\n bucket 32: 10%\n bucket 31: 40%\n bucket 32: 20%\n bucket 31: 50%\n bucket 32: 30%\n bucket 31: 60%\n bucket 32: 40%\n bucket 31: 70%\n bucket 32: 50%\n bucket 31: 80%\n bucket 32: 60%\n bucket 31: 90%\n bucket 31: 100%\n bucket 32: 70%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n bucket 33: 10%\n Calculating Z arrays for bucket 34\n bucket 33: 20%\n Entering block accumulator loop for bucket 34:\n bucket 33: 30%\n bucket 33: 40%\n bucket 34: 10%\n bucket 33: 50%\n bucket 34: 20%\n bucket 33: 60%\n bucket 34: 30%\n bucket 33: 70%\n bucket 34: 40%\n bucket 33: 80%\n bucket 34: 50%\n bucket 33: 90%\n bucket 34: 60%\n bucket 33: 100%\n bucket 34: 70%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 36:\n Entering block accumulator loop for bucket 37:\n Entering block accumulator loop for bucket 35:\n bucket 37: 10%\n bucket 36: 10%\n bucket 37: 20%\n bucket 35: 10%\n bucket 37: 30%\n bucket 36: 20%\n bucket 35: 20%\n bucket 37: 40%\n bucket 36: 30%\n bucket 35: 30%\n bucket 37: 50%\n bucket 36: 40%\n bucket 35: 40%\n bucket 37: 60%\n bucket 36: 50%\n bucket 37: 70%\n bucket 35: 50%\n bucket 37: 80%\n bucket 36: 60%\n bucket 35: 60%\n bucket 37: 90%\n bucket 36: 70%\n bucket 37: 100%\n bucket 35: 70%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 36: 80%\n bucket 35: 80%\n bucket 36: 90%\n bucket 35: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 50%\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 38: 60%\n bucket 39: 30%\n bucket 38: 70%\n bucket 39: 40%\n bucket 38: 80%\n bucket 39: 50%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\nGetting block 41 of 60\n bucket 40: 40%\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 50%\n bucket 40: 60%\n Entering block accumulator loop for bucket 41:\n bucket 40: 70%\n bucket 40: 80%\n bucket 41: 10%\n bucket 40: 90%\n bucket 41: 20%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 43 of 60\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 44:\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 10%\n bucket 44: 10%\n bucket 42: 20%\n bucket 44: 20%\n Entering block accumulator loop for bucket 43:\n bucket 42: 30%\n bucket 44: 30%\n bucket 42: 40%\n bucket 43: 10%\n bucket 44: 40%\n bucket 42: 50%\n bucket 43: 20%\n bucket 42: 60%\n bucket 44: 50%\n bucket 43: 30%\n bucket 44: 60%\n bucket 42: 70%\n bucket 43: 40%\n bucket 44: 70%\n bucket 42: 80%\n bucket 43: 50%\n bucket 44: 80%\n bucket 42: 90%\n bucket 43: 60%\n bucket 44: 90%\n bucket 42: 100%\n bucket 43: 70%\n bucket 44: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Entering block accumulator loop for bucket 45:\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n bucket 45: 20%\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 45: 30%\n Entering block accumulator loop for bucket 46:\n bucket 45: 40%\n Entering block accumulator loop for bucket 47:\n bucket 45: 50%\n bucket 46: 10%\n bucket 47: 10%\n bucket 45: 60%\n bucket 46: 20%\n bucket 47: 20%\n bucket 45: 70%\n bucket 46: 30%\n bucket 45: 80%\n bucket 46: 40%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 50%\n bucket 47: 30%\n bucket 46: 60%\n bucket 47: 40%\n bucket 46: 70%\n bucket 47: 50%\n bucket 46: 80%\n bucket 47: 60%\n bucket 46: 90%\n bucket 47: 70%\n bucket 46: 100%\n bucket 47: 80%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 50%\n bucket 50: 60%\n Entering block accumulator loop for bucket 51:\n bucket 50: 70%\n bucket 50: 80%\n bucket 51: 10%\n bucket 50: 90%\n bucket 51: 20%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n Sorting block time: 00:00:00\n bucket 53: 100%\nReturning block of 107 for bucket 52\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 60%\n Entering block accumulator loop for bucket 55:\n bucket 54: 70%\n bucket 55: 10%\n bucket 54: 80%\n bucket 55: 20%\n bucket 54: 90%\n bucket 55: 30%\n bucket 55: 40%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n Entering block accumulator loop for bucket 57:\n bucket 56: 10%\n bucket 57: 10%\n bucket 56: 20%\n bucket 57: 20%\n bucket 56: 30%\n bucket 57: 30%\n bucket 56: 40%\n bucket 57: 40%\n bucket 56: 50%\n bucket 57: 50%\n bucket 56: 60%\n bucket 57: 60%\n bucket 56: 70%\n bucket 57: 70%\n bucket 56: 80%\n bucket 57: 80%\n bucket 56: 90%\n bucket 57: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Sorting block of length 113 for bucket 58\n Calculating Z arrays for bucket 59\n (Using difference cover)\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were unpaired; of these:\n 0 (0.00%) aligned 0 times\n 10 (100.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n100.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 4\n Calculating Z arrays for bucket 3\n bucket 1: 10%\nGetting block 5 of 60\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 4:\nGetting block 7 of 60\n Calculating Z arrays for bucket 2\n bucket 1: 20%\n bucket 3: 10%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Reserving size (126) for bucket 5\n Entering block accumulator loop for bucket 2:\nGetting block 8 of 60\n Calculating Z arrays for bucket 5\n bucket 3: 20%\n Reserving size (126) for bucket 8\n bucket 3: 30%\n Reserving size (126) for bucket 7\n Entering block accumulator loop for bucket 5:\n Calculating Z arrays for bucket 8\n Calculating Z arrays for bucket 6\n bucket 1: 30%\n bucket 4: 10%\n bucket 3: 40%\n bucket 5: 10%\n Entering block accumulator loop for bucket 8:\n Calculating Z arrays for bucket 7\n bucket 3: 50%\n bucket 2: 10%\n Entering block accumulator loop for bucket 6:\n bucket 4: 20%\n bucket 5: 20%\n bucket 1: 40%\n bucket 2: 20%\n bucket 8: 10%\n bucket 4: 30%\n Entering block accumulator loop for bucket 7:\n bucket 6: 10%\n bucket 5: 30%\n bucket 3: 60%\n bucket 8: 20%\n bucket 2: 30%\n bucket 4: 40%\n bucket 5: 40%\n bucket 1: 50%\n bucket 8: 30%\n bucket 2: 40%\n bucket 4: 50%\n bucket 5: 50%\n bucket 6: 20%\n bucket 8: 40%\n bucket 5: 60%\n bucket 3: 70%\n bucket 1: 60%\n bucket 7: 10%\n bucket 6: 30%\n bucket 8: 50%\n bucket 2: 50%\n bucket 3: 80%\n bucket 5: 70%\n bucket 4: 60%\n bucket 7: 20%\n bucket 1: 70%\n bucket 3: 90%\n bucket 6: 40%\n bucket 4: 70%\n bucket 5: 80%\n bucket 8: 60%\n bucket 3: 100%\n bucket 4: 80%\n bucket 1: 80%\n bucket 2: 60%\n bucket 6: 50%\n bucket 5: 90%\n bucket 7: 30%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 70%\n bucket 1: 90%\n bucket 6: 60%\n bucket 4: 90%\n bucket 2: 70%\n bucket 5: 100%\n bucket 7: 40%\n bucket 1: 100%\n bucket 4: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 70%\n bucket 8: 80%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block of length 42 for bucket 1\n bucket 2: 80%\n bucket 8: 90%\n bucket 2: 90%\n bucket 8: 100%\n bucket 6: 80%\n Sorting block of length 94 for bucket 8\n bucket 2: 100%\n (Using difference cover)\n bucket 6: 90%\n (Using difference cover)\n bucket 7: 50%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n bucket 7: 60%\n (Using difference cover)\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\nGetting block 9 of 60\nGetting block 10 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n bucket 9: 10%\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\n Entering block accumulator loop for bucket 11:\n bucket 9: 60%\n bucket 10: 40%\n bucket 9: 70%\n bucket 11: 10%\n bucket 9: 80%\n bucket 10: 50%\n bucket 11: 20%\n bucket 10: 60%\n bucket 11: 30%\n bucket 9: 90%\n bucket 11: 40%\n bucket 10: 70%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n bucket 11: 50%\n (Using difference cover)\n bucket 10: 80%\n bucket 11: 60%\n bucket 10: 90%\n bucket 10: 100%\n bucket 11: 70%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\nGetting block 13 of 60\n bucket 12: 80%\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 13:\n bucket 12: 90%\n bucket 13: 10%\n bucket 12: 100%\n Entering block accumulator loop for bucket 14:\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 20%\n bucket 14: 10%\n bucket 13: 30%\n bucket 14: 20%\n bucket 13: 40%\n bucket 14: 30%\n bucket 14: 40%\n bucket 13: 50%\n bucket 14: 50%\n bucket 13: 60%\n bucket 14: 60%\n bucket 13: 70%\n bucket 14: 70%\n bucket 13: 80%\n bucket 14: 80%\n bucket 13: 90%\n bucket 14: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 30%\n bucket 15: 40%\n Entering block accumulator loop for bucket 16:\n bucket 15: 50%\n bucket 16: 10%\n bucket 15: 60%\n bucket 16: 20%\n bucket 15: 70%\n bucket 16: 30%\n bucket 15: 80%\n bucket 16: 40%\n bucket 15: 90%\n bucket 16: 50%\n bucket 15: 100%\n bucket 16: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n bucket 17: 50%\n Calculating Z arrays for bucket 18\n bucket 17: 60%\n bucket 17: 70%\n Entering block accumulator loop for bucket 18:\n bucket 17: 80%\n bucket 18: 10%\n bucket 17: 90%\n bucket 18: 20%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n Entering block accumulator loop for bucket 21:\n Entering block accumulator loop for bucket 23:\n bucket 22: 10%\n bucket 21: 10%\n bucket 23: 10%\n bucket 22: 20%\n bucket 21: 20%\n bucket 23: 20%\n bucket 21: 30%\n bucket 22: 30%\n bucket 23: 30%\n bucket 21: 40%\n bucket 22: 40%\n bucket 21: 50%\n bucket 23: 40%\n bucket 22: 50%\n bucket 21: 60%\n bucket 23: 50%\n bucket 21: 70%\n bucket 22: 60%\n bucket 23: 60%\n bucket 21: 80%\n bucket 22: 70%\n bucket 23: 70%\n bucket 21: 90%\n bucket 22: 80%\n bucket 23: 80%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 90%\n bucket 23: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 70%\n bucket 24: 80%\n Entering block accumulator loop for bucket 25:\n bucket 24: 90%\n bucket 25: 10%\n bucket 25: 20%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\nGetting block 27 of 60\n bucket 26: 90%\n Reserving size (126) for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 26: 100%\n Calculating Z arrays for bucket 27\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Entering block accumulator loop for bucket 28:\n Entering block accumulator loop for bucket 27:\n bucket 28: 10%\n bucket 27: 10%\n bucket 28: 20%\n bucket 27: 20%\n bucket 28: 30%\n bucket 27: 30%\n bucket 28: 40%\n bucket 27: 40%\n bucket 28: 50%\n bucket 27: 50%\n bucket 28: 60%\n bucket 27: 60%\n bucket 28: 70%\n bucket 27: 70%\n bucket 28: 80%\n bucket 27: 80%\n bucket 28: 90%\n bucket 27: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\nGetting block 30 of 60\n bucket 29: 60%\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 70%\n bucket 29: 80%\n Entering block accumulator loop for bucket 30:\n bucket 29: 90%\n bucket 30: 10%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 31: 30%\n bucket 32: 10%\n bucket 31: 40%\n bucket 32: 20%\n bucket 31: 50%\n bucket 32: 30%\n bucket 31: 60%\n bucket 32: 40%\n bucket 31: 70%\n bucket 32: 50%\n bucket 31: 80%\n bucket 32: 60%\n bucket 31: 90%\n bucket 31: 100%\n bucket 32: 70%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n bucket 33: 10%\n Calculating Z arrays for bucket 34\n bucket 33: 20%\n Entering block accumulator loop for bucket 34:\n bucket 33: 30%\n bucket 33: 40%\n bucket 34: 10%\n bucket 33: 50%\n bucket 34: 20%\n bucket 33: 60%\n bucket 34: 30%\n bucket 33: 70%\n bucket 34: 40%\n bucket 33: 80%\n bucket 34: 50%\n bucket 33: 90%\n bucket 34: 60%\n bucket 33: 100%\n bucket 34: 70%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 36:\n Entering block accumulator loop for bucket 37:\n Entering block accumulator loop for bucket 35:\n bucket 37: 10%\n bucket 36: 10%\n bucket 37: 20%\n bucket 35: 10%\n bucket 37: 30%\n bucket 36: 20%\n bucket 35: 20%\n bucket 37: 40%\n bucket 36: 30%\n bucket 35: 30%\n bucket 37: 50%\n bucket 36: 40%\n bucket 35: 40%\n bucket 37: 60%\n bucket 36: 50%\n bucket 37: 70%\n bucket 35: 50%\n bucket 37: 80%\n bucket 36: 60%\n bucket 35: 60%\n bucket 37: 90%\n bucket 36: 70%\n bucket 37: 100%\n bucket 35: 70%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 36: 80%\n bucket 35: 80%\n bucket 36: 90%\n bucket 35: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 50%\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 38: 60%\n bucket 39: 30%\n bucket 38: 70%\n bucket 39: 40%\n bucket 38: 80%\n bucket 39: 50%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\nGetting block 41 of 60\n bucket 40: 40%\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 40: 50%\n bucket 40: 60%\n Entering block accumulator loop for bucket 41:\n bucket 40: 70%\n bucket 40: 80%\n bucket 41: 10%\n bucket 40: 90%\n bucket 41: 20%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 43 of 60\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 44:\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 10%\n bucket 44: 10%\n bucket 42: 20%\n bucket 44: 20%\n Entering block accumulator loop for bucket 43:\n bucket 42: 30%\n bucket 44: 30%\n bucket 42: 40%\n bucket 43: 10%\n bucket 44: 40%\n bucket 42: 50%\n bucket 43: 20%\n bucket 42: 60%\n bucket 44: 50%\n bucket 43: 30%\n bucket 44: 60%\n bucket 42: 70%\n bucket 43: 40%\n bucket 44: 70%\n bucket 42: 80%\n bucket 43: 50%\n bucket 44: 80%\n bucket 42: 90%\n bucket 43: 60%\n bucket 44: 90%\n bucket 42: 100%\n bucket 43: 70%\n bucket 44: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Entering block accumulator loop for bucket 45:\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n bucket 45: 20%\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 45: 30%\n Entering block accumulator loop for bucket 46:\n bucket 45: 40%\n Entering block accumulator loop for bucket 47:\n bucket 45: 50%\n bucket 46: 10%\n bucket 47: 10%\n bucket 45: 60%\n bucket 46: 20%\n bucket 47: 20%\n bucket 45: 70%\n bucket 46: 30%\n bucket 45: 80%\n bucket 46: 40%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 50%\n bucket 47: 30%\n bucket 46: 60%\n bucket 47: 40%\n bucket 46: 70%\n bucket 47: 50%\n bucket 46: 80%\n bucket 47: 60%\n bucket 46: 90%\n bucket 47: 70%\n bucket 46: 100%\n bucket 47: 80%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 50%\n bucket 50: 60%\n Entering block accumulator loop for bucket 51:\n bucket 50: 70%\n bucket 50: 80%\n bucket 51: 10%\n bucket 50: 90%\n bucket 51: 20%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n Sorting block time: 00:00:00\n bucket 53: 100%\nReturning block of 107 for bucket 52\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 60%\n Entering block accumulator loop for bucket 55:\n bucket 54: 70%\n bucket 55: 10%\n bucket 54: 80%\n bucket 55: 20%\n bucket 54: 90%\n bucket 55: 30%\n bucket 55: 40%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n Entering block accumulator loop for bucket 57:\n bucket 56: 10%\n bucket 57: 10%\n bucket 56: 20%\n bucket 57: 20%\n bucket 56: 30%\n bucket 57: 30%\n bucket 56: 40%\n bucket 57: 40%\n bucket 56: 50%\n bucket 57: 50%\n bucket 56: 60%\n bucket 57: 60%\n bucket 56: 70%\n bucket 57: 70%\n bucket 56: 80%\n bucket 57: 80%\n bucket 56: 90%\n bucket 57: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Sorting block of length 113 for bucket 58\n Calculating Z arrays for bucket 59\n (Using difference cover)\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were unpaired; of these:\n 0 (0.00%) aligned 0 times\n 10 (100.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n100.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:58:17", "plugin": "core", "name": "end_epoch", "raw_value": "1725001097.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:58:16", "plugin": "core", "name": "start_epoch", "raw_value": "1725001096.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-15", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 15, "time_seconds": 33.84105181694031, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "8a731c16879c5339"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "7c1e613de25469d9"}, "library|rna_strandness": "R", "library|type": "single", "adv|spliced_options|novel_splicesite_outfile": true, "adv|spliced_options|spliced_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "011cf8633ac73a47", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:06:54.238960", "update_time": "2024-08-30T07:07:07.699405", "galaxy_version": "24.1", "external_id": "gxy-58rb5", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/0/7/9/dataset_07964b07-3cf9-475e-bcb0-c5be2fc911e1.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/7/9/6/dataset_796ad3e8-e245-4fa8-95b5-2e6f38366e2f.dat' input_f.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -U 'input_f.fastq' --rna-strandness R --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000 --novel-splicesite-outfile '/galaxy/server/database/objects/b/3/c/dataset_b3c6cb52-aec9-46d0-8a1d-5bb079ba0939.dat' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/a/6/6/dataset_a66be6bc-3de7-4f7d-be23-4c41c34d0baa.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 1, \"canonical_penalty\": \"0\", \"coefficient\": \"1.0\", \"constant_term\": \"-8.0\", \"function_type\": \"G\", \"known_splice_gtf\": null, \"max_intron\": \"500000\", \"min_intron\": \"20\", \"nc_coefficient\": \"1.0\", \"nc_constant_term\": \"-8.0\", \"nc_function_type\": \"G\", \"no_spliced_alignment_options\": {\"__current_case__\": 1, \"no_spliced_alignment\": \"\"}, \"noncanonical_penalty\": \"12\", \"notmplen\": false, \"novel_splicesite_outfile\": true, \"spliced_options_selector\": \"advanced\", \"tma\": \"\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 0, \"input_1\": {\"values\": [{\"id\": 229, \"src\": \"hda\"}]}, \"rna_strandness\": \"R\", \"type\": \"single\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 228, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "8a731c16879c5339", "src": "hda", "uuid": "07964b07-3cf9-475e-bcb0-c5be2fc911e1"}, "library|input_1": {"id": "7c1e613de25469d9", "src": "hda", "uuid": "796ad3e8-e245-4fa8-95b5-2e6f38366e2f"}}, "outputs": {"output_alignments": {"id": "092b784731aa0339", "src": "hda", "uuid": "a66be6bc-3de7-4f7d-be23-4c41c34d0baa"}, "novel_splicesite_output": {"id": "71182d24ecd819de", "src": "hda", "uuid": "b3c6cb52-aec9-46d0-8a1d-5bb079ba0939"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 2: 10%\n bucket 1: 10%\n bucket 2: 20%\n Entering block accumulator loop for bucket 3:\n bucket 1: 20%\n bucket 2: 30%\n bucket 1: 30%\n bucket 2: 40%\nGetting block 4 of 60\nGetting block 5 of 60\n bucket 3: 10%\nGetting block 6 of 60\n bucket 1: 40%\n bucket 3: 20%\nGetting block 8 of 60\n Reserving size (126) for bucket 4\n Reserving size (126) for bucket 8\n bucket 3: 30%\n Calculating Z arrays for bucket 4\n bucket 1: 50%\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 8\n bucket 1: 60%\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 5\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 4:\n bucket 1: 70%\n Entering block accumulator loop for bucket 5:\n bucket 3: 40%\n bucket 2: 50%\n bucket 4: 10%\n bucket 1: 80%\n Entering block accumulator loop for bucket 6:\n bucket 3: 50%\n bucket 5: 10%\n Entering block accumulator loop for bucket 8:\n bucket 4: 20%\n bucket 5: 20%\n bucket 6: 10%\n bucket 3: 60%\n bucket 4: 30%\n bucket 2: 60%\n bucket 8: 10%\n bucket 3: 70%\n bucket 1: 90%\n bucket 8: 20%\n bucket 2: 70%\n bucket 3: 80%\n bucket 4: 40%\n bucket 8: 30%\n Calculating Z arrays for bucket 7\n bucket 4: 50%\n bucket 6: 20%\n bucket 1: 100%\n bucket 4: 60%\n bucket 2: 80%\n bucket 3: 90%\n bucket 5: 30%\n bucket 2: 90%\n bucket 6: 30%\n bucket 3: 100%\n bucket 2: 100%\n bucket 4: 70%\n bucket 6: 40%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Entering block accumulator loop for bucket 7:\n bucket 8: 40%\n bucket 5: 40%\n bucket 6: 50%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 8: 50%\n bucket 5: 50%\n bucket 6: 60%\n bucket 8: 60%\n bucket 7: 10%\n bucket 6: 70%\n bucket 4: 80%\n bucket 8: 70%\n bucket 6: 80%\n bucket 5: 60%\n bucket 7: 20%\n bucket 8: 80%\n bucket 6: 90%\n bucket 7: 30%\n bucket 4: 90%\n bucket 8: 90%\n bucket 7: 40%\n bucket 5: 70%\n bucket 6: 100%\n bucket 8: 100%\n bucket 7: 50%\n bucket 4: 100%\n Sorting block of length 94 for bucket 8\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n (Using difference cover)\n Sorting block of length 68 for bucket 4\n bucket 5: 80%\n (Using difference cover)\n bucket 7: 60%\n bucket 5: 90%\n bucket 7: 70%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Entering block accumulator loop for bucket 9:\n Calculating Z arrays for bucket 10\n bucket 9: 10%\n bucket 9: 20%\n Entering block accumulator loop for bucket 10:\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 9: 30%\n bucket 10: 10%\n bucket 9: 40%\n bucket 10: 20%\n bucket 9: 50%\n Entering block accumulator loop for bucket 11:\n bucket 9: 60%\n bucket 10: 30%\n bucket 11: 10%\n bucket 10: 40%\n bucket 9: 70%\n bucket 11: 20%\n bucket 10: 50%\n bucket 9: 80%\n bucket 11: 30%\n bucket 10: 60%\n bucket 9: 90%\n bucket 11: 40%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 70%\n bucket 11: 50%\n bucket 10: 80%\n bucket 11: 60%\n bucket 10: 90%\n bucket 11: 70%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 13:\n Entering block accumulator loop for bucket 12:\n bucket 13: 10%\n bucket 12: 10%\n bucket 12: 20%\n bucket 13: 20%\n bucket 12: 30%\n bucket 13: 30%\n bucket 12: 40%\n bucket 13: 40%\n bucket 12: 50%\n bucket 13: 50%\n bucket 12: 60%\n bucket 13: 60%\n bucket 12: 70%\n bucket 13: 70%\n bucket 12: 80%\n bucket 13: 80%\n bucket 12: 90%\n bucket 13: 90%\n bucket 12: 100%\n bucket 13: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n Entering block accumulator loop for bucket 15:\n bucket 14: 20%\n bucket 14: 30%\n bucket 15: 10%\n bucket 14: 40%\n bucket 15: 20%\n bucket 14: 50%\n bucket 15: 30%\n bucket 14: 60%\n bucket 15: 40%\n bucket 14: 70%\n bucket 15: 50%\n bucket 14: 80%\n bucket 15: 60%\n bucket 14: 90%\n bucket 15: 70%\n bucket 14: 100%\n bucket 15: 80%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 10%\n bucket 16: 20%\nGetting block 18 of 60\n bucket 16: 30%\n Reserving size (126) for bucket 18\n Entering block accumulator loop for bucket 17:\n bucket 16: 40%\n Calculating Z arrays for bucket 18\n bucket 17: 10%\n bucket 16: 50%\n bucket 17: 20%\n Entering block accumulator loop for bucket 18:\n bucket 16: 60%\n bucket 17: 30%\n bucket 18: 10%\n bucket 16: 70%\n bucket 18: 20%\n bucket 16: 80%\n bucket 17: 40%\n bucket 18: 30%\n bucket 16: 90%\n bucket 17: 50%\n bucket 18: 40%\n bucket 16: 100%\n bucket 17: 60%\n bucket 18: 50%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 70%\n bucket 18: 60%\n bucket 17: 80%\n bucket 18: 70%\n bucket 17: 90%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n bucket 21: 90%\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n (Using difference cover)\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 22: 40%\n bucket 23: 20%\n bucket 22: 50%\n bucket 23: 30%\n bucket 22: 60%\n bucket 23: 40%\n bucket 22: 70%\n bucket 23: 50%\n bucket 22: 80%\n bucket 23: 60%\n bucket 22: 90%\n bucket 23: 70%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Entering block accumulator loop for bucket 24:\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 10%\n bucket 24: 20%\n Entering block accumulator loop for bucket 25:\n bucket 24: 30%\n bucket 25: 10%\n bucket 24: 40%\n bucket 24: 50%\n bucket 25: 20%\n bucket 24: 60%\n bucket 25: 30%\n bucket 24: 70%\n bucket 25: 40%\n bucket 24: 80%\n bucket 25: 50%\n bucket 24: 90%\n bucket 25: 60%\n bucket 24: 100%\n bucket 25: 70%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 60\n Entering block accumulator loop for bucket 27:\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 10%\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 27: 30%\n bucket 28: 10%\n bucket 27: 40%\n bucket 28: 20%\n bucket 27: 50%\n bucket 27: 60%\n bucket 28: 30%\n bucket 27: 70%\n bucket 28: 40%\n bucket 27: 80%\n bucket 28: 50%\n bucket 27: 90%\n bucket 28: 60%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 29: 30%\n Entering block accumulator loop for bucket 31:\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 31: 10%\n bucket 29: 40%\n bucket 31: 20%\n Entering block accumulator loop for bucket 30:\n bucket 29: 50%\n bucket 31: 30%\n bucket 30: 10%\n bucket 29: 60%\n bucket 31: 40%\n bucket 30: 20%\n bucket 29: 70%\n bucket 31: 50%\n bucket 30: 30%\n bucket 29: 80%\n bucket 31: 60%\n bucket 30: 40%\n bucket 29: 90%\n bucket 31: 70%\n bucket 30: 50%\n bucket 29: 100%\n bucket 31: 80%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 60%\n bucket 31: 90%\n bucket 30: 70%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 32:\n Entering block accumulator loop for bucket 33:\n bucket 32: 10%\n bucket 33: 10%\n bucket 32: 20%\n bucket 33: 20%\n bucket 32: 30%\n bucket 33: 30%\n bucket 32: 40%\n bucket 33: 40%\n bucket 32: 50%\n bucket 33: 50%\n bucket 32: 60%\n bucket 33: 60%\n bucket 33: 70%\n bucket 32: 70%\n bucket 33: 80%\n bucket 32: 80%\n bucket 33: 90%\n bucket 33: 100%\n bucket 32: 90%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\nGetting block 35 of 60\n bucket 34: 40%\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 50%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 35:\n bucket 34: 60%\n bucket 34: 70%\n Entering block accumulator loop for bucket 36:\n bucket 35: 10%\n bucket 34: 80%\n bucket 36: 10%\n bucket 34: 90%\n bucket 35: 20%\n bucket 36: 20%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 30%\n bucket 36: 30%\n bucket 35: 40%\n bucket 36: 40%\n bucket 35: 50%\n bucket 36: 50%\n bucket 35: 60%\n bucket 36: 60%\n bucket 35: 70%\n bucket 36: 70%\n bucket 35: 80%\n bucket 36: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Entering block accumulator loop for bucket 37:\n Calculating Z arrays for bucket 38\n bucket 37: 10%\n Entering block accumulator loop for bucket 38:\n bucket 37: 20%\n bucket 37: 30%\n bucket 38: 10%\n bucket 37: 40%\n bucket 38: 20%\n bucket 37: 50%\n bucket 38: 30%\n bucket 37: 60%\n bucket 38: 40%\n bucket 37: 70%\n bucket 38: 50%\n bucket 37: 80%\n bucket 38: 60%\n bucket 37: 90%\n bucket 38: 70%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 41 of 60\n Entering block accumulator loop for bucket 40:\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 39:\n bucket 40: 10%\n bucket 39: 10%\n Entering block accumulator loop for bucket 41:\n bucket 40: 20%\n bucket 39: 20%\n bucket 41: 10%\n bucket 40: 30%\n bucket 39: 30%\n bucket 41: 20%\n bucket 40: 40%\n bucket 39: 40%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 39: 50%\n bucket 40: 60%\n bucket 41: 50%\n bucket 39: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 39: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 39: 80%\n bucket 41: 90%\n bucket 40: 90%\n bucket 39: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 42 of 60\n Reserving size (126) for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Calculating Z arrays for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 43:\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 42: 10%\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 42: 20%\n Entering block accumulator loop for bucket 45:\n bucket 43: 20%\n bucket 42: 30%\n bucket 45: 10%\n bucket 44: 10%\n bucket 42: 40%\n bucket 43: 30%\n bucket 42: 50%\n bucket 44: 20%\n bucket 45: 20%\n bucket 42: 60%\n bucket 43: 40%\n bucket 44: 30%\n bucket 45: 30%\n bucket 42: 70%\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 44: 40%\n bucket 45: 40%\n bucket 42: 80%\n bucket 43: 50%\n bucket 44: 50%\n bucket 45: 50%\n bucket 42: 90%\n Entering block accumulator loop for bucket 46:\n bucket 43: 60%\n bucket 45: 60%\n bucket 44: 60%\n bucket 45: 70%\n bucket 46: 10%\n bucket 43: 70%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 44: 70%\n bucket 46: 20%\n bucket 43: 80%\n bucket 45: 80%\n bucket 44: 80%\n bucket 46: 30%\n bucket 43: 90%\n bucket 45: 90%\n bucket 44: 90%\n bucket 46: 40%\n bucket 45: 100%\n bucket 43: 100%\n Sorting block of length 79 for bucket 45\n bucket 44: 100%\n bucket 46: 50%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n (Using difference cover)\n bucket 46: 60%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 46: 70%\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n Sorting block time: 00:00:00\n bucket 48: 80%\nReturning block of 84 for bucket 47\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 50:\n bucket 49: 10%\n bucket 50: 10%\n bucket 49: 20%\n bucket 50: 20%\n bucket 49: 30%\n bucket 50: 30%\n bucket 49: 40%\n bucket 50: 40%\n bucket 49: 50%\n bucket 50: 50%\n bucket 49: 60%\n bucket 50: 60%\n bucket 49: 70%\n bucket 50: 70%\n bucket 49: 80%\n bucket 50: 80%\n bucket 49: 90%\n bucket 50: 90%\n bucket 49: 100%\n bucket 50: 100%\n Sorting block of length 74 for bucket 49\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n bucket 51: 50%\n Calculating Z arrays for bucket 52\n bucket 51: 60%\n Entering block accumulator loop for bucket 52:\n bucket 51: 70%\n bucket 52: 10%\n bucket 51: 80%\n bucket 52: 20%\n bucket 51: 90%\n bucket 52: 30%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\nGetting block 55 of 60\nGetting block 54 of 60\n Reserving size (126) for bucket 55\n bucket 53: 20%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 55\n Calculating Z arrays for bucket 54\n bucket 53: 30%\n bucket 53: 40%\n Entering block accumulator loop for bucket 55:\n bucket 53: 50%\n Entering block accumulator loop for bucket 54:\n bucket 55: 10%\n bucket 53: 60%\n bucket 54: 10%\n bucket 53: 70%\n bucket 55: 20%\n bucket 54: 20%\n bucket 53: 80%\n bucket 55: 30%\n bucket 54: 30%\n bucket 53: 90%\n bucket 55: 40%\n bucket 53: 100%\n bucket 54: 40%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 55: 50%\n bucket 54: 50%\n bucket 55: 60%\n bucket 54: 60%\n bucket 55: 70%\n bucket 54: 70%\n bucket 55: 80%\n bucket 54: 80%\n bucket 55: 90%\n bucket 54: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n bucket 56: 60%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Calculating Z arrays for bucket 57\n bucket 56: 70%\n bucket 56: 80%\n Entering block accumulator loop for bucket 58:\n bucket 56: 90%\n Entering block accumulator loop for bucket 57:\n bucket 56: 100%\n bucket 58: 10%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 10%\n bucket 58: 20%\n bucket 57: 20%\n bucket 58: 30%\n bucket 57: 30%\n bucket 58: 40%\n bucket 57: 40%\n bucket 58: 50%\n bucket 57: 50%\n bucket 58: 60%\n bucket 57: 60%\n bucket 58: 70%\n bucket 57: 70%\n bucket 58: 80%\n bucket 57: 80%\n bucket 58: 90%\n bucket 58: 100%\n bucket 57: 90%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 60: 20%\n bucket 59: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 59: 30%\n bucket 60: 50%\n bucket 60: 60%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 60: 70%\n bucket 59: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n bucket 59: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were unpaired; of these:\n 0 (0.00%) aligned 0 times\n 10 (100.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n100.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\nGetting block 3 of 60\n Entering block accumulator loop for bucket 1:\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 2: 10%\n bucket 1: 10%\n bucket 2: 20%\n Entering block accumulator loop for bucket 3:\n bucket 1: 20%\n bucket 2: 30%\n bucket 1: 30%\n bucket 2: 40%\nGetting block 4 of 60\nGetting block 5 of 60\n bucket 3: 10%\nGetting block 6 of 60\n bucket 1: 40%\n bucket 3: 20%\nGetting block 8 of 60\n Reserving size (126) for bucket 4\n Reserving size (126) for bucket 8\n bucket 3: 30%\n Calculating Z arrays for bucket 4\n bucket 1: 50%\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 8\n bucket 1: 60%\n Reserving size (126) for bucket 6\n Calculating Z arrays for bucket 5\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 4:\n bucket 1: 70%\n Entering block accumulator loop for bucket 5:\n bucket 3: 40%\n bucket 2: 50%\n bucket 4: 10%\n bucket 1: 80%\n Entering block accumulator loop for bucket 6:\n bucket 3: 50%\n bucket 5: 10%\n Entering block accumulator loop for bucket 8:\n bucket 4: 20%\n bucket 5: 20%\n bucket 6: 10%\n bucket 3: 60%\n bucket 4: 30%\n bucket 2: 60%\n bucket 8: 10%\n bucket 3: 70%\n bucket 1: 90%\n bucket 8: 20%\n bucket 2: 70%\n bucket 3: 80%\n bucket 4: 40%\n bucket 8: 30%\n Calculating Z arrays for bucket 7\n bucket 4: 50%\n bucket 6: 20%\n bucket 1: 100%\n bucket 4: 60%\n bucket 2: 80%\n bucket 3: 90%\n bucket 5: 30%\n bucket 2: 90%\n bucket 6: 30%\n bucket 3: 100%\n bucket 2: 100%\n bucket 4: 70%\n bucket 6: 40%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Entering block accumulator loop for bucket 7:\n bucket 8: 40%\n bucket 5: 40%\n bucket 6: 50%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 8: 50%\n bucket 5: 50%\n bucket 6: 60%\n bucket 8: 60%\n bucket 7: 10%\n bucket 6: 70%\n bucket 4: 80%\n bucket 8: 70%\n bucket 6: 80%\n bucket 5: 60%\n bucket 7: 20%\n bucket 8: 80%\n bucket 6: 90%\n bucket 7: 30%\n bucket 4: 90%\n bucket 8: 90%\n bucket 7: 40%\n bucket 5: 70%\n bucket 6: 100%\n bucket 8: 100%\n bucket 7: 50%\n bucket 4: 100%\n Sorting block of length 94 for bucket 8\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n (Using difference cover)\n Sorting block of length 68 for bucket 4\n bucket 5: 80%\n (Using difference cover)\n bucket 7: 60%\n bucket 5: 90%\n bucket 7: 70%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Entering block accumulator loop for bucket 9:\n Calculating Z arrays for bucket 10\n bucket 9: 10%\n bucket 9: 20%\n Entering block accumulator loop for bucket 10:\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 9: 30%\n bucket 10: 10%\n bucket 9: 40%\n bucket 10: 20%\n bucket 9: 50%\n Entering block accumulator loop for bucket 11:\n bucket 9: 60%\n bucket 10: 30%\n bucket 11: 10%\n bucket 10: 40%\n bucket 9: 70%\n bucket 11: 20%\n bucket 10: 50%\n bucket 9: 80%\n bucket 11: 30%\n bucket 10: 60%\n bucket 9: 90%\n bucket 11: 40%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 70%\n bucket 11: 50%\n bucket 10: 80%\n bucket 11: 60%\n bucket 10: 90%\n bucket 11: 70%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 13:\n Entering block accumulator loop for bucket 12:\n bucket 13: 10%\n bucket 12: 10%\n bucket 12: 20%\n bucket 13: 20%\n bucket 12: 30%\n bucket 13: 30%\n bucket 12: 40%\n bucket 13: 40%\n bucket 12: 50%\n bucket 13: 50%\n bucket 12: 60%\n bucket 13: 60%\n bucket 12: 70%\n bucket 13: 70%\n bucket 12: 80%\n bucket 13: 80%\n bucket 12: 90%\n bucket 13: 90%\n bucket 12: 100%\n bucket 13: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n Entering block accumulator loop for bucket 15:\n bucket 14: 20%\n bucket 14: 30%\n bucket 15: 10%\n bucket 14: 40%\n bucket 15: 20%\n bucket 14: 50%\n bucket 15: 30%\n bucket 14: 60%\n bucket 15: 40%\n bucket 14: 70%\n bucket 15: 50%\n bucket 14: 80%\n bucket 15: 60%\n bucket 14: 90%\n bucket 15: 70%\n bucket 14: 100%\n bucket 15: 80%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 10%\n bucket 16: 20%\nGetting block 18 of 60\n bucket 16: 30%\n Reserving size (126) for bucket 18\n Entering block accumulator loop for bucket 17:\n bucket 16: 40%\n Calculating Z arrays for bucket 18\n bucket 17: 10%\n bucket 16: 50%\n bucket 17: 20%\n Entering block accumulator loop for bucket 18:\n bucket 16: 60%\n bucket 17: 30%\n bucket 18: 10%\n bucket 16: 70%\n bucket 18: 20%\n bucket 16: 80%\n bucket 17: 40%\n bucket 18: 30%\n bucket 16: 90%\n bucket 17: 50%\n bucket 18: 40%\n bucket 16: 100%\n bucket 17: 60%\n bucket 18: 50%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 70%\n bucket 18: 60%\n bucket 17: 80%\n bucket 18: 70%\n bucket 17: 90%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n bucket 21: 90%\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n (Using difference cover)\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 22: 40%\n bucket 23: 20%\n bucket 22: 50%\n bucket 23: 30%\n bucket 22: 60%\n bucket 23: 40%\n bucket 22: 70%\n bucket 23: 50%\n bucket 22: 80%\n bucket 23: 60%\n bucket 22: 90%\n bucket 23: 70%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Entering block accumulator loop for bucket 24:\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 10%\n bucket 24: 20%\n Entering block accumulator loop for bucket 25:\n bucket 24: 30%\n bucket 25: 10%\n bucket 24: 40%\n bucket 24: 50%\n bucket 25: 20%\n bucket 24: 60%\n bucket 25: 30%\n bucket 24: 70%\n bucket 25: 40%\n bucket 24: 80%\n bucket 25: 50%\n bucket 24: 90%\n bucket 25: 60%\n bucket 24: 100%\n bucket 25: 70%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 60\n Entering block accumulator loop for bucket 27:\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 10%\n Entering block accumulator loop for bucket 28:\n bucket 27: 20%\n bucket 27: 30%\n bucket 28: 10%\n bucket 27: 40%\n bucket 28: 20%\n bucket 27: 50%\n bucket 27: 60%\n bucket 28: 30%\n bucket 27: 70%\n bucket 28: 40%\n bucket 27: 80%\n bucket 28: 50%\n bucket 27: 90%\n bucket 28: 60%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 29: 30%\n Entering block accumulator loop for bucket 31:\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 31: 10%\n bucket 29: 40%\n bucket 31: 20%\n Entering block accumulator loop for bucket 30:\n bucket 29: 50%\n bucket 31: 30%\n bucket 30: 10%\n bucket 29: 60%\n bucket 31: 40%\n bucket 30: 20%\n bucket 29: 70%\n bucket 31: 50%\n bucket 30: 30%\n bucket 29: 80%\n bucket 31: 60%\n bucket 30: 40%\n bucket 29: 90%\n bucket 31: 70%\n bucket 30: 50%\n bucket 29: 100%\n bucket 31: 80%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 60%\n bucket 31: 90%\n bucket 30: 70%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 32:\n Entering block accumulator loop for bucket 33:\n bucket 32: 10%\n bucket 33: 10%\n bucket 32: 20%\n bucket 33: 20%\n bucket 32: 30%\n bucket 33: 30%\n bucket 32: 40%\n bucket 33: 40%\n bucket 32: 50%\n bucket 33: 50%\n bucket 32: 60%\n bucket 33: 60%\n bucket 33: 70%\n bucket 32: 70%\n bucket 33: 80%\n bucket 32: 80%\n bucket 33: 90%\n bucket 33: 100%\n bucket 32: 90%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\nGetting block 35 of 60\n bucket 34: 40%\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 50%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 35:\n bucket 34: 60%\n bucket 34: 70%\n Entering block accumulator loop for bucket 36:\n bucket 35: 10%\n bucket 34: 80%\n bucket 36: 10%\n bucket 34: 90%\n bucket 35: 20%\n bucket 36: 20%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 30%\n bucket 36: 30%\n bucket 35: 40%\n bucket 36: 40%\n bucket 35: 50%\n bucket 36: 50%\n bucket 35: 60%\n bucket 36: 60%\n bucket 35: 70%\n bucket 36: 70%\n bucket 35: 80%\n bucket 36: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Entering block accumulator loop for bucket 37:\n Calculating Z arrays for bucket 38\n bucket 37: 10%\n Entering block accumulator loop for bucket 38:\n bucket 37: 20%\n bucket 37: 30%\n bucket 38: 10%\n bucket 37: 40%\n bucket 38: 20%\n bucket 37: 50%\n bucket 38: 30%\n bucket 37: 60%\n bucket 38: 40%\n bucket 37: 70%\n bucket 38: 50%\n bucket 37: 80%\n bucket 38: 60%\n bucket 37: 90%\n bucket 38: 70%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 41 of 60\n Entering block accumulator loop for bucket 40:\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 39:\n bucket 40: 10%\n bucket 39: 10%\n Entering block accumulator loop for bucket 41:\n bucket 40: 20%\n bucket 39: 20%\n bucket 41: 10%\n bucket 40: 30%\n bucket 39: 30%\n bucket 41: 20%\n bucket 40: 40%\n bucket 39: 40%\n bucket 41: 30%\n bucket 40: 50%\n bucket 41: 40%\n bucket 39: 50%\n bucket 40: 60%\n bucket 41: 50%\n bucket 39: 60%\n bucket 41: 60%\n bucket 40: 70%\n bucket 39: 70%\n bucket 41: 70%\n bucket 40: 80%\n bucket 41: 80%\n bucket 39: 80%\n bucket 41: 90%\n bucket 40: 90%\n bucket 39: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 42 of 60\n Reserving size (126) for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Calculating Z arrays for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 43:\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 42: 10%\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 42: 20%\n Entering block accumulator loop for bucket 45:\n bucket 43: 20%\n bucket 42: 30%\n bucket 45: 10%\n bucket 44: 10%\n bucket 42: 40%\n bucket 43: 30%\n bucket 42: 50%\n bucket 44: 20%\n bucket 45: 20%\n bucket 42: 60%\n bucket 43: 40%\n bucket 44: 30%\n bucket 45: 30%\n bucket 42: 70%\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 44: 40%\n bucket 45: 40%\n bucket 42: 80%\n bucket 43: 50%\n bucket 44: 50%\n bucket 45: 50%\n bucket 42: 90%\n Entering block accumulator loop for bucket 46:\n bucket 43: 60%\n bucket 45: 60%\n bucket 44: 60%\n bucket 45: 70%\n bucket 46: 10%\n bucket 43: 70%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 44: 70%\n bucket 46: 20%\n bucket 43: 80%\n bucket 45: 80%\n bucket 44: 80%\n bucket 46: 30%\n bucket 43: 90%\n bucket 45: 90%\n bucket 44: 90%\n bucket 46: 40%\n bucket 45: 100%\n bucket 43: 100%\n Sorting block of length 79 for bucket 45\n bucket 44: 100%\n bucket 46: 50%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n (Using difference cover)\n bucket 46: 60%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 46: 70%\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n Sorting block time: 00:00:00\n bucket 48: 80%\nReturning block of 84 for bucket 47\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 50:\n bucket 49: 10%\n bucket 50: 10%\n bucket 49: 20%\n bucket 50: 20%\n bucket 49: 30%\n bucket 50: 30%\n bucket 49: 40%\n bucket 50: 40%\n bucket 49: 50%\n bucket 50: 50%\n bucket 49: 60%\n bucket 50: 60%\n bucket 49: 70%\n bucket 50: 70%\n bucket 49: 80%\n bucket 50: 80%\n bucket 49: 90%\n bucket 50: 90%\n bucket 49: 100%\n bucket 50: 100%\n Sorting block of length 74 for bucket 49\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n bucket 51: 50%\n Calculating Z arrays for bucket 52\n bucket 51: 60%\n Entering block accumulator loop for bucket 52:\n bucket 51: 70%\n bucket 52: 10%\n bucket 51: 80%\n bucket 52: 20%\n bucket 51: 90%\n bucket 52: 30%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\nGetting block 55 of 60\nGetting block 54 of 60\n Reserving size (126) for bucket 55\n bucket 53: 20%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 55\n Calculating Z arrays for bucket 54\n bucket 53: 30%\n bucket 53: 40%\n Entering block accumulator loop for bucket 55:\n bucket 53: 50%\n Entering block accumulator loop for bucket 54:\n bucket 55: 10%\n bucket 53: 60%\n bucket 54: 10%\n bucket 53: 70%\n bucket 55: 20%\n bucket 54: 20%\n bucket 53: 80%\n bucket 55: 30%\n bucket 54: 30%\n bucket 53: 90%\n bucket 55: 40%\n bucket 53: 100%\n bucket 54: 40%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 55: 50%\n bucket 54: 50%\n bucket 55: 60%\n bucket 54: 60%\n bucket 55: 70%\n bucket 54: 70%\n bucket 55: 80%\n bucket 54: 80%\n bucket 55: 90%\n bucket 54: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n bucket 56: 60%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Calculating Z arrays for bucket 57\n bucket 56: 70%\n bucket 56: 80%\n Entering block accumulator loop for bucket 58:\n bucket 56: 90%\n Entering block accumulator loop for bucket 57:\n bucket 56: 100%\n bucket 58: 10%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 10%\n bucket 58: 20%\n bucket 57: 20%\n bucket 58: 30%\n bucket 57: 30%\n bucket 58: 40%\n bucket 57: 40%\n bucket 58: 50%\n bucket 57: 50%\n bucket 58: 60%\n bucket 57: 60%\n bucket 58: 70%\n bucket 57: 70%\n bucket 58: 80%\n bucket 57: 80%\n bucket 58: 90%\n bucket 58: 100%\n bucket 57: 90%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 60: 20%\n bucket 59: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 59: 30%\n bucket 60: 50%\n bucket 60: 60%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 60: 70%\n bucket 59: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 59: 90%\n bucket 60: 100%\n bucket 59: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were unpaired; of these:\n 0 (0.00%) aligned 0 times\n 10 (100.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n100.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:06:57", "plugin": "core", "name": "end_epoch", "raw_value": "1725001617.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:06:56", "plugin": "core", "name": "start_epoch", "raw_value": "1725001616.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-16", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 16, "time_seconds": 11.858004331588745, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "hisat2/2.2.1+galaxy1-16", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 16, "time_seconds": 34.352033376693726, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "8916ff9dbfc5c821"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "e99911308db98f0d"}, "library|type": "paired_interleaved", "adv|sam_options|no_unal": true, "adv|sam_options|read_groups|read_groups_0|rg": "BC:test1", "adv|sam_options|read_groups|read_groups_1|rg": "CN:test2", "adv|sam_options|read_groups|rg_labels": "Yes", "adv|sam_options|chr_text": "--add-chrname", "adv|sam_options|omit_sec_seq": true, "adv|sam_options|sam_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "33d2eb019e2e20b5", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:07:29.334675", "update_time": "2024-08-30T07:07:42.539555", "galaxy_version": "24.1", "external_id": "gxy-ddxgr", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/e/2/f/dataset_e2f9e556-ecc3-457a-aa96-cc1836e0ff82.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && bzcat '/galaxy/server/database/objects/c/5/2/dataset_c5287dec-668d-4476-8d13-6e90612b2f5f.dat' | seqtk seq -1 /dev/stdin > input_f.fastq && bzcat '/galaxy/server/database/objects/c/5/2/dataset_c5287dec-668d-4476-8d13-6e90612b2f5f.dat' | seqtk seq -2 /dev/stdin > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq --no-unal --rg-id 'read_group' --rg 'BC:test1' --rg 'CN:test2' --add-chrname --omit-sec-seq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/2/1/a/dataset_21a85810-ac97-41a7-a377-dfa2126daced.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 1, \"chr_text\": \"--add-chrname\", \"no_unal\": true, \"omit_sec_seq\": true, \"read_groups\": {\"__current_case__\": 1, \"read_groups\": [{\"__index__\": 0, \"rg\": \"BC:test1\"}, {\"__index__\": 1, \"rg\": \"CN:test2\"}], \"rg_id\": \"read_group\", \"rg_labels\": \"Yes\"}, \"sam_options_selector\": \"advanced\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 233, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 232, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "8916ff9dbfc5c821", "src": "hda", "uuid": "e2f9e556-ecc3-457a-aa96-cc1836e0ff82"}, "library|input_1": {"id": "e99911308db98f0d", "src": "hda", "uuid": "c5287dec-668d-4476-8d13-6e90612b2f5f"}}, "outputs": {"output_alignments": {"id": "9f23ed907fcd9227", "src": "hda", "uuid": "21a85810-ac97-41a7-a377-dfa2126daced"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n bucket 2: 10%\nGetting block 4 of 60\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 2: 20%\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 3:\nGetting block 6 of 60\nGetting block 7 of 60\n Reserving size (126) for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Calculating Z arrays for bucket 7\n bucket 2: 30%\n Calculating Z arrays for bucket 8\n Reserving size (126) for bucket 6\n bucket 1: 20%\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 8:\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 7:\n bucket 1: 30%\n Entering block accumulator loop for bucket 5:\n bucket 8: 10%\n Entering block accumulator loop for bucket 6:\n bucket 7: 10%\n bucket 3: 10%\n bucket 1: 40%\n bucket 5: 10%\n bucket 8: 20%\n Calculating Z arrays for bucket 4\n bucket 6: 10%\n bucket 8: 30%\n bucket 5: 20%\n bucket 7: 20%\n bucket 3: 20%\n bucket 8: 40%\n Entering block accumulator loop for bucket 4:\n bucket 3: 30%\n bucket 8: 50%\n bucket 1: 50%\n bucket 6: 20%\n bucket 5: 30%\n bucket 7: 30%\n bucket 3: 40%\n bucket 8: 60%\n bucket 7: 40%\n bucket 2: 40%\n bucket 3: 50%\n bucket 5: 40%\n bucket 1: 60%\n bucket 6: 30%\n bucket 7: 50%\n bucket 8: 70%\n bucket 1: 70%\n bucket 6: 40%\n bucket 4: 10%\n bucket 2: 50%\n bucket 6: 50%\n bucket 1: 80%\n bucket 5: 50%\n bucket 6: 60%\n bucket 7: 60%\n bucket 5: 60%\n bucket 4: 20%\n bucket 7: 70%\n bucket 8: 80%\n bucket 4: 30%\n bucket 7: 80%\n bucket 3: 60%\n bucket 5: 70%\n bucket 7: 90%\n bucket 3: 70%\n bucket 6: 70%\n bucket 4: 40%\n bucket 1: 90%\n bucket 5: 80%\n bucket 7: 100%\n bucket 2: 60%\n bucket 1: 100%\n bucket 6: 80%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 3: 80%\n bucket 8: 90%\n bucket 6: 90%\n bucket 3: 90%\n bucket 8: 100%\n bucket 2: 70%\n bucket 5: 90%\n bucket 6: 100%\n Sorting block of length 42 for bucket 1\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n (Using difference cover)\n bucket 3: 100%\n bucket 2: 80%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 5: 100%\n bucket 2: 90%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 4: 50%\n bucket 2: 100%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 4: 60%\n bucket 4: 70%\n bucket 4: 80%\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\nGetting block 10 of 60\n bucket 9: 40%\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n Entering block accumulator loop for bucket 10:\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 40%\n bucket 10: 50%\n Entering block accumulator loop for bucket 11:\n bucket 10: 60%\n bucket 11: 10%\n bucket 10: 70%\n bucket 11: 20%\n bucket 10: 80%\n bucket 10: 90%\n bucket 11: 30%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n Entering block accumulator loop for bucket 12:\n bucket 13: 20%\n bucket 12: 10%\n bucket 13: 30%\n bucket 12: 20%\n bucket 13: 40%\n bucket 12: 30%\n bucket 13: 50%\n bucket 12: 40%\n bucket 13: 60%\n bucket 12: 50%\n bucket 13: 70%\n bucket 12: 60%\n bucket 13: 80%\n bucket 13: 90%\n bucket 12: 70%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n bucket 14: 60%\n Calculating Z arrays for bucket 15\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n Entering block accumulator loop for bucket 15:\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Entering block accumulator loop for bucket 17:\n bucket 16: 50%\n bucket 17: 10%\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 20%\n bucket 16: 60%\n bucket 17: 30%\n Entering block accumulator loop for bucket 18:\n bucket 17: 40%\n bucket 16: 70%\n bucket 17: 50%\n bucket 18: 10%\n bucket 17: 60%\n bucket 16: 80%\n bucket 18: 20%\n bucket 17: 70%\n bucket 16: 90%\n bucket 18: 30%\n bucket 17: 80%\n bucket 16: 100%\n bucket 18: 40%\n Sorting block of length 100 for bucket 16\n bucket 17: 90%\n bucket 18: 50%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n (Using difference cover)\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\n Sorting block time: 00:00:00\n Entering block accumulator loop for bucket 21:\nReturning block of 108 for bucket 19\n bucket 20: 10%\n bucket 21: 10%\n bucket 20: 20%\n bucket 21: 20%\n bucket 20: 30%\n bucket 21: 30%\n bucket 20: 40%\n bucket 21: 40%\n bucket 20: 50%\n bucket 21: 50%\n bucket 20: 60%\n bucket 21: 60%\n bucket 20: 70%\n bucket 21: 70%\n bucket 20: 80%\n bucket 21: 80%\n bucket 20: 90%\n bucket 21: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 22: 30%\nGetting block 23 of 60\n bucket 22: 40%\n Entering block accumulator loop for bucket 24:\n Reserving size (126) for bucket 23\n bucket 22: 50%\n Calculating Z arrays for bucket 23\n bucket 24: 10%\n bucket 22: 60%\n bucket 24: 20%\n Entering block accumulator loop for bucket 23:\n bucket 22: 70%\n bucket 24: 30%\n bucket 22: 80%\n bucket 23: 10%\n bucket 24: 40%\n bucket 22: 90%\n bucket 23: 20%\n bucket 24: 50%\n bucket 22: 100%\n bucket 24: 60%\n bucket 23: 30%\n Sorting block of length 80 for bucket 22\n bucket 24: 70%\n bucket 23: 40%\n (Using difference cover)\n bucket 24: 80%\n bucket 23: 50%\n bucket 24: 90%\n bucket 23: 60%\n bucket 24: 100%\n bucket 23: 70%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n bucket 25: 90%\n bucket 25: 100%\n Entering block accumulator loop for bucket 26:\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 20%\n Entering block accumulator loop for bucket 28:\n bucket 27: 30%\n bucket 27: 40%\n bucket 28: 10%\n bucket 27: 50%\n bucket 28: 20%\n bucket 27: 60%\n bucket 28: 30%\n bucket 27: 70%\n bucket 28: 40%\n bucket 27: 80%\n bucket 28: 50%\n bucket 27: 90%\n bucket 28: 60%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 30:\n bucket 29: 10%\n bucket 30: 10%\n bucket 29: 20%\n bucket 30: 20%\n bucket 30: 30%\n bucket 29: 30%\n bucket 30: 40%\n bucket 29: 40%\n bucket 30: 50%\n bucket 29: 50%\n bucket 30: 60%\n bucket 29: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 29: 70%\n bucket 30: 90%\n bucket 29: 80%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\nGetting block 33 of 60\n bucket 32: 20%\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 30%\n bucket 32: 40%\n Entering block accumulator loop for bucket 33:\n bucket 32: 50%\n bucket 33: 10%\n bucket 32: 60%\n bucket 33: 20%\n bucket 32: 70%\n bucket 33: 30%\n bucket 32: 80%\n bucket 33: 40%\n bucket 32: 90%\n bucket 33: 50%\n bucket 32: 100%\n bucket 33: 60%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Entering block accumulator loop for bucket 34:\n Calculating Z arrays for bucket 35\n bucket 34: 10%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n Calculating Z arrays for bucket 36\n bucket 34: 30%\n bucket 35: 10%\n Entering block accumulator loop for bucket 36:\n bucket 34: 40%\n bucket 35: 20%\n bucket 34: 50%\n bucket 36: 10%\n bucket 35: 30%\n bucket 34: 60%\n bucket 36: 20%\n bucket 34: 70%\n bucket 35: 40%\n bucket 36: 30%\n bucket 34: 80%\n bucket 35: 50%\n bucket 36: 40%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 50%\n bucket 35: 60%\n bucket 34: 90%\n bucket 35: 70%\n bucket 36: 60%\n bucket 34: 100%\n Entering block accumulator loop for bucket 37:\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 80%\n bucket 36: 70%\n bucket 37: 10%\n bucket 35: 90%\n bucket 36: 80%\n bucket 35: 100%\n bucket 37: 20%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 90%\n bucket 37: 30%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n Sorting block time: 00:00:00\n bucket 37: 80%\nReturning block of 123 for bucket 34\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 39:\n bucket 40: 10%\n bucket 39: 10%\n bucket 40: 20%\n bucket 39: 20%\n bucket 40: 30%\n bucket 39: 30%\n bucket 40: 40%\n bucket 39: 40%\n bucket 40: 50%\n bucket 39: 50%\n bucket 40: 60%\n bucket 39: 60%\n bucket 40: 70%\n bucket 39: 70%\n bucket 40: 80%\n bucket 39: 80%\n bucket 40: 90%\n bucket 39: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 41:\n bucket 42: 10%\n bucket 41: 10%\n bucket 41: 20%\n bucket 42: 20%\n bucket 41: 30%\n bucket 42: 30%\n bucket 41: 40%\n bucket 42: 40%\n bucket 41: 50%\n bucket 42: 50%\n bucket 41: 60%\n bucket 42: 60%\n bucket 41: 70%\n bucket 42: 70%\n bucket 41: 80%\n bucket 42: 80%\n bucket 41: 90%\n bucket 42: 90%\n bucket 41: 100%\n bucket 42: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 43: 20%\n bucket 43: 30%\n bucket 44: 10%\n bucket 43: 40%\n bucket 44: 20%\n bucket 43: 50%\n bucket 44: 30%\n bucket 43: 60%\n bucket 44: 40%\n bucket 43: 70%\n bucket 43: 80%\n bucket 44: 50%\n bucket 43: 90%\n bucket 44: 60%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n Entering block accumulator loop for bucket 46:\n bucket 45: 20%\n bucket 46: 10%\n bucket 45: 30%\n bucket 46: 20%\n bucket 45: 40%\n bucket 46: 30%\n bucket 45: 50%\n bucket 46: 40%\n bucket 45: 60%\n bucket 46: 50%\n bucket 46: 60%\n bucket 45: 70%\n bucket 46: 70%\n bucket 45: 80%\n bucket 46: 80%\n bucket 45: 90%\n bucket 46: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Entering block accumulator loop for bucket 47:\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 10%\nGetting block 49 of 60\n bucket 47: 20%\n Entering block accumulator loop for bucket 48:\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 47: 30%\n bucket 48: 10%\n bucket 47: 40%\n bucket 48: 20%\n Entering block accumulator loop for bucket 49:\n bucket 47: 50%\n bucket 48: 30%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 47: 60%\n bucket 49: 10%\n bucket 48: 40%\n bucket 47: 70%\n bucket 48: 50%\n bucket 47: 80%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 48: 60%\n bucket 47: 90%\n bucket 49: 30%\n bucket 47: 100%\n bucket 48: 70%\n bucket 50: 10%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 49: 40%\n bucket 48: 80%\n bucket 50: 20%\n bucket 48: 90%\n bucket 49: 50%\n bucket 50: 30%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 60%\n bucket 50: 40%\n bucket 49: 70%\n bucket 50: 50%\n bucket 49: 80%\n bucket 50: 60%\n bucket 49: 90%\n bucket 50: 70%\n bucket 49: 100%\n bucket 50: 80%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 40%\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 51: 50%\n Entering block accumulator loop for bucket 52:\n bucket 51: 60%\n bucket 52: 10%\n Entering block accumulator loop for bucket 53:\n bucket 51: 70%\n bucket 52: 20%\n bucket 53: 10%\n bucket 51: 80%\n bucket 52: 30%\n bucket 53: 20%\n bucket 51: 90%\n bucket 52: 40%\n bucket 53: 30%\n bucket 51: 100%\n bucket 52: 50%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 53: 40%\n bucket 52: 60%\n bucket 53: 50%\n bucket 52: 70%\n bucket 53: 60%\n bucket 52: 80%\n bucket 52: 90%\n bucket 53: 70%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 56:\n bucket 55: 10%\n bucket 56: 10%\n bucket 55: 20%\n bucket 56: 20%\n bucket 55: 30%\n bucket 56: 30%\n bucket 55: 40%\n bucket 56: 40%\n bucket 55: 50%\n bucket 56: 50%\n bucket 55: 60%\n bucket 56: 60%\n bucket 55: 70%\n bucket 56: 70%\n bucket 55: 80%\n bucket 56: 80%\n bucket 55: 90%\n bucket 56: 90%\n bucket 55: 100%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 40%\n bucket 57: 50%\n Entering block accumulator loop for bucket 58:\n bucket 57: 60%\n bucket 58: 10%\n bucket 57: 70%\n bucket 58: 20%\n bucket 57: 80%\n bucket 58: 30%\n bucket 57: 90%\n bucket 58: 40%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n Entering block accumulator loop for bucket 59:\n bucket 60: 10%\n bucket 59: 10%\n bucket 60: 20%\n bucket 59: 20%\n bucket 60: 30%\n bucket 59: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 59: 40%\n bucket 60: 60%\n bucket 59: 50%\n bucket 60: 70%\n bucket 59: 60%\n bucket 60: 80%\n bucket 59: 70%\n bucket 60: 90%\n bucket 60: 100%\n bucket 59: 80%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n bucket 2: 10%\nGetting block 4 of 60\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 2: 20%\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 3:\nGetting block 6 of 60\nGetting block 7 of 60\n Reserving size (126) for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Calculating Z arrays for bucket 7\n bucket 2: 30%\n Calculating Z arrays for bucket 8\n Reserving size (126) for bucket 6\n bucket 1: 20%\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 8:\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 7:\n bucket 1: 30%\n Entering block accumulator loop for bucket 5:\n bucket 8: 10%\n Entering block accumulator loop for bucket 6:\n bucket 7: 10%\n bucket 3: 10%\n bucket 1: 40%\n bucket 5: 10%\n bucket 8: 20%\n Calculating Z arrays for bucket 4\n bucket 6: 10%\n bucket 8: 30%\n bucket 5: 20%\n bucket 7: 20%\n bucket 3: 20%\n bucket 8: 40%\n Entering block accumulator loop for bucket 4:\n bucket 3: 30%\n bucket 8: 50%\n bucket 1: 50%\n bucket 6: 20%\n bucket 5: 30%\n bucket 7: 30%\n bucket 3: 40%\n bucket 8: 60%\n bucket 7: 40%\n bucket 2: 40%\n bucket 3: 50%\n bucket 5: 40%\n bucket 1: 60%\n bucket 6: 30%\n bucket 7: 50%\n bucket 8: 70%\n bucket 1: 70%\n bucket 6: 40%\n bucket 4: 10%\n bucket 2: 50%\n bucket 6: 50%\n bucket 1: 80%\n bucket 5: 50%\n bucket 6: 60%\n bucket 7: 60%\n bucket 5: 60%\n bucket 4: 20%\n bucket 7: 70%\n bucket 8: 80%\n bucket 4: 30%\n bucket 7: 80%\n bucket 3: 60%\n bucket 5: 70%\n bucket 7: 90%\n bucket 3: 70%\n bucket 6: 70%\n bucket 4: 40%\n bucket 1: 90%\n bucket 5: 80%\n bucket 7: 100%\n bucket 2: 60%\n bucket 1: 100%\n bucket 6: 80%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 3: 80%\n bucket 8: 90%\n bucket 6: 90%\n bucket 3: 90%\n bucket 8: 100%\n bucket 2: 70%\n bucket 5: 90%\n bucket 6: 100%\n Sorting block of length 42 for bucket 1\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n (Using difference cover)\n bucket 3: 100%\n bucket 2: 80%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 5: 100%\n bucket 2: 90%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 4: 50%\n bucket 2: 100%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 4: 60%\n bucket 4: 70%\n bucket 4: 80%\n bucket 4: 90%\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\nGetting block 10 of 60\n bucket 9: 40%\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n Entering block accumulator loop for bucket 10:\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 40%\n bucket 10: 50%\n Entering block accumulator loop for bucket 11:\n bucket 10: 60%\n bucket 11: 10%\n bucket 10: 70%\n bucket 11: 20%\n bucket 10: 80%\n bucket 10: 90%\n bucket 11: 30%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n Entering block accumulator loop for bucket 12:\n bucket 13: 20%\n bucket 12: 10%\n bucket 13: 30%\n bucket 12: 20%\n bucket 13: 40%\n bucket 12: 30%\n bucket 13: 50%\n bucket 12: 40%\n bucket 13: 60%\n bucket 12: 50%\n bucket 13: 70%\n bucket 12: 60%\n bucket 13: 80%\n bucket 13: 90%\n bucket 12: 70%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n bucket 14: 60%\n Calculating Z arrays for bucket 15\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n Entering block accumulator loop for bucket 15:\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Entering block accumulator loop for bucket 17:\n bucket 16: 50%\n bucket 17: 10%\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 20%\n bucket 16: 60%\n bucket 17: 30%\n Entering block accumulator loop for bucket 18:\n bucket 17: 40%\n bucket 16: 70%\n bucket 17: 50%\n bucket 18: 10%\n bucket 17: 60%\n bucket 16: 80%\n bucket 18: 20%\n bucket 17: 70%\n bucket 16: 90%\n bucket 18: 30%\n bucket 17: 80%\n bucket 16: 100%\n bucket 18: 40%\n Sorting block of length 100 for bucket 16\n bucket 17: 90%\n bucket 18: 50%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n (Using difference cover)\n bucket 18: 60%\n bucket 18: 70%\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\n Sorting block time: 00:00:00\n Entering block accumulator loop for bucket 21:\nReturning block of 108 for bucket 19\n bucket 20: 10%\n bucket 21: 10%\n bucket 20: 20%\n bucket 21: 20%\n bucket 20: 30%\n bucket 21: 30%\n bucket 20: 40%\n bucket 21: 40%\n bucket 20: 50%\n bucket 21: 50%\n bucket 20: 60%\n bucket 21: 60%\n bucket 20: 70%\n bucket 21: 70%\n bucket 20: 80%\n bucket 21: 80%\n bucket 20: 90%\n bucket 21: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 22: 30%\nGetting block 23 of 60\n bucket 22: 40%\n Entering block accumulator loop for bucket 24:\n Reserving size (126) for bucket 23\n bucket 22: 50%\n Calculating Z arrays for bucket 23\n bucket 24: 10%\n bucket 22: 60%\n bucket 24: 20%\n Entering block accumulator loop for bucket 23:\n bucket 22: 70%\n bucket 24: 30%\n bucket 22: 80%\n bucket 23: 10%\n bucket 24: 40%\n bucket 22: 90%\n bucket 23: 20%\n bucket 24: 50%\n bucket 22: 100%\n bucket 24: 60%\n bucket 23: 30%\n Sorting block of length 80 for bucket 22\n bucket 24: 70%\n bucket 23: 40%\n (Using difference cover)\n bucket 24: 80%\n bucket 23: 50%\n bucket 24: 90%\n bucket 23: 60%\n bucket 24: 100%\n bucket 23: 70%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n bucket 25: 90%\n bucket 25: 100%\n Entering block accumulator loop for bucket 26:\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 20%\n Entering block accumulator loop for bucket 28:\n bucket 27: 30%\n bucket 27: 40%\n bucket 28: 10%\n bucket 27: 50%\n bucket 28: 20%\n bucket 27: 60%\n bucket 28: 30%\n bucket 27: 70%\n bucket 28: 40%\n bucket 27: 80%\n bucket 28: 50%\n bucket 27: 90%\n bucket 28: 60%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n Entering block accumulator loop for bucket 30:\n bucket 29: 10%\n bucket 30: 10%\n bucket 29: 20%\n bucket 30: 20%\n bucket 30: 30%\n bucket 29: 30%\n bucket 30: 40%\n bucket 29: 40%\n bucket 30: 50%\n bucket 29: 50%\n bucket 30: 60%\n bucket 29: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 29: 70%\n bucket 30: 90%\n bucket 29: 80%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n bucket 31: 60%\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\nGetting block 33 of 60\n bucket 32: 20%\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 30%\n bucket 32: 40%\n Entering block accumulator loop for bucket 33:\n bucket 32: 50%\n bucket 33: 10%\n bucket 32: 60%\n bucket 33: 20%\n bucket 32: 70%\n bucket 33: 30%\n bucket 32: 80%\n bucket 33: 40%\n bucket 32: 90%\n bucket 33: 50%\n bucket 32: 100%\n bucket 33: 60%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Entering block accumulator loop for bucket 34:\n Calculating Z arrays for bucket 35\n bucket 34: 10%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n Calculating Z arrays for bucket 36\n bucket 34: 30%\n bucket 35: 10%\n Entering block accumulator loop for bucket 36:\n bucket 34: 40%\n bucket 35: 20%\n bucket 34: 50%\n bucket 36: 10%\n bucket 35: 30%\n bucket 34: 60%\n bucket 36: 20%\n bucket 34: 70%\n bucket 35: 40%\n bucket 36: 30%\n bucket 34: 80%\n bucket 35: 50%\n bucket 36: 40%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 50%\n bucket 35: 60%\n bucket 34: 90%\n bucket 35: 70%\n bucket 36: 60%\n bucket 34: 100%\n Entering block accumulator loop for bucket 37:\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 80%\n bucket 36: 70%\n bucket 37: 10%\n bucket 35: 90%\n bucket 36: 80%\n bucket 35: 100%\n bucket 37: 20%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 90%\n bucket 37: 30%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n Sorting block time: 00:00:00\n bucket 37: 80%\nReturning block of 123 for bucket 34\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 40:\n Entering block accumulator loop for bucket 39:\n bucket 40: 10%\n bucket 39: 10%\n bucket 40: 20%\n bucket 39: 20%\n bucket 40: 30%\n bucket 39: 30%\n bucket 40: 40%\n bucket 39: 40%\n bucket 40: 50%\n bucket 39: 50%\n bucket 40: 60%\n bucket 39: 60%\n bucket 40: 70%\n bucket 39: 70%\n bucket 40: 80%\n bucket 39: 80%\n bucket 40: 90%\n bucket 39: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 41:\n bucket 42: 10%\n bucket 41: 10%\n bucket 41: 20%\n bucket 42: 20%\n bucket 41: 30%\n bucket 42: 30%\n bucket 41: 40%\n bucket 42: 40%\n bucket 41: 50%\n bucket 42: 50%\n bucket 41: 60%\n bucket 42: 60%\n bucket 41: 70%\n bucket 42: 70%\n bucket 41: 80%\n bucket 42: 80%\n bucket 41: 90%\n bucket 42: 90%\n bucket 41: 100%\n bucket 42: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n Entering block accumulator loop for bucket 44:\n bucket 43: 20%\n bucket 43: 30%\n bucket 44: 10%\n bucket 43: 40%\n bucket 44: 20%\n bucket 43: 50%\n bucket 44: 30%\n bucket 43: 60%\n bucket 44: 40%\n bucket 43: 70%\n bucket 43: 80%\n bucket 44: 50%\n bucket 43: 90%\n bucket 44: 60%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n Entering block accumulator loop for bucket 46:\n bucket 45: 20%\n bucket 46: 10%\n bucket 45: 30%\n bucket 46: 20%\n bucket 45: 40%\n bucket 46: 30%\n bucket 45: 50%\n bucket 46: 40%\n bucket 45: 60%\n bucket 46: 50%\n bucket 46: 60%\n bucket 45: 70%\n bucket 46: 70%\n bucket 45: 80%\n bucket 46: 80%\n bucket 45: 90%\n bucket 46: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Entering block accumulator loop for bucket 47:\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n bucket 47: 10%\nGetting block 49 of 60\n bucket 47: 20%\n Entering block accumulator loop for bucket 48:\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 47: 30%\n bucket 48: 10%\n bucket 47: 40%\n bucket 48: 20%\n Entering block accumulator loop for bucket 49:\n bucket 47: 50%\n bucket 48: 30%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 47: 60%\n bucket 49: 10%\n bucket 48: 40%\n bucket 47: 70%\n bucket 48: 50%\n bucket 47: 80%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 48: 60%\n bucket 47: 90%\n bucket 49: 30%\n bucket 47: 100%\n bucket 48: 70%\n bucket 50: 10%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 49: 40%\n bucket 48: 80%\n bucket 50: 20%\n bucket 48: 90%\n bucket 49: 50%\n bucket 50: 30%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 60%\n bucket 50: 40%\n bucket 49: 70%\n bucket 50: 50%\n bucket 49: 80%\n bucket 50: 60%\n bucket 49: 90%\n bucket 50: 70%\n bucket 49: 100%\n bucket 50: 80%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 40%\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 51: 50%\n Entering block accumulator loop for bucket 52:\n bucket 51: 60%\n bucket 52: 10%\n Entering block accumulator loop for bucket 53:\n bucket 51: 70%\n bucket 52: 20%\n bucket 53: 10%\n bucket 51: 80%\n bucket 52: 30%\n bucket 53: 20%\n bucket 51: 90%\n bucket 52: 40%\n bucket 53: 30%\n bucket 51: 100%\n bucket 52: 50%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 53: 40%\n bucket 52: 60%\n bucket 53: 50%\n bucket 52: 70%\n bucket 53: 60%\n bucket 52: 80%\n bucket 52: 90%\n bucket 53: 70%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n Entering block accumulator loop for bucket 56:\n bucket 55: 10%\n bucket 56: 10%\n bucket 55: 20%\n bucket 56: 20%\n bucket 55: 30%\n bucket 56: 30%\n bucket 55: 40%\n bucket 56: 40%\n bucket 55: 50%\n bucket 56: 50%\n bucket 55: 60%\n bucket 56: 60%\n bucket 55: 70%\n bucket 56: 70%\n bucket 55: 80%\n bucket 56: 80%\n bucket 55: 90%\n bucket 56: 90%\n bucket 55: 100%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 40%\n bucket 57: 50%\n Entering block accumulator loop for bucket 58:\n bucket 57: 60%\n bucket 58: 10%\n bucket 57: 70%\n bucket 58: 20%\n bucket 57: 80%\n bucket 58: 30%\n bucket 57: 90%\n bucket 58: 40%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 60 of 60\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n Entering block accumulator loop for bucket 59:\n bucket 60: 10%\n bucket 59: 10%\n bucket 60: 20%\n bucket 59: 20%\n bucket 60: 30%\n bucket 59: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 59: 40%\n bucket 60: 60%\n bucket 59: 50%\n bucket 60: 70%\n bucket 59: 60%\n bucket 60: 80%\n bucket 59: 70%\n bucket 60: 90%\n bucket 60: 100%\n bucket 59: 80%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:07:31", "plugin": "core", "name": "end_epoch", "raw_value": "1725001651.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:07:30", "plugin": "core", "name": "start_epoch", "raw_value": "1725001650.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-2", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 2, "time_seconds": 54.60550594329834, "inputs": {"reference_genome|source": "indexed", "library|input_1": {"src": "hda", "id": "3b6c8dfcda395d47"}, "library|input_2": {"src": "hda", "id": "a69c3e75a061b64e"}, "library|type": "paired"}, "job": {"model_class": "Job", "id": "cd3f8a909dc3fb52", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:51:47.864746", "update_time": "2024-08-30T06:52:22.785455", "galaxy_version": "24.1", "external_id": "gxy-4mhj7", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -f -s '/galaxy/server/database/objects/c/6/d/dataset_c6d3ceee-f687-46ff-92ee-a56e660134d0.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/d/3/8/dataset_d3835e61-05ca-4ac1-b7b8-0ef663f85689.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x '/cvmfs/data.galaxyproject.org/managed/hisat2_index/apiMel4/apiMel4' -1 'input_f.fastq' -2 'input_r.fastq' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/f/5/6/dataset_f56c6840-b84d-49e1-a93f-9f69fe4a4e30.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"phiX\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/phiX.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 124, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 125, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 0, \"index\": \"apiMel4\", \"source\": \"indexed\"}"}, "inputs": {"library|input_1": {"id": "3b6c8dfcda395d47", "src": "hda", "uuid": "c6d3ceee-f687-46ff-92ee-a56e660134d0"}, "library|input_2": {"id": "a69c3e75a061b64e", "src": "hda", "uuid": "d3835e61-05ca-4ac1-b7b8-0ef663f85689"}}, "outputs": {"output_alignments": {"id": "58faae816ea8ef23", "src": "hda", "uuid": "f56c6840-b84d-49e1-a93f-9f69fe4a4e30"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "10 reads; of these:\n 10 (100.00%) were paired; of these:\n 10 (100.00%) aligned concordantly 0 times\n 0 (0.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 10 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 10 pairs aligned 0 times concordantly or discordantly; of these:\n 20 mates make up the pairs; of these:\n 20 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "10 reads; of these:\n 10 (100.00%) were paired; of these:\n 10 (100.00%) aligned concordantly 0 times\n 0 (0.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 10 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 10 pairs aligned 0 times concordantly or discordantly; of these:\n 20 mates make up the pairs; of these:\n 20 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "22 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "22.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:52:11", "plugin": "core", "name": "end_epoch", "raw_value": "1725000731.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:51:49", "plugin": "core", "name": "start_epoch", "raw_value": "1725000709.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "output_problems": ["Output output_alignments: different than expected, difference (using diff):\n( /tmp/local_bam_converted_to_sam_7wjjugps.sam v. /tmp/history_bam_converted_to_sam__q0wilm0.sam )\n--- local_file\n+++ history_data\n@@ -1,23 +1,5343 @@\n @HD\tVN:1.0\tSO:coordinate\n-@PG\tID:hisat2\tPN:hisat2\tVN:2.1.0\tCL:\"/home/maria/miniconda3/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin/hisat2-align-s --wrapper basic-0 -p 1 -x genome -1 input_f.fastq -2 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GTTCATCAGCAAACGCAGA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:14A55\tYS:i:0\tYT:Z:CP\tNH:i:1\n-phiX174_3199_3732_0:0:0_1:0:0_7\t99\tphiX174\t3199\t60\t70M\t=\t3663\t534\tCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAA\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:0\tXN:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tNM:i:0\tMD:Z:70\tYS:i:-3\tYT:Z:CP\tNH:i:1\n-phiX174_36_572_1:0:0_0:0:0_8\t163\tphiX174\t36\t60\t70M\t=\t503\t537\tTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATTACTACTGCTTGTTTACGAAT\t2222222222222222222222222222222222222222222222222222222222222222222222\tAS:i:-3\tXN:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tNM:i:1\tMD:Z:45G24\tYS:i:0\tYT:Z:CP\tNH:i:1\n********\n*SNIP 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"status": "failure"}}, {"id": "hisat2/2.2.1+galaxy1-2", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 2, "time_seconds": 13.158743858337402, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "hisat2/2.2.1+galaxy1-3", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 3, "time_seconds": 10.402784824371338, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "hisat2/2.2.1+galaxy1-3", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 3, "time_seconds": 39.521541118621826, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "e70b5c7d6296e58d"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "9b653325fbca9371"}, "library|input_2": {"src": "hda", "id": "b5cd130555fb95b9"}, "library|type": "paired", "adv|input_options|trim5": "15", "adv|input_options|trim3": "15", "adv|input_options|input_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "568deb7e518268f5", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:00:36.801196", "update_time": "2024-08-30T07:00:50.932966", "galaxy_version": "24.1", "external_id": "gxy-mffdm", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/b/5/0/dataset_b508b4b7-288c-4f9d-81f2-43d2907d8997.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/c/d/1/dataset_cd11bad5-f550-45e9-ac08-8322e88ecf6e.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/b/7/3/dataset_b73ebe41-9f9b-4655-80c6-e8a0c02e9dd1.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' --trim5 '15' --trim3 '15' --phred33 | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/d/9/5/dataset_d9590cb4-ed5e-4b3c-8628-2a5d70962173.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 1, \"input_options_selector\": \"advanced\", \"int_quals\": false, \"qupto\": \"0\", \"qv_encoding\": \"--phred33\", \"skip\": \"0\", \"solexa_quals\": false, \"trim3\": \"15\", \"trim5\": \"15\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 186, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 187, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 185, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "e70b5c7d6296e58d", "src": "hda", "uuid": "b508b4b7-288c-4f9d-81f2-43d2907d8997"}, "library|input_1": {"id": "9b653325fbca9371", "src": "hda", "uuid": "cd11bad5-f550-45e9-ac08-8322e88ecf6e"}, "library|input_2": {"id": "b5cd130555fb95b9", "src": "hda", "uuid": "b73ebe41-9f9b-4655-80c6-e8a0c02e9dd1"}}, "outputs": {"output_alignments": {"id": "9cd2ea9e0fa020ae", "src": "hda", "uuid": "d9590cb4-ed5e-4b3c-8628-2a5d70962173"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n bucket 1: 20%\nGetting block 5 of 60\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 3:\n Reserving size (126) for bucket 5\nGetting block 4 of 60\n bucket 3: 10%\n bucket 2: 10%\n Calculating Z arrays for bucket 5\n Reserving size (126) for bucket 4\n bucket 2: 20%\n bucket 3: 20%\nGetting block 6 of 60\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 6\n bucket 1: 30%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 5: 10%\n Entering block accumulator loop for bucket 4:\n bucket 1: 40%\n Calculating Z arrays for bucket 8\n bucket 3: 30%\n bucket 2: 30%\n Calculating Z arrays for bucket 6\n bucket 3: 40%\n bucket 4: 10%\n Entering block accumulator loop for bucket 8:\n bucket 1: 50%\n bucket 3: 50%\n Entering block accumulator loop for bucket 6:\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 1: 60%\n bucket 3: 60%\n bucket 2: 40%\n bucket 6: 10%\n bucket 1: 70%\n bucket 3: 70%\n bucket 4: 20%\n bucket 2: 50%\n bucket 6: 20%\n bucket 3: 80%\n bucket 8: 10%\n bucket 5: 20%\n Calculating Z arrays for bucket 7\n bucket 4: 30%\n bucket 8: 20%\n bucket 6: 30%\n bucket 2: 60%\n bucket 5: 30%\n bucket 8: 30%\n Entering block accumulator loop for bucket 7:\n bucket 1: 80%\n bucket 3: 90%\n bucket 4: 40%\n bucket 1: 90%\n bucket 8: 40%\n bucket 2: 70%\n bucket 3: 100%\n bucket 1: 100%\n bucket 4: 50%\n bucket 8: 50%\n bucket 5: 40%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 2: 80%\n bucket 4: 60%\n bucket 5: 50%\n bucket 7: 10%\n bucket 4: 70%\n bucket 2: 90%\n bucket 7: 20%\n bucket 6: 40%\n bucket 5: 60%\n bucket 8: 60%\n bucket 2: 100%\n bucket 7: 30%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 6: 50%\n bucket 8: 70%\n bucket 5: 70%\n bucket 7: 40%\n bucket 8: 80%\n bucket 6: 60%\n bucket 5: 80%\n bucket 8: 90%\n bucket 7: 50%\n bucket 6: 70%\n bucket 8: 100%\n bucket 4: 80%\n bucket 5: 90%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 6: 80%\n bucket 4: 90%\n bucket 5: 100%\n bucket 7: 60%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 90%\n bucket 7: 70%\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Entering block accumulator loop for bucket 9:\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\nGetting block 11 of 60\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n Reserving size (126) for bucket 11\n bucket 9: 30%\n Calculating Z arrays for bucket 11\n bucket 10: 10%\n bucket 9: 40%\n bucket 10: 20%\n bucket 9: 50%\n Entering block accumulator loop for bucket 11:\n bucket 10: 30%\n bucket 9: 60%\n bucket 11: 10%\n bucket 10: 40%\n bucket 11: 20%\n bucket 9: 70%\n bucket 10: 50%\n bucket 11: 30%\n bucket 10: 60%\n bucket 11: 40%\n bucket 10: 70%\n bucket 11: 50%\n bucket 10: 80%\n bucket 11: 60%\n bucket 10: 90%\n bucket 11: 70%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 80%\n bucket 11: 90%\n bucket 9: 80%\n bucket 11: 100%\n bucket 9: 90%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Entering block accumulator loop for bucket 13:\n Entering block accumulator loop for bucket 14:\n bucket 13: 10%\n bucket 13: 20%\n bucket 14: 10%\n bucket 13: 30%\n bucket 14: 20%\n bucket 13: 40%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 13: 80%\n bucket 14: 50%\n bucket 13: 90%\n bucket 14: 60%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\nGetting block 16 of 60\n bucket 15: 100%\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nGetting block 18 of 60\nReturning block of 40 for bucket 17\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Entering block accumulator loop for bucket 18:\n Calculating Z arrays for bucket 19\n bucket 18: 10%\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 18: 20%\n Entering block accumulator loop for bucket 19:\n bucket 18: 30%\n bucket 18: 40%\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 18: 50%\n bucket 19: 20%\n bucket 18: 60%\n bucket 20: 10%\n bucket 18: 70%\n bucket 19: 30%\n bucket 20: 20%\n bucket 18: 80%\n bucket 20: 30%\n bucket 18: 90%\n bucket 19: 40%\n bucket 20: 40%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 20: 50%\n bucket 19: 50%\n bucket 20: 60%\n bucket 19: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 19: 70%\n bucket 20: 90%\n bucket 19: 80%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\nGetting block 22 of 60\n bucket 21: 60%\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n Entering block accumulator loop for bucket 22:\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Entering block accumulator loop for bucket 23:\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 23: 60%\n bucket 24: 40%\n bucket 23: 70%\n bucket 24: 50%\n bucket 23: 80%\n bucket 24: 60%\n bucket 23: 90%\n bucket 24: 70%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Entering block accumulator loop for bucket 25:\n Calculating Z arrays for bucket 26\n bucket 25: 10%\n bucket 25: 20%\n Entering block accumulator loop for bucket 26:\n bucket 25: 30%\n bucket 25: 40%\n bucket 26: 10%\n bucket 25: 50%\n bucket 25: 60%\n bucket 26: 20%\n bucket 25: 70%\n bucket 25: 80%\n bucket 26: 30%\n bucket 25: 90%\n bucket 26: 40%\n bucket 26: 50%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 28:\n bucket 27: 10%\n bucket 28: 10%\n bucket 27: 20%\n bucket 28: 20%\n bucket 27: 30%\n bucket 28: 30%\n bucket 27: 40%\n bucket 28: 40%\n bucket 27: 50%\n bucket 28: 50%\n bucket 27: 60%\n bucket 28: 60%\n bucket 27: 70%\n bucket 28: 70%\n bucket 27: 80%\n bucket 28: 80%\n bucket 27: 90%\n bucket 28: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 40%\n bucket 29: 50%\n Entering block accumulator loop for bucket 30:\n bucket 29: 60%\n bucket 30: 10%\n bucket 29: 70%\n bucket 30: 20%\n bucket 29: 80%\n bucket 30: 30%\n bucket 29: 90%\n bucket 30: 40%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 32: 10%\n bucket 31: 30%\n bucket 32: 20%\n bucket 31: 40%\n bucket 32: 30%\n bucket 31: 50%\n bucket 32: 40%\n bucket 31: 60%\n bucket 32: 50%\n bucket 31: 70%\n bucket 32: 60%\n bucket 31: 80%\n bucket 32: 70%\n bucket 31: 90%\n bucket 32: 80%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 60\n Entering block accumulator loop for bucket 33:\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 10%\n Entering block accumulator loop for bucket 34:\n bucket 33: 20%\n bucket 34: 10%\n bucket 33: 30%\n bucket 34: 20%\n bucket 33: 40%\n bucket 34: 30%\n bucket 33: 50%\n bucket 34: 40%\n bucket 33: 60%\n bucket 34: 50%\n bucket 34: 60%\n bucket 33: 70%\n bucket 34: 70%\n bucket 33: 80%\n bucket 34: 80%\n bucket 33: 90%\n bucket 34: 90%\n bucket 33: 100%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 40: 20%\n bucket 39: 30%\n bucket 40: 30%\n bucket 39: 40%\n bucket 40: 40%\n bucket 39: 50%\n bucket 40: 50%\n bucket 39: 60%\n bucket 40: 60%\n bucket 39: 70%\n bucket 40: 70%\n bucket 39: 80%\n bucket 40: 80%\n bucket 39: 90%\n bucket 40: 90%\n bucket 39: 100%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\nGetting block 42 of 60\n Calculating Z arrays for bucket 41\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 42:\n bucket 41: 10%\n bucket 42: 10%\n bucket 41: 20%\n bucket 42: 20%\n bucket 41: 30%\n bucket 42: 30%\n bucket 41: 40%\n bucket 42: 40%\n bucket 41: 50%\n bucket 42: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 42: 60%\n bucket 41: 80%\n bucket 42: 70%\n bucket 41: 90%\n bucket 42: 80%\n bucket 41: 100%\n bucket 42: 90%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n Sorting block time: 00:00:00\n bucket 44: 90%\nReturning block of 122 for bucket 43\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 46 of 60\n Reserving size (126) for bucket 46\nGetting block 45 of 60\n Reserving size (126) for bucket 45\nGetting block 47 of 60\n Calculating Z arrays for bucket 46\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 46:\n Entering block accumulator loop for bucket 47:\n Entering block accumulator loop for bucket 45:\n bucket 46: 10%\n bucket 47: 10%\n bucket 46: 20%\n bucket 47: 20%\n bucket 45: 10%\n bucket 46: 30%\n bucket 47: 30%\n bucket 46: 40%\n bucket 47: 40%\n bucket 45: 20%\n bucket 46: 50%\n bucket 47: 50%\n bucket 45: 30%\n bucket 47: 60%\n bucket 46: 60%\n bucket 47: 70%\n bucket 45: 40%\n bucket 46: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 46: 80%\n bucket 45: 50%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 46: 90%\n bucket 45: 60%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n bucket 45: 70%\n bucket 45: 80%\n (Using difference cover)\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 60\n Entering block accumulator loop for bucket 48:\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n bucket 48: 10%\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 50\n bucket 48: 20%\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 49:\n bucket 48: 30%\n Entering block accumulator loop for bucket 50:\n Entering block accumulator loop for bucket 51:\n bucket 49: 10%\n bucket 48: 40%\n bucket 50: 10%\n bucket 51: 10%\n bucket 49: 20%\n bucket 48: 50%\n bucket 50: 20%\n bucket 51: 20%\n bucket 49: 30%\n bucket 48: 60%\n bucket 51: 30%\n bucket 50: 30%\n bucket 48: 70%\n bucket 49: 40%\n bucket 51: 40%\n bucket 48: 80%\n bucket 50: 40%\n bucket 49: 50%\n bucket 51: 50%\n bucket 48: 90%\n bucket 50: 50%\n bucket 49: 60%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 50: 60%\n bucket 51: 60%\n bucket 49: 70%\n bucket 50: 70%\n bucket 49: 80%\n bucket 51: 70%\n bucket 50: 80%\n bucket 51: 80%\n bucket 49: 90%\n bucket 50: 90%\n bucket 51: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 100%\n bucket 51: 100%\n Sorting block of length 108 for bucket 50\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\nGetting block 55 of 60\n bucket 53: 10%\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 52: 10%\n Entering block accumulator loop for bucket 54:\n bucket 53: 20%\n bucket 52: 20%\n Entering block accumulator loop for bucket 55:\n bucket 53: 30%\n bucket 54: 10%\n bucket 52: 30%\n bucket 55: 10%\n bucket 53: 40%\n bucket 54: 20%\n bucket 52: 40%\n bucket 55: 20%\n bucket 53: 50%\n bucket 54: 30%\n bucket 52: 50%\n bucket 55: 30%\n bucket 54: 40%\n bucket 55: 40%\n bucket 52: 60%\n bucket 53: 60%\n bucket 54: 50%\n bucket 55: 50%\n bucket 52: 70%\n bucket 53: 70%\n bucket 54: 60%\n bucket 55: 60%\n bucket 52: 80%\n bucket 54: 70%\n bucket 53: 80%\n bucket 55: 70%\n bucket 52: 90%\n bucket 54: 80%\n bucket 53: 90%\n bucket 55: 80%\n bucket 52: 100%\n bucket 54: 90%\n Sorting block of length 106 for bucket 52\n bucket 53: 100%\n bucket 55: 90%\n bucket 54: 100%\n bucket 55: 100%\n (Using difference cover)\n Sorting block of length 78 for bucket 53\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 56: 80%\n Entering block accumulator loop for bucket 57:\n bucket 56: 90%\n Entering block accumulator loop for bucket 58:\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 10%\n bucket 58: 10%\n bucket 58: 20%\n bucket 57: 20%\n bucket 58: 30%\n bucket 57: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 57: 40%\n bucket 58: 60%\n bucket 57: 50%\n bucket 58: 70%\n bucket 58: 80%\n bucket 57: 60%\n bucket 58: 90%\n bucket 57: 70%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 57: 80%\n Sorting block time: 00:00:00\n bucket 57: 90%\nReturning block of 56 for bucket 56\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n Entering block accumulator loop for bucket 59:\n bucket 60: 30%\n bucket 60: 40%\n bucket 59: 10%\n bucket 60: 50%\n bucket 59: 20%\n bucket 60: 60%\n bucket 59: 30%\n bucket 60: 70%\n bucket 60: 80%\n bucket 59: 40%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 71 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 71 pairs aligned 0 times concordantly or discordantly; of these:\n 142 mates make up the pairs; of these:\n 74 (52.11%) aligned 0 times\n 68 (47.89%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n92.60% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 3\n bucket 1: 20%\nGetting block 5 of 60\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 3:\n Reserving size (126) for bucket 5\nGetting block 4 of 60\n bucket 3: 10%\n bucket 2: 10%\n Calculating Z arrays for bucket 5\n Reserving size (126) for bucket 4\n bucket 2: 20%\n bucket 3: 20%\nGetting block 6 of 60\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 6\n bucket 1: 30%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 5: 10%\n Entering block accumulator loop for bucket 4:\n bucket 1: 40%\n Calculating Z arrays for bucket 8\n bucket 3: 30%\n bucket 2: 30%\n Calculating Z arrays for bucket 6\n bucket 3: 40%\n bucket 4: 10%\n Entering block accumulator loop for bucket 8:\n bucket 1: 50%\n bucket 3: 50%\n Entering block accumulator loop for bucket 6:\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 1: 60%\n bucket 3: 60%\n bucket 2: 40%\n bucket 6: 10%\n bucket 1: 70%\n bucket 3: 70%\n bucket 4: 20%\n bucket 2: 50%\n bucket 6: 20%\n bucket 3: 80%\n bucket 8: 10%\n bucket 5: 20%\n Calculating Z arrays for bucket 7\n bucket 4: 30%\n bucket 8: 20%\n bucket 6: 30%\n bucket 2: 60%\n bucket 5: 30%\n bucket 8: 30%\n Entering block accumulator loop for bucket 7:\n bucket 1: 80%\n bucket 3: 90%\n bucket 4: 40%\n bucket 1: 90%\n bucket 8: 40%\n bucket 2: 70%\n bucket 3: 100%\n bucket 1: 100%\n bucket 4: 50%\n bucket 8: 50%\n bucket 5: 40%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 2: 80%\n bucket 4: 60%\n bucket 5: 50%\n bucket 7: 10%\n bucket 4: 70%\n bucket 2: 90%\n bucket 7: 20%\n bucket 6: 40%\n bucket 5: 60%\n bucket 8: 60%\n bucket 2: 100%\n bucket 7: 30%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 6: 50%\n bucket 8: 70%\n bucket 5: 70%\n bucket 7: 40%\n bucket 8: 80%\n bucket 6: 60%\n bucket 5: 80%\n bucket 8: 90%\n bucket 7: 50%\n bucket 6: 70%\n bucket 8: 100%\n bucket 4: 80%\n bucket 5: 90%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 6: 80%\n bucket 4: 90%\n bucket 5: 100%\n bucket 7: 60%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 90%\n bucket 7: 70%\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Entering block accumulator loop for bucket 9:\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\nGetting block 11 of 60\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n Reserving size (126) for bucket 11\n bucket 9: 30%\n Calculating Z arrays for bucket 11\n bucket 10: 10%\n bucket 9: 40%\n bucket 10: 20%\n bucket 9: 50%\n Entering block accumulator loop for bucket 11:\n bucket 10: 30%\n bucket 9: 60%\n bucket 11: 10%\n bucket 10: 40%\n bucket 11: 20%\n bucket 9: 70%\n bucket 10: 50%\n bucket 11: 30%\n bucket 10: 60%\n bucket 11: 40%\n bucket 10: 70%\n bucket 11: 50%\n bucket 10: 80%\n bucket 11: 60%\n bucket 10: 90%\n bucket 11: 70%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 80%\n bucket 11: 90%\n bucket 9: 80%\n bucket 11: 100%\n bucket 9: 90%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Entering block accumulator loop for bucket 13:\n Entering block accumulator loop for bucket 14:\n bucket 13: 10%\n bucket 13: 20%\n bucket 14: 10%\n bucket 13: 30%\n bucket 14: 20%\n bucket 13: 40%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 13: 80%\n bucket 14: 50%\n bucket 13: 90%\n bucket 14: 60%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\nGetting block 16 of 60\n bucket 15: 100%\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nGetting block 18 of 60\nReturning block of 40 for bucket 17\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Entering block accumulator loop for bucket 18:\n Calculating Z arrays for bucket 19\n bucket 18: 10%\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 18: 20%\n Entering block accumulator loop for bucket 19:\n bucket 18: 30%\n bucket 18: 40%\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 18: 50%\n bucket 19: 20%\n bucket 18: 60%\n bucket 20: 10%\n bucket 18: 70%\n bucket 19: 30%\n bucket 20: 20%\n bucket 18: 80%\n bucket 20: 30%\n bucket 18: 90%\n bucket 19: 40%\n bucket 20: 40%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 20: 50%\n bucket 19: 50%\n bucket 20: 60%\n bucket 19: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 19: 70%\n bucket 20: 90%\n bucket 19: 80%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\nGetting block 22 of 60\n bucket 21: 60%\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n Entering block accumulator loop for bucket 22:\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\nGetting block 24 of 60\n Entering block accumulator loop for bucket 23:\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n bucket 23: 10%\n Entering block accumulator loop for bucket 24:\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 23: 60%\n bucket 24: 40%\n bucket 23: 70%\n bucket 24: 50%\n bucket 23: 80%\n bucket 24: 60%\n bucket 23: 90%\n bucket 24: 70%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Entering block accumulator loop for bucket 25:\n Calculating Z arrays for bucket 26\n bucket 25: 10%\n bucket 25: 20%\n Entering block accumulator loop for bucket 26:\n bucket 25: 30%\n bucket 25: 40%\n bucket 26: 10%\n bucket 25: 50%\n bucket 25: 60%\n bucket 26: 20%\n bucket 25: 70%\n bucket 25: 80%\n bucket 26: 30%\n bucket 25: 90%\n bucket 26: 40%\n bucket 26: 50%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 27:\n Entering block accumulator loop for bucket 28:\n bucket 27: 10%\n bucket 28: 10%\n bucket 27: 20%\n bucket 28: 20%\n bucket 27: 30%\n bucket 28: 30%\n bucket 27: 40%\n bucket 28: 40%\n bucket 27: 50%\n bucket 28: 50%\n bucket 27: 60%\n bucket 28: 60%\n bucket 27: 70%\n bucket 28: 70%\n bucket 27: 80%\n bucket 28: 80%\n bucket 27: 90%\n bucket 28: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 40%\n bucket 29: 50%\n Entering block accumulator loop for bucket 30:\n bucket 29: 60%\n bucket 30: 10%\n bucket 29: 70%\n bucket 30: 20%\n bucket 29: 80%\n bucket 30: 30%\n bucket 29: 90%\n bucket 30: 40%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n bucket 31: 20%\n bucket 32: 10%\n bucket 31: 30%\n bucket 32: 20%\n bucket 31: 40%\n bucket 32: 30%\n bucket 31: 50%\n bucket 32: 40%\n bucket 31: 60%\n bucket 32: 50%\n bucket 31: 70%\n bucket 32: 60%\n bucket 31: 80%\n bucket 32: 70%\n bucket 31: 90%\n bucket 32: 80%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 60\n Entering block accumulator loop for bucket 33:\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 10%\n Entering block accumulator loop for bucket 34:\n bucket 33: 20%\n bucket 34: 10%\n bucket 33: 30%\n bucket 34: 20%\n bucket 33: 40%\n bucket 34: 30%\n bucket 33: 50%\n bucket 34: 40%\n bucket 33: 60%\n bucket 34: 50%\n bucket 34: 60%\n bucket 33: 70%\n bucket 34: 70%\n bucket 33: 80%\n bucket 34: 80%\n bucket 33: 90%\n bucket 34: 90%\n bucket 33: 100%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\n bucket 35: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n bucket 38: 10%\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 40: 20%\n bucket 39: 30%\n bucket 40: 30%\n bucket 39: 40%\n bucket 40: 40%\n bucket 39: 50%\n bucket 40: 50%\n bucket 39: 60%\n bucket 40: 60%\n bucket 39: 70%\n bucket 40: 70%\n bucket 39: 80%\n bucket 40: 80%\n bucket 39: 90%\n bucket 40: 90%\n bucket 39: 100%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\nGetting block 42 of 60\n Calculating Z arrays for bucket 41\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 41:\n Entering block accumulator loop for bucket 42:\n bucket 41: 10%\n bucket 42: 10%\n bucket 41: 20%\n bucket 42: 20%\n bucket 41: 30%\n bucket 42: 30%\n bucket 41: 40%\n bucket 42: 40%\n bucket 41: 50%\n bucket 42: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 42: 60%\n bucket 41: 80%\n bucket 42: 70%\n bucket 41: 90%\n bucket 42: 80%\n bucket 41: 100%\n bucket 42: 90%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n Sorting block time: 00:00:00\n bucket 44: 90%\nReturning block of 122 for bucket 43\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 46 of 60\n Reserving size (126) for bucket 46\nGetting block 45 of 60\n Reserving size (126) for bucket 45\nGetting block 47 of 60\n Calculating Z arrays for bucket 46\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 46:\n Entering block accumulator loop for bucket 47:\n Entering block accumulator loop for bucket 45:\n bucket 46: 10%\n bucket 47: 10%\n bucket 46: 20%\n bucket 47: 20%\n bucket 45: 10%\n bucket 46: 30%\n bucket 47: 30%\n bucket 46: 40%\n bucket 47: 40%\n bucket 45: 20%\n bucket 46: 50%\n bucket 47: 50%\n bucket 45: 30%\n bucket 47: 60%\n bucket 46: 60%\n bucket 47: 70%\n bucket 45: 40%\n bucket 46: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 46: 80%\n bucket 45: 50%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 46: 90%\n bucket 45: 60%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n bucket 45: 70%\n bucket 45: 80%\n (Using difference cover)\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\nGetting block 49 of 60\n Entering block accumulator loop for bucket 48:\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n bucket 48: 10%\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 50\n bucket 48: 20%\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 49:\n bucket 48: 30%\n Entering block accumulator loop for bucket 50:\n Entering block accumulator loop for bucket 51:\n bucket 49: 10%\n bucket 48: 40%\n bucket 50: 10%\n bucket 51: 10%\n bucket 49: 20%\n bucket 48: 50%\n bucket 50: 20%\n bucket 51: 20%\n bucket 49: 30%\n bucket 48: 60%\n bucket 51: 30%\n bucket 50: 30%\n bucket 48: 70%\n bucket 49: 40%\n bucket 51: 40%\n bucket 48: 80%\n bucket 50: 40%\n bucket 49: 50%\n bucket 51: 50%\n bucket 48: 90%\n bucket 50: 50%\n bucket 49: 60%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 50: 60%\n bucket 51: 60%\n bucket 49: 70%\n bucket 50: 70%\n bucket 49: 80%\n bucket 51: 70%\n bucket 50: 80%\n bucket 51: 80%\n bucket 49: 90%\n bucket 50: 90%\n bucket 51: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 100%\n bucket 51: 100%\n Sorting block of length 108 for bucket 50\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\nGetting block 55 of 60\n bucket 53: 10%\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 52: 10%\n Entering block accumulator loop for bucket 54:\n bucket 53: 20%\n bucket 52: 20%\n Entering block accumulator loop for bucket 55:\n bucket 53: 30%\n bucket 54: 10%\n bucket 52: 30%\n bucket 55: 10%\n bucket 53: 40%\n bucket 54: 20%\n bucket 52: 40%\n bucket 55: 20%\n bucket 53: 50%\n bucket 54: 30%\n bucket 52: 50%\n bucket 55: 30%\n bucket 54: 40%\n bucket 55: 40%\n bucket 52: 60%\n bucket 53: 60%\n bucket 54: 50%\n bucket 55: 50%\n bucket 52: 70%\n bucket 53: 70%\n bucket 54: 60%\n bucket 55: 60%\n bucket 52: 80%\n bucket 54: 70%\n bucket 53: 80%\n bucket 55: 70%\n bucket 52: 90%\n bucket 54: 80%\n bucket 53: 90%\n bucket 55: 80%\n bucket 52: 100%\n bucket 54: 90%\n Sorting block of length 106 for bucket 52\n bucket 53: 100%\n bucket 55: 90%\n bucket 54: 100%\n bucket 55: 100%\n (Using difference cover)\n Sorting block of length 78 for bucket 53\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 56: 80%\n Entering block accumulator loop for bucket 57:\n bucket 56: 90%\n Entering block accumulator loop for bucket 58:\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 10%\n bucket 58: 10%\n bucket 58: 20%\n bucket 57: 20%\n bucket 58: 30%\n bucket 57: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 57: 40%\n bucket 58: 60%\n bucket 57: 50%\n bucket 58: 70%\n bucket 58: 80%\n bucket 57: 60%\n bucket 58: 90%\n bucket 57: 70%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 57: 80%\n Sorting block time: 00:00:00\n bucket 57: 90%\nReturning block of 56 for bucket 56\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n Entering block accumulator loop for bucket 59:\n bucket 60: 30%\n bucket 60: 40%\n bucket 59: 10%\n bucket 60: 50%\n bucket 59: 20%\n bucket 60: 60%\n bucket 59: 30%\n bucket 60: 70%\n bucket 60: 80%\n bucket 59: 40%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 71 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 71 pairs aligned 0 times concordantly or discordantly; of these:\n 142 mates make up the pairs; of these:\n 74 (52.11%) aligned 0 times\n 68 (47.89%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n92.60% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 07:00:39", "plugin": "core", "name": "end_epoch", "raw_value": "1725001239.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:00:39", "plugin": "core", "name": "start_epoch", "raw_value": "1725001239.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-4", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 4, "time_seconds": 38.752811908721924, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "30588cafbd94a1cd"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "b4ac6a1c72b1396c"}, "library|input_2": {"src": "hda", "id": "12a0d8e93377a2d3"}, "library|paired_options|no_mixed": true, "library|paired_options|no_discordant": true, "library|paired_options|paired_options_selector": "advanced", "library|type": "paired", "adv|input_options|trim5": "15", "adv|input_options|trim3": "15", "adv|input_options|input_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "3cfb09a11cdf160e", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:52:58.229007", "update_time": "2024-08-30T06:53:11.861468", "galaxy_version": "24.1", "external_id": "gxy-2gsft", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/f/b/0/dataset_fb08bccf-2967-47ca-8d23-bed96d58cd21.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/6/9/b/dataset_69b8d557-557f-4517-a09c-23288a1a7e7a.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/b/1/c/dataset_b1c540ce-6040-4d66-a87b-e72b133d7cb9.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' --fr --no-mixed --no-discordant --trim5 '15' --trim3 '15' --phred33 | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/3/1/f/dataset_31fbe374-f401-436a-82b2-1189367b4507.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 1, \"input_options_selector\": \"advanced\", \"int_quals\": false, \"qupto\": \"0\", \"qv_encoding\": \"--phred33\", \"skip\": \"0\", \"solexa_quals\": false, \"trim3\": \"15\", \"trim5\": \"15\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 131, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 132, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"fr_rf_ff\": \"--fr\", \"no_discordant\": true, \"no_mixed\": true, \"paired_options_selector\": \"advanced\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 130, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "30588cafbd94a1cd", "src": "hda", "uuid": "fb08bccf-2967-47ca-8d23-bed96d58cd21"}, "library|input_1": {"id": "b4ac6a1c72b1396c", "src": "hda", "uuid": "69b8d557-557f-4517-a09c-23288a1a7e7a"}, "library|input_2": {"id": "12a0d8e93377a2d3", "src": "hda", "uuid": "b1c540ce-6040-4d66-a87b-e72b133d7cb9"}}, "outputs": {"output_alignments": {"id": "b388024b55b62cb5", "src": "hda", "uuid": "31fbe374-f401-436a-82b2-1189367b4507"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n bucket 1: 20%\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n bucket 1: 40%\n bucket 2: 10%\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n bucket 1: 50%\n Calculating Z arrays for bucket 4\n bucket 1: 60%\n bucket 2: 20%\nGetting block 5 of 60\n bucket 1: 70%\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 4:\n bucket 2: 30%\n bucket 3: 10%\n bucket 2: 40%\n bucket 1: 80%\n Reserving size (126) for bucket 5\n bucket 3: 20%\n bucket 1: 90%\n Calculating Z arrays for bucket 5\n bucket 3: 30%\n bucket 1: 100%\n Sorting block of length 42 for bucket 1\n bucket 2: 50%\n (Using difference cover)\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 2: 60%\n bucket 3: 40%\nGetting block 7 of 60\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 7\n bucket 4: 10%\n bucket 3: 50%\n Calculating Z arrays for bucket 7\n bucket 2: 70%\n Entering block accumulator loop for bucket 6:\n bucket 2: 80%\n bucket 4: 20%\n Entering block accumulator loop for bucket 7:\n bucket 3: 60%\n bucket 6: 10%\n bucket 5: 10%\n bucket 2: 90%\n bucket 7: 10%\n Sorting block time: 00:00:00\nGetting block 8 of 60\n bucket 3: 70%\nReturning block of 43 for bucket 1\n bucket 7: 20%\n bucket 4: 30%\n bucket 3: 80%\n bucket 5: 20%\n bucket 7: 30%\n Reserving size (126) for bucket 8\n bucket 5: 30%\n bucket 7: 40%\n bucket 6: 20%\n bucket 5: 40%\n bucket 4: 40%\n Calculating Z arrays for bucket 8\n bucket 3: 90%\n bucket 7: 50%\n bucket 6: 30%\n bucket 5: 50%\n bucket 2: 100%\n bucket 6: 40%\n bucket 7: 60%\n bucket 5: 60%\n bucket 3: 100%\n bucket 6: 50%\n bucket 7: 70%\n bucket 5: 70%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 5: 80%\n bucket 6: 60%\n Entering block accumulator loop for bucket 8:\n bucket 4: 50%\n bucket 6: 70%\n bucket 5: 90%\n bucket 7: 80%\n bucket 6: 80%\n bucket 4: 60%\n bucket 7: 90%\n bucket 8: 10%\n bucket 5: 100%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 90%\n bucket 8: 20%\n bucket 4: 70%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 4: 80%\n bucket 8: 30%\n bucket 4: 90%\n bucket 8: 40%\n bucket 4: 100%\n bucket 8: 50%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 9: 30%\n bucket 10: 10%\n bucket 9: 40%\n bucket 10: 20%\n bucket 9: 50%\n bucket 10: 30%\n bucket 9: 60%\n bucket 10: 40%\n bucket 9: 70%\n bucket 10: 50%\n bucket 9: 80%\n bucket 10: 60%\n bucket 9: 90%\n bucket 10: 70%\n bucket 9: 100%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 80%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 90%\n bucket 10: 100%\n Entering block accumulator loop for bucket 11:\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Entering block accumulator loop for bucket 12:\n Calculating Z arrays for bucket 13\n bucket 12: 10%\n Entering block accumulator loop for bucket 13:\n bucket 12: 20%\n bucket 12: 30%\n bucket 13: 10%\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\n bucket 13: 40%\n bucket 12: 70%\n bucket 12: 80%\n bucket 13: 50%\n bucket 12: 90%\n bucket 13: 60%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Entering block accumulator loop for bucket 14:\n Calculating Z arrays for bucket 15\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n Entering block accumulator loop for bucket 15:\n bucket 14: 40%\n bucket 15: 10%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 60\n bucket 15: 20%\n bucket 14: 50%\n Entering block accumulator loop for bucket 16:\n bucket 15: 30%\n bucket 14: 60%\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 15: 40%\n bucket 14: 70%\n bucket 16: 10%\n bucket 14: 80%\n bucket 15: 50%\n bucket 16: 20%\n Entering block accumulator loop for bucket 17:\n bucket 14: 90%\n bucket 15: 60%\n bucket 16: 30%\n bucket 17: 10%\n bucket 14: 100%\n bucket 15: 70%\n bucket 17: 20%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 16: 40%\n bucket 17: 30%\n bucket 15: 80%\n bucket 17: 40%\n bucket 16: 50%\n bucket 15: 90%\n bucket 17: 50%\n bucket 16: 60%\n bucket 15: 100%\n bucket 17: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 70%\n bucket 17: 70%\n bucket 17: 80%\n bucket 16: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 50%\n bucket 18: 60%\n Entering block accumulator loop for bucket 19:\n bucket 18: 70%\n bucket 19: 10%\n bucket 18: 80%\n bucket 19: 20%\n bucket 18: 90%\n bucket 19: 30%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n Sorting block time: 00:00:00\n bucket 21: 30%\nReturning block of 98 for bucket 20\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 23:\n Entering block accumulator loop for bucket 22:\n bucket 23: 10%\n bucket 22: 10%\n bucket 23: 20%\n bucket 22: 20%\n bucket 23: 30%\n bucket 22: 30%\n bucket 23: 40%\n bucket 22: 40%\n bucket 23: 50%\n bucket 22: 50%\n bucket 23: 60%\n bucket 22: 60%\n bucket 23: 70%\n bucket 22: 70%\n bucket 23: 80%\n bucket 22: 80%\n bucket 23: 90%\n bucket 22: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 24: 20%\n bucket 25: 10%\n bucket 24: 30%\n bucket 25: 20%\n bucket 24: 40%\n bucket 25: 30%\n bucket 24: 50%\n bucket 25: 40%\n bucket 24: 60%\n bucket 25: 50%\n bucket 24: 70%\n bucket 25: 60%\n bucket 24: 80%\n bucket 25: 70%\n bucket 24: 90%\n bucket 25: 80%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 28:\n bucket 26: 10%\n Entering block accumulator loop for bucket 27:\n bucket 26: 20%\n bucket 28: 10%\n bucket 26: 30%\n bucket 27: 10%\n bucket 28: 20%\n bucket 26: 40%\n bucket 27: 20%\n bucket 26: 50%\n bucket 28: 30%\n bucket 26: 60%\n bucket 27: 30%\n bucket 28: 40%\n bucket 26: 70%\n bucket 28: 50%\n bucket 26: 80%\n bucket 27: 40%\n bucket 28: 60%\n bucket 26: 90%\n bucket 27: 50%\n bucket 28: 70%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 60%\n bucket 28: 80%\n bucket 27: 70%\n bucket 28: 90%\n bucket 27: 80%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 29: 10%\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n Entering block accumulator loop for bucket 31:\n bucket 30: 10%\n bucket 29: 30%\n bucket 31: 10%\n bucket 29: 40%\n bucket 30: 20%\n bucket 31: 20%\n bucket 29: 50%\n bucket 30: 30%\n bucket 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n bucket 30: 50%\n bucket 29: 60%\n bucket 31: 50%\n bucket 30: 60%\n bucket 29: 70%\n bucket 31: 60%\n bucket 30: 70%\n bucket 29: 80%\n bucket 31: 70%\n bucket 30: 80%\n bucket 29: 90%\n bucket 31: 80%\n bucket 30: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n bucket 31: 90%\n (Using difference cover)\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 40%\n Entering block accumulator loop for bucket 33:\n bucket 32: 50%\n bucket 33: 10%\n bucket 32: 60%\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n bucket 33: 20%\n bucket 32: 70%\n Calculating Z arrays for bucket 34\n bucket 33: 30%\n bucket 32: 80%\n bucket 33: 40%\n bucket 32: 90%\n bucket 33: 50%\n Entering block accumulator loop for bucket 34:\n bucket 32: 100%\n bucket 33: 60%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 70%\n bucket 33: 80%\n bucket 34: 10%\n bucket 33: 90%\n bucket 33: 100%\n bucket 34: 20%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 35:\n Entering block accumulator loop for bucket 36:\n bucket 35: 10%\n bucket 35: 20%\n bucket 36: 10%\n bucket 35: 30%\n bucket 36: 20%\n bucket 35: 40%\n bucket 36: 30%\n bucket 35: 50%\n bucket 36: 40%\n bucket 35: 60%\n bucket 36: 50%\n bucket 35: 70%\n bucket 36: 60%\n bucket 35: 80%\n bucket 36: 70%\n bucket 35: 90%\n bucket 36: 80%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n bucket 36: 90%\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\nGetting block 38 of 60\n bucket 37: 60%\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 70%\n bucket 37: 80%\n Entering block accumulator loop for bucket 38:\n bucket 37: 90%\n bucket 38: 10%\n bucket 37: 100%\n bucket 38: 20%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n bucket 39: 20%\n bucket 39: 30%\n Entering block accumulator loop for bucket 40:\n bucket 39: 40%\n bucket 39: 50%\n bucket 40: 10%\n bucket 39: 60%\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 39: 70%\n bucket 40: 20%\n bucket 39: 80%\n Entering block accumulator loop for bucket 41:\n bucket 40: 30%\n bucket 39: 90%\n bucket 41: 10%\n bucket 40: 40%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 41: 20%\n bucket 40: 50%\n bucket 41: 30%\n bucket 40: 60%\n bucket 41: 40%\n bucket 40: 70%\n bucket 41: 50%\n bucket 40: 80%\n bucket 41: 60%\n bucket 40: 90%\n bucket 41: 70%\n bucket 40: 100%\n bucket 41: 80%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 20%\n bucket 42: 30%\n Entering block accumulator loop for bucket 43:\n bucket 42: 40%\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 42: 50%\n bucket 43: 40%\n bucket 42: 60%\n bucket 42: 70%\n bucket 43: 50%\n bucket 42: 80%\n bucket 43: 60%\n bucket 42: 90%\n bucket 43: 70%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\nGetting block 46 of 60\n bucket 45: 50%\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n Entering block accumulator loop for bucket 46:\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 10%\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n bucket 47: 10%\n Calculating Z arrays for bucket 48\n bucket 47: 20%\n bucket 47: 30%\n Entering block accumulator loop for bucket 48:\n bucket 47: 40%\n bucket 48: 10%\n bucket 47: 50%\n bucket 48: 20%\n bucket 47: 60%\n bucket 48: 30%\n bucket 47: 70%\n bucket 48: 40%\n bucket 47: 80%\n bucket 48: 50%\n bucket 47: 90%\n bucket 48: 60%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 49: 30%\n bucket 50: 10%\n bucket 49: 40%\n bucket 50: 20%\n bucket 49: 50%\n bucket 50: 30%\n bucket 49: 60%\n bucket 50: 40%\n bucket 49: 70%\n bucket 50: 50%\n bucket 49: 80%\n bucket 50: 60%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n bucket 50: 70%\n Calculating Z arrays for bucket 51\n bucket 50: 80%\n bucket 49: 90%\n bucket 50: 90%\n Entering block accumulator loop for bucket 51:\n bucket 49: 100%\n bucket 50: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n bucket 52: 10%\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Entering block accumulator loop for bucket 53:\n bucket 52: 20%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 52: 30%\n bucket 53: 10%\n bucket 52: 40%\n bucket 53: 20%\n bucket 52: 50%\n Entering block accumulator loop for bucket 54:\n bucket 53: 30%\n bucket 52: 60%\n bucket 54: 10%\n bucket 53: 40%\n bucket 52: 70%\n bucket 54: 20%\n bucket 53: 50%\n bucket 52: 80%\n bucket 54: 30%\n bucket 52: 90%\n bucket 53: 60%\n bucket 52: 100%\n bucket 54: 40%\n bucket 53: 70%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 80%\n bucket 54: 50%\n bucket 53: 90%\n bucket 54: 60%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n Entering block accumulator loop for bucket 56:\n bucket 55: 70%\n bucket 56: 10%\n bucket 55: 80%\n bucket 56: 20%\n bucket 55: 90%\n bucket 55: 100%\n bucket 56: 30%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n bucket 57: 40%\n Calculating Z arrays for bucket 58\n bucket 57: 50%\n Entering block accumulator loop for bucket 58:\n bucket 57: 60%\n bucket 58: 10%\n bucket 57: 70%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 57: 80%\n bucket 58: 60%\n bucket 57: 90%\n bucket 58: 70%\n bucket 57: 100%\n bucket 58: 80%\n Sorting block of length 85 for bucket 57\n bucket 58: 90%\n (Using difference cover)\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 59: 20%\n bucket 60: 20%\n bucket 59: 30%\n bucket 60: 30%\n bucket 59: 40%\n bucket 60: 40%\n bucket 59: 50%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 59: 80%\n bucket 60: 80%\n bucket 59: 90%\n bucket 60: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n bucket 1: 20%\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 2:\n bucket 1: 30%\n bucket 1: 40%\n bucket 2: 10%\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n bucket 1: 50%\n Calculating Z arrays for bucket 4\n bucket 1: 60%\n bucket 2: 20%\nGetting block 5 of 60\n bucket 1: 70%\n Entering block accumulator loop for bucket 3:\n Entering block accumulator loop for bucket 4:\n bucket 2: 30%\n bucket 3: 10%\n bucket 2: 40%\n bucket 1: 80%\n Reserving size (126) for bucket 5\n bucket 3: 20%\n bucket 1: 90%\n Calculating Z arrays for bucket 5\n bucket 3: 30%\n bucket 1: 100%\n Sorting block of length 42 for bucket 1\n bucket 2: 50%\n (Using difference cover)\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 2: 60%\n bucket 3: 40%\nGetting block 7 of 60\n Calculating Z arrays for bucket 6\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 7\n bucket 4: 10%\n bucket 3: 50%\n Calculating Z arrays for bucket 7\n bucket 2: 70%\n Entering block accumulator loop for bucket 6:\n bucket 2: 80%\n bucket 4: 20%\n Entering block accumulator loop for bucket 7:\n bucket 3: 60%\n bucket 6: 10%\n bucket 5: 10%\n bucket 2: 90%\n bucket 7: 10%\n Sorting block time: 00:00:00\nGetting block 8 of 60\n bucket 3: 70%\nReturning block of 43 for bucket 1\n bucket 7: 20%\n bucket 4: 30%\n bucket 3: 80%\n bucket 5: 20%\n bucket 7: 30%\n Reserving size (126) for bucket 8\n bucket 5: 30%\n bucket 7: 40%\n bucket 6: 20%\n bucket 5: 40%\n bucket 4: 40%\n Calculating Z arrays for bucket 8\n bucket 3: 90%\n bucket 7: 50%\n bucket 6: 30%\n bucket 5: 50%\n bucket 2: 100%\n bucket 6: 40%\n bucket 7: 60%\n bucket 5: 60%\n bucket 3: 100%\n bucket 6: 50%\n bucket 7: 70%\n bucket 5: 70%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 5: 80%\n bucket 6: 60%\n Entering block accumulator loop for bucket 8:\n bucket 4: 50%\n bucket 6: 70%\n bucket 5: 90%\n bucket 7: 80%\n bucket 6: 80%\n bucket 4: 60%\n bucket 7: 90%\n bucket 8: 10%\n bucket 5: 100%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 90%\n bucket 8: 20%\n bucket 4: 70%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 4: 80%\n bucket 8: 30%\n bucket 4: 90%\n bucket 8: 40%\n bucket 4: 100%\n bucket 8: 50%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 8: 60%\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 9: 30%\n bucket 10: 10%\n bucket 9: 40%\n bucket 10: 20%\n bucket 9: 50%\n bucket 10: 30%\n bucket 9: 60%\n bucket 10: 40%\n bucket 9: 70%\n bucket 10: 50%\n bucket 9: 80%\n bucket 10: 60%\n bucket 9: 90%\n bucket 10: 70%\n bucket 9: 100%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n bucket 10: 80%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 90%\n bucket 10: 100%\n Entering block accumulator loop for bucket 11:\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Entering block accumulator loop for bucket 12:\n Calculating Z arrays for bucket 13\n bucket 12: 10%\n Entering block accumulator loop for bucket 13:\n bucket 12: 20%\n bucket 12: 30%\n bucket 13: 10%\n bucket 12: 40%\n bucket 13: 20%\n bucket 12: 50%\n bucket 13: 30%\n bucket 12: 60%\n bucket 13: 40%\n bucket 12: 70%\n bucket 12: 80%\n bucket 13: 50%\n bucket 12: 90%\n bucket 13: 60%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Entering block accumulator loop for bucket 14:\n Calculating Z arrays for bucket 15\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n Entering block accumulator loop for bucket 15:\n bucket 14: 40%\n bucket 15: 10%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 60\n bucket 15: 20%\n bucket 14: 50%\n Entering block accumulator loop for bucket 16:\n bucket 15: 30%\n bucket 14: 60%\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 15: 40%\n bucket 14: 70%\n bucket 16: 10%\n bucket 14: 80%\n bucket 15: 50%\n bucket 16: 20%\n Entering block accumulator loop for bucket 17:\n bucket 14: 90%\n bucket 15: 60%\n bucket 16: 30%\n bucket 17: 10%\n bucket 14: 100%\n bucket 15: 70%\n bucket 17: 20%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 16: 40%\n bucket 17: 30%\n bucket 15: 80%\n bucket 17: 40%\n bucket 16: 50%\n bucket 15: 90%\n bucket 17: 50%\n bucket 16: 60%\n bucket 15: 100%\n bucket 17: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 70%\n bucket 17: 70%\n bucket 17: 80%\n bucket 16: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 50%\n bucket 18: 60%\n Entering block accumulator loop for bucket 19:\n bucket 18: 70%\n bucket 19: 10%\n bucket 18: 80%\n bucket 19: 20%\n bucket 18: 90%\n bucket 19: 30%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n Sorting block time: 00:00:00\n bucket 21: 30%\nReturning block of 98 for bucket 20\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 23:\n Entering block accumulator loop for bucket 22:\n bucket 23: 10%\n bucket 22: 10%\n bucket 23: 20%\n bucket 22: 20%\n bucket 23: 30%\n bucket 22: 30%\n bucket 23: 40%\n bucket 22: 40%\n bucket 23: 50%\n bucket 22: 50%\n bucket 23: 60%\n bucket 22: 60%\n bucket 23: 70%\n bucket 22: 70%\n bucket 23: 80%\n bucket 22: 80%\n bucket 23: 90%\n bucket 22: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 24: 20%\n bucket 25: 10%\n bucket 24: 30%\n bucket 25: 20%\n bucket 24: 40%\n bucket 25: 30%\n bucket 24: 50%\n bucket 25: 40%\n bucket 24: 60%\n bucket 25: 50%\n bucket 24: 70%\n bucket 25: 60%\n bucket 24: 80%\n bucket 25: 70%\n bucket 24: 90%\n bucket 25: 80%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 28:\n bucket 26: 10%\n Entering block accumulator loop for bucket 27:\n bucket 26: 20%\n bucket 28: 10%\n bucket 26: 30%\n bucket 27: 10%\n bucket 28: 20%\n bucket 26: 40%\n bucket 27: 20%\n bucket 26: 50%\n bucket 28: 30%\n bucket 26: 60%\n bucket 27: 30%\n bucket 28: 40%\n bucket 26: 70%\n bucket 28: 50%\n bucket 26: 80%\n bucket 27: 40%\n bucket 28: 60%\n bucket 26: 90%\n bucket 27: 50%\n bucket 28: 70%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 60%\n bucket 28: 80%\n bucket 27: 70%\n bucket 28: 90%\n bucket 27: 80%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 29: 10%\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n Entering block accumulator loop for bucket 31:\n bucket 30: 10%\n bucket 29: 30%\n bucket 31: 10%\n bucket 29: 40%\n bucket 30: 20%\n bucket 31: 20%\n bucket 29: 50%\n bucket 30: 30%\n bucket 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n bucket 30: 50%\n bucket 29: 60%\n bucket 31: 50%\n bucket 30: 60%\n bucket 29: 70%\n bucket 31: 60%\n bucket 30: 70%\n bucket 29: 80%\n bucket 31: 70%\n bucket 30: 80%\n bucket 29: 90%\n bucket 31: 80%\n bucket 30: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n bucket 31: 90%\n (Using difference cover)\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 32:\n bucket 32: 10%\n bucket 32: 20%\n bucket 32: 30%\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 32: 40%\n Entering block accumulator loop for bucket 33:\n bucket 32: 50%\n bucket 33: 10%\n bucket 32: 60%\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n bucket 33: 20%\n bucket 32: 70%\n Calculating Z arrays for bucket 34\n bucket 33: 30%\n bucket 32: 80%\n bucket 33: 40%\n bucket 32: 90%\n bucket 33: 50%\n Entering block accumulator loop for bucket 34:\n bucket 32: 100%\n bucket 33: 60%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 70%\n bucket 33: 80%\n bucket 34: 10%\n bucket 33: 90%\n bucket 33: 100%\n bucket 34: 20%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 35:\n Entering block accumulator loop for bucket 36:\n bucket 35: 10%\n bucket 35: 20%\n bucket 36: 10%\n bucket 35: 30%\n bucket 36: 20%\n bucket 35: 40%\n bucket 36: 30%\n bucket 35: 50%\n bucket 36: 40%\n bucket 35: 60%\n bucket 36: 50%\n bucket 35: 70%\n bucket 36: 60%\n bucket 35: 80%\n bucket 36: 70%\n bucket 35: 90%\n bucket 36: 80%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n bucket 36: 90%\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\nGetting block 38 of 60\n bucket 37: 60%\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 70%\n bucket 37: 80%\n Entering block accumulator loop for bucket 38:\n bucket 37: 90%\n bucket 38: 10%\n bucket 37: 100%\n bucket 38: 20%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n bucket 39: 20%\n bucket 39: 30%\n Entering block accumulator loop for bucket 40:\n bucket 39: 40%\n bucket 39: 50%\n bucket 40: 10%\n bucket 39: 60%\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n bucket 39: 70%\n bucket 40: 20%\n bucket 39: 80%\n Entering block accumulator loop for bucket 41:\n bucket 40: 30%\n bucket 39: 90%\n bucket 41: 10%\n bucket 40: 40%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 41: 20%\n bucket 40: 50%\n bucket 41: 30%\n bucket 40: 60%\n bucket 41: 40%\n bucket 40: 70%\n bucket 41: 50%\n bucket 40: 80%\n bucket 41: 60%\n bucket 40: 90%\n bucket 41: 70%\n bucket 40: 100%\n bucket 41: 80%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 20%\n bucket 42: 30%\n Entering block accumulator loop for bucket 43:\n bucket 42: 40%\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 42: 50%\n bucket 43: 40%\n bucket 42: 60%\n bucket 42: 70%\n bucket 43: 50%\n bucket 42: 80%\n bucket 43: 60%\n bucket 42: 90%\n bucket 43: 70%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 44: 20%\n bucket 44: 30%\n bucket 44: 40%\n bucket 44: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\nGetting block 46 of 60\n bucket 45: 50%\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n Entering block accumulator loop for bucket 46:\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 10%\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n bucket 47: 10%\n Calculating Z arrays for bucket 48\n bucket 47: 20%\n bucket 47: 30%\n Entering block accumulator loop for bucket 48:\n bucket 47: 40%\n bucket 48: 10%\n bucket 47: 50%\n bucket 48: 20%\n bucket 47: 60%\n bucket 48: 30%\n bucket 47: 70%\n bucket 48: 40%\n bucket 47: 80%\n bucket 48: 50%\n bucket 47: 90%\n bucket 48: 60%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 10%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 49: 30%\n bucket 50: 10%\n bucket 49: 40%\n bucket 50: 20%\n bucket 49: 50%\n bucket 50: 30%\n bucket 49: 60%\n bucket 50: 40%\n bucket 49: 70%\n bucket 50: 50%\n bucket 49: 80%\n bucket 50: 60%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n bucket 50: 70%\n Calculating Z arrays for bucket 51\n bucket 50: 80%\n bucket 49: 90%\n bucket 50: 90%\n Entering block accumulator loop for bucket 51:\n bucket 49: 100%\n bucket 50: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n bucket 52: 10%\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Entering block accumulator loop for bucket 53:\n bucket 52: 20%\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 52: 30%\n bucket 53: 10%\n bucket 52: 40%\n bucket 53: 20%\n bucket 52: 50%\n Entering block accumulator loop for bucket 54:\n bucket 53: 30%\n bucket 52: 60%\n bucket 54: 10%\n bucket 53: 40%\n bucket 52: 70%\n bucket 54: 20%\n bucket 53: 50%\n bucket 52: 80%\n bucket 54: 30%\n bucket 52: 90%\n bucket 53: 60%\n bucket 52: 100%\n bucket 54: 40%\n bucket 53: 70%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 80%\n bucket 54: 50%\n bucket 53: 90%\n bucket 54: 60%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n Entering block accumulator loop for bucket 56:\n bucket 55: 70%\n bucket 56: 10%\n bucket 55: 80%\n bucket 56: 20%\n bucket 55: 90%\n bucket 55: 100%\n bucket 56: 30%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n bucket 57: 40%\n Calculating Z arrays for bucket 58\n bucket 57: 50%\n Entering block accumulator loop for bucket 58:\n bucket 57: 60%\n bucket 58: 10%\n bucket 57: 70%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 57: 80%\n bucket 58: 60%\n bucket 57: 90%\n bucket 58: 70%\n bucket 57: 100%\n bucket 58: 80%\n Sorting block of length 85 for bucket 57\n bucket 58: 90%\n (Using difference cover)\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 60: 10%\n bucket 59: 20%\n bucket 60: 20%\n bucket 59: 30%\n bucket 60: 30%\n bucket 59: 40%\n bucket 60: 40%\n bucket 59: 50%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 59: 70%\n bucket 60: 70%\n bucket 59: 80%\n bucket 60: 80%\n bucket 59: 90%\n bucket 60: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:53:01", "plugin": "core", "name": "end_epoch", "raw_value": "1725000781.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:53:00", "plugin": "core", "name": "start_epoch", "raw_value": "1725000780.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-4", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 4, "time_seconds": 39.13515067100525, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "f4bbadf0a55281e1"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "745271ac39632b43"}, "library|input_2": {"src": "hda", "id": "1f2589c0628914d3"}, "library|paired_options|no_mixed": true, "library|paired_options|no_discordant": true, "library|paired_options|paired_options_selector": "advanced", "library|type": "paired", "adv|input_options|trim5": "15", "adv|input_options|trim3": "15", "adv|input_options|input_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "4eea5e6094bb2d99", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:01:16.384760", "update_time": "2024-08-30T07:01:29.996159", "galaxy_version": "24.1", "external_id": "gxy-p2jgm", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/4/0/3/dataset_40313fa8-5b99-4c73-8c0f-8d942acc6da0.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/f/7/a/dataset_f7ac6827-c300-40b0-88cd-7b4876687dfc.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/e/a/1/dataset_ea178a9a-37bd-46f7-94bf-4be7f673089f.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' --fr --no-mixed --no-discordant --trim5 '15' --trim3 '15' --phred33 | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/c/4/a/dataset_c4aaaf69-419a-4fa9-837a-6a0a96d18c04.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 1, \"input_options_selector\": \"advanced\", \"int_quals\": false, \"qupto\": \"0\", \"qv_encoding\": \"--phred33\", \"skip\": \"0\", \"solexa_quals\": false, \"trim3\": \"15\", \"trim5\": \"15\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 190, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 191, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"fr_rf_ff\": \"--fr\", \"no_discordant\": true, \"no_mixed\": true, \"paired_options_selector\": \"advanced\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 189, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "f4bbadf0a55281e1", "src": "hda", "uuid": "40313fa8-5b99-4c73-8c0f-8d942acc6da0"}, "library|input_1": {"id": "745271ac39632b43", "src": "hda", "uuid": "f7ac6827-c300-40b0-88cd-7b4876687dfc"}, "library|input_2": {"id": "1f2589c0628914d3", "src": "hda", "uuid": "ea178a9a-37bd-46f7-94bf-4be7f673089f"}}, "outputs": {"output_alignments": {"id": "716e327cba368c7d", "src": "hda", "uuid": "c4aaaf69-419a-4fa9-837a-6a0a96d18c04"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\n bucket 1: 20%\n bucket 1: 30%\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 40%\n Calculating Z arrays for bucket 2\n bucket 1: 50%\nGetting block 3 of 60\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 1: 60%\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 6\n bucket 2: 10%\n Calculating Z arrays for bucket 4\n bucket 1: 70%\n Entering block accumulator loop for bucket 3:\nGetting block 7 of 60\n bucket 2: 20%\nGetting block 5 of 60\nGetting block 8 of 60\n Entering block accumulator loop for bucket 6:\n Reserving size (126) for bucket 7\n Reserving size (126) for bucket 5\n bucket 3: 10%\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 7\n bucket 2: 30%\n bucket 6: 10%\n bucket 3: 20%\n Reserving size (126) for bucket 8\n bucket 2: 40%\n bucket 1: 80%\n Entering block accumulator loop for bucket 5:\n bucket 6: 20%\n bucket 1: 90%\n bucket 2: 50%\n Entering block accumulator loop for bucket 7:\n bucket 4: 10%\n bucket 5: 10%\n bucket 2: 60%\n bucket 7: 10%\n Calculating Z arrays for bucket 8\n bucket 3: 30%\n bucket 6: 30%\n bucket 4: 20%\n bucket 5: 20%\n bucket 3: 40%\n bucket 1: 100%\n bucket 2: 70%\n bucket 5: 30%\n bucket 3: 50%\n bucket 7: 20%\n Entering block accumulator loop for bucket 8:\n bucket 4: 30%\n bucket 2: 80%\n bucket 5: 40%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 2: 90%\n bucket 3: 60%\n bucket 8: 10%\n bucket 6: 40%\n bucket 5: 50%\n bucket 7: 30%\n bucket 6: 50%\n bucket 8: 20%\n bucket 5: 60%\n bucket 7: 40%\n bucket 3: 70%\n bucket 4: 40%\n bucket 5: 70%\n bucket 8: 30%\n bucket 4: 50%\n bucket 7: 50%\n bucket 5: 80%\n bucket 4: 60%\n bucket 2: 100%\n bucket 4: 70%\n bucket 3: 80%\n Sorting block of length 84 for bucket 2\n bucket 5: 90%\n bucket 4: 80%\n (Using difference cover)\n bucket 6: 60%\n bucket 4: 90%\n bucket 7: 60%\n Sorting block time: 00:00:00\n bucket 8: 40%\n bucket 6: 70%\n bucket 5: 100%\n bucket 7: 70%\n bucket 3: 90%\n bucket 4: 100%\n bucket 8: 50%\n bucket 6: 80%\nReturning block of 43 for bucket 1\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 80%\n bucket 3: 100%\n Sorting block of length 68 for bucket 4\n bucket 7: 90%\n bucket 6: 90%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 60%\n (Using difference cover)\n bucket 7: 100%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 30%\n bucket 9: 40%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n bucket 9: 50%\n Entering block accumulator loop for bucket 10:\n Calculating Z arrays for bucket 11\n bucket 9: 60%\n bucket 10: 10%\n bucket 9: 70%\n bucket 10: 20%\n bucket 9: 80%\n bucket 10: 30%\n bucket 9: 90%\n bucket 10: 40%\n Entering block accumulator loop for bucket 11:\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 50%\n bucket 11: 10%\n bucket 10: 60%\n bucket 11: 20%\n bucket 10: 70%\n bucket 10: 80%\n bucket 11: 30%\n bucket 10: 90%\n bucket 11: 40%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 13:\n bucket 12: 10%\n bucket 13: 10%\n bucket 12: 20%\n bucket 13: 20%\n bucket 12: 30%\n bucket 13: 30%\n bucket 12: 40%\n bucket 13: 40%\n bucket 12: 50%\n bucket 13: 50%\n bucket 12: 60%\n bucket 13: 60%\n bucket 12: 70%\n bucket 13: 70%\n bucket 12: 80%\n bucket 13: 80%\n bucket 12: 90%\n bucket 13: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n Entering block accumulator loop for bucket 15:\n bucket 14: 20%\n bucket 15: 10%\n bucket 14: 30%\n bucket 15: 20%\n bucket 14: 40%\n bucket 15: 30%\n bucket 14: 50%\n bucket 15: 40%\n bucket 14: 60%\n bucket 15: 50%\n bucket 14: 70%\n bucket 15: 60%\n bucket 14: 80%\n bucket 15: 70%\n bucket 14: 90%\n bucket 15: 80%\n bucket 14: 100%\n bucket 15: 90%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 60\n Entering block accumulator loop for bucket 16:\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n Entering block accumulator loop for bucket 17:\n bucket 16: 40%\n bucket 16: 50%\n bucket 17: 10%\n bucket 16: 60%\n bucket 17: 20%\n bucket 16: 70%\n bucket 17: 30%\n bucket 16: 80%\n bucket 17: 40%\n bucket 16: 90%\n bucket 17: 50%\n bucket 16: 100%\n bucket 17: 60%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n Entering block accumulator loop for bucket 19:\n bucket 18: 20%\n bucket 19: 10%\n bucket 18: 30%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 18: 80%\n bucket 19: 50%\n bucket 18: 90%\n bucket 19: 60%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\nGetting block 21 of 60\n Calculating Z arrays for bucket 20\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\n Entering block accumulator loop for bucket 21:\n bucket 20: 10%\n bucket 21: 10%\n bucket 20: 20%\n bucket 21: 20%\n bucket 20: 30%\n bucket 21: 30%\n bucket 20: 40%\n bucket 21: 40%\n bucket 20: 50%\n bucket 21: 50%\n bucket 20: 60%\n bucket 21: 60%\n bucket 20: 70%\n bucket 21: 70%\n bucket 20: 80%\n bucket 21: 80%\n bucket 20: 90%\n bucket 21: 90%\n bucket 20: 100%\n bucket 21: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 23:\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 22: 50%\n bucket 23: 40%\n bucket 22: 60%\n bucket 23: 50%\n bucket 22: 70%\n bucket 23: 60%\n bucket 22: 80%\n bucket 23: 70%\n bucket 22: 90%\n bucket 23: 80%\n bucket 22: 100%\n bucket 23: 90%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Entering block accumulator loop for bucket 24:\n Calculating Z arrays for bucket 25\n bucket 24: 10%\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n bucket 24: 20%\n Entering block accumulator loop for bucket 26:\n bucket 25: 10%\n bucket 24: 30%\n bucket 25: 20%\n bucket 26: 10%\n bucket 24: 40%\n bucket 25: 30%\n bucket 24: 50%\n bucket 25: 40%\n bucket 24: 60%\n bucket 25: 50%\n bucket 24: 70%\n bucket 25: 60%\n bucket 24: 80%\n bucket 25: 70%\n bucket 24: 90%\n bucket 25: 80%\n bucket 26: 20%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 25: 90%\n bucket 26: 60%\n bucket 26: 70%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\nGetting block 28 of 60\n bucket 27: 100%\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 80%\nGetting block 31 of 60\n Entering block accumulator loop for bucket 30:\n bucket 29: 90%\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 30: 10%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n Entering block accumulator loop for bucket 31:\n bucket 30: 90%\n bucket 31: 10%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n Sorting block time: 00:00:00\n bucket 31: 60%\nReturning block of 52 for bucket 29\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Entering block accumulator loop for bucket 32:\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n bucket 32: 10%\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 33:\n bucket 32: 20%\n bucket 32: 30%\n bucket 33: 10%\n Entering block accumulator loop for bucket 34:\n bucket 32: 40%\n bucket 33: 20%\n bucket 32: 50%\n bucket 33: 30%\n bucket 32: 60%\n bucket 33: 40%\n bucket 32: 70%\n bucket 33: 50%\n bucket 32: 80%\n bucket 33: 60%\n bucket 32: 90%\n bucket 33: 70%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n bucket 33: 80%\n (Using difference cover)\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block time: 00:00:00\n Sorting block of length 122 for bucket 34\n (Using difference cover)\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n Entering block accumulator loop for bucket 36:\n bucket 35: 10%\n bucket 36: 10%\n bucket 35: 20%\n bucket 36: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 36: 30%\n bucket 35: 50%\n bucket 36: 40%\n bucket 35: 60%\n bucket 36: 50%\n bucket 35: 70%\n bucket 35: 80%\n bucket 36: 60%\n bucket 35: 90%\n bucket 36: 70%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n Entering block accumulator loop for bucket 38:\n bucket 37: 40%\n bucket 38: 10%\n bucket 37: 50%\n bucket 38: 20%\n bucket 37: 60%\n bucket 38: 30%\n bucket 37: 70%\n bucket 38: 40%\n bucket 37: 80%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n bucket 39: 90%\n bucket 39: 100%\n Entering block accumulator loop for bucket 40:\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n Sorting block time: 00:00:00\n bucket 40: 40%\nReturning block of 126 for bucket 39\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 60\n Entering block accumulator loop for bucket 41:\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 41: 10%\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n Sorting block time: 00:00:00\n bucket 41: 100%\nReturning block of 120 for bucket 42\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 43: 60%\n bucket 44: 20%\n bucket 43: 70%\n bucket 44: 30%\n bucket 44: 40%\n bucket 43: 80%\n bucket 44: 50%\n bucket 43: 90%\n bucket 44: 60%\n bucket 43: 100%\n bucket 44: 70%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 46:\n bucket 45: 10%\n bucket 46: 10%\n bucket 46: 20%\n bucket 45: 20%\n bucket 46: 30%\n bucket 45: 30%\n bucket 46: 40%\n bucket 45: 40%\n bucket 46: 50%\n bucket 45: 50%\n bucket 45: 60%\n bucket 46: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 70%\n bucket 45: 90%\n bucket 45: 100%\n bucket 46: 80%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\nGetting block 48 of 60\n Calculating Z arrays for bucket 47\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 47:\n Entering block accumulator loop for bucket 48:\n bucket 47: 10%\n bucket 48: 10%\n bucket 47: 20%\n bucket 48: 20%\n bucket 47: 30%\n bucket 48: 30%\n bucket 47: 40%\n bucket 48: 40%\n bucket 47: 50%\n bucket 48: 50%\n bucket 47: 60%\n bucket 48: 60%\n bucket 48: 70%\n bucket 47: 70%\n bucket 48: 80%\n bucket 47: 80%\n bucket 47: 90%\n bucket 48: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 40%\n bucket 51: 50%\n Entering block accumulator loop for bucket 52:\n bucket 51: 60%\n bucket 52: 10%\n bucket 51: 70%\n bucket 52: 20%\n bucket 52: 30%\n bucket 51: 80%\n bucket 52: 40%\n bucket 51: 90%\n bucket 52: 50%\n bucket 51: 100%\n bucket 52: 60%\n Sorting block of length 91 for bucket 51\n bucket 52: 70%\n bucket 52: 80%\n (Using difference cover)\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 55: 10%\n bucket 56: 30%\n bucket 55: 20%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 40%\n bucket 55: 30%\n bucket 56: 50%\n Entering block accumulator loop for bucket 57:\n bucket 55: 40%\n bucket 57: 10%\n bucket 56: 60%\n bucket 57: 20%\n bucket 55: 50%\n bucket 57: 30%\n bucket 56: 70%\n bucket 55: 60%\n bucket 57: 40%\n bucket 56: 80%\n bucket 57: 50%\n bucket 56: 90%\n bucket 57: 60%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\n bucket 1: 20%\n bucket 1: 30%\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 40%\n Calculating Z arrays for bucket 2\n bucket 1: 50%\nGetting block 3 of 60\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 1: 60%\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 6\n bucket 2: 10%\n Calculating Z arrays for bucket 4\n bucket 1: 70%\n Entering block accumulator loop for bucket 3:\nGetting block 7 of 60\n bucket 2: 20%\nGetting block 5 of 60\nGetting block 8 of 60\n Entering block accumulator loop for bucket 6:\n Reserving size (126) for bucket 7\n Reserving size (126) for bucket 5\n bucket 3: 10%\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 7\n bucket 2: 30%\n bucket 6: 10%\n bucket 3: 20%\n Reserving size (126) for bucket 8\n bucket 2: 40%\n bucket 1: 80%\n Entering block accumulator loop for bucket 5:\n bucket 6: 20%\n bucket 1: 90%\n bucket 2: 50%\n Entering block accumulator loop for bucket 7:\n bucket 4: 10%\n bucket 5: 10%\n bucket 2: 60%\n bucket 7: 10%\n Calculating Z arrays for bucket 8\n bucket 3: 30%\n bucket 6: 30%\n bucket 4: 20%\n bucket 5: 20%\n bucket 3: 40%\n bucket 1: 100%\n bucket 2: 70%\n bucket 5: 30%\n bucket 3: 50%\n bucket 7: 20%\n Entering block accumulator loop for bucket 8:\n bucket 4: 30%\n bucket 2: 80%\n bucket 5: 40%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 2: 90%\n bucket 3: 60%\n bucket 8: 10%\n bucket 6: 40%\n bucket 5: 50%\n bucket 7: 30%\n bucket 6: 50%\n bucket 8: 20%\n bucket 5: 60%\n bucket 7: 40%\n bucket 3: 70%\n bucket 4: 40%\n bucket 5: 70%\n bucket 8: 30%\n bucket 4: 50%\n bucket 7: 50%\n bucket 5: 80%\n bucket 4: 60%\n bucket 2: 100%\n bucket 4: 70%\n bucket 3: 80%\n Sorting block of length 84 for bucket 2\n bucket 5: 90%\n bucket 4: 80%\n (Using difference cover)\n bucket 6: 60%\n bucket 4: 90%\n bucket 7: 60%\n Sorting block time: 00:00:00\n bucket 8: 40%\n bucket 6: 70%\n bucket 5: 100%\n bucket 7: 70%\n bucket 3: 90%\n bucket 4: 100%\n bucket 8: 50%\n bucket 6: 80%\nReturning block of 43 for bucket 1\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 80%\n bucket 3: 100%\n Sorting block of length 68 for bucket 4\n bucket 7: 90%\n bucket 6: 90%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 60%\n (Using difference cover)\n bucket 7: 100%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 30%\n bucket 9: 40%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n bucket 9: 50%\n Entering block accumulator loop for bucket 10:\n Calculating Z arrays for bucket 11\n bucket 9: 60%\n bucket 10: 10%\n bucket 9: 70%\n bucket 10: 20%\n bucket 9: 80%\n bucket 10: 30%\n bucket 9: 90%\n bucket 10: 40%\n Entering block accumulator loop for bucket 11:\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 50%\n bucket 11: 10%\n bucket 10: 60%\n bucket 11: 20%\n bucket 10: 70%\n bucket 10: 80%\n bucket 11: 30%\n bucket 10: 90%\n bucket 11: 40%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 13:\n bucket 12: 10%\n bucket 13: 10%\n bucket 12: 20%\n bucket 13: 20%\n bucket 12: 30%\n bucket 13: 30%\n bucket 12: 40%\n bucket 13: 40%\n bucket 12: 50%\n bucket 13: 50%\n bucket 12: 60%\n bucket 13: 60%\n bucket 12: 70%\n bucket 13: 70%\n bucket 12: 80%\n bucket 13: 80%\n bucket 12: 90%\n bucket 13: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n Entering block accumulator loop for bucket 15:\n bucket 14: 20%\n bucket 15: 10%\n bucket 14: 30%\n bucket 15: 20%\n bucket 14: 40%\n bucket 15: 30%\n bucket 14: 50%\n bucket 15: 40%\n bucket 14: 60%\n bucket 15: 50%\n bucket 14: 70%\n bucket 15: 60%\n bucket 14: 80%\n bucket 15: 70%\n bucket 14: 90%\n bucket 15: 80%\n bucket 14: 100%\n bucket 15: 90%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\nGetting block 17 of 60\n Entering block accumulator loop for bucket 16:\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n Entering block accumulator loop for bucket 17:\n bucket 16: 40%\n bucket 16: 50%\n bucket 17: 10%\n bucket 16: 60%\n bucket 17: 20%\n bucket 16: 70%\n bucket 17: 30%\n bucket 16: 80%\n bucket 17: 40%\n bucket 16: 90%\n bucket 17: 50%\n bucket 16: 100%\n bucket 17: 60%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n Entering block accumulator loop for bucket 19:\n bucket 18: 20%\n bucket 19: 10%\n bucket 18: 30%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 18: 80%\n bucket 19: 50%\n bucket 18: 90%\n bucket 19: 60%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\nGetting block 21 of 60\n Calculating Z arrays for bucket 20\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 20:\n Entering block accumulator loop for bucket 21:\n bucket 20: 10%\n bucket 21: 10%\n bucket 20: 20%\n bucket 21: 20%\n bucket 20: 30%\n bucket 21: 30%\n bucket 20: 40%\n bucket 21: 40%\n bucket 20: 50%\n bucket 21: 50%\n bucket 20: 60%\n bucket 21: 60%\n bucket 20: 70%\n bucket 21: 70%\n bucket 20: 80%\n bucket 21: 80%\n bucket 20: 90%\n bucket 21: 90%\n bucket 20: 100%\n bucket 21: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 23:\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 22: 50%\n bucket 23: 40%\n bucket 22: 60%\n bucket 23: 50%\n bucket 22: 70%\n bucket 23: 60%\n bucket 22: 80%\n bucket 23: 70%\n bucket 22: 90%\n bucket 23: 80%\n bucket 22: 100%\n bucket 23: 90%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Entering block accumulator loop for bucket 24:\n Calculating Z arrays for bucket 25\n bucket 24: 10%\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 25:\n bucket 24: 20%\n Entering block accumulator loop for bucket 26:\n bucket 25: 10%\n bucket 24: 30%\n bucket 25: 20%\n bucket 26: 10%\n bucket 24: 40%\n bucket 25: 30%\n bucket 24: 50%\n bucket 25: 40%\n bucket 24: 60%\n bucket 25: 50%\n bucket 24: 70%\n bucket 25: 60%\n bucket 24: 80%\n bucket 25: 70%\n bucket 24: 90%\n bucket 25: 80%\n bucket 26: 20%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 26: 30%\n bucket 26: 40%\n bucket 26: 50%\n bucket 25: 90%\n bucket 26: 60%\n bucket 26: 70%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\nGetting block 28 of 60\n bucket 27: 100%\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 29: 20%\n bucket 29: 30%\n bucket 29: 40%\n bucket 29: 50%\n bucket 29: 60%\n bucket 29: 70%\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 80%\nGetting block 31 of 60\n Entering block accumulator loop for bucket 30:\n bucket 29: 90%\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n bucket 30: 10%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 30: 80%\n Entering block accumulator loop for bucket 31:\n bucket 30: 90%\n bucket 31: 10%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 20%\n bucket 31: 30%\n bucket 31: 40%\n bucket 31: 50%\n Sorting block time: 00:00:00\n bucket 31: 60%\nReturning block of 52 for bucket 29\n bucket 31: 70%\n bucket 31: 80%\n bucket 31: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Entering block accumulator loop for bucket 32:\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n bucket 32: 10%\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 33:\n bucket 32: 20%\n bucket 32: 30%\n bucket 33: 10%\n Entering block accumulator loop for bucket 34:\n bucket 32: 40%\n bucket 33: 20%\n bucket 32: 50%\n bucket 33: 30%\n bucket 32: 60%\n bucket 33: 40%\n bucket 32: 70%\n bucket 33: 50%\n bucket 32: 80%\n bucket 33: 60%\n bucket 32: 90%\n bucket 33: 70%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n bucket 33: 80%\n (Using difference cover)\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 10%\n bucket 34: 20%\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block time: 00:00:00\n Sorting block of length 122 for bucket 34\n (Using difference cover)\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n Entering block accumulator loop for bucket 36:\n bucket 35: 10%\n bucket 36: 10%\n bucket 35: 20%\n bucket 36: 20%\n bucket 35: 30%\n bucket 35: 40%\n bucket 36: 30%\n bucket 35: 50%\n bucket 36: 40%\n bucket 35: 60%\n bucket 36: 50%\n bucket 35: 70%\n bucket 35: 80%\n bucket 36: 60%\n bucket 35: 90%\n bucket 36: 70%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n Entering block accumulator loop for bucket 38:\n bucket 37: 40%\n bucket 38: 10%\n bucket 37: 50%\n bucket 38: 20%\n bucket 37: 60%\n bucket 38: 30%\n bucket 37: 70%\n bucket 38: 40%\n bucket 37: 80%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 39:\n bucket 39: 10%\n bucket 39: 20%\n bucket 39: 30%\n bucket 39: 40%\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n bucket 39: 90%\n bucket 39: 100%\n Entering block accumulator loop for bucket 40:\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n Sorting block time: 00:00:00\n bucket 40: 40%\nReturning block of 126 for bucket 39\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 60\n Entering block accumulator loop for bucket 41:\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 41: 10%\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n Sorting block time: 00:00:00\n bucket 41: 100%\nReturning block of 120 for bucket 42\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n bucket 43: 60%\n bucket 44: 20%\n bucket 43: 70%\n bucket 44: 30%\n bucket 44: 40%\n bucket 43: 80%\n bucket 44: 50%\n bucket 43: 90%\n bucket 44: 60%\n bucket 43: 100%\n bucket 44: 70%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 45 of 60\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 46:\n bucket 45: 10%\n bucket 46: 10%\n bucket 46: 20%\n bucket 45: 20%\n bucket 46: 30%\n bucket 45: 30%\n bucket 46: 40%\n bucket 45: 40%\n bucket 46: 50%\n bucket 45: 50%\n bucket 45: 60%\n bucket 46: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 46: 70%\n bucket 45: 90%\n bucket 45: 100%\n bucket 46: 80%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\nGetting block 48 of 60\n Calculating Z arrays for bucket 47\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 47:\n Entering block accumulator loop for bucket 48:\n bucket 47: 10%\n bucket 48: 10%\n bucket 47: 20%\n bucket 48: 20%\n bucket 47: 30%\n bucket 48: 30%\n bucket 47: 40%\n bucket 48: 40%\n bucket 47: 50%\n bucket 48: 50%\n bucket 47: 60%\n bucket 48: 60%\n bucket 48: 70%\n bucket 47: 70%\n bucket 48: 80%\n bucket 47: 80%\n bucket 47: 90%\n bucket 48: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 40%\n bucket 51: 50%\n Entering block accumulator loop for bucket 52:\n bucket 51: 60%\n bucket 52: 10%\n bucket 51: 70%\n bucket 52: 20%\n bucket 52: 30%\n bucket 51: 80%\n bucket 52: 40%\n bucket 51: 90%\n bucket 52: 50%\n bucket 51: 100%\n bucket 52: 60%\n Sorting block of length 91 for bucket 51\n bucket 52: 70%\n bucket 52: 80%\n (Using difference cover)\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 53: 20%\n bucket 53: 30%\n bucket 53: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 55: 10%\n bucket 56: 30%\n bucket 55: 20%\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 40%\n bucket 55: 30%\n bucket 56: 50%\n Entering block accumulator loop for bucket 57:\n bucket 55: 40%\n bucket 57: 10%\n bucket 56: 60%\n bucket 57: 20%\n bucket 55: 50%\n bucket 57: 30%\n bucket 56: 70%\n bucket 55: 60%\n bucket 57: 40%\n bucket 56: 80%\n bucket 57: 50%\n bucket 56: 90%\n bucket 57: 60%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 07:01:18", "plugin": "core", "name": "end_epoch", "raw_value": "1725001278.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:01:18", "plugin": "core", "name": "start_epoch", "raw_value": "1725001278.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-5", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 5, "time_seconds": 11.22361946105957, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "hisat2/2.2.1+galaxy1-5", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 5, "time_seconds": 11.216285705566406, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "hisat2/2.2.1+galaxy1-6", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 6, "time_seconds": 33.94484877586365, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "2d50454efb2c16ca"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "74ce2bf6b3b2a9b0"}, "library|input_2": {"src": "hda", "id": "74ce2bf6b3b2a9b0"}, "library|type": "paired", "adv|output_options|unaligned_file": true, "adv|output_options|aligned_file": true, "adv|output_options|output_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "6cb8c88a9ee438e5", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:53:43.674954", "update_time": "2024-08-30T06:53:57.064126", "galaxy_version": "24.1", "external_id": "gxy-5gqdw", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/5/e/d/dataset_5edd5de4-9bdb-4beb-8fe8-34a76eb6def6.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/2/f/1/dataset_2f1e4da1-d70b-4e00-8c93-0687837c5bc2.dat' input_f.fasta && ln -f -s '/galaxy/server/database/objects/2/f/1/dataset_2f1e4da1-d70b-4e00-8c93-0687837c5bc2.dat' input_r.fasta && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -f -1 'input_f.fasta' -2 'input_r.fasta' --un-conc '/galaxy/server/database/objects/5/c/a/dataset_5caec423-ec49-4187-979d-a64cfa8e7bfe.dat' --al-conc '/galaxy/server/database/objects/8/e/1/dataset_8e1b1edf-e7c3-427f-8d5a-d734427c854f.dat' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/0/0/d/dataset_00ddae32-c637-473a-ad24-00236d1750c3.dat' && mv '/galaxy/server/database/objects/5/c/a/dataset_5caec423-ec49-4187-979d-a64cfa8e7bfe.1.dat' '/galaxy/server/database/objects/5/c/a/dataset_5caec423-ec49-4187-979d-a64cfa8e7bfe.dat' && mv '/galaxy/server/database/objects/5/c/a/dataset_5caec423-ec49-4187-979d-a64cfa8e7bfe.2.dat' '/galaxy/server/database/objects/c/e/8/dataset_ce85231e-003e-43cc-b47b-40985d4ab75e.dat' && mv '/galaxy/server/database/objects/8/e/1/dataset_8e1b1edf-e7c3-427f-8d5a-d734427c854f.1.dat' '/galaxy/server/database/objects/8/e/1/dataset_8e1b1edf-e7c3-427f-8d5a-d734427c854f.dat' && mv '/galaxy/server/database/objects/8/e/1/dataset_8e1b1edf-e7c3-427f-8d5a-d734427c854f.2.dat' '/galaxy/server/database/objects/9/e/6/dataset_9e690adf-5418-49fd-9969-bb582b19dda3.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 1, \"aligned_file\": true, \"output_options_selector\": \"advanced\", \"unaligned_file\": true}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 137, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 137, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 136, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "2d50454efb2c16ca", "src": "hda", "uuid": "5edd5de4-9bdb-4beb-8fe8-34a76eb6def6"}, "library|input_1": {"id": "74ce2bf6b3b2a9b0", "src": "hda", "uuid": "2f1e4da1-d70b-4e00-8c93-0687837c5bc2"}, "library|input_2": {"id": "74ce2bf6b3b2a9b0", "src": "hda", "uuid": "2f1e4da1-d70b-4e00-8c93-0687837c5bc2"}}, "outputs": {"output_alignments": {"id": "18a21a304df93622", "src": "hda", "uuid": "00ddae32-c637-473a-ad24-00236d1750c3"}, "output_unaligned_reads_l": {"id": "eef7d7b823935650", "src": "hda", "uuid": "5caec423-ec49-4187-979d-a64cfa8e7bfe"}, "output_aligned_reads_l": {"id": "53b0e16a29081cba", "src": "hda", "uuid": "8e1b1edf-e7c3-427f-8d5a-d734427c854f"}, "output_unaligned_reads_r": {"id": "ffa36cfcb4321d19", "src": "hda", "uuid": "ce85231e-003e-43cc-b47b-40985d4ab75e"}, "output_aligned_reads_r": {"id": "e8ce6f51c192a43d", "src": "hda", "uuid": "9e690adf-5418-49fd-9969-bb582b19dda3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Entering block accumulator loop for bucket 2:\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n bucket 2: 10%\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 3\n bucket 2: 20%\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 4\nGetting block 5 of 60\n bucket 2: 30%\nGetting block 7 of 60\nGetting block 8 of 60\n Reserving size (126) for bucket 8\nGetting block 6 of 60\n Reserving size (126) for bucket 5\n Entering block accumulator loop for bucket 4:\n bucket 3: 10%\n Calculating Z arrays for bucket 8\n bucket 1: 10%\n Reserving size (126) for bucket 7\n bucket 2: 40%\n bucket 3: 20%\n Reserving size (126) for bucket 6\n bucket 1: 20%\n bucket 4: 10%\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 8:\n bucket 1: 30%\n Calculating Z arrays for bucket 6\n bucket 3: 30%\n bucket 1: 40%\n bucket 8: 10%\n bucket 4: 20%\n bucket 3: 40%\n Calculating Z arrays for bucket 5\n bucket 1: 50%\n Entering block accumulator loop for bucket 6:\n bucket 8: 20%\n Entering block accumulator loop for bucket 7:\n bucket 1: 60%\n bucket 4: 30%\n bucket 2: 50%\n bucket 7: 10%\n bucket 1: 70%\n bucket 8: 30%\n bucket 3: 50%\n bucket 2: 60%\n bucket 8: 40%\n bucket 7: 20%\n bucket 6: 10%\n bucket 1: 80%\n bucket 2: 70%\n bucket 7: 30%\n bucket 8: 50%\n bucket 3: 60%\n bucket 4: 40%\n bucket 1: 90%\n bucket 7: 40%\n Entering block accumulator loop for bucket 5:\n bucket 7: 50%\n bucket 6: 20%\n bucket 4: 50%\n bucket 8: 60%\n bucket 3: 70%\n bucket 5: 10%\n bucket 4: 60%\n bucket 1: 100%\n bucket 6: 30%\n bucket 2: 80%\n bucket 7: 60%\n Sorting block of length 42 for bucket 1\n bucket 6: 40%\n bucket 5: 20%\n bucket 4: 70%\n bucket 6: 50%\n (Using difference cover)\n bucket 7: 70%\n bucket 4: 80%\n bucket 3: 80%\n bucket 6: 60%\n bucket 5: 30%\n bucket 3: 90%\n bucket 7: 80%\n bucket 4: 90%\n bucket 8: 70%\n bucket 6: 70%\n bucket 7: 90%\n bucket 2: 90%\n bucket 4: 100%\n bucket 6: 80%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 3: 100%\n bucket 7: 100%\n bucket 5: 40%\n bucket 8: 80%\n bucket 2: 100%\n Sorting block of length 75 for bucket 7\n bucket 6: 90%\n (Using difference cover)\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 5: 50%\n bucket 8: 90%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 80%\n bucket 13: 90%\n Entering block accumulator loop for bucket 14:\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 16: 20%\n bucket 15: 40%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n bucket 16: 30%\n Calculating Z arrays for bucket 17\n bucket 15: 50%\n bucket 16: 40%\n bucket 15: 60%\n bucket 16: 50%\n Entering block accumulator loop for bucket 17:\n bucket 15: 70%\n bucket 16: 60%\n bucket 17: 10%\n bucket 15: 80%\n bucket 17: 20%\n bucket 16: 70%\n bucket 17: 30%\n bucket 15: 90%\n bucket 16: 80%\n bucket 17: 40%\n bucket 15: 100%\n bucket 17: 50%\n bucket 16: 90%\n Sorting block of length 68 for bucket 15\n bucket 17: 60%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n (Using difference cover)\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n Entering block accumulator loop for bucket 19:\n bucket 18: 20%\n bucket 18: 30%\n bucket 19: 10%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 19: 50%\n bucket 18: 80%\n bucket 19: 60%\n bucket 18: 90%\n bucket 19: 70%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 20%\n bucket 20: 30%\n Entering block accumulator loop for bucket 21:\n bucket 20: 40%\n bucket 21: 10%\n bucket 20: 50%\n bucket 21: 20%\n bucket 20: 60%\n bucket 21: 30%\n bucket 20: 70%\n bucket 21: 40%\n bucket 20: 80%\n bucket 21: 50%\n bucket 20: 90%\n bucket 21: 60%\n bucket 20: 100%\n bucket 21: 70%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 60%\n bucket 22: 70%\n Entering block accumulator loop for bucket 23:\n bucket 22: 80%\n bucket 23: 10%\n bucket 22: 90%\n bucket 23: 20%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 30%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n bucket 23: 40%\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Calculating Z arrays for bucket 25\n bucket 23: 50%\n Entering block accumulator loop for bucket 24:\n bucket 23: 60%\n Entering block accumulator loop for bucket 25:\n bucket 23: 70%\n Sorting block time: 00:00:00\n bucket 24: 10%\n bucket 25: 10%\nReturning block of 81 for bucket 22\n bucket 23: 80%\n bucket 25: 20%\n bucket 24: 20%\n bucket 23: 90%\n bucket 25: 30%\n bucket 24: 30%\n bucket 23: 100%\n bucket 25: 40%\n bucket 24: 40%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 25: 50%\n bucket 24: 50%\n bucket 25: 60%\n bucket 24: 60%\n bucket 25: 70%\n bucket 24: 70%\n bucket 25: 80%\n bucket 24: 80%\n bucket 25: 90%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n Entering block accumulator loop for bucket 27:\n bucket 26: 20%\n bucket 27: 10%\n bucket 26: 30%\n bucket 27: 20%\n bucket 26: 40%\n bucket 27: 30%\n bucket 26: 50%\n bucket 27: 40%\n bucket 26: 60%\n bucket 27: 50%\n bucket 26: 70%\n bucket 27: 60%\n bucket 26: 80%\n bucket 27: 70%\n bucket 26: 90%\n bucket 27: 80%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n bucket 28: 10%\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n bucket 28: 20%\n bucket 28: 30%\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 28: 40%\n bucket 29: 20%\n bucket 30: 10%\n bucket 28: 50%\n bucket 29: 30%\n bucket 28: 60%\n bucket 30: 20%\n bucket 28: 70%\n bucket 29: 40%\n bucket 30: 30%\n bucket 28: 80%\n bucket 29: 50%\n bucket 28: 90%\n bucket 30: 40%\n bucket 29: 60%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 30: 50%\n bucket 29: 70%\n bucket 30: 60%\n bucket 29: 80%\n bucket 30: 70%\n bucket 29: 90%\n bucket 30: 80%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\nGetting block 33 of 60\n Entering block accumulator loop for bucket 32:\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 31: 10%\n bucket 32: 10%\n bucket 31: 20%\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 31: 30%\n bucket 32: 30%\n bucket 33: 10%\n bucket 32: 40%\n bucket 31: 40%\n bucket 32: 50%\n bucket 33: 20%\n bucket 31: 50%\n bucket 32: 60%\n bucket 33: 30%\n bucket 32: 70%\n bucket 31: 60%\n bucket 33: 40%\n bucket 32: 80%\n bucket 31: 70%\n bucket 33: 50%\n bucket 32: 90%\n bucket 31: 80%\n bucket 33: 60%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 31: 90%\n bucket 33: 70%\n bucket 31: 100%\n bucket 33: 80%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n Entering block accumulator loop for bucket 35:\n bucket 34: 10%\n bucket 35: 10%\n bucket 34: 20%\n bucket 35: 20%\n bucket 34: 30%\n bucket 35: 30%\n bucket 34: 40%\n bucket 35: 40%\n bucket 34: 50%\n bucket 35: 50%\n bucket 34: 60%\n bucket 35: 60%\n bucket 34: 70%\n bucket 35: 70%\n bucket 34: 80%\n bucket 35: 80%\n bucket 34: 90%\n bucket 35: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 20%\n Entering block accumulator loop for bucket 37:\n bucket 36: 30%\n bucket 37: 10%\n bucket 36: 40%\n bucket 37: 20%\n bucket 36: 50%\n bucket 37: 30%\n bucket 37: 40%\n bucket 36: 60%\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n bucket 37: 50%\n bucket 36: 70%\n Calculating Z arrays for bucket 38\n bucket 37: 60%\n bucket 36: 80%\n bucket 37: 70%\n bucket 37: 80%\n Entering block accumulator loop for bucket 38:\n bucket 36: 90%\n bucket 37: 90%\n bucket 37: 100%\n bucket 38: 10%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 40: 20%\n bucket 40: 30%\n bucket 39: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 39: 40%\n bucket 40: 60%\n bucket 40: 70%\n bucket 39: 50%\n bucket 40: 80%\n bucket 39: 60%\n bucket 40: 90%\n bucket 39: 70%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 41: 10%\n bucket 41: 20%\n Entering block accumulator loop for bucket 42:\n bucket 41: 30%\n bucket 42: 10%\n bucket 41: 40%\n bucket 42: 20%\n bucket 41: 50%\n bucket 42: 30%\n bucket 41: 60%\n bucket 42: 40%\n bucket 41: 70%\n bucket 42: 50%\n bucket 41: 80%\n bucket 42: 60%\n bucket 41: 90%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\nGetting block 45 of 60\n Reserving size (126) for bucket 44\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 44:\n bucket 45: 10%\n bucket 44: 10%\n bucket 45: 20%\n bucket 44: 20%\n bucket 45: 30%\n bucket 44: 30%\n bucket 45: 40%\n bucket 44: 40%\n bucket 45: 50%\n bucket 44: 50%\n bucket 45: 60%\n bucket 44: 60%\n bucket 45: 70%\n bucket 44: 70%\n bucket 45: 80%\n bucket 44: 80%\n bucket 45: 90%\n bucket 44: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n Entering block accumulator loop for bucket 47:\n bucket 46: 20%\n bucket 46: 30%\n bucket 47: 10%\n bucket 46: 40%\n bucket 47: 20%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n bucket 46: 50%\n Calculating Z arrays for bucket 48\n bucket 47: 30%\n bucket 46: 60%\n bucket 47: 40%\n Entering block accumulator loop for bucket 48:\n bucket 46: 70%\n bucket 47: 50%\n bucket 46: 80%\n bucket 48: 10%\n bucket 47: 60%\n bucket 46: 90%\n bucket 48: 20%\n bucket 47: 70%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 80%\n bucket 48: 30%\n bucket 48: 40%\n bucket 47: 90%\n bucket 48: 50%\n bucket 48: 60%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n bucket 48: 70%\n (Using difference cover)\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 50%\n bucket 49: 60%\n Entering block accumulator loop for bucket 50:\n bucket 49: 70%\n bucket 50: 10%\n bucket 49: 80%\n bucket 50: 20%\n bucket 49: 90%\n bucket 50: 30%\n bucket 49: 100%\n bucket 50: 40%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 51: 70%\n Entering block accumulator loop for bucket 52:\n bucket 51: 80%\n Entering block accumulator loop for bucket 53:\n bucket 52: 10%\n bucket 53: 10%\n bucket 51: 90%\n bucket 52: 20%\n bucket 53: 20%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n bucket 52: 30%\n (Using difference cover)\n bucket 53: 30%\n bucket 52: 40%\n bucket 53: 40%\n bucket 52: 50%\n bucket 53: 50%\n bucket 52: 60%\n bucket 53: 60%\n bucket 52: 70%\n bucket 53: 70%\n bucket 52: 80%\n bucket 53: 80%\n bucket 52: 90%\n bucket 53: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 20%\n Entering block accumulator loop for bucket 55:\n bucket 54: 30%\n bucket 55: 10%\n bucket 54: 40%\n bucket 55: 20%\n bucket 55: 30%\n bucket 54: 50%\n bucket 55: 40%\n bucket 54: 60%\n bucket 55: 50%\n bucket 54: 70%\n bucket 55: 60%\n bucket 54: 80%\n bucket 55: 70%\n bucket 54: 90%\n bucket 55: 80%\n bucket 55: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n bucket 55: 100%\n (Using difference cover)\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\nGetting block 57 of 60\n bucket 56: 70%\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 80%\n bucket 56: 90%\n Entering block accumulator loop for bucket 57:\n bucket 56: 100%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 10%\n Entering block accumulator loop for bucket 58:\n bucket 57: 20%\n bucket 58: 10%\n bucket 57: 30%\n bucket 58: 20%\n bucket 57: 40%\n bucket 58: 30%\n bucket 58: 40%\n bucket 57: 50%\n bucket 58: 50%\n bucket 57: 60%\n bucket 58: 60%\n bucket 58: 70%\n bucket 57: 70%\n bucket 58: 80%\n Sorting block time: 00:00:00\n bucket 57: 80%\nReturning block of 56 for bucket 56\n bucket 58: 90%\n bucket 57: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n3 reads; of these:\n 3 (100.00%) were paired; of these:\n 3 (100.00%) aligned concordantly 0 times\n 0 (0.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 6 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Entering block accumulator loop for bucket 2:\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n bucket 2: 10%\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 3\n bucket 2: 20%\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 4\nGetting block 5 of 60\n bucket 2: 30%\nGetting block 7 of 60\nGetting block 8 of 60\n Reserving size (126) for bucket 8\nGetting block 6 of 60\n Reserving size (126) for bucket 5\n Entering block accumulator loop for bucket 4:\n bucket 3: 10%\n Calculating Z arrays for bucket 8\n bucket 1: 10%\n Reserving size (126) for bucket 7\n bucket 2: 40%\n bucket 3: 20%\n Reserving size (126) for bucket 6\n bucket 1: 20%\n bucket 4: 10%\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 8:\n bucket 1: 30%\n Calculating Z arrays for bucket 6\n bucket 3: 30%\n bucket 1: 40%\n bucket 8: 10%\n bucket 4: 20%\n bucket 3: 40%\n Calculating Z arrays for bucket 5\n bucket 1: 50%\n Entering block accumulator loop for bucket 6:\n bucket 8: 20%\n Entering block accumulator loop for bucket 7:\n bucket 1: 60%\n bucket 4: 30%\n bucket 2: 50%\n bucket 7: 10%\n bucket 1: 70%\n bucket 8: 30%\n bucket 3: 50%\n bucket 2: 60%\n bucket 8: 40%\n bucket 7: 20%\n bucket 6: 10%\n bucket 1: 80%\n bucket 2: 70%\n bucket 7: 30%\n bucket 8: 50%\n bucket 3: 60%\n bucket 4: 40%\n bucket 1: 90%\n bucket 7: 40%\n Entering block accumulator loop for bucket 5:\n bucket 7: 50%\n bucket 6: 20%\n bucket 4: 50%\n bucket 8: 60%\n bucket 3: 70%\n bucket 5: 10%\n bucket 4: 60%\n bucket 1: 100%\n bucket 6: 30%\n bucket 2: 80%\n bucket 7: 60%\n Sorting block of length 42 for bucket 1\n bucket 6: 40%\n bucket 5: 20%\n bucket 4: 70%\n bucket 6: 50%\n (Using difference cover)\n bucket 7: 70%\n bucket 4: 80%\n bucket 3: 80%\n bucket 6: 60%\n bucket 5: 30%\n bucket 3: 90%\n bucket 7: 80%\n bucket 4: 90%\n bucket 8: 70%\n bucket 6: 70%\n bucket 7: 90%\n bucket 2: 90%\n bucket 4: 100%\n bucket 6: 80%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 3: 100%\n bucket 7: 100%\n bucket 5: 40%\n bucket 8: 80%\n bucket 2: 100%\n Sorting block of length 75 for bucket 7\n bucket 6: 90%\n (Using difference cover)\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 5: 50%\n bucket 8: 90%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 5: 60%\n bucket 5: 70%\n bucket 5: 80%\n bucket 5: 90%\n bucket 5: 100%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 80%\n bucket 13: 90%\n Entering block accumulator loop for bucket 14:\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n bucket 14: 70%\n bucket 14: 80%\n bucket 14: 90%\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n Entering block accumulator loop for bucket 16:\n bucket 15: 20%\n bucket 16: 10%\n bucket 15: 30%\n bucket 16: 20%\n bucket 15: 40%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n bucket 16: 30%\n Calculating Z arrays for bucket 17\n bucket 15: 50%\n bucket 16: 40%\n bucket 15: 60%\n bucket 16: 50%\n Entering block accumulator loop for bucket 17:\n bucket 15: 70%\n bucket 16: 60%\n bucket 17: 10%\n bucket 15: 80%\n bucket 17: 20%\n bucket 16: 70%\n bucket 17: 30%\n bucket 15: 90%\n bucket 16: 80%\n bucket 17: 40%\n bucket 15: 100%\n bucket 17: 50%\n bucket 16: 90%\n Sorting block of length 68 for bucket 15\n bucket 17: 60%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n (Using difference cover)\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n Entering block accumulator loop for bucket 19:\n bucket 18: 20%\n bucket 18: 30%\n bucket 19: 10%\n bucket 18: 40%\n bucket 19: 20%\n bucket 18: 50%\n bucket 19: 30%\n bucket 18: 60%\n bucket 19: 40%\n bucket 18: 70%\n bucket 19: 50%\n bucket 18: 80%\n bucket 19: 60%\n bucket 18: 90%\n bucket 19: 70%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 20%\n bucket 20: 30%\n Entering block accumulator loop for bucket 21:\n bucket 20: 40%\n bucket 21: 10%\n bucket 20: 50%\n bucket 21: 20%\n bucket 20: 60%\n bucket 21: 30%\n bucket 20: 70%\n bucket 21: 40%\n bucket 20: 80%\n bucket 21: 50%\n bucket 20: 90%\n bucket 21: 60%\n bucket 20: 100%\n bucket 21: 70%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n bucket 22: 60%\n bucket 22: 70%\n Entering block accumulator loop for bucket 23:\n bucket 22: 80%\n bucket 23: 10%\n bucket 22: 90%\n bucket 23: 20%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 30%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n bucket 23: 40%\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Calculating Z arrays for bucket 25\n bucket 23: 50%\n Entering block accumulator loop for bucket 24:\n bucket 23: 60%\n Entering block accumulator loop for bucket 25:\n bucket 23: 70%\n Sorting block time: 00:00:00\n bucket 24: 10%\n bucket 25: 10%\nReturning block of 81 for bucket 22\n bucket 23: 80%\n bucket 25: 20%\n bucket 24: 20%\n bucket 23: 90%\n bucket 25: 30%\n bucket 24: 30%\n bucket 23: 100%\n bucket 25: 40%\n bucket 24: 40%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 25: 50%\n bucket 24: 50%\n bucket 25: 60%\n bucket 24: 60%\n bucket 25: 70%\n bucket 24: 70%\n bucket 25: 80%\n bucket 24: 80%\n bucket 25: 90%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n Entering block accumulator loop for bucket 27:\n bucket 26: 20%\n bucket 27: 10%\n bucket 26: 30%\n bucket 27: 20%\n bucket 26: 40%\n bucket 27: 30%\n bucket 26: 50%\n bucket 27: 40%\n bucket 26: 60%\n bucket 27: 50%\n bucket 26: 70%\n bucket 27: 60%\n bucket 26: 80%\n bucket 27: 70%\n bucket 26: 90%\n bucket 27: 80%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n bucket 28: 10%\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 29:\n bucket 28: 20%\n bucket 28: 30%\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 28: 40%\n bucket 29: 20%\n bucket 30: 10%\n bucket 28: 50%\n bucket 29: 30%\n bucket 28: 60%\n bucket 30: 20%\n bucket 28: 70%\n bucket 29: 40%\n bucket 30: 30%\n bucket 28: 80%\n bucket 29: 50%\n bucket 28: 90%\n bucket 30: 40%\n bucket 29: 60%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 30: 50%\n bucket 29: 70%\n bucket 30: 60%\n bucket 29: 80%\n bucket 30: 70%\n bucket 29: 90%\n bucket 30: 80%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\nGetting block 33 of 60\n Entering block accumulator loop for bucket 32:\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 31: 10%\n bucket 32: 10%\n bucket 31: 20%\n bucket 32: 20%\n Entering block accumulator loop for bucket 33:\n bucket 31: 30%\n bucket 32: 30%\n bucket 33: 10%\n bucket 32: 40%\n bucket 31: 40%\n bucket 32: 50%\n bucket 33: 20%\n bucket 31: 50%\n bucket 32: 60%\n bucket 33: 30%\n bucket 32: 70%\n bucket 31: 60%\n bucket 33: 40%\n bucket 32: 80%\n bucket 31: 70%\n bucket 33: 50%\n bucket 32: 90%\n bucket 31: 80%\n bucket 33: 60%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 31: 90%\n bucket 33: 70%\n bucket 31: 100%\n bucket 33: 80%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n Entering block accumulator loop for bucket 35:\n bucket 34: 10%\n bucket 35: 10%\n bucket 34: 20%\n bucket 35: 20%\n bucket 34: 30%\n bucket 35: 30%\n bucket 34: 40%\n bucket 35: 40%\n bucket 34: 50%\n bucket 35: 50%\n bucket 34: 60%\n bucket 35: 60%\n bucket 34: 70%\n bucket 35: 70%\n bucket 34: 80%\n bucket 35: 80%\n bucket 34: 90%\n bucket 35: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 20%\n Entering block accumulator loop for bucket 37:\n bucket 36: 30%\n bucket 37: 10%\n bucket 36: 40%\n bucket 37: 20%\n bucket 36: 50%\n bucket 37: 30%\n bucket 37: 40%\n bucket 36: 60%\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n bucket 37: 50%\n bucket 36: 70%\n Calculating Z arrays for bucket 38\n bucket 37: 60%\n bucket 36: 80%\n bucket 37: 70%\n bucket 37: 80%\n Entering block accumulator loop for bucket 38:\n bucket 36: 90%\n bucket 37: 90%\n bucket 37: 100%\n bucket 38: 10%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 38: 20%\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 40: 20%\n bucket 40: 30%\n bucket 39: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 39: 40%\n bucket 40: 60%\n bucket 40: 70%\n bucket 39: 50%\n bucket 40: 80%\n bucket 39: 60%\n bucket 40: 90%\n bucket 39: 70%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 41: 10%\n bucket 41: 20%\n Entering block accumulator loop for bucket 42:\n bucket 41: 30%\n bucket 42: 10%\n bucket 41: 40%\n bucket 42: 20%\n bucket 41: 50%\n bucket 42: 30%\n bucket 41: 60%\n bucket 42: 40%\n bucket 41: 70%\n bucket 42: 50%\n bucket 41: 80%\n bucket 42: 60%\n bucket 41: 90%\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Entering block accumulator loop for bucket 43:\n bucket 43: 10%\n bucket 43: 20%\n bucket 43: 30%\n bucket 43: 40%\n bucket 43: 50%\n bucket 43: 60%\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n bucket 43: 70%\n bucket 43: 80%\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\nGetting block 45 of 60\n Reserving size (126) for bucket 44\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 44:\n bucket 45: 10%\n bucket 44: 10%\n bucket 45: 20%\n bucket 44: 20%\n bucket 45: 30%\n bucket 44: 30%\n bucket 45: 40%\n bucket 44: 40%\n bucket 45: 50%\n bucket 44: 50%\n bucket 45: 60%\n bucket 44: 60%\n bucket 45: 70%\n bucket 44: 70%\n bucket 45: 80%\n bucket 44: 80%\n bucket 45: 90%\n bucket 44: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n Entering block accumulator loop for bucket 47:\n bucket 46: 20%\n bucket 46: 30%\n bucket 47: 10%\n bucket 46: 40%\n bucket 47: 20%\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n bucket 46: 50%\n Calculating Z arrays for bucket 48\n bucket 47: 30%\n bucket 46: 60%\n bucket 47: 40%\n Entering block accumulator loop for bucket 48:\n bucket 46: 70%\n bucket 47: 50%\n bucket 46: 80%\n bucket 48: 10%\n bucket 47: 60%\n bucket 46: 90%\n bucket 48: 20%\n bucket 47: 70%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 80%\n bucket 48: 30%\n bucket 48: 40%\n bucket 47: 90%\n bucket 48: 50%\n bucket 48: 60%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n bucket 48: 70%\n (Using difference cover)\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 49: 50%\n bucket 49: 60%\n Entering block accumulator loop for bucket 50:\n bucket 49: 70%\n bucket 50: 10%\n bucket 49: 80%\n bucket 50: 20%\n bucket 49: 90%\n bucket 50: 30%\n bucket 49: 100%\n bucket 50: 40%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 51: 70%\n Entering block accumulator loop for bucket 52:\n bucket 51: 80%\n Entering block accumulator loop for bucket 53:\n bucket 52: 10%\n bucket 53: 10%\n bucket 51: 90%\n bucket 52: 20%\n bucket 53: 20%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n bucket 52: 30%\n (Using difference cover)\n bucket 53: 30%\n bucket 52: 40%\n bucket 53: 40%\n bucket 52: 50%\n bucket 53: 50%\n bucket 52: 60%\n bucket 53: 60%\n bucket 52: 70%\n bucket 53: 70%\n bucket 52: 80%\n bucket 53: 80%\n bucket 52: 90%\n bucket 53: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 20%\n Entering block accumulator loop for bucket 55:\n bucket 54: 30%\n bucket 55: 10%\n bucket 54: 40%\n bucket 55: 20%\n bucket 55: 30%\n bucket 54: 50%\n bucket 55: 40%\n bucket 54: 60%\n bucket 55: 50%\n bucket 54: 70%\n bucket 55: 60%\n bucket 54: 80%\n bucket 55: 70%\n bucket 54: 90%\n bucket 55: 80%\n bucket 55: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n bucket 55: 100%\n (Using difference cover)\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\nGetting block 57 of 60\n bucket 56: 70%\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n bucket 56: 80%\n bucket 56: 90%\n Entering block accumulator loop for bucket 57:\n bucket 56: 100%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 10%\n Entering block accumulator loop for bucket 58:\n bucket 57: 20%\n bucket 58: 10%\n bucket 57: 30%\n bucket 58: 20%\n bucket 57: 40%\n bucket 58: 30%\n bucket 58: 40%\n bucket 57: 50%\n bucket 58: 50%\n bucket 57: 60%\n bucket 58: 60%\n bucket 58: 70%\n bucket 57: 70%\n bucket 58: 80%\n Sorting block time: 00:00:00\n bucket 57: 80%\nReturning block of 56 for bucket 56\n bucket 58: 90%\n bucket 57: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\n bucket 59: 30%\n bucket 59: 40%\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n3 reads; of these:\n 3 (100.00%) were paired; of these:\n 3 (100.00%) aligned concordantly 0 times\n 0 (0.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 6 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:53:46", "plugin": "core", "name": "end_epoch", "raw_value": "1725000826.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:53:45", "plugin": "core", "name": "start_epoch", "raw_value": "1725000825.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-6", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 6, "time_seconds": 35.15934753417969, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "5a4278ced56f35e8"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "71238fffda61b52d"}, "library|input_2": {"src": "hda", "id": "71238fffda61b52d"}, "library|type": "paired", "adv|output_options|unaligned_file": true, "adv|output_options|aligned_file": true, "adv|output_options|output_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "74698d208f06f7f8", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:02:01.698464", "update_time": "2024-08-30T07:02:16.231612", "galaxy_version": "24.1", "external_id": "gxy-x6zb5", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/8/b/1/dataset_8b14f4c0-f7a6-4222-befc-4e75b89209cd.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/d/f/b/dataset_dfba74c5-9a54-4172-b574-5510e74b64e7.dat' input_f.fasta && ln -f -s '/galaxy/server/database/objects/d/f/b/dataset_dfba74c5-9a54-4172-b574-5510e74b64e7.dat' input_r.fasta && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -f -1 'input_f.fasta' -2 'input_r.fasta' --un-conc '/galaxy/server/database/objects/a/e/f/dataset_aef8f4b5-6a96-486f-9dc2-32fc248ffd8d.dat' --al-conc '/galaxy/server/database/objects/a/a/4/dataset_aa4f3dc6-4e73-47c3-94d3-68f27acc6473.dat' | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/6/8/c/dataset_68c0f89a-3379-44f2-bbde-84ef95bbe1f2.dat' && mv '/galaxy/server/database/objects/a/e/f/dataset_aef8f4b5-6a96-486f-9dc2-32fc248ffd8d.1.dat' '/galaxy/server/database/objects/a/e/f/dataset_aef8f4b5-6a96-486f-9dc2-32fc248ffd8d.dat' && mv '/galaxy/server/database/objects/a/e/f/dataset_aef8f4b5-6a96-486f-9dc2-32fc248ffd8d.2.dat' '/galaxy/server/database/objects/d/f/0/dataset_df07945d-2a19-426a-b41c-5c3972f8ec51.dat' && mv '/galaxy/server/database/objects/a/a/4/dataset_aa4f3dc6-4e73-47c3-94d3-68f27acc6473.1.dat' '/galaxy/server/database/objects/a/a/4/dataset_aa4f3dc6-4e73-47c3-94d3-68f27acc6473.dat' && mv '/galaxy/server/database/objects/a/a/4/dataset_aa4f3dc6-4e73-47c3-94d3-68f27acc6473.2.dat' '/galaxy/server/database/objects/d/0/b/dataset_d0b562b4-9418-4917-a3b0-2f9382913b5b.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 1, \"aligned_file\": true, \"output_options_selector\": \"advanced\", \"unaligned_file\": true}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 196, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 196, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 195, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "5a4278ced56f35e8", "src": "hda", "uuid": "8b14f4c0-f7a6-4222-befc-4e75b89209cd"}, "library|input_1": {"id": "71238fffda61b52d", "src": "hda", "uuid": "dfba74c5-9a54-4172-b574-5510e74b64e7"}, "library|input_2": {"id": "71238fffda61b52d", "src": "hda", "uuid": "dfba74c5-9a54-4172-b574-5510e74b64e7"}}, "outputs": {"output_alignments": {"id": "33d2eb019e2e20b5", "src": "hda", "uuid": "68c0f89a-3379-44f2-bbde-84ef95bbe1f2"}, "output_unaligned_reads_l": {"id": "aeb32d475429697d", "src": "hda", "uuid": "aef8f4b5-6a96-486f-9dc2-32fc248ffd8d"}, "output_aligned_reads_l": {"id": "aaed36200ff80f35", "src": "hda", "uuid": "aa4f3dc6-4e73-47c3-94d3-68f27acc6473"}, "output_unaligned_reads_r": {"id": "cc136686b8ded45a", "src": "hda", "uuid": "df07945d-2a19-426a-b41c-5c3972f8ec51"}, "output_aligned_reads_r": {"id": "34bc419e944da75c", "src": "hda", "uuid": "d0b562b4-9418-4917-a3b0-2f9382913b5b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 2:\n bucket 1: 20%\n Reserving size (126) for bucket 3\n bucket 1: 30%\n bucket 2: 10%\n Calculating Z arrays for bucket 3\n bucket 1: 40%\n bucket 2: 20%\n bucket 1: 50%\n bucket 2: 30%\n Entering block accumulator loop for bucket 3:\nGetting block 4 of 60\n bucket 3: 10%\n bucket 2: 40%\n bucket 1: 60%\n Reserving size (126) for bucket 4\n bucket 2: 50%\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 3: 20%\n bucket 2: 60%\n Calculating Z arrays for bucket 5\n bucket 3: 30%\n bucket 2: 70%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 3: 40%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 2: 80%\n Calculating Z arrays for bucket 4\n bucket 3: 50%\n Entering block accumulator loop for bucket 5:\n bucket 1: 70%\n bucket 3: 60%\n Calculating Z arrays for bucket 7\n Calculating Z arrays for bucket 6\n bucket 5: 10%\n bucket 1: 80%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 2: 90%\n bucket 5: 20%\n bucket 1: 90%\n bucket 2: 100%\n bucket 5: 30%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 5: 40%\n Calculating Z arrays for bucket 8\n bucket 1: 100%\n Entering block accumulator loop for bucket 4:\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 3: 70%\n bucket 6: 10%\n bucket 5: 50%\n bucket 7: 10%\n bucket 5: 60%\n bucket 6: 20%\n bucket 4: 10%\n Entering block accumulator loop for bucket 8:\n bucket 5: 70%\n bucket 6: 30%\n bucket 4: 20%\n bucket 3: 80%\n bucket 8: 10%\n bucket 5: 80%\n bucket 3: 90%\n bucket 4: 30%\n bucket 5: 90%\n bucket 6: 40%\n bucket 3: 100%\n bucket 7: 20%\n bucket 5: 100%\n bucket 8: 20%\n bucket 4: 40%\n bucket 7: 30%\n bucket 6: 50%\n bucket 4: 50%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 40%\n bucket 8: 30%\n bucket 4: 60%\n bucket 6: 60%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 40%\n Sorting block time: 00:00:00\n bucket 6: 70%\n bucket 7: 50%\nReturning block of 85 for bucket 2\n bucket 7: 60%\n bucket 4: 70%\n bucket 6: 80%\n bucket 7: 70%\n bucket 4: 80%\n bucket 8: 50%\n bucket 7: 80%\n bucket 4: 90%\n bucket 6: 90%\n bucket 8: 60%\n bucket 7: 90%\n bucket 4: 100%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n bucket 13: 100%\n Calculating Z arrays for bucket 14\n Sorting block of length 85 for bucket 13\n (Using difference cover)\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n Entering block accumulator loop for bucket 15:\n bucket 14: 30%\n bucket 14: 40%\n bucket 15: 10%\n bucket 14: 50%\n bucket 15: 20%\n bucket 14: 60%\n Sorting block time: 00:00:00\n bucket 15: 30%\nReturning block of 86 for bucket 13\n bucket 14: 70%\n bucket 15: 40%\n bucket 14: 80%\n bucket 14: 90%\n bucket 15: 50%\n bucket 14: 100%\n bucket 15: 60%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 50%\n bucket 16: 60%\n Entering block accumulator loop for bucket 17:\n bucket 16: 70%\n bucket 17: 10%\n bucket 16: 80%\n bucket 17: 20%\n bucket 16: 90%\n bucket 17: 30%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 19:\n Entering block accumulator loop for bucket 18:\n bucket 19: 10%\n bucket 19: 20%\n bucket 18: 10%\n bucket 19: 30%\n bucket 18: 20%\n bucket 19: 40%\n bucket 19: 50%\n bucket 18: 30%\n bucket 19: 60%\n bucket 18: 40%\n bucket 19: 70%\n bucket 18: 50%\n bucket 19: 80%\n bucket 18: 60%\n bucket 19: 90%\n bucket 18: 70%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 20%\n bucket 21: 30%\n Entering block accumulator loop for bucket 22:\n bucket 21: 40%\n bucket 21: 50%\n bucket 22: 10%\n bucket 21: 60%\n bucket 22: 20%\n bucket 21: 70%\n bucket 21: 80%\n bucket 22: 30%\n bucket 21: 90%\n bucket 22: 40%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n Sorting block time: 00:00:00\n bucket 24: 60%\nReturning block of 65 for bucket 23\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\n bucket 27: 20%\n bucket 26: 30%\n bucket 27: 30%\n bucket 26: 40%\n bucket 27: 40%\n bucket 26: 50%\n bucket 27: 50%\n bucket 26: 60%\n bucket 27: 60%\n bucket 26: 70%\n bucket 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 26: 90%\n bucket 27: 90%\n bucket 26: 100%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n Entering block accumulator loop for bucket 29:\n bucket 28: 20%\n bucket 29: 10%\n bucket 28: 30%\n bucket 29: 20%\n bucket 28: 40%\n bucket 29: 30%\n bucket 28: 50%\n bucket 29: 40%\n bucket 28: 60%\n bucket 29: 50%\n bucket 28: 70%\n bucket 29: 60%\n bucket 28: 80%\n bucket 29: 70%\n bucket 28: 90%\n bucket 29: 80%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n Sorting block time: 00:00:00\n bucket 30: 70%\nReturning block of 52 for bucket 29\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n Entering block accumulator loop for bucket 33:\n bucket 31: 20%\n bucket 32: 10%\n bucket 33: 10%\n bucket 31: 30%\n bucket 32: 20%\n bucket 33: 20%\n bucket 31: 40%\n bucket 32: 30%\n bucket 33: 30%\n bucket 32: 40%\n bucket 31: 50%\n bucket 33: 40%\n bucket 32: 50%\n bucket 31: 60%\n bucket 33: 50%\n bucket 31: 70%\n bucket 32: 60%\n bucket 33: 60%\n bucket 32: 70%\n bucket 31: 80%\n bucket 32: 80%\n bucket 33: 70%\n bucket 31: 90%\n bucket 32: 90%\n bucket 33: 80%\n bucket 31: 100%\n bucket 32: 100%\n Sorting block of length 110 for bucket 31\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 90%\n (Using difference cover)\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n bucket 35: 10%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 35: 30%\n bucket 34: 50%\n bucket 35: 40%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\n bucket 35: 70%\n bucket 34: 90%\n bucket 35: 80%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Entering block accumulator loop for bucket 36:\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n bucket 36: 20%\n Entering block accumulator loop for bucket 37:\n bucket 36: 30%\n bucket 36: 40%\n bucket 37: 10%\n bucket 36: 50%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 36: 60%\n bucket 37: 50%\n bucket 36: 70%\n bucket 37: 60%\n bucket 36: 80%\n bucket 37: 70%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n Entering block accumulator loop for bucket 39:\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 39: 20%\n bucket 38: 40%\n bucket 39: 30%\n bucket 38: 50%\n bucket 39: 40%\n bucket 38: 60%\n bucket 39: 50%\n bucket 38: 70%\n bucket 39: 60%\n bucket 38: 80%\n bucket 39: 70%\n bucket 38: 90%\n bucket 39: 80%\n bucket 38: 100%\n bucket 39: 90%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n bucket 40: 30%\n Calculating Z arrays for bucket 41\n bucket 40: 40%\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 40: 50%\n Entering block accumulator loop for bucket 41:\n bucket 40: 60%\n Entering block accumulator loop for bucket 42:\n bucket 41: 10%\n bucket 40: 70%\n bucket 42: 10%\n bucket 41: 20%\n bucket 40: 80%\n bucket 42: 20%\n bucket 41: 30%\n bucket 40: 90%\n bucket 42: 30%\n bucket 41: 40%\n bucket 42: 40%\n bucket 41: 50%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n bucket 42: 50%\n (Using difference cover)\n bucket 41: 60%\n bucket 42: 60%\n bucket 41: 70%\n bucket 42: 70%\n bucket 41: 80%\n bucket 42: 80%\n bucket 41: 90%\n bucket 42: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n bucket 43: 10%\n Calculating Z arrays for bucket 44\n bucket 43: 20%\n bucket 43: 30%\n Entering block accumulator loop for bucket 44:\n bucket 43: 40%\n bucket 44: 10%\n bucket 43: 50%\n bucket 44: 20%\n bucket 43: 60%\n bucket 44: 30%\n bucket 43: 70%\n bucket 44: 40%\n bucket 43: 80%\n bucket 44: 50%\n bucket 43: 90%\n bucket 43: 100%\n bucket 44: 60%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Entering block accumulator loop for bucket 45:\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n Entering block accumulator loop for bucket 46:\n bucket 45: 40%\n bucket 45: 50%\n bucket 46: 10%\n bucket 45: 60%\n bucket 46: 20%\n bucket 45: 70%\n bucket 46: 30%\n bucket 45: 80%\n bucket 46: 40%\n bucket 45: 90%\n bucket 46: 50%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Entering block accumulator loop for bucket 47:\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n bucket 47: 20%\n Entering block accumulator loop for bucket 48:\n bucket 47: 30%\n bucket 47: 40%\n bucket 48: 10%\n bucket 47: 50%\n bucket 48: 20%\n bucket 47: 60%\n bucket 47: 70%\n bucket 48: 30%\n bucket 47: 80%\n bucket 47: 90%\n bucket 48: 40%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\nGetting block 50 of 60\n Calculating Z arrays for bucket 49\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Entering block accumulator loop for bucket 49:\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n Entering block accumulator loop for bucket 51:\n bucket 49: 10%\n bucket 50: 10%\n bucket 51: 10%\n bucket 49: 20%\n bucket 50: 20%\n bucket 51: 20%\n bucket 51: 30%\n bucket 49: 30%\n bucket 50: 30%\n bucket 51: 40%\n bucket 50: 40%\n bucket 49: 40%\n bucket 51: 50%\n bucket 50: 50%\n bucket 51: 60%\n bucket 49: 50%\n bucket 50: 60%\n bucket 51: 70%\n bucket 50: 70%\n bucket 51: 80%\n bucket 49: 60%\n bucket 50: 80%\n bucket 51: 90%\n bucket 49: 70%\n bucket 51: 100%\n bucket 50: 90%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 49: 80%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Reserving size (126) for bucket 52\n Entering block accumulator loop for bucket 53:\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 54:\n bucket 53: 10%\n bucket 54: 10%\n bucket 53: 20%\n Entering block accumulator loop for bucket 52:\n bucket 54: 20%\n bucket 53: 30%\n bucket 54: 30%\n bucket 53: 40%\n bucket 52: 10%\n bucket 54: 40%\n bucket 53: 50%\n bucket 54: 50%\n bucket 52: 20%\n bucket 53: 60%\n bucket 54: 60%\n bucket 52: 30%\n bucket 54: 70%\n bucket 53: 70%\n bucket 52: 40%\n bucket 54: 80%\n bucket 53: 80%\n bucket 54: 90%\n bucket 53: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 52: 50%\n bucket 53: 100%\n bucket 52: 60%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 40%\n bucket 55: 50%\n Entering block accumulator loop for bucket 56:\n bucket 55: 60%\n bucket 56: 10%\n bucket 55: 70%\n bucket 56: 20%\n bucket 56: 30%\n bucket 55: 80%\n bucket 56: 40%\n bucket 55: 90%\n bucket 56: 50%\n bucket 55: 100%\n bucket 56: 60%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n bucket 57: 100%\n Calculating Z arrays for bucket 58\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block time: 00:00:00\n Sorting block of length 113 for bucket 58\n (Using difference cover)\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 20%\n Entering block accumulator loop for bucket 60:\n bucket 59: 30%\n bucket 60: 10%\n bucket 59: 40%\n bucket 60: 20%\n bucket 59: 50%\n bucket 60: 30%\n bucket 59: 60%\n bucket 60: 40%\n bucket 59: 70%\n bucket 60: 50%\n bucket 59: 80%\n bucket 60: 60%\n bucket 60: 70%\n bucket 59: 90%\n bucket 60: 80%\n bucket 60: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n3 reads; of these:\n 3 (100.00%) were paired; of these:\n 3 (100.00%) aligned concordantly 0 times\n 0 (0.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 6 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\n Entering block accumulator loop for bucket 1:\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n bucket 1: 10%\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Entering block accumulator loop for bucket 2:\n bucket 1: 20%\n Reserving size (126) for bucket 3\n bucket 1: 30%\n bucket 2: 10%\n Calculating Z arrays for bucket 3\n bucket 1: 40%\n bucket 2: 20%\n bucket 1: 50%\n bucket 2: 30%\n Entering block accumulator loop for bucket 3:\nGetting block 4 of 60\n bucket 3: 10%\n bucket 2: 40%\n bucket 1: 60%\n Reserving size (126) for bucket 4\n bucket 2: 50%\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 3: 20%\n bucket 2: 60%\n Calculating Z arrays for bucket 5\n bucket 3: 30%\n bucket 2: 70%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 3: 40%\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n bucket 2: 80%\n Calculating Z arrays for bucket 4\n bucket 3: 50%\n Entering block accumulator loop for bucket 5:\n bucket 1: 70%\n bucket 3: 60%\n Calculating Z arrays for bucket 7\n Calculating Z arrays for bucket 6\n bucket 5: 10%\n bucket 1: 80%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n bucket 2: 90%\n bucket 5: 20%\n bucket 1: 90%\n bucket 2: 100%\n bucket 5: 30%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 7:\n bucket 5: 40%\n Calculating Z arrays for bucket 8\n bucket 1: 100%\n Entering block accumulator loop for bucket 4:\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 3: 70%\n bucket 6: 10%\n bucket 5: 50%\n bucket 7: 10%\n bucket 5: 60%\n bucket 6: 20%\n bucket 4: 10%\n Entering block accumulator loop for bucket 8:\n bucket 5: 70%\n bucket 6: 30%\n bucket 4: 20%\n bucket 3: 80%\n bucket 8: 10%\n bucket 5: 80%\n bucket 3: 90%\n bucket 4: 30%\n bucket 5: 90%\n bucket 6: 40%\n bucket 3: 100%\n bucket 7: 20%\n bucket 5: 100%\n bucket 8: 20%\n bucket 4: 40%\n bucket 7: 30%\n bucket 6: 50%\n bucket 4: 50%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 40%\n bucket 8: 30%\n bucket 4: 60%\n bucket 6: 60%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 40%\n Sorting block time: 00:00:00\n bucket 6: 70%\n bucket 7: 50%\nReturning block of 85 for bucket 2\n bucket 7: 60%\n bucket 4: 70%\n bucket 6: 80%\n bucket 7: 70%\n bucket 4: 80%\n bucket 8: 50%\n bucket 7: 80%\n bucket 4: 90%\n bucket 6: 90%\n bucket 8: 60%\n bucket 7: 90%\n bucket 4: 100%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 8: 70%\n bucket 8: 80%\n bucket 8: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n bucket 11: 20%\n bucket 11: 30%\n bucket 11: 40%\n bucket 11: 50%\n bucket 11: 60%\n bucket 11: 70%\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\n bucket 12: 90%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n bucket 13: 50%\n bucket 13: 60%\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n bucket 13: 100%\n Calculating Z arrays for bucket 14\n Sorting block of length 85 for bucket 13\n (Using difference cover)\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n Entering block accumulator loop for bucket 15:\n bucket 14: 30%\n bucket 14: 40%\n bucket 15: 10%\n bucket 14: 50%\n bucket 15: 20%\n bucket 14: 60%\n Sorting block time: 00:00:00\n bucket 15: 30%\nReturning block of 86 for bucket 13\n bucket 14: 70%\n bucket 15: 40%\n bucket 14: 80%\n bucket 14: 90%\n bucket 15: 50%\n bucket 14: 100%\n bucket 15: 60%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 70%\n bucket 15: 80%\n bucket 15: 90%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 50%\n bucket 16: 60%\n Entering block accumulator loop for bucket 17:\n bucket 16: 70%\n bucket 17: 10%\n bucket 16: 80%\n bucket 17: 20%\n bucket 16: 90%\n bucket 17: 30%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 19:\n Entering block accumulator loop for bucket 18:\n bucket 19: 10%\n bucket 19: 20%\n bucket 18: 10%\n bucket 19: 30%\n bucket 18: 20%\n bucket 19: 40%\n bucket 19: 50%\n bucket 18: 30%\n bucket 19: 60%\n bucket 18: 40%\n bucket 19: 70%\n bucket 18: 50%\n bucket 19: 80%\n bucket 18: 60%\n bucket 19: 90%\n bucket 18: 70%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n bucket 21: 20%\n bucket 21: 30%\n Entering block accumulator loop for bucket 22:\n bucket 21: 40%\n bucket 21: 50%\n bucket 22: 10%\n bucket 21: 60%\n bucket 22: 20%\n bucket 21: 70%\n bucket 21: 80%\n bucket 22: 30%\n bucket 21: 90%\n bucket 22: 40%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 50%\n bucket 22: 60%\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 23: 10%\n bucket 23: 20%\n bucket 23: 30%\n bucket 23: 40%\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\n bucket 24: 40%\n bucket 24: 50%\n Sorting block time: 00:00:00\n bucket 24: 60%\nReturning block of 65 for bucket 23\n bucket 24: 70%\n bucket 24: 80%\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\n bucket 25: 20%\n bucket 25: 30%\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\n bucket 27: 20%\n bucket 26: 30%\n bucket 27: 30%\n bucket 26: 40%\n bucket 27: 40%\n bucket 26: 50%\n bucket 27: 50%\n bucket 26: 60%\n bucket 27: 60%\n bucket 26: 70%\n bucket 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 26: 90%\n bucket 27: 90%\n bucket 26: 100%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n Entering block accumulator loop for bucket 29:\n bucket 28: 20%\n bucket 29: 10%\n bucket 28: 30%\n bucket 29: 20%\n bucket 28: 40%\n bucket 29: 30%\n bucket 28: 50%\n bucket 29: 40%\n bucket 28: 60%\n bucket 29: 50%\n bucket 28: 70%\n bucket 29: 60%\n bucket 28: 80%\n bucket 29: 70%\n bucket 28: 90%\n bucket 29: 80%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n bucket 30: 20%\n bucket 30: 30%\n bucket 30: 40%\n bucket 30: 50%\n bucket 30: 60%\n Sorting block time: 00:00:00\n bucket 30: 70%\nReturning block of 52 for bucket 29\n bucket 30: 80%\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n bucket 31: 10%\n Entering block accumulator loop for bucket 32:\n Entering block accumulator loop for bucket 33:\n bucket 31: 20%\n bucket 32: 10%\n bucket 33: 10%\n bucket 31: 30%\n bucket 32: 20%\n bucket 33: 20%\n bucket 31: 40%\n bucket 32: 30%\n bucket 33: 30%\n bucket 32: 40%\n bucket 31: 50%\n bucket 33: 40%\n bucket 32: 50%\n bucket 31: 60%\n bucket 33: 50%\n bucket 31: 70%\n bucket 32: 60%\n bucket 33: 60%\n bucket 32: 70%\n bucket 31: 80%\n bucket 32: 80%\n bucket 33: 70%\n bucket 31: 90%\n bucket 32: 90%\n bucket 33: 80%\n bucket 31: 100%\n bucket 32: 100%\n Sorting block of length 110 for bucket 31\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 90%\n (Using difference cover)\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n bucket 35: 10%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 35: 30%\n bucket 34: 50%\n bucket 35: 40%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\n bucket 35: 70%\n bucket 34: 90%\n bucket 35: 80%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Entering block accumulator loop for bucket 36:\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n bucket 36: 20%\n Entering block accumulator loop for bucket 37:\n bucket 36: 30%\n bucket 36: 40%\n bucket 37: 10%\n bucket 36: 50%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 36: 60%\n bucket 37: 50%\n bucket 36: 70%\n bucket 37: 60%\n bucket 36: 80%\n bucket 37: 70%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n Entering block accumulator loop for bucket 39:\n bucket 38: 20%\n bucket 39: 10%\n bucket 38: 30%\n bucket 39: 20%\n bucket 38: 40%\n bucket 39: 30%\n bucket 38: 50%\n bucket 39: 40%\n bucket 38: 60%\n bucket 39: 50%\n bucket 38: 70%\n bucket 39: 60%\n bucket 38: 80%\n bucket 39: 70%\n bucket 38: 90%\n bucket 39: 80%\n bucket 38: 100%\n bucket 39: 90%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n bucket 40: 30%\n Calculating Z arrays for bucket 41\n bucket 40: 40%\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 40: 50%\n Entering block accumulator loop for bucket 41:\n bucket 40: 60%\n Entering block accumulator loop for bucket 42:\n bucket 41: 10%\n bucket 40: 70%\n bucket 42: 10%\n bucket 41: 20%\n bucket 40: 80%\n bucket 42: 20%\n bucket 41: 30%\n bucket 40: 90%\n bucket 42: 30%\n bucket 41: 40%\n bucket 42: 40%\n bucket 41: 50%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n bucket 42: 50%\n (Using difference cover)\n bucket 41: 60%\n bucket 42: 60%\n bucket 41: 70%\n bucket 42: 70%\n bucket 41: 80%\n bucket 42: 80%\n bucket 41: 90%\n bucket 42: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 43:\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n bucket 43: 10%\n Calculating Z arrays for bucket 44\n bucket 43: 20%\n bucket 43: 30%\n Entering block accumulator loop for bucket 44:\n bucket 43: 40%\n bucket 44: 10%\n bucket 43: 50%\n bucket 44: 20%\n bucket 43: 60%\n bucket 44: 30%\n bucket 43: 70%\n bucket 44: 40%\n bucket 43: 80%\n bucket 44: 50%\n bucket 43: 90%\n bucket 43: 100%\n bucket 44: 60%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 70%\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Entering block accumulator loop for bucket 45:\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n Entering block accumulator loop for bucket 46:\n bucket 45: 40%\n bucket 45: 50%\n bucket 46: 10%\n bucket 45: 60%\n bucket 46: 20%\n bucket 45: 70%\n bucket 46: 30%\n bucket 45: 80%\n bucket 46: 40%\n bucket 45: 90%\n bucket 46: 50%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Entering block accumulator loop for bucket 47:\n Calculating Z arrays for bucket 48\n bucket 47: 10%\n bucket 47: 20%\n Entering block accumulator loop for bucket 48:\n bucket 47: 30%\n bucket 47: 40%\n bucket 48: 10%\n bucket 47: 50%\n bucket 48: 20%\n bucket 47: 60%\n bucket 47: 70%\n bucket 48: 30%\n bucket 47: 80%\n bucket 47: 90%\n bucket 48: 40%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 49 of 60\n Reserving size (126) for bucket 49\nGetting block 50 of 60\n Calculating Z arrays for bucket 49\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Entering block accumulator loop for bucket 49:\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n Entering block accumulator loop for bucket 51:\n bucket 49: 10%\n bucket 50: 10%\n bucket 51: 10%\n bucket 49: 20%\n bucket 50: 20%\n bucket 51: 20%\n bucket 51: 30%\n bucket 49: 30%\n bucket 50: 30%\n bucket 51: 40%\n bucket 50: 40%\n bucket 49: 40%\n bucket 51: 50%\n bucket 50: 50%\n bucket 51: 60%\n bucket 49: 50%\n bucket 50: 60%\n bucket 51: 70%\n bucket 50: 70%\n bucket 51: 80%\n bucket 49: 60%\n bucket 50: 80%\n bucket 51: 90%\n bucket 49: 70%\n bucket 51: 100%\n bucket 50: 90%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 49: 80%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Reserving size (126) for bucket 52\n Entering block accumulator loop for bucket 53:\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 54:\n bucket 53: 10%\n bucket 54: 10%\n bucket 53: 20%\n Entering block accumulator loop for bucket 52:\n bucket 54: 20%\n bucket 53: 30%\n bucket 54: 30%\n bucket 53: 40%\n bucket 52: 10%\n bucket 54: 40%\n bucket 53: 50%\n bucket 54: 50%\n bucket 52: 20%\n bucket 53: 60%\n bucket 54: 60%\n bucket 52: 30%\n bucket 54: 70%\n bucket 53: 70%\n bucket 52: 40%\n bucket 54: 80%\n bucket 53: 80%\n bucket 54: 90%\n bucket 53: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 52: 50%\n bucket 53: 100%\n bucket 52: 60%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 40%\n bucket 55: 50%\n Entering block accumulator loop for bucket 56:\n bucket 55: 60%\n bucket 56: 10%\n bucket 55: 70%\n bucket 56: 20%\n bucket 56: 30%\n bucket 55: 80%\n bucket 56: 40%\n bucket 55: 90%\n bucket 56: 50%\n bucket 55: 100%\n bucket 56: 60%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n bucket 57: 70%\n bucket 57: 80%\n bucket 57: 90%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n bucket 57: 100%\n Calculating Z arrays for bucket 58\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block time: 00:00:00\n Sorting block of length 113 for bucket 58\n (Using difference cover)\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 20%\n Entering block accumulator loop for bucket 60:\n bucket 59: 30%\n bucket 60: 10%\n bucket 59: 40%\n bucket 60: 20%\n bucket 59: 50%\n bucket 60: 30%\n bucket 59: 60%\n bucket 60: 40%\n bucket 59: 70%\n bucket 60: 50%\n bucket 59: 80%\n bucket 60: 60%\n bucket 60: 70%\n bucket 59: 90%\n bucket 60: 80%\n bucket 60: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n3 reads; of these:\n 3 (100.00%) were paired; of these:\n 3 (100.00%) aligned concordantly 0 times\n 0 (0.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 3 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 3 pairs aligned 0 times concordantly or discordantly; of these:\n 6 mates make up the pairs; of these:\n 6 (100.00%) aligned 0 times\n 0 (0.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n0.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:02:04", "plugin": "core", "name": "end_epoch", "raw_value": "1725001324.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:02:03", "plugin": "core", "name": "start_epoch", "raw_value": "1725001323.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-7", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 7, "time_seconds": 38.33867263793945, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "fa174e715819986b"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "0cd591fe269f46c1"}, "library|input_2": {"src": "hda", "id": "d4f5642823b84ea6"}, "library|paired_options|no_mixed": true, "library|paired_options|no_discordant": true, "library|paired_options|paired_options_selector": "advanced", "library|type": "paired", "adv|input_options|trim5": "15", "adv|input_options|trim3": "15", "adv|input_options|input_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "57b498026778ca1b", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:54:21.760554", "update_time": "2024-08-30T06:54:35.760952", "galaxy_version": "24.1", "external_id": "gxy-xdmn6", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/8/c/0/dataset_8c087e05-165e-4659-ba64-d5c8eda4ea20.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/a/5/2/dataset_a5235c64-5073-4560-8547-39efe8a48936.dat' input_f.fastq.gz && ln -f -s '/galaxy/server/database/objects/a/0/1/dataset_a012fe62-e8fa-4067-9cd4-bda8bb24bd58.dat' input_r.fastq.gz && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq.gz' -2 'input_r.fastq.gz' --fr --no-mixed --no-discordant --trim5 '15' --trim3 '15' --phred33 | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/9/1/3/dataset_913263aa-301a-43c3-9f35-e168768e9511.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 1, \"input_options_selector\": \"advanced\", \"int_quals\": false, \"qupto\": \"0\", \"qv_encoding\": \"--phred33\", \"skip\": \"0\", \"solexa_quals\": false, \"trim3\": \"15\", \"trim5\": \"15\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 144, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 145, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"fr_rf_ff\": \"--fr\", \"no_discordant\": true, \"no_mixed\": true, \"paired_options_selector\": \"advanced\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 143, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "fa174e715819986b", "src": "hda", "uuid": "8c087e05-165e-4659-ba64-d5c8eda4ea20"}, "library|input_1": {"id": "0cd591fe269f46c1", "src": "hda", "uuid": "a5235c64-5073-4560-8547-39efe8a48936"}, "library|input_2": {"id": "d4f5642823b84ea6", "src": "hda", "uuid": "a012fe62-e8fa-4067-9cd4-bda8bb24bd58"}}, "outputs": {"output_alignments": {"id": "01547d2d72cffcb2", "src": "hda", "uuid": "913263aa-301a-43c3-9f35-e168768e9511"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n bucket 1: 20%\n bucket 1: 30%\n bucket 1: 40%\n Entering block accumulator loop for bucket 2:\nGetting block 4 of 60\nGetting block 3 of 60\n bucket 1: 50%\n Reserving size (126) for bucket 3\n bucket 2: 10%\nGetting block 5 of 60\n bucket 1: 60%\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 4\n bucket 2: 20%\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 3\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 6\n bucket 4: 10%\n Entering block accumulator loop for bucket 3:\n bucket 1: 70%\n bucket 4: 20%\n bucket 2: 30%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 5:\n bucket 2: 40%\nGetting block 8 of 60\n bucket 3: 10%\n bucket 5: 10%\n bucket 6: 10%\n Reserving size (126) for bucket 8\n bucket 5: 20%\n bucket 4: 30%\n Calculating Z arrays for bucket 8\n bucket 5: 30%\n bucket 4: 40%\n bucket 2: 50%\n bucket 1: 80%\nGetting block 7 of 60\n bucket 3: 20%\n bucket 6: 20%\n bucket 1: 90%\n Entering block accumulator loop for bucket 8:\n Reserving size (126) for bucket 7\n bucket 5: 40%\n bucket 4: 50%\n bucket 1: 100%\n bucket 3: 30%\n Calculating Z arrays for bucket 7\n bucket 4: 60%\n bucket 2: 60%\n bucket 8: 10%\n bucket 3: 40%\n bucket 2: 70%\n bucket 4: 70%\n bucket 8: 20%\n bucket 5: 50%\n bucket 4: 80%\n bucket 3: 50%\n bucket 6: 30%\n bucket 2: 80%\n bucket 6: 40%\n bucket 4: 90%\n bucket 8: 30%\n bucket 3: 60%\n Sorting block of length 42 for bucket 1\n bucket 8: 40%\n (Using difference cover)\n bucket 4: 100%\n Entering block accumulator loop for bucket 7:\n bucket 5: 60%\n bucket 6: 50%\n bucket 3: 70%\n bucket 8: 50%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 2: 90%\n bucket 7: 10%\n bucket 6: 60%\n bucket 3: 80%\n bucket 8: 60%\n bucket 7: 20%\n bucket 2: 100%\n bucket 3: 90%\n bucket 5: 70%\n bucket 8: 70%\n Sorting block of length 84 for bucket 2\n bucket 6: 70%\n (Using difference cover)\n bucket 5: 80%\n bucket 3: 100%\n bucket 8: 80%\n bucket 7: 30%\n bucket 8: 90%\n bucket 6: 80%\n bucket 5: 90%\n bucket 7: 40%\n bucket 6: 90%\n bucket 8: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 7: 50%\n bucket 6: 100%\n bucket 5: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block of length 63 for bucket 5\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n (Using difference cover)\n bucket 7: 60%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n Entering block accumulator loop for bucket 10:\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 10%\nGetting block 13 of 60\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 12:\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n bucket 11: 20%\n bucket 12: 10%\n Entering block accumulator loop for bucket 13:\n Entering block accumulator loop for bucket 14:\n bucket 12: 20%\n bucket 13: 10%\n bucket 14: 10%\n bucket 11: 30%\n bucket 12: 30%\n bucket 13: 20%\n bucket 14: 20%\n bucket 12: 40%\n bucket 11: 40%\n bucket 13: 30%\n bucket 14: 30%\n bucket 12: 50%\n bucket 11: 50%\n bucket 14: 40%\n bucket 13: 40%\n bucket 11: 60%\n bucket 12: 60%\n bucket 14: 50%\n bucket 12: 70%\n bucket 11: 70%\n bucket 14: 60%\n bucket 12: 80%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n bucket 12: 90%\n bucket 14: 70%\n Calculating Z arrays for bucket 15\n bucket 13: 50%\n bucket 14: 80%\n bucket 12: 100%\n bucket 11: 80%\nGetting block 16 of 60\n bucket 11: 90%\n bucket 13: 60%\n Entering block accumulator loop for bucket 15:\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 13: 70%\n bucket 11: 100%\n bucket 14: 90%\n bucket 15: 10%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 13: 80%\n bucket 15: 20%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Entering block accumulator loop for bucket 16:\n bucket 13: 90%\n bucket 15: 30%\n bucket 16: 10%\n bucket 15: 40%\n bucket 13: 100%\n bucket 16: 20%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 15: 50%\n bucket 16: 30%\n bucket 16: 40%\n bucket 15: 60%\n bucket 16: 50%\n bucket 15: 70%\n bucket 16: 60%\n bucket 15: 80%\n bucket 16: 70%\n bucket 15: 90%\n bucket 16: 80%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n Entering block accumulator loop for bucket 18:\n bucket 17: 20%\n bucket 17: 30%\n bucket 18: 10%\n bucket 17: 40%\n bucket 18: 20%\n bucket 17: 50%\n bucket 18: 30%\n bucket 17: 60%\n bucket 18: 40%\n bucket 17: 70%\n bucket 18: 50%\n bucket 17: 80%\n bucket 18: 60%\n bucket 17: 90%\n bucket 18: 70%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 30%\n bucket 19: 40%\n Entering block accumulator loop for bucket 20:\n bucket 19: 50%\n bucket 19: 60%\n bucket 20: 10%\n bucket 19: 70%\n bucket 19: 80%\n bucket 20: 20%\n bucket 19: 90%\n bucket 20: 30%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n bucket 23: 10%\n Calculating Z arrays for bucket 24\n bucket 23: 20%\n Entering block accumulator loop for bucket 24:\n bucket 23: 30%\n bucket 24: 10%\n bucket 23: 40%\n bucket 24: 20%\n bucket 24: 30%\n bucket 23: 50%\n bucket 24: 40%\n bucket 23: 60%\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n bucket 25: 20%\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 26\n Calculating Z arrays for bucket 27\n bucket 25: 30%\n bucket 25: 40%\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 25: 50%\n bucket 26: 10%\n bucket 25: 60%\n bucket 27: 10%\n bucket 26: 20%\n bucket 25: 70%\n bucket 27: 20%\n bucket 25: 80%\n bucket 26: 30%\n bucket 27: 30%\n bucket 25: 90%\n bucket 26: 40%\n bucket 27: 40%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 50%\n bucket 27: 50%\n bucket 26: 60%\n bucket 27: 60%\n bucket 26: 70%\n bucket 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 26: 90%\n bucket 27: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\n Entering block accumulator loop for bucket 29:\n bucket 28: 10%\n bucket 29: 10%\n bucket 28: 20%\n bucket 29: 20%\n bucket 28: 30%\n bucket 29: 30%\n bucket 29: 40%\n bucket 28: 40%\n bucket 29: 50%\n bucket 28: 50%\n bucket 29: 60%\n bucket 28: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 28: 70%\n bucket 29: 90%\n bucket 28: 80%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 28: 90%\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 31:\n bucket 30: 10%\n bucket 31: 10%\n bucket 30: 20%\n bucket 31: 20%\n bucket 30: 30%\n bucket 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n Sorting block time: 00:00:00\n bucket 30: 50%\nReturning block of 52 for bucket 29\n bucket 31: 50%\n bucket 30: 60%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n bucket 31: 60%\n bucket 30: 70%\n bucket 31: 70%\n bucket 30: 80%\n bucket 31: 80%\n bucket 31: 90%\n bucket 30: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 32:\n Entering block accumulator loop for bucket 33:\n bucket 32: 10%\n bucket 33: 10%\n bucket 32: 20%\n bucket 33: 20%\n bucket 32: 30%\n bucket 33: 30%\n bucket 32: 40%\n bucket 33: 40%\n bucket 32: 50%\n bucket 33: 50%\n bucket 32: 60%\n bucket 33: 60%\n bucket 32: 70%\n bucket 33: 70%\n bucket 32: 80%\n bucket 33: 80%\n bucket 32: 90%\n bucket 33: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n bucket 35: 10%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 35: 30%\n bucket 34: 50%\n bucket 35: 40%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\n bucket 35: 70%\n bucket 34: 90%\n bucket 35: 80%\n bucket 34: 100%\n bucket 35: 90%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Entering block accumulator loop for bucket 36:\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n Entering block accumulator loop for bucket 37:\n bucket 36: 20%\n bucket 37: 10%\n bucket 36: 30%\n bucket 37: 20%\n bucket 36: 40%\n bucket 37: 30%\n bucket 36: 50%\n bucket 37: 40%\n bucket 36: 60%\n bucket 37: 50%\n bucket 36: 70%\n bucket 37: 60%\n bucket 36: 80%\n bucket 37: 70%\n bucket 36: 90%\n bucket 37: 80%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 30%\n bucket 38: 40%\n Entering block accumulator loop for bucket 39:\n bucket 38: 50%\n bucket 39: 10%\n bucket 38: 60%\n bucket 39: 20%\n bucket 38: 70%\n bucket 39: 30%\n bucket 38: 80%\n bucket 38: 90%\n bucket 39: 40%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n Entering block accumulator loop for bucket 43:\n bucket 42: 20%\n bucket 43: 10%\n bucket 42: 30%\n bucket 43: 20%\n bucket 42: 40%\n bucket 43: 30%\n bucket 42: 50%\n bucket 43: 40%\n bucket 42: 60%\n bucket 43: 50%\n bucket 42: 70%\n bucket 43: 60%\n bucket 43: 70%\n bucket 42: 80%\n bucket 43: 80%\n bucket 43: 90%\n bucket 42: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 44:\n bucket 45: 10%\n bucket 44: 10%\n bucket 45: 20%\n bucket 44: 20%\n bucket 45: 30%\n bucket 44: 30%\n bucket 45: 40%\n bucket 44: 40%\n bucket 44: 50%\n bucket 45: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 45: 60%\n bucket 44: 80%\n bucket 45: 70%\n bucket 45: 80%\n bucket 44: 90%\n bucket 45: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n bucket 48: 10%\n Calculating Z arrays for bucket 49\n bucket 48: 20%\n Entering block accumulator loop for bucket 49:\n bucket 48: 30%\n bucket 48: 40%\n bucket 49: 10%\n bucket 48: 50%\n bucket 48: 60%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 49: 30%\n bucket 50: 10%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 40%\n bucket 50: 20%\n bucket 49: 50%\n bucket 50: 30%\n bucket 49: 60%\n bucket 50: 40%\n bucket 49: 70%\n bucket 50: 50%\n bucket 49: 80%\n bucket 50: 60%\n bucket 49: 90%\n bucket 50: 70%\n Sorting block time: 00:00:00\n bucket 49: 100%\n bucket 50: 80%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\nReturning block of 114 for bucket 48\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 40%\n bucket 51: 50%\n Entering block accumulator loop for bucket 52:\n bucket 51: 60%\n bucket 52: 10%\n bucket 51: 70%\n bucket 52: 20%\n bucket 51: 80%\n bucket 52: 30%\n bucket 51: 90%\n bucket 52: 40%\n bucket 52: 50%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Entering block accumulator loop for bucket 53:\n Calculating Z arrays for bucket 54\n bucket 53: 10%\n Entering block accumulator loop for bucket 54:\n bucket 53: 20%\n bucket 53: 30%\n bucket 54: 10%\n bucket 53: 40%\n bucket 54: 20%\n bucket 53: 50%\n bucket 54: 30%\n bucket 53: 60%\n bucket 54: 40%\n bucket 53: 70%\n bucket 54: 50%\n bucket 53: 80%\n bucket 54: 60%\n bucket 53: 90%\n bucket 54: 70%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n Entering block accumulator loop for bucket 56:\n bucket 55: 20%\n bucket 56: 10%\n bucket 55: 30%\n bucket 56: 20%\n bucket 55: 40%\n bucket 56: 30%\n bucket 55: 50%\n bucket 56: 40%\n bucket 55: 60%\n bucket 56: 50%\n bucket 55: 70%\n bucket 56: 60%\n bucket 55: 80%\n bucket 56: 70%\n bucket 55: 90%\n bucket 56: 80%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 10%\n bucket 57: 20%\n Entering block accumulator loop for bucket 58:\n bucket 57: 30%\n bucket 57: 40%\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 57: 50%\n bucket 58: 70%\n bucket 57: 60%\n bucket 58: 80%\n bucket 57: 70%\n bucket 58: 90%\n bucket 57: 80%\n bucket 57: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 30%\n Entering block accumulator loop for bucket 60:\n bucket 59: 40%\n bucket 60: 10%\n bucket 59: 50%\n bucket 60: 20%\n bucket 59: 60%\n bucket 60: 30%\n bucket 59: 70%\n bucket 60: 40%\n bucket 59: 80%\n bucket 59: 90%\n bucket 60: 50%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Calculating Z arrays for bucket 1\n Reserving size (126) for bucket 2\n Entering block accumulator loop for bucket 1:\n bucket 1: 10%\n Calculating Z arrays for bucket 2\n bucket 1: 20%\n bucket 1: 30%\n bucket 1: 40%\n Entering block accumulator loop for bucket 2:\nGetting block 4 of 60\nGetting block 3 of 60\n bucket 1: 50%\n Reserving size (126) for bucket 3\n bucket 2: 10%\nGetting block 5 of 60\n bucket 1: 60%\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 4\n bucket 2: 20%\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 3\nGetting block 6 of 60\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 6\n bucket 4: 10%\n Entering block accumulator loop for bucket 3:\n bucket 1: 70%\n bucket 4: 20%\n bucket 2: 30%\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 5:\n bucket 2: 40%\nGetting block 8 of 60\n bucket 3: 10%\n bucket 5: 10%\n bucket 6: 10%\n Reserving size (126) for bucket 8\n bucket 5: 20%\n bucket 4: 30%\n Calculating Z arrays for bucket 8\n bucket 5: 30%\n bucket 4: 40%\n bucket 2: 50%\n bucket 1: 80%\nGetting block 7 of 60\n bucket 3: 20%\n bucket 6: 20%\n bucket 1: 90%\n Entering block accumulator loop for bucket 8:\n Reserving size (126) for bucket 7\n bucket 5: 40%\n bucket 4: 50%\n bucket 1: 100%\n bucket 3: 30%\n Calculating Z arrays for bucket 7\n bucket 4: 60%\n bucket 2: 60%\n bucket 8: 10%\n bucket 3: 40%\n bucket 2: 70%\n bucket 4: 70%\n bucket 8: 20%\n bucket 5: 50%\n bucket 4: 80%\n bucket 3: 50%\n bucket 6: 30%\n bucket 2: 80%\n bucket 6: 40%\n bucket 4: 90%\n bucket 8: 30%\n bucket 3: 60%\n Sorting block of length 42 for bucket 1\n bucket 8: 40%\n (Using difference cover)\n bucket 4: 100%\n Entering block accumulator loop for bucket 7:\n bucket 5: 60%\n bucket 6: 50%\n bucket 3: 70%\n bucket 8: 50%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 2: 90%\n bucket 7: 10%\n bucket 6: 60%\n bucket 3: 80%\n bucket 8: 60%\n bucket 7: 20%\n bucket 2: 100%\n bucket 3: 90%\n bucket 5: 70%\n bucket 8: 70%\n Sorting block of length 84 for bucket 2\n bucket 6: 70%\n (Using difference cover)\n bucket 5: 80%\n bucket 3: 100%\n bucket 8: 80%\n bucket 7: 30%\n bucket 8: 90%\n bucket 6: 80%\n bucket 5: 90%\n bucket 7: 40%\n bucket 6: 90%\n bucket 8: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 7: 50%\n bucket 6: 100%\n bucket 5: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block of length 63 for bucket 5\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n (Using difference cover)\n bucket 7: 60%\n bucket 7: 70%\n bucket 7: 80%\n bucket 7: 90%\n bucket 7: 100%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n Entering block accumulator loop for bucket 10:\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 11:\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n bucket 11: 10%\nGetting block 13 of 60\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 12:\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n bucket 11: 20%\n bucket 12: 10%\n Entering block accumulator loop for bucket 13:\n Entering block accumulator loop for bucket 14:\n bucket 12: 20%\n bucket 13: 10%\n bucket 14: 10%\n bucket 11: 30%\n bucket 12: 30%\n bucket 13: 20%\n bucket 14: 20%\n bucket 12: 40%\n bucket 11: 40%\n bucket 13: 30%\n bucket 14: 30%\n bucket 12: 50%\n bucket 11: 50%\n bucket 14: 40%\n bucket 13: 40%\n bucket 11: 60%\n bucket 12: 60%\n bucket 14: 50%\n bucket 12: 70%\n bucket 11: 70%\n bucket 14: 60%\n bucket 12: 80%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n bucket 12: 90%\n bucket 14: 70%\n Calculating Z arrays for bucket 15\n bucket 13: 50%\n bucket 14: 80%\n bucket 12: 100%\n bucket 11: 80%\nGetting block 16 of 60\n bucket 11: 90%\n bucket 13: 60%\n Entering block accumulator loop for bucket 15:\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 13: 70%\n bucket 11: 100%\n bucket 14: 90%\n bucket 15: 10%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 13: 80%\n bucket 15: 20%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Entering block accumulator loop for bucket 16:\n bucket 13: 90%\n bucket 15: 30%\n bucket 16: 10%\n bucket 15: 40%\n bucket 13: 100%\n bucket 16: 20%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 15: 50%\n bucket 16: 30%\n bucket 16: 40%\n bucket 15: 60%\n bucket 16: 50%\n bucket 15: 70%\n bucket 16: 60%\n bucket 15: 80%\n bucket 16: 70%\n bucket 15: 90%\n bucket 16: 80%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n Entering block accumulator loop for bucket 18:\n bucket 17: 20%\n bucket 17: 30%\n bucket 18: 10%\n bucket 17: 40%\n bucket 18: 20%\n bucket 17: 50%\n bucket 18: 30%\n bucket 17: 60%\n bucket 18: 40%\n bucket 17: 70%\n bucket 18: 50%\n bucket 17: 80%\n bucket 18: 60%\n bucket 17: 90%\n bucket 18: 70%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n Entering block accumulator loop for bucket 19:\n bucket 19: 10%\n bucket 19: 20%\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n bucket 19: 30%\n bucket 19: 40%\n Entering block accumulator loop for bucket 20:\n bucket 19: 50%\n bucket 19: 60%\n bucket 20: 10%\n bucket 19: 70%\n bucket 19: 80%\n bucket 20: 20%\n bucket 19: 90%\n bucket 20: 30%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n bucket 22: 30%\n bucket 22: 40%\n bucket 22: 50%\n bucket 22: 60%\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n bucket 22: 70%\n bucket 22: 80%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n bucket 23: 10%\n Calculating Z arrays for bucket 24\n bucket 23: 20%\n Entering block accumulator loop for bucket 24:\n bucket 23: 30%\n bucket 24: 10%\n bucket 23: 40%\n bucket 24: 20%\n bucket 24: 30%\n bucket 23: 50%\n bucket 24: 40%\n bucket 23: 60%\n bucket 24: 50%\n bucket 23: 70%\n bucket 24: 60%\n bucket 23: 80%\n bucket 24: 70%\n bucket 23: 90%\n bucket 24: 80%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n bucket 24: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 25:\n bucket 25: 10%\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n bucket 25: 20%\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 26\n Calculating Z arrays for bucket 27\n bucket 25: 30%\n bucket 25: 40%\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 25: 50%\n bucket 26: 10%\n bucket 25: 60%\n bucket 27: 10%\n bucket 26: 20%\n bucket 25: 70%\n bucket 27: 20%\n bucket 25: 80%\n bucket 26: 30%\n bucket 27: 30%\n bucket 25: 90%\n bucket 26: 40%\n bucket 27: 40%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 50%\n bucket 27: 50%\n bucket 26: 60%\n bucket 27: 60%\n bucket 26: 70%\n bucket 27: 70%\n bucket 26: 80%\n bucket 27: 80%\n bucket 26: 90%\n bucket 27: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n Entering block accumulator loop for bucket 28:\n Entering block accumulator loop for bucket 29:\n bucket 28: 10%\n bucket 29: 10%\n bucket 28: 20%\n bucket 29: 20%\n bucket 28: 30%\n bucket 29: 30%\n bucket 29: 40%\n bucket 28: 40%\n bucket 29: 50%\n bucket 28: 50%\n bucket 29: 60%\n bucket 28: 60%\n bucket 29: 70%\n bucket 29: 80%\n bucket 28: 70%\n bucket 29: 90%\n bucket 28: 80%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 28: 90%\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 31:\n bucket 30: 10%\n bucket 31: 10%\n bucket 30: 20%\n bucket 31: 20%\n bucket 30: 30%\n bucket 31: 30%\n bucket 30: 40%\n bucket 31: 40%\n Sorting block time: 00:00:00\n bucket 30: 50%\nReturning block of 52 for bucket 29\n bucket 31: 50%\n bucket 30: 60%\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n bucket 31: 60%\n bucket 30: 70%\n bucket 31: 70%\n bucket 30: 80%\n bucket 31: 80%\n bucket 31: 90%\n bucket 30: 90%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 32:\n Entering block accumulator loop for bucket 33:\n bucket 32: 10%\n bucket 33: 10%\n bucket 32: 20%\n bucket 33: 20%\n bucket 32: 30%\n bucket 33: 30%\n bucket 32: 40%\n bucket 33: 40%\n bucket 32: 50%\n bucket 33: 50%\n bucket 32: 60%\n bucket 33: 60%\n bucket 32: 70%\n bucket 33: 70%\n bucket 32: 80%\n bucket 33: 80%\n bucket 32: 90%\n bucket 33: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\n Entering block accumulator loop for bucket 35:\n bucket 34: 20%\n bucket 35: 10%\n bucket 34: 30%\n bucket 35: 20%\n bucket 34: 40%\n bucket 35: 30%\n bucket 34: 50%\n bucket 35: 40%\n bucket 34: 60%\n bucket 35: 50%\n bucket 34: 70%\n bucket 35: 60%\n bucket 34: 80%\n bucket 35: 70%\n bucket 34: 90%\n bucket 35: 80%\n bucket 34: 100%\n bucket 35: 90%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Entering block accumulator loop for bucket 36:\n Calculating Z arrays for bucket 37\n bucket 36: 10%\n Entering block accumulator loop for bucket 37:\n bucket 36: 20%\n bucket 37: 10%\n bucket 36: 30%\n bucket 37: 20%\n bucket 36: 40%\n bucket 37: 30%\n bucket 36: 50%\n bucket 37: 40%\n bucket 36: 60%\n bucket 37: 50%\n bucket 36: 70%\n bucket 37: 60%\n bucket 36: 80%\n bucket 37: 70%\n bucket 36: 90%\n bucket 37: 80%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n bucket 38: 30%\n bucket 38: 40%\n Entering block accumulator loop for bucket 39:\n bucket 38: 50%\n bucket 39: 10%\n bucket 38: 60%\n bucket 39: 20%\n bucket 38: 70%\n bucket 39: 30%\n bucket 38: 80%\n bucket 38: 90%\n bucket 39: 40%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 39: 50%\n bucket 39: 60%\n bucket 39: 70%\n bucket 39: 80%\n bucket 39: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n Entering block accumulator loop for bucket 43:\n bucket 42: 20%\n bucket 43: 10%\n bucket 42: 30%\n bucket 43: 20%\n bucket 42: 40%\n bucket 43: 30%\n bucket 42: 50%\n bucket 43: 40%\n bucket 42: 60%\n bucket 43: 50%\n bucket 42: 70%\n bucket 43: 60%\n bucket 43: 70%\n bucket 42: 80%\n bucket 43: 80%\n bucket 43: 90%\n bucket 42: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 45:\n Entering block accumulator loop for bucket 44:\n bucket 45: 10%\n bucket 44: 10%\n bucket 45: 20%\n bucket 44: 20%\n bucket 45: 30%\n bucket 44: 30%\n bucket 45: 40%\n bucket 44: 40%\n bucket 44: 50%\n bucket 45: 50%\n bucket 44: 60%\n bucket 44: 70%\n bucket 45: 60%\n bucket 44: 80%\n bucket 45: 70%\n bucket 45: 80%\n bucket 44: 90%\n bucket 45: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n bucket 48: 10%\n Calculating Z arrays for bucket 49\n bucket 48: 20%\n Entering block accumulator loop for bucket 49:\n bucket 48: 30%\n bucket 48: 40%\n bucket 49: 10%\n bucket 48: 50%\n bucket 48: 60%\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 49: 20%\n Entering block accumulator loop for bucket 50:\n bucket 49: 30%\n bucket 50: 10%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 40%\n bucket 50: 20%\n bucket 49: 50%\n bucket 50: 30%\n bucket 49: 60%\n bucket 50: 40%\n bucket 49: 70%\n bucket 50: 50%\n bucket 49: 80%\n bucket 50: 60%\n bucket 49: 90%\n bucket 50: 70%\n Sorting block time: 00:00:00\n bucket 49: 100%\n bucket 50: 80%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\nReturning block of 114 for bucket 48\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 51: 40%\n bucket 51: 50%\n Entering block accumulator loop for bucket 52:\n bucket 51: 60%\n bucket 52: 10%\n bucket 51: 70%\n bucket 52: 20%\n bucket 51: 80%\n bucket 52: 30%\n bucket 51: 90%\n bucket 52: 40%\n bucket 52: 50%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n bucket 52: 60%\n bucket 52: 70%\n bucket 52: 80%\n bucket 52: 90%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Entering block accumulator loop for bucket 53:\n Calculating Z arrays for bucket 54\n bucket 53: 10%\n Entering block accumulator loop for bucket 54:\n bucket 53: 20%\n bucket 53: 30%\n bucket 54: 10%\n bucket 53: 40%\n bucket 54: 20%\n bucket 53: 50%\n bucket 54: 30%\n bucket 53: 60%\n bucket 54: 40%\n bucket 53: 70%\n bucket 54: 50%\n bucket 53: 80%\n bucket 54: 60%\n bucket 53: 90%\n bucket 54: 70%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n Entering block accumulator loop for bucket 56:\n bucket 55: 20%\n bucket 56: 10%\n bucket 55: 30%\n bucket 56: 20%\n bucket 55: 40%\n bucket 56: 30%\n bucket 55: 50%\n bucket 56: 40%\n bucket 55: 60%\n bucket 56: 50%\n bucket 55: 70%\n bucket 56: 60%\n bucket 55: 80%\n bucket 56: 70%\n bucket 55: 90%\n bucket 56: 80%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 10%\n bucket 57: 20%\n Entering block accumulator loop for bucket 58:\n bucket 57: 30%\n bucket 57: 40%\n bucket 58: 10%\n bucket 58: 20%\n bucket 58: 30%\n bucket 58: 40%\n bucket 58: 50%\n bucket 58: 60%\n bucket 57: 50%\n bucket 58: 70%\n bucket 57: 60%\n bucket 58: 80%\n bucket 57: 70%\n bucket 58: 90%\n bucket 57: 80%\n bucket 57: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n Entering block accumulator loop for bucket 59:\n bucket 59: 10%\n bucket 59: 20%\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n bucket 59: 30%\n Entering block accumulator loop for bucket 60:\n bucket 59: 40%\n bucket 60: 10%\n bucket 59: 50%\n bucket 60: 20%\n bucket 59: 60%\n bucket 60: 30%\n bucket 59: 70%\n bucket 60: 40%\n bucket 59: 80%\n bucket 59: 90%\n bucket 60: 50%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:54:24", "plugin": "core", "name": "end_epoch", "raw_value": "1725000864.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:54:23", "plugin": "core", "name": "start_epoch", "raw_value": "1725000863.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-7", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 7, "time_seconds": 37.49690818786621, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "45235b8c70a9698c"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "e189963b696cfa6a"}, "library|input_2": {"src": "hda", "id": "9984a0e231dfae1c"}, "library|paired_options|no_mixed": true, "library|paired_options|no_discordant": true, "library|paired_options|paired_options_selector": "advanced", "library|type": "paired", "adv|input_options|trim5": "15", "adv|input_options|trim3": "15", "adv|input_options|input_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "3b6b6ae24dc1e01e", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:02:41.343255", "update_time": "2024-08-30T07:02:54.027356", "galaxy_version": "24.1", "external_id": "gxy-dlxv9", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/6/1/5/dataset_615bf557-20db-4c54-a53a-533064eead88.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/4/2/d/dataset_42dcd6ce-e569-455c-8b86-aafc63509117.dat' input_f.fastq.gz && ln -f -s '/galaxy/server/database/objects/9/4/0/dataset_940c33d8-f2e2-4632-828b-f3218b51d663.dat' input_r.fastq.gz && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq.gz' -2 'input_r.fastq.gz' --fr --no-mixed --no-discordant --trim5 '15' --trim3 '15' --phred33 | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/2/4/d/dataset_24d116bb-7f23-4cdb-96e1-d786c3ecd7dc.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 1, \"input_options_selector\": \"advanced\", \"int_quals\": false, \"qupto\": \"0\", \"qv_encoding\": \"--phred33\", \"skip\": \"0\", \"solexa_quals\": false, \"trim3\": \"15\", \"trim5\": \"15\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 203, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 204, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"fr_rf_ff\": \"--fr\", \"no_discordant\": true, \"no_mixed\": true, \"paired_options_selector\": \"advanced\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 202, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "45235b8c70a9698c", "src": "hda", "uuid": "615bf557-20db-4c54-a53a-533064eead88"}, "library|input_1": {"id": "e189963b696cfa6a", "src": "hda", "uuid": "42dcd6ce-e569-455c-8b86-aafc63509117"}, "library|input_2": {"id": "9984a0e231dfae1c", "src": "hda", "uuid": "940c33d8-f2e2-4632-828b-f3218b51d663"}}, "outputs": {"output_alignments": {"id": "d963144abd1822c5", "src": "hda", "uuid": "24d116bb-7f23-4cdb-96e1-d786c3ecd7dc"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n bucket 2: 10%\n bucket 1: 20%\nGetting block 4 of 60\n Entering block accumulator loop for bucket 3:\n bucket 2: 20%\nGetting block 5 of 60\n bucket 1: 30%\n Reserving size (126) for bucket 5\n Reserving size (126) for bucket 4\n bucket 3: 10%\n bucket 1: 40%\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 4\n bucket 1: 50%\nGetting block 6 of 60\nGetting block 7 of 60\n Entering block accumulator loop for bucket 4:\n bucket 3: 20%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 7\n bucket 1: 60%\n bucket 5: 10%\n bucket 4: 10%\n bucket 1: 70%\n Calculating Z arrays for bucket 7\n bucket 3: 30%\n bucket 2: 30%\n bucket 1: 80%\n bucket 4: 20%\n bucket 2: 40%\n bucket 5: 20%\n bucket 3: 40%\n bucket 2: 50%\n bucket 5: 30%\n bucket 1: 90%\n bucket 3: 50%\n bucket 5: 40%\n Entering block accumulator loop for bucket 7:\n bucket 4: 30%\n bucket 3: 60%\n bucket 5: 50%\n bucket 1: 100%\n bucket 2: 60%\n bucket 4: 40%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 8\n bucket 3: 70%\n Sorting block of length 42 for bucket 1\n bucket 5: 60%\n bucket 3: 80%\n bucket 2: 70%\n bucket 5: 70%\n (Using difference cover)\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 8:\n bucket 2: 80%\n bucket 7: 10%\n bucket 2: 90%\n bucket 3: 90%\n bucket 8: 10%\n bucket 2: 100%\n bucket 6: 10%\n bucket 7: 20%\n bucket 8: 20%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 5: 80%\n bucket 7: 30%\n bucket 4: 50%\n bucket 5: 90%\n bucket 6: 20%\n bucket 8: 30%\n bucket 4: 60%\n bucket 5: 100%\n bucket 7: 40%\n bucket 3: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 4: 70%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 30%\n bucket 8: 40%\n bucket 7: 50%\n bucket 6: 40%\n bucket 8: 50%\n bucket 7: 60%\n bucket 6: 50%\n bucket 8: 60%\n bucket 7: 70%\n bucket 6: 60%\n bucket 8: 70%\n bucket 7: 80%\n bucket 6: 70%\n bucket 8: 80%\n bucket 6: 80%\n bucket 8: 90%\n bucket 7: 90%\n bucket 6: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 6: 100%\n bucket 4: 80%\n bucket 7: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 4: 90%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 40%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n bucket 9: 50%\n Entering block accumulator loop for bucket 10:\n Calculating Z arrays for bucket 11\n bucket 9: 60%\n bucket 10: 10%\n bucket 9: 70%\n bucket 10: 20%\n Entering block accumulator loop for bucket 11:\n bucket 10: 30%\n bucket 11: 10%\n bucket 9: 80%\n bucket 11: 20%\n bucket 10: 40%\n bucket 9: 90%\n bucket 11: 30%\n bucket 10: 50%\n bucket 11: 40%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n bucket 10: 60%\n (Using difference cover)\n bucket 11: 50%\n bucket 10: 70%\n bucket 11: 60%\n bucket 10: 80%\n bucket 11: 70%\n bucket 11: 80%\n bucket 10: 90%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n Entering block accumulator loop for bucket 12:\n bucket 13: 20%\n bucket 13: 30%\n bucket 12: 10%\n bucket 13: 40%\n bucket 12: 20%\n bucket 13: 50%\n bucket 12: 30%\n bucket 13: 60%\n bucket 12: 40%\n bucket 13: 70%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 80%\n bucket 12: 50%\n bucket 13: 90%\n bucket 12: 60%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 12: 70%\n Entering block accumulator loop for bucket 14:\n bucket 12: 80%\n bucket 14: 10%\n bucket 12: 90%\n bucket 14: 20%\n bucket 12: 100%\n bucket 14: 30%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n Sorting block time: 00:00:00\n bucket 14: 70%\nReturning block of 86 for bucket 13\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Entering block accumulator loop for bucket 15:\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n bucket 15: 20%\n Entering block accumulator loop for bucket 16:\n bucket 15: 30%\n bucket 15: 40%\n bucket 16: 10%\n bucket 15: 50%\n bucket 16: 20%\n bucket 15: 60%\n bucket 15: 70%\n bucket 16: 30%\n bucket 15: 80%\n bucket 16: 40%\n bucket 15: 90%\n bucket 16: 50%\n bucket 15: 100%\n bucket 16: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Entering block accumulator loop for bucket 17:\n Calculating Z arrays for bucket 18\n bucket 17: 10%\n Entering block accumulator loop for bucket 18:\n bucket 17: 20%\n bucket 18: 10%\n bucket 17: 30%\n bucket 18: 20%\n bucket 17: 40%\n bucket 18: 30%\n bucket 17: 50%\n bucket 18: 40%\n bucket 17: 60%\n bucket 18: 50%\n bucket 17: 70%\n bucket 17: 80%\n bucket 18: 60%\n bucket 17: 90%\n bucket 18: 70%\n bucket 17: 100%\n bucket 18: 80%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n Entering block accumulator loop for bucket 20:\n bucket 19: 10%\n bucket 20: 10%\n bucket 19: 20%\n bucket 20: 20%\n bucket 19: 30%\n bucket 20: 30%\n bucket 19: 40%\n bucket 20: 40%\n bucket 19: 50%\n bucket 20: 50%\n bucket 19: 60%\n bucket 20: 60%\n bucket 19: 70%\n bucket 20: 70%\n bucket 19: 80%\n bucket 20: 80%\n bucket 19: 90%\n bucket 20: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n bucket 21: 90%\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 22: 50%\n bucket 23: 40%\n bucket 22: 60%\n bucket 23: 50%\n bucket 22: 70%\n bucket 23: 60%\n bucket 22: 80%\n bucket 23: 70%\n bucket 22: 90%\n bucket 23: 80%\n bucket 22: 100%\n bucket 23: 90%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 25: 10%\n bucket 24: 20%\n bucket 25: 20%\n bucket 24: 30%\n bucket 25: 30%\n bucket 24: 40%\n bucket 25: 40%\n bucket 24: 50%\n bucket 25: 50%\n bucket 24: 60%\n bucket 25: 60%\n bucket 24: 70%\n bucket 25: 70%\n bucket 24: 80%\n bucket 25: 80%\n bucket 24: 90%\n bucket 25: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\n bucket 27: 20%\n bucket 26: 30%\n bucket 27: 30%\n bucket 27: 40%\n bucket 26: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 26: 50%\n bucket 27: 70%\n bucket 27: 80%\n bucket 26: 60%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\nGetting block 29 of 60\n bucket 28: 30%\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 40%\n Entering block accumulator loop for bucket 29:\n bucket 28: 50%\n bucket 29: 10%\n bucket 28: 60%\n bucket 29: 20%\n bucket 29: 30%\n bucket 28: 70%\n bucket 29: 40%\n bucket 28: 80%\n bucket 29: 50%\n bucket 29: 60%\n bucket 28: 90%\n bucket 29: 70%\n bucket 29: 80%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n bucket 29: 90%\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 40%\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n bucket 30: 50%\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 30: 60%\n bucket 31: 10%\n bucket 30: 70%\n bucket 31: 20%\n Entering block accumulator loop for bucket 32:\n bucket 30: 80%\n bucket 31: 30%\n bucket 30: 90%\n bucket 32: 10%\n bucket 30: 100%\n bucket 31: 40%\n bucket 32: 20%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 50%\n bucket 32: 30%\n bucket 31: 60%\n bucket 32: 40%\n bucket 31: 70%\n bucket 32: 50%\n bucket 31: 80%\n bucket 32: 60%\n bucket 31: 90%\n bucket 32: 70%\n bucket 31: 100%\n bucket 32: 80%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 33:\n Entering block accumulator loop for bucket 34:\n bucket 33: 10%\n bucket 34: 10%\n bucket 33: 20%\n bucket 34: 20%\n bucket 33: 30%\n bucket 34: 30%\n bucket 33: 40%\n bucket 34: 40%\n bucket 33: 50%\n bucket 34: 50%\n bucket 33: 60%\n bucket 34: 60%\n bucket 33: 70%\n bucket 34: 70%\n bucket 33: 80%\n bucket 34: 80%\n bucket 33: 90%\n bucket 34: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\nGetting block 36 of 60\n bucket 35: 20%\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 30%\n bucket 35: 40%\n Entering block accumulator loop for bucket 36:\n bucket 35: 50%\n bucket 35: 60%\n bucket 36: 10%\n bucket 35: 70%\n bucket 36: 20%\n bucket 35: 80%\n bucket 36: 30%\n bucket 35: 90%\n bucket 36: 40%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n Entering block accumulator loop for bucket 37:\n bucket 38: 30%\n bucket 37: 10%\n bucket 38: 40%\n bucket 37: 20%\n bucket 38: 50%\n bucket 37: 30%\n bucket 38: 60%\n bucket 37: 40%\n bucket 38: 70%\n bucket 37: 50%\n bucket 38: 80%\n bucket 37: 60%\n bucket 38: 90%\n bucket 37: 70%\n bucket 38: 100%\n bucket 37: 80%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Entering block accumulator loop for bucket 39:\n Calculating Z arrays for bucket 40\n bucket 39: 10%\n Entering block accumulator loop for bucket 40:\n bucket 39: 20%\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n bucket 40: 10%\n bucket 39: 30%\n Calculating Z arrays for bucket 41\n bucket 40: 20%\n bucket 39: 40%\n Entering block accumulator loop for bucket 41:\n bucket 40: 30%\n bucket 39: 50%\n bucket 41: 10%\n bucket 40: 40%\n bucket 39: 60%\n bucket 41: 20%\n bucket 39: 70%\n bucket 41: 30%\n bucket 40: 50%\n bucket 39: 80%\n bucket 41: 40%\n bucket 39: 90%\n bucket 41: 50%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n bucket 41: 60%\n bucket 40: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 40: 70%\n bucket 41: 90%\n bucket 40: 80%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n Entering block accumulator loop for bucket 43:\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 43: 10%\n bucket 42: 50%\n bucket 43: 20%\n bucket 42: 60%\n bucket 43: 30%\n bucket 42: 70%\n bucket 43: 40%\n bucket 43: 50%\n bucket 42: 80%\n bucket 43: 60%\n bucket 42: 90%\n bucket 43: 70%\n bucket 42: 100%\n bucket 43: 80%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n Entering block accumulator loop for bucket 45:\n bucket 44: 20%\n bucket 45: 10%\n bucket 44: 30%\n bucket 45: 20%\n bucket 44: 40%\n bucket 45: 30%\n bucket 44: 50%\n bucket 45: 40%\n bucket 44: 60%\n bucket 44: 70%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 48:\n bucket 49: 10%\n bucket 48: 10%\n bucket 49: 20%\n bucket 48: 20%\n bucket 49: 30%\n bucket 48: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 48: 40%\n bucket 49: 60%\n bucket 49: 70%\n bucket 48: 50%\n bucket 49: 80%\n bucket 48: 60%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n Entering block accumulator loop for bucket 51:\n bucket 50: 20%\n bucket 51: 10%\n bucket 50: 30%\n bucket 50: 40%\n bucket 51: 20%\n bucket 50: 50%\n bucket 51: 30%\n bucket 50: 60%\n bucket 51: 40%\n bucket 50: 70%\n bucket 51: 50%\n bucket 50: 80%\n bucket 51: 60%\n bucket 50: 90%\n bucket 51: 70%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 40%\n bucket 52: 50%\n Entering block accumulator loop for bucket 53:\n bucket 52: 60%\n bucket 53: 10%\n bucket 52: 70%\n bucket 53: 20%\n bucket 52: 80%\n bucket 53: 30%\n bucket 52: 90%\n bucket 53: 40%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 20%\n bucket 54: 30%\n Entering block accumulator loop for bucket 55:\n bucket 54: 40%\n bucket 55: 10%\n bucket 54: 50%\n bucket 55: 20%\n bucket 54: 60%\n bucket 54: 70%\n bucket 55: 30%\n bucket 54: 80%\n bucket 55: 40%\n bucket 54: 90%\n bucket 55: 50%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n bucket 57: 30%\n Calculating Z arrays for bucket 58\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n Entering block accumulator loop for bucket 58:\n bucket 57: 70%\n bucket 57: 80%\n bucket 58: 10%\nGetting block 59 of 60\n bucket 58: 20%\n Reserving size (126) for bucket 59\n bucket 57: 90%\n Calculating Z arrays for bucket 59\n bucket 58: 30%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 40%\n Entering block accumulator loop for bucket 59:\n bucket 58: 50%\n bucket 59: 10%\n bucket 58: 60%\n bucket 59: 20%\n bucket 58: 70%\n bucket 59: 30%\n bucket 58: 80%\n bucket 59: 40%\n bucket 58: 90%\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 1:\n Entering block accumulator loop for bucket 2:\n bucket 1: 10%\n Calculating Z arrays for bucket 3\n bucket 2: 10%\n bucket 1: 20%\nGetting block 4 of 60\n Entering block accumulator loop for bucket 3:\n bucket 2: 20%\nGetting block 5 of 60\n bucket 1: 30%\n Reserving size (126) for bucket 5\n Reserving size (126) for bucket 4\n bucket 3: 10%\n bucket 1: 40%\n Calculating Z arrays for bucket 5\n Calculating Z arrays for bucket 4\n bucket 1: 50%\nGetting block 6 of 60\nGetting block 7 of 60\n Entering block accumulator loop for bucket 4:\n bucket 3: 20%\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 7\n bucket 1: 60%\n bucket 5: 10%\n bucket 4: 10%\n bucket 1: 70%\n Calculating Z arrays for bucket 7\n bucket 3: 30%\n bucket 2: 30%\n bucket 1: 80%\n bucket 4: 20%\n bucket 2: 40%\n bucket 5: 20%\n bucket 3: 40%\n bucket 2: 50%\n bucket 5: 30%\n bucket 1: 90%\n bucket 3: 50%\n bucket 5: 40%\n Entering block accumulator loop for bucket 7:\n bucket 4: 30%\n bucket 3: 60%\n bucket 5: 50%\n bucket 1: 100%\n bucket 2: 60%\n bucket 4: 40%\n Calculating Z arrays for bucket 6\n Calculating Z arrays for bucket 8\n bucket 3: 70%\n Sorting block of length 42 for bucket 1\n bucket 5: 60%\n bucket 3: 80%\n bucket 2: 70%\n bucket 5: 70%\n (Using difference cover)\n Entering block accumulator loop for bucket 6:\n Entering block accumulator loop for bucket 8:\n bucket 2: 80%\n bucket 7: 10%\n bucket 2: 90%\n bucket 3: 90%\n bucket 8: 10%\n bucket 2: 100%\n bucket 6: 10%\n bucket 7: 20%\n bucket 8: 20%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 5: 80%\n bucket 7: 30%\n bucket 4: 50%\n bucket 5: 90%\n bucket 6: 20%\n bucket 8: 30%\n bucket 4: 60%\n bucket 5: 100%\n bucket 7: 40%\n bucket 3: 100%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 4: 70%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 30%\n bucket 8: 40%\n bucket 7: 50%\n bucket 6: 40%\n bucket 8: 50%\n bucket 7: 60%\n bucket 6: 50%\n bucket 8: 60%\n bucket 7: 70%\n bucket 6: 60%\n bucket 8: 70%\n bucket 7: 80%\n bucket 6: 70%\n bucket 8: 80%\n bucket 6: 80%\n bucket 8: 90%\n bucket 7: 90%\n bucket 6: 90%\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 6: 100%\n bucket 4: 80%\n bucket 7: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 4: 90%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n bucket 9: 40%\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n bucket 9: 50%\n Entering block accumulator loop for bucket 10:\n Calculating Z arrays for bucket 11\n bucket 9: 60%\n bucket 10: 10%\n bucket 9: 70%\n bucket 10: 20%\n Entering block accumulator loop for bucket 11:\n bucket 10: 30%\n bucket 11: 10%\n bucket 9: 80%\n bucket 11: 20%\n bucket 10: 40%\n bucket 9: 90%\n bucket 11: 30%\n bucket 10: 50%\n bucket 11: 40%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n bucket 10: 60%\n (Using difference cover)\n bucket 11: 50%\n bucket 10: 70%\n bucket 11: 60%\n bucket 10: 80%\n bucket 11: 70%\n bucket 11: 80%\n bucket 10: 90%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 12 of 60\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n Entering block accumulator loop for bucket 12:\n bucket 13: 20%\n bucket 13: 30%\n bucket 12: 10%\n bucket 13: 40%\n bucket 12: 20%\n bucket 13: 50%\n bucket 12: 30%\n bucket 13: 60%\n bucket 12: 40%\n bucket 13: 70%\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 13: 80%\n bucket 12: 50%\n bucket 13: 90%\n bucket 12: 60%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 12: 70%\n Entering block accumulator loop for bucket 14:\n bucket 12: 80%\n bucket 14: 10%\n bucket 12: 90%\n bucket 14: 20%\n bucket 12: 100%\n bucket 14: 30%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 14: 40%\n bucket 14: 50%\n bucket 14: 60%\n Sorting block time: 00:00:00\n bucket 14: 70%\nReturning block of 86 for bucket 13\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\nGetting block 16 of 60\n Entering block accumulator loop for bucket 15:\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 10%\n bucket 15: 20%\n Entering block accumulator loop for bucket 16:\n bucket 15: 30%\n bucket 15: 40%\n bucket 16: 10%\n bucket 15: 50%\n bucket 16: 20%\n bucket 15: 60%\n bucket 15: 70%\n bucket 16: 30%\n bucket 15: 80%\n bucket 16: 40%\n bucket 15: 90%\n bucket 16: 50%\n bucket 15: 100%\n bucket 16: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Entering block accumulator loop for bucket 17:\n Calculating Z arrays for bucket 18\n bucket 17: 10%\n Entering block accumulator loop for bucket 18:\n bucket 17: 20%\n bucket 18: 10%\n bucket 17: 30%\n bucket 18: 20%\n bucket 17: 40%\n bucket 18: 30%\n bucket 17: 50%\n bucket 18: 40%\n bucket 17: 60%\n bucket 18: 50%\n bucket 17: 70%\n bucket 17: 80%\n bucket 18: 60%\n bucket 17: 90%\n bucket 18: 70%\n bucket 17: 100%\n bucket 18: 80%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 19:\n Entering block accumulator loop for bucket 20:\n bucket 19: 10%\n bucket 20: 10%\n bucket 19: 20%\n bucket 20: 20%\n bucket 19: 30%\n bucket 20: 30%\n bucket 19: 40%\n bucket 20: 40%\n bucket 19: 50%\n bucket 20: 50%\n bucket 19: 60%\n bucket 20: 60%\n bucket 19: 70%\n bucket 20: 70%\n bucket 19: 80%\n bucket 20: 80%\n bucket 19: 90%\n bucket 20: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n bucket 21: 90%\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 22: 50%\n bucket 23: 40%\n bucket 22: 60%\n bucket 23: 50%\n bucket 22: 70%\n bucket 23: 60%\n bucket 22: 80%\n bucket 23: 70%\n bucket 22: 90%\n bucket 23: 80%\n bucket 22: 100%\n bucket 23: 90%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n Entering block accumulator loop for bucket 25:\n bucket 24: 10%\n bucket 25: 10%\n bucket 24: 20%\n bucket 25: 20%\n bucket 24: 30%\n bucket 25: 30%\n bucket 24: 40%\n bucket 25: 40%\n bucket 24: 50%\n bucket 25: 50%\n bucket 24: 60%\n bucket 25: 60%\n bucket 24: 70%\n bucket 25: 70%\n bucket 24: 80%\n bucket 25: 80%\n bucket 24: 90%\n bucket 25: 90%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\n bucket 27: 20%\n bucket 26: 30%\n bucket 27: 30%\n bucket 27: 40%\n bucket 26: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 26: 50%\n bucket 27: 70%\n bucket 27: 80%\n bucket 26: 60%\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\nGetting block 29 of 60\n bucket 28: 30%\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 40%\n Entering block accumulator loop for bucket 29:\n bucket 28: 50%\n bucket 29: 10%\n bucket 28: 60%\n bucket 29: 20%\n bucket 29: 30%\n bucket 28: 70%\n bucket 29: 40%\n bucket 28: 80%\n bucket 29: 50%\n bucket 29: 60%\n bucket 28: 90%\n bucket 29: 70%\n bucket 29: 80%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n bucket 29: 90%\n (Using difference cover)\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 30 of 60\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n Entering block accumulator loop for bucket 30:\n bucket 30: 10%\n bucket 30: 20%\n bucket 30: 30%\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n bucket 30: 40%\n Calculating Z arrays for bucket 31\nGetting block 32 of 60\n Entering block accumulator loop for bucket 31:\n bucket 30: 50%\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 30: 60%\n bucket 31: 10%\n bucket 30: 70%\n bucket 31: 20%\n Entering block accumulator loop for bucket 32:\n bucket 30: 80%\n bucket 31: 30%\n bucket 30: 90%\n bucket 32: 10%\n bucket 30: 100%\n bucket 31: 40%\n bucket 32: 20%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 50%\n bucket 32: 30%\n bucket 31: 60%\n bucket 32: 40%\n bucket 31: 70%\n bucket 32: 50%\n bucket 31: 80%\n bucket 32: 60%\n bucket 31: 90%\n bucket 32: 70%\n bucket 31: 100%\n bucket 32: 80%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 33:\n Entering block accumulator loop for bucket 34:\n bucket 33: 10%\n bucket 34: 10%\n bucket 33: 20%\n bucket 34: 20%\n bucket 33: 30%\n bucket 34: 30%\n bucket 33: 40%\n bucket 34: 40%\n bucket 33: 50%\n bucket 34: 50%\n bucket 33: 60%\n bucket 34: 60%\n bucket 33: 70%\n bucket 34: 70%\n bucket 33: 80%\n bucket 34: 80%\n bucket 33: 90%\n bucket 34: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n Entering block accumulator loop for bucket 35:\n bucket 35: 10%\nGetting block 36 of 60\n bucket 35: 20%\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n bucket 35: 30%\n bucket 35: 40%\n Entering block accumulator loop for bucket 36:\n bucket 35: 50%\n bucket 35: 60%\n bucket 36: 10%\n bucket 35: 70%\n bucket 36: 20%\n bucket 35: 80%\n bucket 36: 30%\n bucket 35: 90%\n bucket 36: 40%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\nGetting block 37 of 60\n Reserving size (126) for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 38:\n bucket 38: 10%\n bucket 38: 20%\n Entering block accumulator loop for bucket 37:\n bucket 38: 30%\n bucket 37: 10%\n bucket 38: 40%\n bucket 37: 20%\n bucket 38: 50%\n bucket 37: 30%\n bucket 38: 60%\n bucket 37: 40%\n bucket 38: 70%\n bucket 37: 50%\n bucket 38: 80%\n bucket 37: 60%\n bucket 38: 90%\n bucket 37: 70%\n bucket 38: 100%\n bucket 37: 80%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Entering block accumulator loop for bucket 39:\n Calculating Z arrays for bucket 40\n bucket 39: 10%\n Entering block accumulator loop for bucket 40:\n bucket 39: 20%\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n bucket 40: 10%\n bucket 39: 30%\n Calculating Z arrays for bucket 41\n bucket 40: 20%\n bucket 39: 40%\n Entering block accumulator loop for bucket 41:\n bucket 40: 30%\n bucket 39: 50%\n bucket 41: 10%\n bucket 40: 40%\n bucket 39: 60%\n bucket 41: 20%\n bucket 39: 70%\n bucket 41: 30%\n bucket 40: 50%\n bucket 39: 80%\n bucket 41: 40%\n bucket 39: 90%\n bucket 41: 50%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n bucket 41: 60%\n bucket 40: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 40: 70%\n bucket 41: 90%\n bucket 40: 80%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n bucket 42: 10%\n Entering block accumulator loop for bucket 43:\n bucket 42: 20%\n bucket 42: 30%\n bucket 42: 40%\n bucket 43: 10%\n bucket 42: 50%\n bucket 43: 20%\n bucket 42: 60%\n bucket 43: 30%\n bucket 42: 70%\n bucket 43: 40%\n bucket 43: 50%\n bucket 42: 80%\n bucket 43: 60%\n bucket 42: 90%\n bucket 43: 70%\n bucket 42: 100%\n bucket 43: 80%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n bucket 43: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n Entering block accumulator loop for bucket 44:\n bucket 44: 10%\n Entering block accumulator loop for bucket 45:\n bucket 44: 20%\n bucket 45: 10%\n bucket 44: 30%\n bucket 45: 20%\n bucket 44: 40%\n bucket 45: 30%\n bucket 44: 50%\n bucket 45: 40%\n bucket 44: 60%\n bucket 44: 70%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 44: 80%\n bucket 44: 90%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n Entering block accumulator loop for bucket 48:\n bucket 49: 10%\n bucket 48: 10%\n bucket 49: 20%\n bucket 48: 20%\n bucket 49: 30%\n bucket 48: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 48: 40%\n bucket 49: 60%\n bucket 49: 70%\n bucket 48: 50%\n bucket 49: 80%\n bucket 48: 60%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n bucket 48: 70%\n bucket 48: 80%\n bucket 48: 90%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n Entering block accumulator loop for bucket 51:\n bucket 50: 20%\n bucket 51: 10%\n bucket 50: 30%\n bucket 50: 40%\n bucket 51: 20%\n bucket 50: 50%\n bucket 51: 30%\n bucket 50: 60%\n bucket 51: 40%\n bucket 50: 70%\n bucket 51: 50%\n bucket 50: 80%\n bucket 51: 60%\n bucket 50: 90%\n bucket 51: 70%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n bucket 52: 20%\n bucket 52: 30%\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n bucket 52: 40%\n bucket 52: 50%\n Entering block accumulator loop for bucket 53:\n bucket 52: 60%\n bucket 53: 10%\n bucket 52: 70%\n bucket 53: 20%\n bucket 52: 80%\n bucket 53: 30%\n bucket 52: 90%\n bucket 53: 40%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 50%\n bucket 53: 60%\n bucket 53: 70%\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 20%\n bucket 54: 30%\n Entering block accumulator loop for bucket 55:\n bucket 54: 40%\n bucket 55: 10%\n bucket 54: 50%\n bucket 55: 20%\n bucket 54: 60%\n bucket 54: 70%\n bucket 55: 30%\n bucket 54: 80%\n bucket 55: 40%\n bucket 54: 90%\n bucket 55: 50%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n bucket 57: 30%\n Calculating Z arrays for bucket 58\n bucket 57: 40%\n bucket 57: 50%\n bucket 57: 60%\n Entering block accumulator loop for bucket 58:\n bucket 57: 70%\n bucket 57: 80%\n bucket 58: 10%\nGetting block 59 of 60\n bucket 58: 20%\n Reserving size (126) for bucket 59\n bucket 57: 90%\n Calculating Z arrays for bucket 59\n bucket 58: 30%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 40%\n Entering block accumulator loop for bucket 59:\n bucket 58: 50%\n bucket 59: 10%\n bucket 58: 60%\n bucket 59: 20%\n bucket 58: 70%\n bucket 59: 30%\n bucket 58: 80%\n bucket 59: 40%\n bucket 58: 90%\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:02:43", "plugin": "core", "name": "end_epoch", "raw_value": "1725001363.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:02:42", "plugin": "core", "name": "start_epoch", "raw_value": "1725001362.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-8", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 8, "time_seconds": 11.017140865325928, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "hisat2/2.2.1+galaxy1-8", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 8, "time_seconds": 38.58284068107605, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "cc8321173c4a3910"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "cfbcb78557262785"}, "library|input_2": {"src": "hda", "id": "a8f76721d2ec609e"}, "library|paired_options|no_mixed": true, "library|paired_options|no_discordant": true, "library|paired_options|paired_options_selector": "advanced", "library|type": "paired", "adv|input_options|trim5": "15", "adv|input_options|trim3": "15", "adv|input_options|input_options_selector": "advanced"}, "job": {"model_class": "Job", "id": "689bab7197243cdc", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:03:19.641751", "update_time": "2024-08-30T07:03:32.855704", "galaxy_version": "24.1", "external_id": "gxy-7bddr", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/2/5/c/dataset_25ce7ce1-9a23-429d-bfc3-e822e1d999c6.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/b/a/f/dataset_baf223fc-1367-4e82-b394-e5088db309bc.dat' input_f.fastq.bz2 && ln -f -s '/galaxy/server/database/objects/0/3/c/dataset_03cd559e-cb19-4137-9d43-573c0d636a44.dat' input_r.fastq.bz2 && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq.bz2' -2 'input_r.fastq.bz2' --fr --no-mixed --no-discordant --trim5 '15' --trim3 '15' --phred33 | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/a/f/c/dataset_afc7b12f-bed0-4d9d-b019-b4d0db713233.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 1, \"input_options_selector\": \"advanced\", \"int_quals\": false, \"qupto\": \"0\", \"qv_encoding\": \"--phred33\", \"skip\": \"0\", \"solexa_quals\": false, \"trim3\": \"15\", \"trim5\": \"15\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 207, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 208, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"fr_rf_ff\": \"--fr\", \"no_discordant\": true, \"no_mixed\": true, \"paired_options_selector\": \"advanced\"}, \"rna_strandness\": \"\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 206, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "cc8321173c4a3910", "src": "hda", "uuid": "25ce7ce1-9a23-429d-bfc3-e822e1d999c6"}, "library|input_1": {"id": "cfbcb78557262785", "src": "hda", "uuid": "baf223fc-1367-4e82-b394-e5088db309bc"}, "library|input_2": {"id": "a8f76721d2ec609e", "src": "hda", "uuid": "03cd559e-cb19-4137-9d43-573c0d636a44"}}, "outputs": {"output_alignments": {"id": "0875251307385fa4", "src": "hda", "uuid": "afc7b12f-bed0-4d9d-b019-b4d0db713233"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n bucket 1: 10%\n bucket 2: 10%\n Entering block accumulator loop for bucket 3:\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 2: 20%\n bucket 3: 10%\n bucket 2: 30%\n bucket 1: 20%\n Calculating Z arrays for bucket 4\n bucket 2: 40%\n bucket 3: 20%\n bucket 1: 30%\n bucket 2: 50%\n bucket 3: 30%\n Calculating Z arrays for bucket 5\n bucket 2: 60%\n Entering block accumulator loop for bucket 4:\n bucket 3: 40%\n bucket 1: 40%\n bucket 2: 70%\n bucket 4: 10%\n Entering block accumulator loop for bucket 5:\n bucket 2: 80%\n bucket 1: 50%\n bucket 3: 50%\nGetting block 6 of 60\n bucket 4: 20%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 4: 30%\n bucket 5: 10%\n bucket 4: 40%\nGetting block 8 of 60\n bucket 4: 50%\n Reserving size (126) for bucket 8\n bucket 1: 60%\n Calculating Z arrays for bucket 7\n bucket 4: 60%\n bucket 3: 60%\n bucket 2: 90%\n bucket 1: 70%\n bucket 4: 70%\n bucket 5: 20%\n bucket 2: 100%\n Calculating Z arrays for bucket 8\n Sorting block of length 84 for bucket 2\n bucket 5: 30%\n (Using difference cover)\n bucket 3: 70%\n bucket 4: 80%\n Reserving size (126) for bucket 6\n bucket 5: 40%\n Entering block accumulator loop for bucket 7:\n bucket 4: 90%\n bucket 1: 80%\n bucket 5: 50%\n Calculating Z arrays for bucket 6\n bucket 4: 100%\n bucket 3: 80%\n bucket 1: 90%\n Entering block accumulator loop for bucket 8:\n bucket 5: 60%\n bucket 7: 10%\n bucket 1: 100%\n bucket 5: 70%\n bucket 3: 90%\n bucket 8: 10%\n bucket 3: 100%\n Sorting block of length 42 for bucket 1\n bucket 5: 80%\n (Using difference cover)\n bucket 7: 20%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 20%\n bucket 5: 90%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Entering block accumulator loop for bucket 6:\n bucket 7: 30%\n bucket 5: 100%\n bucket 8: 30%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 40%\n bucket 8: 40%\n bucket 7: 50%\n bucket 6: 10%\n bucket 8: 50%\n bucket 7: 60%\n bucket 6: 20%\n bucket 8: 60%\n bucket 7: 70%\n bucket 6: 30%\n bucket 8: 70%\n bucket 7: 80%\n bucket 6: 40%\n bucket 8: 80%\n bucket 7: 90%\n bucket 6: 50%\n bucket 7: 100%\n bucket 6: 60%\n bucket 8: 90%\n Sorting block of length 75 for bucket 7\n bucket 6: 70%\n bucket 8: 100%\n (Using difference cover)\n bucket 6: 80%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Calculating Z arrays for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n Calculating Z arrays for bucket 11\n bucket 9: 10%\n bucket 10: 10%\n Entering block accumulator loop for bucket 11:\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 11: 10%\n bucket 9: 40%\n bucket 10: 30%\n bucket 11: 20%\n bucket 9: 50%\n bucket 10: 40%\n bucket 9: 60%\n bucket 11: 30%\n bucket 10: 50%\n bucket 9: 70%\n bucket 11: 40%\n bucket 10: 60%\n bucket 9: 80%\n bucket 11: 50%\n bucket 9: 90%\n bucket 10: 70%\n bucket 9: 100%\n bucket 11: 60%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 80%\n bucket 11: 70%\n bucket 10: 90%\n bucket 11: 80%\n bucket 10: 100%\n bucket 11: 90%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n bucket 12: 90%\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Entering block accumulator loop for bucket 13:\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 13: 10%\n bucket 13: 20%\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 15:\n bucket 13: 30%\n bucket 14: 10%\n bucket 15: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 15: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 15: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 15: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 15: 50%\n bucket 14: 60%\n bucket 13: 90%\n bucket 15: 60%\n bucket 13: 100%\n bucket 14: 70%\n Sorting block of length 85 for bucket 13\n Sorting block time: 00:00:00\n (Using difference cover)\n bucket 15: 70%\n bucket 14: 80%\nReturning block of 83 for bucket 12\n bucket 15: 80%\n bucket 14: 90%\n bucket 15: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 50%\n bucket 18: 60%\n Entering block accumulator loop for bucket 19:\n bucket 18: 70%\n bucket 19: 10%\n bucket 18: 80%\n bucket 19: 20%\n bucket 18: 90%\n bucket 19: 30%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n Entering block accumulator loop for bucket 23:\n bucket 22: 30%\n bucket 22: 40%\n bucket 23: 10%\n bucket 22: 50%\n bucket 23: 20%\n bucket 22: 60%\n bucket 23: 30%\n bucket 22: 70%\n bucket 23: 40%\n bucket 23: 50%\n bucket 22: 80%\n bucket 23: 60%\n bucket 22: 90%\n bucket 23: 70%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n Entering block accumulator loop for bucket 25:\n bucket 24: 20%\n bucket 25: 10%\n bucket 24: 30%\n bucket 25: 20%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 25: 30%\n bucket 24: 70%\n bucket 24: 80%\n bucket 25: 40%\n bucket 24: 90%\n bucket 25: 50%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 30%\n bucket 26: 40%\n Entering block accumulator loop for bucket 27:\n bucket 26: 50%\n bucket 27: 10%\n bucket 26: 60%\n bucket 27: 20%\n bucket 26: 70%\n bucket 26: 80%\n bucket 27: 30%\n bucket 26: 90%\n bucket 27: 40%\n bucket 26: 100%\n bucket 27: 50%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Entering block accumulator loop for bucket 29:\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 30: 10%\n bucket 29: 30%\n bucket 30: 20%\n bucket 29: 40%\n bucket 30: 30%\n bucket 29: 50%\n bucket 30: 40%\n bucket 29: 60%\n bucket 30: 50%\n bucket 29: 70%\n bucket 30: 60%\n bucket 29: 80%\n bucket 30: 70%\n bucket 29: 90%\n bucket 30: 80%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 32:\n Entering block accumulator loop for bucket 31:\n bucket 32: 10%\n bucket 31: 10%\n bucket 32: 20%\n bucket 31: 20%\n bucket 32: 30%\n bucket 31: 30%\n bucket 32: 40%\n bucket 31: 40%\n bucket 32: 50%\n bucket 31: 50%\n bucket 32: 60%\n bucket 31: 60%\n bucket 32: 70%\n bucket 31: 70%\n bucket 32: 80%\n bucket 31: 80%\n bucket 32: 90%\n bucket 31: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n bucket 31: 100%\n (Using difference cover)\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\nGetting block 34 of 60\n bucket 33: 20%\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 30%\n bucket 33: 40%\n Entering block accumulator loop for bucket 34:\n bucket 33: 50%\n bucket 34: 10%\n bucket 33: 60%\n bucket 34: 20%\n bucket 33: 70%\n bucket 34: 30%\n bucket 33: 80%\n bucket 33: 90%\n bucket 34: 40%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 35\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 35:\n Entering block accumulator loop for bucket 36:\n bucket 35: 10%\n bucket 36: 10%\n bucket 36: 20%\n bucket 35: 20%\n bucket 36: 30%\n bucket 35: 30%\n bucket 36: 40%\n bucket 35: 40%\n bucket 36: 50%\n bucket 35: 50%\n bucket 36: 60%\n bucket 35: 60%\n bucket 36: 70%\n bucket 35: 70%\n bucket 36: 80%\n bucket 35: 80%\n bucket 36: 90%\n bucket 35: 90%\n bucket 36: 100%\n bucket 35: 100%\n Sorting block of length 120 for bucket 36\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 50%\n bucket 37: 60%\n Entering block accumulator loop for bucket 38:\n bucket 37: 70%\n bucket 37: 80%\n bucket 38: 10%\n bucket 37: 90%\n bucket 38: 20%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 40: 20%\n bucket 40: 30%\n bucket 39: 30%\n bucket 40: 40%\n bucket 39: 40%\n bucket 40: 50%\n bucket 39: 50%\n bucket 40: 60%\n bucket 39: 60%\n bucket 40: 70%\n bucket 39: 70%\n bucket 40: 80%\n bucket 39: 80%\n bucket 40: 90%\n bucket 39: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 60\n Entering block accumulator loop for bucket 41:\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 41: 10%\n bucket 41: 20%\n Entering block accumulator loop for bucket 42:\n bucket 41: 30%\n bucket 41: 40%\n bucket 42: 10%\n bucket 41: 50%\n bucket 41: 60%\n bucket 42: 20%\n bucket 41: 70%\n bucket 42: 30%\n bucket 41: 80%\n bucket 41: 90%\n bucket 42: 40%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n Entering block accumulator loop for bucket 44:\n bucket 43: 10%\n bucket 44: 10%\n bucket 43: 20%\n bucket 44: 20%\n bucket 43: 30%\n bucket 44: 30%\n bucket 43: 40%\n bucket 44: 40%\n bucket 43: 50%\n bucket 44: 50%\n bucket 43: 60%\n bucket 44: 60%\n bucket 43: 70%\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 70%\n bucket 43: 80%\n bucket 44: 80%\n bucket 43: 90%\n Entering block accumulator loop for bucket 45:\n bucket 44: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n bucket 46: 10%\n Calculating Z arrays for bucket 47\n bucket 46: 20%\n bucket 46: 30%\n Entering block accumulator loop for bucket 47:\n bucket 46: 40%\n bucket 46: 50%\n bucket 47: 10%\n bucket 46: 60%\n bucket 47: 20%\n bucket 46: 70%\n bucket 46: 80%\n bucket 47: 30%\n bucket 46: 90%\n bucket 46: 100%\n bucket 47: 40%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 48: 80%\n bucket 48: 90%\n Entering block accumulator loop for bucket 49:\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Sorting block time: 00:00:00\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nReturning block of 92 for bucket 51\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 52: 10%\n bucket 53: 10%\n bucket 52: 20%\n bucket 53: 20%\n bucket 52: 30%\n bucket 53: 30%\n bucket 53: 40%\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 53: 50%\n bucket 52: 80%\n bucket 53: 60%\n bucket 52: 90%\n bucket 53: 70%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\nGetting block 55 of 60\n bucket 54: 50%\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n Entering block accumulator loop for bucket 55:\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n Entering block accumulator loop for bucket 57:\n bucket 56: 20%\n bucket 57: 10%\n bucket 56: 30%\n bucket 57: 20%\n bucket 56: 40%\n bucket 57: 30%\n bucket 56: 50%\n bucket 57: 40%\n bucket 56: 60%\n bucket 57: 50%\n bucket 56: 70%\n bucket 57: 60%\n bucket 56: 80%\n bucket 57: 70%\n bucket 56: 90%\n bucket 57: 80%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n bucket 58: 20%\n Calculating Z arrays for bucket 59\n bucket 58: 30%\n Entering block accumulator loop for bucket 59:\n bucket 58: 40%\n bucket 58: 50%\n bucket 59: 10%\n bucket 58: 60%\n bucket 59: 20%\n bucket 58: 70%\n bucket 58: 80%\n bucket 59: 30%\n bucket 58: 90%\n bucket 59: 40%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\n Reserving size (126) for bucket 1\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 2\n Calculating Z arrays for bucket 1\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Entering block accumulator loop for bucket 2:\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n bucket 1: 10%\n bucket 2: 10%\n Entering block accumulator loop for bucket 3:\n Reserving size (126) for bucket 4\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 2: 20%\n bucket 3: 10%\n bucket 2: 30%\n bucket 1: 20%\n Calculating Z arrays for bucket 4\n bucket 2: 40%\n bucket 3: 20%\n bucket 1: 30%\n bucket 2: 50%\n bucket 3: 30%\n Calculating Z arrays for bucket 5\n bucket 2: 60%\n Entering block accumulator loop for bucket 4:\n bucket 3: 40%\n bucket 1: 40%\n bucket 2: 70%\n bucket 4: 10%\n Entering block accumulator loop for bucket 5:\n bucket 2: 80%\n bucket 1: 50%\n bucket 3: 50%\nGetting block 6 of 60\n bucket 4: 20%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 4: 30%\n bucket 5: 10%\n bucket 4: 40%\nGetting block 8 of 60\n bucket 4: 50%\n Reserving size (126) for bucket 8\n bucket 1: 60%\n Calculating Z arrays for bucket 7\n bucket 4: 60%\n bucket 3: 60%\n bucket 2: 90%\n bucket 1: 70%\n bucket 4: 70%\n bucket 5: 20%\n bucket 2: 100%\n Calculating Z arrays for bucket 8\n Sorting block of length 84 for bucket 2\n bucket 5: 30%\n (Using difference cover)\n bucket 3: 70%\n bucket 4: 80%\n Reserving size (126) for bucket 6\n bucket 5: 40%\n Entering block accumulator loop for bucket 7:\n bucket 4: 90%\n bucket 1: 80%\n bucket 5: 50%\n Calculating Z arrays for bucket 6\n bucket 4: 100%\n bucket 3: 80%\n bucket 1: 90%\n Entering block accumulator loop for bucket 8:\n bucket 5: 60%\n bucket 7: 10%\n bucket 1: 100%\n bucket 5: 70%\n bucket 3: 90%\n bucket 8: 10%\n bucket 3: 100%\n Sorting block of length 42 for bucket 1\n bucket 5: 80%\n (Using difference cover)\n bucket 7: 20%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 8: 20%\n bucket 5: 90%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n Entering block accumulator loop for bucket 6:\n bucket 7: 30%\n bucket 5: 100%\n bucket 8: 30%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 7: 40%\n bucket 8: 40%\n bucket 7: 50%\n bucket 6: 10%\n bucket 8: 50%\n bucket 7: 60%\n bucket 6: 20%\n bucket 8: 60%\n bucket 7: 70%\n bucket 6: 30%\n bucket 8: 70%\n bucket 7: 80%\n bucket 6: 40%\n bucket 8: 80%\n bucket 7: 90%\n bucket 6: 50%\n bucket 7: 100%\n bucket 6: 60%\n bucket 8: 90%\n Sorting block of length 75 for bucket 7\n bucket 6: 70%\n bucket 8: 100%\n (Using difference cover)\n bucket 6: 80%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n bucket 6: 90%\n bucket 6: 100%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Calculating Z arrays for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Entering block accumulator loop for bucket 9:\n Entering block accumulator loop for bucket 10:\n Calculating Z arrays for bucket 11\n bucket 9: 10%\n bucket 10: 10%\n Entering block accumulator loop for bucket 11:\n bucket 9: 20%\n bucket 10: 20%\n bucket 9: 30%\n bucket 11: 10%\n bucket 9: 40%\n bucket 10: 30%\n bucket 11: 20%\n bucket 9: 50%\n bucket 10: 40%\n bucket 9: 60%\n bucket 11: 30%\n bucket 10: 50%\n bucket 9: 70%\n bucket 11: 40%\n bucket 10: 60%\n bucket 9: 80%\n bucket 11: 50%\n bucket 9: 90%\n bucket 10: 70%\n bucket 9: 100%\n bucket 11: 60%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 80%\n bucket 11: 70%\n bucket 10: 90%\n bucket 11: 80%\n bucket 10: 100%\n bucket 11: 90%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 12:\n bucket 12: 10%\n bucket 12: 20%\n bucket 12: 30%\n bucket 12: 40%\n bucket 12: 50%\n bucket 12: 60%\n bucket 12: 70%\n bucket 12: 80%\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n bucket 12: 90%\n Calculating Z arrays for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Entering block accumulator loop for bucket 13:\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 13: 10%\n bucket 13: 20%\n Entering block accumulator loop for bucket 14:\n Entering block accumulator loop for bucket 15:\n bucket 13: 30%\n bucket 14: 10%\n bucket 15: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 15: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 15: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 15: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 15: 50%\n bucket 14: 60%\n bucket 13: 90%\n bucket 15: 60%\n bucket 13: 100%\n bucket 14: 70%\n Sorting block of length 85 for bucket 13\n Sorting block time: 00:00:00\n (Using difference cover)\n bucket 15: 70%\n bucket 14: 80%\nReturning block of 83 for bucket 12\n bucket 15: 80%\n bucket 14: 90%\n bucket 15: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n Entering block accumulator loop for bucket 16:\n bucket 16: 10%\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\n bucket 18: 50%\n bucket 18: 60%\n Entering block accumulator loop for bucket 19:\n bucket 18: 70%\n bucket 19: 10%\n bucket 18: 80%\n bucket 19: 20%\n bucket 18: 90%\n bucket 19: 30%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Entering block accumulator loop for bucket 20:\n bucket 20: 10%\n bucket 20: 20%\n bucket 20: 30%\n bucket 20: 40%\n bucket 20: 50%\n bucket 20: 60%\n bucket 20: 70%\n bucket 20: 80%\n bucket 20: 90%\nGetting block 21 of 60\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Entering block accumulator loop for bucket 21:\n bucket 21: 10%\n bucket 21: 20%\n bucket 21: 30%\n bucket 21: 40%\n bucket 21: 50%\n bucket 21: 60%\n bucket 21: 70%\n bucket 21: 80%\n bucket 21: 90%\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n bucket 22: 20%\n Entering block accumulator loop for bucket 23:\n bucket 22: 30%\n bucket 22: 40%\n bucket 23: 10%\n bucket 22: 50%\n bucket 23: 20%\n bucket 22: 60%\n bucket 23: 30%\n bucket 22: 70%\n bucket 23: 40%\n bucket 23: 50%\n bucket 22: 80%\n bucket 23: 60%\n bucket 22: 90%\n bucket 23: 70%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n Entering block accumulator loop for bucket 25:\n bucket 24: 20%\n bucket 25: 10%\n bucket 24: 30%\n bucket 25: 20%\n bucket 24: 40%\n bucket 24: 50%\n bucket 24: 60%\n bucket 25: 30%\n bucket 24: 70%\n bucket 24: 80%\n bucket 25: 40%\n bucket 24: 90%\n bucket 25: 50%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n Entering block accumulator loop for bucket 26:\n bucket 26: 10%\n bucket 26: 20%\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n bucket 26: 30%\n bucket 26: 40%\n Entering block accumulator loop for bucket 27:\n bucket 26: 50%\n bucket 27: 10%\n bucket 26: 60%\n bucket 27: 20%\n bucket 26: 70%\n bucket 26: 80%\n bucket 27: 30%\n bucket 26: 90%\n bucket 27: 40%\n bucket 26: 100%\n bucket 27: 50%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 60%\n bucket 27: 70%\n bucket 27: 80%\n bucket 27: 90%\n bucket 27: 100%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Entering block accumulator loop for bucket 28:\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n bucket 28: 80%\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Entering block accumulator loop for bucket 29:\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 30: 10%\n bucket 29: 30%\n bucket 30: 20%\n bucket 29: 40%\n bucket 30: 30%\n bucket 29: 50%\n bucket 30: 40%\n bucket 29: 60%\n bucket 30: 50%\n bucket 29: 70%\n bucket 30: 60%\n bucket 29: 80%\n bucket 30: 70%\n bucket 29: 90%\n bucket 30: 80%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 30: 90%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\nGetting block 31 of 60\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 32:\n Entering block accumulator loop for bucket 31:\n bucket 32: 10%\n bucket 31: 10%\n bucket 32: 20%\n bucket 31: 20%\n bucket 32: 30%\n bucket 31: 30%\n bucket 32: 40%\n bucket 31: 40%\n bucket 32: 50%\n bucket 31: 50%\n bucket 32: 60%\n bucket 31: 60%\n bucket 32: 70%\n bucket 31: 70%\n bucket 32: 80%\n bucket 31: 80%\n bucket 32: 90%\n bucket 31: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n bucket 31: 100%\n (Using difference cover)\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\nGetting block 34 of 60\n bucket 33: 20%\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 30%\n bucket 33: 40%\n Entering block accumulator loop for bucket 34:\n bucket 33: 50%\n bucket 34: 10%\n bucket 33: 60%\n bucket 34: 20%\n bucket 33: 70%\n bucket 34: 30%\n bucket 33: 80%\n bucket 33: 90%\n bucket 34: 40%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 50%\n bucket 34: 60%\n bucket 34: 70%\n bucket 34: 80%\n bucket 34: 90%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\nGetting block 35 of 60\n Reserving size (126) for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 35\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 35:\n Entering block accumulator loop for bucket 36:\n bucket 35: 10%\n bucket 36: 10%\n bucket 36: 20%\n bucket 35: 20%\n bucket 36: 30%\n bucket 35: 30%\n bucket 36: 40%\n bucket 35: 40%\n bucket 36: 50%\n bucket 35: 50%\n bucket 36: 60%\n bucket 35: 60%\n bucket 36: 70%\n bucket 35: 70%\n bucket 36: 80%\n bucket 35: 80%\n bucket 36: 90%\n bucket 35: 90%\n bucket 36: 100%\n bucket 35: 100%\n Sorting block of length 120 for bucket 36\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\nGetting block 38 of 60\n Reserving size (126) for bucket 38\n Calculating Z arrays for bucket 38\n bucket 37: 50%\n bucket 37: 60%\n Entering block accumulator loop for bucket 38:\n bucket 37: 70%\n bucket 37: 80%\n bucket 38: 10%\n bucket 37: 90%\n bucket 38: 20%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 30%\n bucket 38: 40%\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 40: 20%\n bucket 40: 30%\n bucket 39: 30%\n bucket 40: 40%\n bucket 39: 40%\n bucket 40: 50%\n bucket 39: 50%\n bucket 40: 60%\n bucket 39: 60%\n bucket 40: 70%\n bucket 39: 70%\n bucket 40: 80%\n bucket 39: 80%\n bucket 40: 90%\n bucket 39: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\nGetting block 42 of 60\n Entering block accumulator loop for bucket 41:\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\n bucket 41: 10%\n bucket 41: 20%\n Entering block accumulator loop for bucket 42:\n bucket 41: 30%\n bucket 41: 40%\n bucket 42: 10%\n bucket 41: 50%\n bucket 41: 60%\n bucket 42: 20%\n bucket 41: 70%\n bucket 42: 30%\n bucket 41: 80%\n bucket 41: 90%\n bucket 42: 40%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n bucket 42: 50%\n bucket 42: 60%\n bucket 42: 70%\n bucket 42: 80%\n bucket 42: 90%\n bucket 42: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 43:\n Entering block accumulator loop for bucket 44:\n bucket 43: 10%\n bucket 44: 10%\n bucket 43: 20%\n bucket 44: 20%\n bucket 43: 30%\n bucket 44: 30%\n bucket 43: 40%\n bucket 44: 40%\n bucket 43: 50%\n bucket 44: 50%\n bucket 43: 60%\n bucket 44: 60%\n bucket 43: 70%\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 70%\n bucket 43: 80%\n bucket 44: 80%\n bucket 43: 90%\n Entering block accumulator loop for bucket 45:\n bucket 44: 90%\n bucket 43: 100%\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 10%\n bucket 45: 20%\n bucket 45: 30%\n bucket 45: 40%\n bucket 45: 50%\n bucket 45: 60%\n bucket 45: 70%\n bucket 45: 80%\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n bucket 46: 10%\n Calculating Z arrays for bucket 47\n bucket 46: 20%\n bucket 46: 30%\n Entering block accumulator loop for bucket 47:\n bucket 46: 40%\n bucket 46: 50%\n bucket 47: 10%\n bucket 46: 60%\n bucket 47: 20%\n bucket 46: 70%\n bucket 46: 80%\n bucket 47: 30%\n bucket 46: 90%\n bucket 46: 100%\n bucket 47: 40%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 70 for bucket 46\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\n bucket 48: 50%\n bucket 48: 60%\n bucket 48: 70%\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 48: 80%\n bucket 48: 90%\n Entering block accumulator loop for bucket 49:\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Sorting block time: 00:00:00\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\nReturning block of 92 for bucket 51\n Entering block accumulator loop for bucket 52:\n Entering block accumulator loop for bucket 53:\n bucket 52: 10%\n bucket 53: 10%\n bucket 52: 20%\n bucket 53: 20%\n bucket 52: 30%\n bucket 53: 30%\n bucket 53: 40%\n bucket 52: 40%\n bucket 52: 50%\n bucket 52: 60%\n bucket 52: 70%\n bucket 53: 50%\n bucket 52: 80%\n bucket 53: 60%\n bucket 52: 90%\n bucket 53: 70%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 53: 80%\n bucket 53: 90%\n bucket 53: 100%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n Entering block accumulator loop for bucket 54:\n bucket 54: 10%\n bucket 54: 20%\n bucket 54: 30%\n bucket 54: 40%\nGetting block 55 of 60\n bucket 54: 50%\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n Entering block accumulator loop for bucket 55:\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n bucket 55: 60%\n bucket 55: 70%\n bucket 55: 80%\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n Entering block accumulator loop for bucket 57:\n bucket 56: 20%\n bucket 57: 10%\n bucket 56: 30%\n bucket 57: 20%\n bucket 56: 40%\n bucket 57: 30%\n bucket 56: 50%\n bucket 57: 40%\n bucket 56: 60%\n bucket 57: 50%\n bucket 56: 70%\n bucket 57: 60%\n bucket 56: 80%\n bucket 57: 70%\n bucket 56: 90%\n bucket 57: 80%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 57: 90%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n Entering block accumulator loop for bucket 58:\n bucket 58: 10%\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n bucket 58: 20%\n Calculating Z arrays for bucket 59\n bucket 58: 30%\n Entering block accumulator loop for bucket 59:\n bucket 58: 40%\n bucket 58: 50%\n bucket 59: 10%\n bucket 58: 60%\n bucket 59: 20%\n bucket 58: 70%\n bucket 58: 80%\n bucket 59: 30%\n bucket 58: 90%\n bucket 59: 40%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 50%\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n500 reads; of these:\n 500 (100.00%) were paired; of these:\n 71 (14.20%) aligned concordantly 0 times\n 429 (85.80%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n85.80% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 07:03:21", "plugin": "core", "name": "end_epoch", "raw_value": "1725001401.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:03:21", "plugin": "core", "name": "start_epoch", "raw_value": "1725001401.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-9", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 9, "time_seconds": 38.62207221984863, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "289fd1d4cda0dfe4"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "428d6406e93d9d09"}, "library|input_2": {"src": "hda", "id": "48126e373a98ad3c"}, "library|rna_strandness": "FR", "library|type": "paired"}, "job": {"model_class": "Job", "id": "ffde76bc567fd181", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:55:12.397460", "update_time": "2024-08-30T06:55:25.535243", "galaxy_version": "24.1", "external_id": "gxy-sfdnk", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/c/8/8/dataset_c88c98a6-fc9b-4718-9a61-15d7ee18a442.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/8/e/8/dataset_8e8b418c-8db6-457a-9464-dba31242d272.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/b/6/0/dataset_b6041d3e-f0a6-43d4-87fe-bb5fd44bdba4.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' --rna-strandness FR | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/3/9/2/dataset_39270284-2ca4-4b94-ad48-9460c5437138.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 151, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 152, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"FR\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 150, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "289fd1d4cda0dfe4", "src": "hda", "uuid": "c88c98a6-fc9b-4718-9a61-15d7ee18a442"}, "library|input_1": {"id": "428d6406e93d9d09", "src": "hda", "uuid": "8e8b418c-8db6-457a-9464-dba31242d272"}, "library|input_2": {"id": "48126e373a98ad3c", "src": "hda", "uuid": "b6041d3e-f0a6-43d4-87fe-bb5fd44bdba4"}}, "outputs": {"output_alignments": {"id": "036aaf3293d35c28", "src": "hda", "uuid": "39270284-2ca4-4b94-ad48-9460c5437138"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 2 of 60\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\nGetting block 4 of 60\n Entering block accumulator loop for bucket 1:\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 3\n bucket 1: 10%\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 4\nGetting block 7 of 60\n bucket 1: 20%\nGetting block 6 of 60\n Reserving size (126) for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 8\n bucket 2: 10%\n Entering block accumulator loop for bucket 7:\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 7: 10%\n bucket 1: 30%\n Calculating Z arrays for bucket 6\n bucket 7: 20%\n Entering block accumulator loop for bucket 8:\n bucket 3: 10%\n bucket 7: 30%\n bucket 5: 10%\n bucket 2: 20%\n bucket 7: 40%\n bucket 4: 10%\n bucket 2: 30%\n bucket 3: 20%\n bucket 5: 20%\n bucket 4: 20%\n bucket 3: 30%\n bucket 7: 50%\n Entering block accumulator loop for bucket 6:\n bucket 1: 40%\n bucket 2: 40%\n bucket 3: 40%\n bucket 7: 60%\n bucket 5: 30%\n bucket 2: 50%\n bucket 3: 50%\n bucket 7: 70%\n bucket 2: 60%\n bucket 1: 50%\n bucket 2: 70%\n bucket 6: 10%\n bucket 3: 60%\n bucket 7: 80%\n bucket 2: 80%\n bucket 6: 20%\n bucket 1: 60%\n bucket 5: 40%\n bucket 7: 90%\n bucket 6: 30%\n bucket 8: 10%\n bucket 7: 100%\n bucket 3: 70%\n bucket 8: 20%\n bucket 5: 50%\n bucket 4: 30%\n bucket 6: 40%\n bucket 3: 80%\n bucket 5: 60%\n bucket 2: 90%\n bucket 3: 90%\n bucket 6: 50%\n bucket 5: 70%\n bucket 8: 30%\n bucket 2: 100%\n bucket 3: 100%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 4: 40%\n bucket 5: 80%\n bucket 8: 40%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 90%\n bucket 8: 50%\n bucket 6: 60%\n Sorting block of length 106 for bucket 3\n bucket 5: 100%\n bucket 6: 70%\n bucket 1: 70%\n bucket 4: 50%\n bucket 1: 80%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 80%\n (Using difference cover)\n bucket 8: 60%\n bucket 1: 90%\n bucket 4: 60%\n bucket 8: 70%\n bucket 1: 100%\n bucket 6: 90%\n bucket 4: 70%\n bucket 8: 80%\n bucket 6: 100%\n bucket 4: 80%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 90%\n bucket 4: 90%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 11:\n bucket 12: 10%\n bucket 12: 20%\n bucket 11: 10%\n bucket 12: 30%\n bucket 11: 20%\n bucket 12: 40%\n bucket 11: 30%\n bucket 12: 50%\n bucket 11: 40%\n bucket 12: 60%\n bucket 11: 50%\n bucket 12: 70%\n bucket 11: 60%\n bucket 12: 80%\n bucket 12: 90%\n bucket 11: 70%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n bucket 13: 50%\n bucket 13: 60%\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 40%\n bucket 14: 50%\n Entering block accumulator loop for bucket 15:\n bucket 14: 60%\n bucket 15: 10%\n bucket 14: 70%\n bucket 15: 20%\n bucket 14: 80%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n bucket 14: 90%\n Calculating Z arrays for bucket 16\n bucket 15: 30%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 40%\n Entering block accumulator loop for bucket 16:\n bucket 15: 50%\n bucket 16: 10%\n bucket 15: 60%\n bucket 16: 20%\n bucket 15: 70%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 30%\n bucket 15: 80%\n bucket 16: 40%\n bucket 15: 90%\n bucket 16: 50%\n Entering block accumulator loop for bucket 17:\n bucket 15: 100%\n Sorting block time: 00:00:00\n bucket 16: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 17: 10%\n bucket 16: 70%\n bucket 17: 20%\n bucket 16: 80%\n bucket 17: 30%\n bucket 16: 90%\nReturning block of 83 for bucket 14\n bucket 16: 100%\n bucket 17: 40%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n bucket 18: 60%\n Calculating Z arrays for bucket 19\n bucket 18: 70%\n bucket 18: 80%\n Entering block accumulator loop for bucket 19:\n bucket 18: 90%\n bucket 19: 10%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Entering block accumulator loop for bucket 20:\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 10%\n Entering block accumulator loop for bucket 21:\n bucket 20: 20%\n bucket 21: 10%\n bucket 20: 30%\n bucket 21: 20%\n bucket 20: 40%\n bucket 21: 30%\n bucket 20: 50%\n bucket 21: 40%\n bucket 20: 60%\n bucket 21: 50%\n bucket 20: 70%\n bucket 21: 60%\n bucket 20: 80%\n bucket 21: 70%\n bucket 20: 90%\n bucket 21: 80%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 22: 50%\n bucket 22: 60%\n bucket 23: 40%\n bucket 22: 70%\n bucket 22: 80%\n bucket 23: 50%\n bucket 22: 90%\n bucket 23: 60%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 40%\n bucket 24: 50%\n Entering block accumulator loop for bucket 25:\n bucket 24: 60%\n bucket 24: 70%\n bucket 25: 10%\n bucket 24: 80%\n bucket 25: 20%\n bucket 24: 90%\n bucket 25: 30%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 27: 20%\n bucket 26: 40%\n bucket 27: 30%\n bucket 26: 50%\n bucket 27: 40%\n bucket 26: 60%\n bucket 27: 50%\n bucket 26: 70%\n bucket 27: 60%\n bucket 26: 80%\n bucket 27: 70%\n bucket 26: 90%\n bucket 27: 80%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 10%\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 28: 20%\n bucket 29: 20%\n bucket 28: 30%\n bucket 29: 30%\n bucket 28: 40%\n bucket 29: 40%\n bucket 29: 50%\n bucket 28: 50%\n bucket 29: 60%\n bucket 28: 60%\n bucket 29: 70%\n bucket 28: 70%\n bucket 29: 80%\n bucket 28: 80%\n bucket 29: 90%\n bucket 28: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Reserving size (126) for bucket 30\nGetting block 32 of 60\n Calculating Z arrays for bucket 30\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 32:\n bucket 30: 10%\n bucket 31: 10%\n bucket 30: 20%\n bucket 32: 10%\n bucket 31: 20%\n bucket 30: 30%\n bucket 32: 20%\n bucket 31: 30%\n bucket 30: 40%\n bucket 32: 30%\n bucket 31: 40%\n bucket 30: 50%\n bucket 31: 50%\n bucket 32: 40%\n bucket 30: 60%\n bucket 32: 50%\n bucket 31: 60%\n bucket 30: 70%\n bucket 32: 60%\n bucket 31: 70%\n bucket 30: 80%\n bucket 31: 80%\n bucket 32: 70%\n bucket 30: 90%\n bucket 31: 90%\n bucket 30: 100%\n bucket 32: 80%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 20%\n bucket 34: 30%\n Entering block accumulator loop for bucket 35:\n bucket 34: 40%\n bucket 35: 10%\n bucket 34: 50%\n bucket 35: 20%\n bucket 34: 60%\n bucket 35: 30%\n bucket 34: 70%\n bucket 35: 40%\n bucket 34: 80%\n bucket 35: 50%\n bucket 34: 90%\n bucket 35: 60%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 38:\n bucket 39: 10%\n bucket 38: 10%\n bucket 39: 20%\n bucket 38: 20%\n bucket 39: 30%\n bucket 38: 30%\n bucket 39: 40%\n bucket 38: 40%\n bucket 39: 50%\n bucket 38: 50%\n bucket 39: 60%\n bucket 38: 60%\n bucket 39: 70%\n bucket 38: 70%\n bucket 39: 80%\n bucket 38: 80%\n bucket 39: 90%\n bucket 38: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 43:\n bucket 42: 10%\n bucket 43: 10%\n bucket 42: 20%\n bucket 43: 20%\n bucket 42: 30%\n bucket 43: 30%\n bucket 42: 40%\n bucket 43: 40%\n bucket 42: 50%\n bucket 43: 50%\n bucket 42: 60%\n bucket 43: 60%\n bucket 42: 70%\n bucket 43: 70%\n bucket 42: 80%\n bucket 43: 80%\n bucket 42: 90%\n bucket 43: 90%\n bucket 42: 100%\n bucket 43: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n bucket 44: 10%\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n bucket 44: 20%\n Entering block accumulator loop for bucket 45:\n Calculating Z arrays for bucket 46\n bucket 44: 30%\n bucket 44: 40%\n Entering block accumulator loop for bucket 46:\n bucket 45: 10%\n bucket 44: 50%\n bucket 46: 10%\n bucket 45: 20%\n bucket 44: 60%\n bucket 45: 30%\n bucket 44: 70%\n bucket 45: 40%\n bucket 44: 80%\n bucket 45: 50%\n bucket 46: 20%\n bucket 44: 90%\n bucket 45: 60%\n bucket 46: 30%\n bucket 44: 100%\n bucket 45: 70%\n Sorting block of length 66 for bucket 44\n bucket 46: 40%\n bucket 45: 80%\n bucket 46: 50%\n bucket 45: 90%\n (Using difference cover)\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\nGetting block 49 of 60\n bucket 48: 50%\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 48: 60%\n bucket 48: 70%\n Entering block accumulator loop for bucket 49:\n bucket 48: 80%\n bucket 49: 10%\n bucket 48: 90%\n bucket 49: 20%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 30%\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 50: 40%\n bucket 51: 10%\n Entering block accumulator loop for bucket 52:\n bucket 50: 50%\n bucket 51: 20%\n bucket 52: 10%\n bucket 50: 60%\n bucket 51: 30%\n bucket 52: 20%\n bucket 50: 70%\n bucket 51: 40%\n bucket 52: 30%\n bucket 50: 80%\n bucket 52: 40%\n bucket 50: 90%\n bucket 51: 50%\n bucket 52: 50%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 60%\n bucket 52: 60%\n bucket 51: 70%\n bucket 52: 70%\n bucket 51: 80%\n bucket 52: 80%\n bucket 51: 90%\n bucket 52: 90%\n bucket 52: 100%\n bucket 51: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 54:\n bucket 53: 10%\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Entering block accumulator loop for bucket 55:\n bucket 53: 20%\n bucket 54: 10%\n Calculating Z arrays for bucket 56\n bucket 53: 30%\n bucket 54: 20%\n bucket 55: 10%\n bucket 53: 40%\n bucket 54: 30%\n Entering block accumulator loop for bucket 56:\n bucket 53: 50%\n bucket 55: 20%\n bucket 54: 40%\n bucket 53: 60%\n bucket 54: 50%\n bucket 53: 70%\n bucket 56: 10%\n bucket 55: 30%\n bucket 54: 60%\n bucket 53: 80%\n bucket 56: 20%\n bucket 54: 70%\n bucket 53: 90%\n bucket 55: 40%\n bucket 56: 30%\n bucket 53: 100%\n bucket 54: 80%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 56: 40%\n bucket 54: 90%\n bucket 56: 50%\n bucket 55: 50%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 56: 60%\n bucket 55: 60%\n bucket 56: 70%\n bucket 55: 70%\n bucket 56: 80%\n bucket 55: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n bucket 57: 20%\n Calculating Z arrays for bucket 58\n bucket 57: 30%\n bucket 57: 40%\n Entering block accumulator loop for bucket 58:\n bucket 57: 50%\n bucket 58: 10%\n bucket 57: 60%\n bucket 58: 20%\n bucket 57: 70%\n bucket 58: 30%\n bucket 57: 80%\n bucket 58: 40%\n bucket 57: 90%\n bucket 58: 50%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 59: 20%\n bucket 60: 10%\n bucket 59: 30%\n bucket 60: 20%\n bucket 60: 30%\n bucket 59: 40%\n bucket 60: 40%\n bucket 59: 50%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 60: 70%\n bucket 59: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n bucket 59: 90%\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 2 of 60\nGetting block 1 of 60\n Reserving size (126) for bucket 1\n Reserving size (126) for bucket 2\n Calculating Z arrays for bucket 1\n Calculating Z arrays for bucket 2\nGetting block 3 of 60\n Reserving size (126) for bucket 3\nGetting block 4 of 60\n Entering block accumulator loop for bucket 1:\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n Calculating Z arrays for bucket 3\n bucket 1: 10%\n Entering block accumulator loop for bucket 2:\n Reserving size (126) for bucket 4\n Calculating Z arrays for bucket 5\n Entering block accumulator loop for bucket 3:\n Calculating Z arrays for bucket 4\nGetting block 7 of 60\n bucket 1: 20%\nGetting block 6 of 60\n Reserving size (126) for bucket 7\nGetting block 8 of 60\n Reserving size (126) for bucket 8\n Calculating Z arrays for bucket 7\n Entering block accumulator loop for bucket 4:\n Calculating Z arrays for bucket 8\n bucket 2: 10%\n Entering block accumulator loop for bucket 7:\n Reserving size (126) for bucket 6\n Entering block accumulator loop for bucket 5:\n bucket 7: 10%\n bucket 1: 30%\n Calculating Z arrays for bucket 6\n bucket 7: 20%\n Entering block accumulator loop for bucket 8:\n bucket 3: 10%\n bucket 7: 30%\n bucket 5: 10%\n bucket 2: 20%\n bucket 7: 40%\n bucket 4: 10%\n bucket 2: 30%\n bucket 3: 20%\n bucket 5: 20%\n bucket 4: 20%\n bucket 3: 30%\n bucket 7: 50%\n Entering block accumulator loop for bucket 6:\n bucket 1: 40%\n bucket 2: 40%\n bucket 3: 40%\n bucket 7: 60%\n bucket 5: 30%\n bucket 2: 50%\n bucket 3: 50%\n bucket 7: 70%\n bucket 2: 60%\n bucket 1: 50%\n bucket 2: 70%\n bucket 6: 10%\n bucket 3: 60%\n bucket 7: 80%\n bucket 2: 80%\n bucket 6: 20%\n bucket 1: 60%\n bucket 5: 40%\n bucket 7: 90%\n bucket 6: 30%\n bucket 8: 10%\n bucket 7: 100%\n bucket 3: 70%\n bucket 8: 20%\n bucket 5: 50%\n bucket 4: 30%\n bucket 6: 40%\n bucket 3: 80%\n bucket 5: 60%\n bucket 2: 90%\n bucket 3: 90%\n bucket 6: 50%\n bucket 5: 70%\n bucket 8: 30%\n bucket 2: 100%\n bucket 3: 100%\n Sorting block of length 84 for bucket 2\n (Using difference cover)\n bucket 4: 40%\n bucket 5: 80%\n bucket 8: 40%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 5: 90%\n bucket 8: 50%\n bucket 6: 60%\n Sorting block of length 106 for bucket 3\n bucket 5: 100%\n bucket 6: 70%\n bucket 1: 70%\n bucket 4: 50%\n bucket 1: 80%\n Sorting block of length 63 for bucket 5\n (Using difference cover)\n bucket 6: 80%\n (Using difference cover)\n bucket 8: 60%\n bucket 1: 90%\n bucket 4: 60%\n bucket 8: 70%\n bucket 1: 100%\n bucket 6: 90%\n bucket 4: 70%\n bucket 8: 80%\n bucket 6: 100%\n bucket 4: 80%\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 90%\n bucket 4: 90%\n Sorting block of length 42 for bucket 1\n (Using difference cover)\n bucket 4: 100%\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n bucket 9: 20%\n bucket 9: 30%\n bucket 9: 40%\n bucket 9: 50%\n bucket 9: 60%\n bucket 9: 70%\n bucket 9: 80%\n bucket 9: 90%\n bucket 9: 100%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 10:\n bucket 10: 10%\n bucket 10: 20%\n bucket 10: 30%\n bucket 10: 40%\n bucket 10: 50%\n bucket 10: 60%\n bucket 10: 70%\n bucket 10: 80%\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\nGetting block 11 of 60\n Reserving size (126) for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Calculating Z arrays for bucket 11\n Entering block accumulator loop for bucket 12:\n Entering block accumulator loop for bucket 11:\n bucket 12: 10%\n bucket 12: 20%\n bucket 11: 10%\n bucket 12: 30%\n bucket 11: 20%\n bucket 12: 40%\n bucket 11: 30%\n bucket 12: 50%\n bucket 11: 40%\n bucket 12: 60%\n bucket 11: 50%\n bucket 12: 70%\n bucket 11: 60%\n bucket 12: 80%\n bucket 12: 90%\n bucket 11: 70%\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n bucket 11: 80%\n bucket 11: 90%\n bucket 11: 100%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\n bucket 13: 20%\n bucket 13: 30%\n bucket 13: 40%\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n bucket 13: 50%\n bucket 13: 60%\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\n bucket 13: 70%\n bucket 13: 80%\n bucket 13: 90%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\nGetting block 14 of 60\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 14: 10%\n bucket 14: 20%\n bucket 14: 30%\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n bucket 14: 40%\n bucket 14: 50%\n Entering block accumulator loop for bucket 15:\n bucket 14: 60%\n bucket 15: 10%\n bucket 14: 70%\n bucket 15: 20%\n bucket 14: 80%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n bucket 14: 90%\n Calculating Z arrays for bucket 16\n bucket 15: 30%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n bucket 15: 40%\n Entering block accumulator loop for bucket 16:\n bucket 15: 50%\n bucket 16: 10%\n bucket 15: 60%\n bucket 16: 20%\n bucket 15: 70%\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n bucket 16: 30%\n bucket 15: 80%\n bucket 16: 40%\n bucket 15: 90%\n bucket 16: 50%\n Entering block accumulator loop for bucket 17:\n bucket 15: 100%\n Sorting block time: 00:00:00\n bucket 16: 60%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 17: 10%\n bucket 16: 70%\n bucket 17: 20%\n bucket 16: 80%\n bucket 17: 30%\n bucket 16: 90%\nReturning block of 83 for bucket 14\n bucket 16: 100%\n bucket 17: 40%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n bucket 18: 60%\n Calculating Z arrays for bucket 19\n bucket 18: 70%\n bucket 18: 80%\n Entering block accumulator loop for bucket 19:\n bucket 18: 90%\n bucket 19: 10%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n bucket 19: 20%\n bucket 19: 30%\n bucket 19: 40%\n bucket 19: 50%\n bucket 19: 60%\n bucket 19: 70%\n bucket 19: 80%\n bucket 19: 90%\n bucket 19: 100%\n Sorting block of length 107 for bucket 19\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 20 of 60\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\nGetting block 21 of 60\n Entering block accumulator loop for bucket 20:\n Reserving size (126) for bucket 21\n Calculating Z arrays for bucket 21\n bucket 20: 10%\n Entering block accumulator loop for bucket 21:\n bucket 20: 20%\n bucket 21: 10%\n bucket 20: 30%\n bucket 21: 20%\n bucket 20: 40%\n bucket 21: 30%\n bucket 20: 50%\n bucket 21: 40%\n bucket 20: 60%\n bucket 21: 50%\n bucket 20: 70%\n bucket 21: 60%\n bucket 20: 80%\n bucket 21: 70%\n bucket 20: 90%\n bucket 21: 80%\n bucket 20: 100%\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n bucket 21: 90%\n bucket 21: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 23: 10%\n bucket 22: 30%\n bucket 23: 20%\n bucket 22: 40%\n bucket 23: 30%\n bucket 22: 50%\n bucket 22: 60%\n bucket 23: 40%\n bucket 22: 70%\n bucket 22: 80%\n bucket 23: 50%\n bucket 22: 90%\n bucket 23: 60%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\n bucket 24: 30%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 40%\n bucket 24: 50%\n Entering block accumulator loop for bucket 25:\n bucket 24: 60%\n bucket 24: 70%\n bucket 25: 10%\n bucket 24: 80%\n bucket 25: 20%\n bucket 24: 90%\n bucket 25: 30%\n bucket 24: 100%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 40%\n bucket 25: 50%\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n bucket 25: 90%\n bucket 25: 100%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\nGetting block 26 of 60\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 26:\n Entering block accumulator loop for bucket 27:\n bucket 26: 10%\n bucket 27: 10%\n bucket 26: 20%\n bucket 26: 30%\n bucket 27: 20%\n bucket 26: 40%\n bucket 27: 30%\n bucket 26: 50%\n bucket 27: 40%\n bucket 26: 60%\n bucket 27: 50%\n bucket 26: 70%\n bucket 27: 60%\n bucket 26: 80%\n bucket 27: 70%\n bucket 26: 90%\n bucket 27: 80%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n bucket 27: 90%\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n Entering block accumulator loop for bucket 28:\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\n bucket 28: 10%\n Entering block accumulator loop for bucket 29:\n bucket 29: 10%\n bucket 28: 20%\n bucket 29: 20%\n bucket 28: 30%\n bucket 29: 30%\n bucket 28: 40%\n bucket 29: 40%\n bucket 29: 50%\n bucket 28: 50%\n bucket 29: 60%\n bucket 28: 60%\n bucket 29: 70%\n bucket 28: 70%\n bucket 29: 80%\n bucket 28: 80%\n bucket 29: 90%\n bucket 28: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 30 of 60\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Reserving size (126) for bucket 30\nGetting block 32 of 60\n Calculating Z arrays for bucket 30\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n Entering block accumulator loop for bucket 31:\n Entering block accumulator loop for bucket 30:\n Entering block accumulator loop for bucket 32:\n bucket 30: 10%\n bucket 31: 10%\n bucket 30: 20%\n bucket 32: 10%\n bucket 31: 20%\n bucket 30: 30%\n bucket 32: 20%\n bucket 31: 30%\n bucket 30: 40%\n bucket 32: 30%\n bucket 31: 40%\n bucket 30: 50%\n bucket 31: 50%\n bucket 32: 40%\n bucket 30: 60%\n bucket 32: 50%\n bucket 31: 60%\n bucket 30: 70%\n bucket 32: 60%\n bucket 31: 70%\n bucket 30: 80%\n bucket 31: 80%\n bucket 32: 70%\n bucket 30: 90%\n bucket 31: 90%\n bucket 30: 100%\n bucket 32: 80%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\n bucket 33: 70%\n bucket 33: 80%\n bucket 33: 90%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 45 for bucket 33\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n Entering block accumulator loop for bucket 34:\n bucket 34: 10%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 20%\n bucket 34: 30%\n Entering block accumulator loop for bucket 35:\n bucket 34: 40%\n bucket 35: 10%\n bucket 34: 50%\n bucket 35: 20%\n bucket 34: 60%\n bucket 35: 30%\n bucket 34: 70%\n bucket 35: 40%\n bucket 34: 80%\n bucket 35: 50%\n bucket 34: 90%\n bucket 35: 60%\n bucket 34: 100%\n Sorting block of length 122 for bucket 34\n (Using difference cover)\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\n bucket 36: 20%\n bucket 36: 30%\n bucket 36: 40%\n bucket 36: 50%\n bucket 36: 60%\n bucket 36: 70%\n bucket 36: 80%\n bucket 36: 90%\n bucket 36: 100%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n Entering block accumulator loop for bucket 37:\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n bucket 37: 10%\n bucket 37: 20%\n bucket 37: 30%\n bucket 37: 40%\n bucket 37: 50%\n bucket 37: 60%\n bucket 37: 70%\n bucket 37: 80%\n bucket 37: 90%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\nGetting block 38 of 60\n Reserving size (126) for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\n Calculating Z arrays for bucket 38\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 38:\n bucket 39: 10%\n bucket 38: 10%\n bucket 39: 20%\n bucket 38: 20%\n bucket 39: 30%\n bucket 38: 30%\n bucket 39: 40%\n bucket 38: 40%\n bucket 39: 50%\n bucket 38: 50%\n bucket 39: 60%\n bucket 38: 60%\n bucket 39: 70%\n bucket 38: 70%\n bucket 39: 80%\n bucket 38: 80%\n bucket 39: 90%\n bucket 38: 90%\n bucket 39: 100%\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 40:\n bucket 40: 10%\n bucket 40: 20%\n bucket 40: 30%\n bucket 40: 40%\n bucket 40: 50%\n bucket 40: 60%\n bucket 40: 70%\n bucket 40: 80%\n bucket 40: 90%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 43:\n bucket 42: 10%\n bucket 43: 10%\n bucket 42: 20%\n bucket 43: 20%\n bucket 42: 30%\n bucket 43: 30%\n bucket 42: 40%\n bucket 43: 40%\n bucket 42: 50%\n bucket 43: 50%\n bucket 42: 60%\n bucket 43: 60%\n bucket 42: 70%\n bucket 43: 70%\n bucket 42: 80%\n bucket 43: 80%\n bucket 42: 90%\n bucket 43: 90%\n bucket 42: 100%\n bucket 43: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n bucket 44: 10%\n Calculating Z arrays for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n bucket 44: 20%\n Entering block accumulator loop for bucket 45:\n Calculating Z arrays for bucket 46\n bucket 44: 30%\n bucket 44: 40%\n Entering block accumulator loop for bucket 46:\n bucket 45: 10%\n bucket 44: 50%\n bucket 46: 10%\n bucket 45: 20%\n bucket 44: 60%\n bucket 45: 30%\n bucket 44: 70%\n bucket 45: 40%\n bucket 44: 80%\n bucket 45: 50%\n bucket 46: 20%\n bucket 44: 90%\n bucket 45: 60%\n bucket 46: 30%\n bucket 44: 100%\n bucket 45: 70%\n Sorting block of length 66 for bucket 44\n bucket 46: 40%\n bucket 45: 80%\n bucket 46: 50%\n bucket 45: 90%\n (Using difference cover)\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\nGetting block 47 of 60\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 47:\n bucket 47: 10%\n bucket 47: 20%\n bucket 47: 30%\n bucket 47: 40%\n bucket 47: 50%\n bucket 47: 60%\n bucket 47: 70%\n bucket 47: 80%\n bucket 47: 90%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Entering block accumulator loop for bucket 48:\n bucket 48: 10%\n bucket 48: 20%\n bucket 48: 30%\n bucket 48: 40%\nGetting block 49 of 60\n bucket 48: 50%\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n bucket 48: 60%\n bucket 48: 70%\n Entering block accumulator loop for bucket 49:\n bucket 48: 80%\n bucket 49: 10%\n bucket 48: 90%\n bucket 49: 20%\n bucket 48: 100%\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 30%\nGetting block 52 of 60\n Entering block accumulator loop for bucket 51:\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\n bucket 50: 40%\n bucket 51: 10%\n Entering block accumulator loop for bucket 52:\n bucket 50: 50%\n bucket 51: 20%\n bucket 52: 10%\n bucket 50: 60%\n bucket 51: 30%\n bucket 52: 20%\n bucket 50: 70%\n bucket 51: 40%\n bucket 52: 30%\n bucket 50: 80%\n bucket 52: 40%\n bucket 50: 90%\n bucket 51: 50%\n bucket 52: 50%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n bucket 51: 60%\n bucket 52: 60%\n bucket 51: 70%\n bucket 52: 70%\n bucket 51: 80%\n bucket 52: 80%\n bucket 51: 90%\n bucket 52: 90%\n bucket 52: 100%\n bucket 51: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 53:\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 54:\n bucket 53: 10%\nGetting block 56 of 60\n Reserving size (126) for bucket 56\n Entering block accumulator loop for bucket 55:\n bucket 53: 20%\n bucket 54: 10%\n Calculating Z arrays for bucket 56\n bucket 53: 30%\n bucket 54: 20%\n bucket 55: 10%\n bucket 53: 40%\n bucket 54: 30%\n Entering block accumulator loop for bucket 56:\n bucket 53: 50%\n bucket 55: 20%\n bucket 54: 40%\n bucket 53: 60%\n bucket 54: 50%\n bucket 53: 70%\n bucket 56: 10%\n bucket 55: 30%\n bucket 54: 60%\n bucket 53: 80%\n bucket 56: 20%\n bucket 54: 70%\n bucket 53: 90%\n bucket 55: 40%\n bucket 56: 30%\n bucket 53: 100%\n bucket 54: 80%\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 56: 40%\n bucket 54: 90%\n bucket 56: 50%\n bucket 55: 50%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n bucket 56: 60%\n bucket 55: 60%\n bucket 56: 70%\n bucket 55: 70%\n bucket 56: 80%\n bucket 55: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n (Using difference cover)\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 55\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n bucket 57: 20%\n Calculating Z arrays for bucket 58\n bucket 57: 30%\n bucket 57: 40%\n Entering block accumulator loop for bucket 58:\n bucket 57: 50%\n bucket 58: 10%\n bucket 57: 60%\n bucket 58: 20%\n bucket 57: 70%\n bucket 58: 30%\n bucket 57: 80%\n bucket 58: 40%\n bucket 57: 90%\n bucket 58: 50%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 58: 60%\n bucket 58: 70%\n bucket 58: 80%\n bucket 58: 90%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\nGetting block 59 of 60\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 59:\n Entering block accumulator loop for bucket 60:\n bucket 59: 10%\n bucket 59: 20%\n bucket 60: 10%\n bucket 59: 30%\n bucket 60: 20%\n bucket 60: 30%\n bucket 59: 40%\n bucket 60: 40%\n bucket 59: 50%\n bucket 60: 50%\n bucket 59: 60%\n bucket 60: 60%\n bucket 60: 70%\n bucket 59: 70%\n bucket 60: 80%\n bucket 59: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n bucket 59: 90%\n (Using difference cover)\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:01\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:55:14", "plugin": "core", "name": "end_epoch", "raw_value": "1725000914.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:55:13", "plugin": "core", "name": "start_epoch", "raw_value": "1725000913.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "hisat2/2.2.1+galaxy1-9", "has_data": true, "data": {"tool_id": "hisat2", "tool_version": "2.2.1+galaxy1", "test_index": 9, "time_seconds": 38.61113953590393, "inputs": {"reference_genome|history_item": {"src": "hda", "id": "f91b2de9e5168308"}, "reference_genome|source": "history", "library|input_1": {"src": "hda", "id": "2ad1195a969703b8"}, "library|input_2": {"src": "hda", "id": "361b5ee0a3110f70"}, "library|rna_strandness": "FR", "library|type": "paired"}, "job": {"model_class": "Job", "id": "5d65279e7ef66f7a", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:03:57.476845", "update_time": "2024-08-30T07:04:11.573244", "galaxy_version": "24.1", "external_id": "gxy-zdqh9", "handler": null, "job_runner_name": null, "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/f/f/9/dataset_ff90c5f3-2061-4c88-a2ef-521c2522a63c.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s '/galaxy/server/database/objects/f/f/3/dataset_ff326c6c-bd2d-4e75-8f4d-24f2c30b5e89.dat' input_f.fastq && ln -f -s '/galaxy/server/database/objects/9/a/5/dataset_9a532ed7-58ae-4500-bffb-7b8addb3aaa4.dat' input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 'input_f.fastq' -2 'input_r.fastq' --rna-strandness FR | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/3/9/b/dataset_39b674db-0476-466f-ace7-6cccc92d86a1.dat'", "user_email": "tests@fake.org", "command_version": "/usr/local/bin/hisat2-align-s version 2.2.1\n64-bit\nBuilt on fv-az198-998\nSat Mar 27 17:02:15 UTC 2021\nCompiler: collect2: error: ld returned 1 exit status\nOptions: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11\nSizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", "sum": "{\"new_summary\": false, \"summary_file\": false}", "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 211, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 212, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"FR\", \"type\": \"paired\"}", "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 210, \"src\": \"hda\"}]}, \"source\": \"history\"}"}, "inputs": {"reference_genome|history_item": {"id": "f91b2de9e5168308", "src": "hda", "uuid": "ff90c5f3-2061-4c88-a2ef-521c2522a63c"}, "library|input_1": {"id": "2ad1195a969703b8", "src": "hda", "uuid": "ff326c6c-bd2d-4e75-8f4d-24f2c30b5e89"}, "library|input_2": {"id": "361b5ee0a3110f70", "src": "hda", "uuid": "9a532ed7-58ae-4500-bffb-7b8addb3aaa4"}}, "outputs": {"output_alignments": {"id": "579f0927073ae283", "src": "hda", "uuid": "39b674db-0476-466f-ace7-6cccc92d86a1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 3:\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 1: 10%\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 5\n bucket 1: 20%\n bucket 2: 10%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 1: 30%\n Calculating Z arrays for bucket 7\n bucket 3: 10%\nGetting block 6 of 60\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 7:\n bucket 2: 20%\nGetting block 8 of 60\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 6\n bucket 3: 20%\n bucket 5: 10%\n bucket 1: 40%\n Calculating Z arrays for bucket 6\n bucket 7: 10%\n Entering block accumulator loop for bucket 4:\n bucket 2: 30%\n bucket 5: 20%\n Reserving size (126) for bucket 8\n bucket 3: 30%\n bucket 4: 10%\n bucket 7: 20%\n bucket 5: 30%\n Calculating Z arrays for bucket 8\n bucket 2: 40%\n Entering block accumulator loop for bucket 6:\n bucket 3: 40%\n bucket 7: 30%\n bucket 2: 50%\n bucket 1: 50%\n Entering block accumulator loop for bucket 8:\n bucket 5: 40%\n bucket 6: 10%\n bucket 2: 60%\n bucket 5: 50%\n bucket 1: 60%\n bucket 2: 70%\n bucket 8: 10%\n bucket 3: 50%\n bucket 7: 40%\n bucket 1: 70%\n bucket 8: 20%\n bucket 4: 20%\n bucket 5: 60%\n bucket 7: 50%\n bucket 1: 80%\n bucket 4: 30%\n bucket 6: 20%\n bucket 1: 90%\n bucket 3: 60%\n bucket 2: 80%\n bucket 6: 30%\n bucket 8: 30%\n bucket 1: 100%\n bucket 7: 60%\n bucket 4: 40%\n Sorting block of length 42 for bucket 1\n bucket 3: 70%\n (Using difference cover)\n bucket 7: 70%\n bucket 2: 90%\n bucket 7: 80%\n bucket 3: 80%\n bucket 6: 40%\n bucket 7: 90%\n bucket 4: 50%\n bucket 2: 100%\n bucket 8: 40%\n bucket 3: 90%\n bucket 6: 50%\n bucket 7: 100%\n bucket 3: 100%\n bucket 8: 50%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 6: 60%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 5: 70%\n bucket 8: 60%\n bucket 4: 60%\n bucket 6: 70%\n bucket 5: 80%\n bucket 8: 70%\n bucket 4: 70%\n bucket 6: 80%\n Sorting block of length 84 for bucket 2\n bucket 4: 80%\n bucket 5: 90%\n bucket 4: 90%\n (Using difference cover)\n bucket 8: 80%\n bucket 6: 90%\n bucket 8: 90%\n bucket 5: 100%\n bucket 4: 100%\n bucket 6: 100%\n Sorting block of length 63 for bucket 5\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n (Using difference cover)\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\n bucket 10: 40%\n bucket 9: 60%\n bucket 10: 50%\n bucket 9: 70%\n bucket 10: 60%\n bucket 9: 80%\n bucket 9: 90%\n bucket 10: 70%\n bucket 9: 100%\n bucket 10: 80%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n Entering block accumulator loop for bucket 12:\n bucket 11: 20%\n bucket 12: 10%\n bucket 11: 30%\n bucket 12: 20%\n bucket 11: 40%\n bucket 12: 30%\n bucket 11: 50%\n bucket 12: 40%\n bucket 11: 60%\n bucket 12: 50%\n bucket 11: 70%\n bucket 12: 60%\n bucket 11: 80%\n bucket 12: 70%\n bucket 11: 90%\n bucket 12: 80%\n bucket 11: 100%\n bucket 12: 90%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\nGetting block 14 of 60\n bucket 13: 20%\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 14: 60%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n Entering block accumulator loop for bucket 16:\n bucket 15: 90%\n bucket 16: 10%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\nGetting block 20 of 60\n Entering block accumulator loop for bucket 19:\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Calculating Z arrays for bucket 21\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n Entering block accumulator loop for bucket 21:\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 21: 10%\n bucket 20: 30%\n bucket 19: 50%\n bucket 21: 20%\n bucket 19: 60%\n bucket 20: 40%\n bucket 21: 30%\n bucket 19: 70%\n bucket 20: 50%\n bucket 21: 40%\n bucket 19: 80%\n bucket 21: 50%\n bucket 20: 60%\n bucket 19: 90%\n bucket 21: 60%\n bucket 20: 70%\n bucket 21: 70%\n bucket 21: 80%\n bucket 20: 80%\n bucket 19: 100%\n bucket 21: 90%\n bucket 20: 90%\n Sorting block of length 107 for bucket 19\n bucket 21: 100%\n (Using difference cover)\n bucket 20: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n bucket 22: 50%\n bucket 23: 20%\n bucket 22: 60%\n bucket 22: 70%\n bucket 23: 30%\n bucket 22: 80%\n bucket 23: 40%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 30%\n bucket 24: 40%\n Entering block accumulator loop for bucket 25:\n bucket 24: 50%\n bucket 25: 10%\n bucket 24: 60%\n bucket 25: 20%\n bucket 24: 70%\n bucket 25: 30%\n bucket 24: 80%\n bucket 25: 40%\nGetting block 26 of 60\n bucket 25: 50%\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n Entering block accumulator loop for bucket 26:\n bucket 24: 90%\n bucket 26: 10%\n bucket 25: 90%\n bucket 26: 20%\n bucket 24: 100%\n bucket 26: 30%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 100%\n bucket 26: 40%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 80%\n bucket 27: 90%\n Entering block accumulator loop for bucket 28:\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Entering block accumulator loop for bucket 29:\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 30: 10%\n bucket 30: 20%\n bucket 29: 30%\n bucket 30: 30%\n bucket 29: 40%\n bucket 30: 40%\n bucket 30: 50%\n bucket 29: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 29: 60%\n bucket 30: 80%\n bucket 30: 90%\n bucket 29: 70%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 20%\n bucket 31: 30%\n Entering block accumulator loop for bucket 32:\n bucket 31: 40%\n bucket 32: 10%\n bucket 31: 50%\n bucket 32: 20%\n bucket 31: 60%\n bucket 32: 30%\n bucket 31: 70%\n bucket 32: 40%\n bucket 31: 80%\n bucket 32: 50%\n bucket 31: 90%\n bucket 32: 60%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 70%\n Entering block accumulator loop for bucket 34:\n bucket 33: 80%\n bucket 34: 10%\n bucket 33: 90%\n bucket 34: 20%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 60%\n bucket 34: 70%\n Entering block accumulator loop for bucket 35:\n bucket 34: 80%\n bucket 35: 10%\n bucket 34: 90%\n bucket 35: 20%\n bucket 34: 100%\n bucket 35: 30%\n Sorting block of length 122 for bucket 34\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 45 for bucket 33\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 20%\nGetting block 38 of 60\n bucket 36: 30%\n Reserving size (126) for bucket 38\n Entering block accumulator loop for bucket 37:\n Calculating Z arrays for bucket 38\n bucket 36: 40%\n bucket 37: 10%\n bucket 36: 50%\n bucket 37: 20%\n Entering block accumulator loop for bucket 38:\n bucket 37: 30%\n bucket 36: 60%\n bucket 37: 40%\n bucket 38: 10%\n bucket 37: 50%\n bucket 36: 70%\n bucket 37: 60%\n bucket 38: 20%\n bucket 36: 80%\n bucket 37: 70%\n bucket 36: 90%\n bucket 37: 80%\n bucket 38: 30%\n bucket 36: 100%\n bucket 37: 90%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 38: 40%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 40: 20%\n bucket 39: 30%\n bucket 40: 30%\n bucket 39: 40%\n bucket 40: 40%\n bucket 39: 50%\n bucket 40: 50%\n bucket 39: 60%\n bucket 40: 60%\n bucket 39: 70%\n bucket 40: 70%\n bucket 39: 80%\n bucket 40: 80%\n bucket 39: 90%\n bucket 40: 90%\n bucket 39: 100%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 43:\n bucket 42: 10%\n bucket 43: 10%\n bucket 42: 20%\n bucket 43: 20%\n bucket 42: 30%\n bucket 43: 30%\n bucket 42: 40%\n bucket 43: 40%\n bucket 42: 50%\n bucket 43: 50%\n bucket 42: 60%\n bucket 43: 60%\n bucket 42: 70%\n bucket 43: 70%\n bucket 42: 80%\n bucket 43: 80%\n bucket 42: 90%\n bucket 43: 90%\n bucket 42: 100%\n bucket 43: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 10%\n bucket 44: 20%\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 44: 30%\n bucket 45: 20%\n bucket 44: 40%\n bucket 45: 30%\n bucket 44: 50%\n bucket 45: 40%\n bucket 44: 60%\n bucket 45: 50%\n bucket 44: 70%\n bucket 45: 60%\n bucket 44: 80%\n bucket 45: 70%\n bucket 44: 90%\n bucket 45: 80%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\nGetting block 47 of 60\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 47:\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 48: 10%\n bucket 47: 10%\n bucket 48: 20%\n bucket 47: 20%\n bucket 48: 30%\n bucket 47: 30%\n bucket 48: 40%\n bucket 47: 40%\n bucket 48: 50%\n bucket 47: 50%\n bucket 48: 60%\n bucket 47: 60%\n bucket 48: 70%\n bucket 47: 70%\n bucket 48: 80%\n bucket 47: 80%\n bucket 48: 90%\n bucket 47: 90%\n bucket 48: 100%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 52: 20%\n bucket 53: 20%\n bucket 53: 30%\n bucket 52: 30%\n bucket 53: 40%\n bucket 52: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 52: 50%\n bucket 53: 70%\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 80%\n bucket 52: 60%\n bucket 53: 90%\n bucket 52: 70%\n bucket 53: 100%\n Entering block accumulator loop for bucket 54:\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 52: 80%\n bucket 54: 10%\n bucket 52: 90%\n bucket 54: 20%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\nGetting block 56 of 60\n bucket 55: 80%\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 50%\n bucket 57: 60%\n Entering block accumulator loop for bucket 58:\nGetting block 59 of 60\n bucket 58: 10%\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n bucket 58: 20%\n bucket 57: 70%\n bucket 58: 30%\n Entering block accumulator loop for bucket 59:\n bucket 58: 40%\n bucket 57: 80%\n bucket 58: 50%\n bucket 59: 10%\n bucket 57: 90%\n bucket 58: 60%\n bucket 59: 20%\n bucket 58: 70%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 59: 30%\n bucket 58: 80%\n bucket 59: 40%\n bucket 58: 90%\n bucket 59: 50%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "tool_stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_stdout": "", "job_stderr": "", "stdout": "Building DifferenceCoverSample\n Building sPrime\n Building sPrimeOrder\n V-Sorting samples\n V-Sorting samples time: 00:00:00\n Allocating rank array\n Ranking v-sort output\n Ranking v-sort output time: 00:00:00\n Invoking Larsson-Sadakane on ranks\n Invoking Larsson-Sadakane on ranks time: 00:00:00\n Sanity-checking and returning\nBuilding samples\nReserving space for 88 sample suffixes\nGenerating random suffixes\nQSorting 88 sample offsets, eliminating duplicates\nQSorting sample offsets, eliminating duplicates time: 00:00:00\nMultikey QSorting 88 samples\n (Using difference cover)\n Multikey QSorting samples time: 00:00:00\nCalculating bucket sizes\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 8, merged 39; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 6, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nSplit 2, merged 3; iterating...\nSplitting and merging\n Splitting and merging time: 00:00:00\nAvg bucket size: 88.7833 (target: 125)\nGetting block 1 of 60\nGetting block 2 of 60\n Reserving size (126) for bucket 2\n Reserving size (126) for bucket 1\n Calculating Z arrays for bucket 1\nGetting block 3 of 60\n Reserving size (126) for bucket 3\n Calculating Z arrays for bucket 2\n Entering block accumulator loop for bucket 1:\n Calculating Z arrays for bucket 3\nGetting block 4 of 60\n Reserving size (126) for bucket 4\n Entering block accumulator loop for bucket 3:\nGetting block 5 of 60\n Reserving size (126) for bucket 5\n bucket 1: 10%\n Entering block accumulator loop for bucket 2:\n Calculating Z arrays for bucket 5\n bucket 1: 20%\n bucket 2: 10%\nGetting block 7 of 60\n Reserving size (126) for bucket 7\n bucket 1: 30%\n Calculating Z arrays for bucket 7\n bucket 3: 10%\nGetting block 6 of 60\n Calculating Z arrays for bucket 4\n Entering block accumulator loop for bucket 7:\n bucket 2: 20%\nGetting block 8 of 60\n Entering block accumulator loop for bucket 5:\n Reserving size (126) for bucket 6\n bucket 3: 20%\n bucket 5: 10%\n bucket 1: 40%\n Calculating Z arrays for bucket 6\n bucket 7: 10%\n Entering block accumulator loop for bucket 4:\n bucket 2: 30%\n bucket 5: 20%\n Reserving size (126) for bucket 8\n bucket 3: 30%\n bucket 4: 10%\n bucket 7: 20%\n bucket 5: 30%\n Calculating Z arrays for bucket 8\n bucket 2: 40%\n Entering block accumulator loop for bucket 6:\n bucket 3: 40%\n bucket 7: 30%\n bucket 2: 50%\n bucket 1: 50%\n Entering block accumulator loop for bucket 8:\n bucket 5: 40%\n bucket 6: 10%\n bucket 2: 60%\n bucket 5: 50%\n bucket 1: 60%\n bucket 2: 70%\n bucket 8: 10%\n bucket 3: 50%\n bucket 7: 40%\n bucket 1: 70%\n bucket 8: 20%\n bucket 4: 20%\n bucket 5: 60%\n bucket 7: 50%\n bucket 1: 80%\n bucket 4: 30%\n bucket 6: 20%\n bucket 1: 90%\n bucket 3: 60%\n bucket 2: 80%\n bucket 6: 30%\n bucket 8: 30%\n bucket 1: 100%\n bucket 7: 60%\n bucket 4: 40%\n Sorting block of length 42 for bucket 1\n bucket 3: 70%\n (Using difference cover)\n bucket 7: 70%\n bucket 2: 90%\n bucket 7: 80%\n bucket 3: 80%\n bucket 6: 40%\n bucket 7: 90%\n bucket 4: 50%\n bucket 2: 100%\n bucket 8: 40%\n bucket 3: 90%\n bucket 6: 50%\n bucket 7: 100%\n bucket 3: 100%\n bucket 8: 50%\n Sorting block of length 75 for bucket 7\n (Using difference cover)\n bucket 6: 60%\n Sorting block of length 106 for bucket 3\n (Using difference cover)\n bucket 5: 70%\n bucket 8: 60%\n bucket 4: 60%\n bucket 6: 70%\n bucket 5: 80%\n bucket 8: 70%\n bucket 4: 70%\n bucket 6: 80%\n Sorting block of length 84 for bucket 2\n bucket 4: 80%\n bucket 5: 90%\n bucket 4: 90%\n (Using difference cover)\n bucket 8: 80%\n bucket 6: 90%\n bucket 8: 90%\n bucket 5: 100%\n bucket 4: 100%\n bucket 6: 100%\n Sorting block of length 63 for bucket 5\n Sorting block of length 68 for bucket 4\n (Using difference cover)\n (Using difference cover)\n Sorting block of length 90 for bucket 6\n (Using difference cover)\n bucket 8: 100%\n Sorting block of length 94 for bucket 8\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 85 for bucket 2\n Sorting block time: 00:00:00\nReturning block of 43 for bucket 1\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 4\n Sorting block time: 00:00:00\nReturning block of 76 for bucket 7\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 3\n Sorting block time: 00:00:00\nReturning block of 91 for bucket 6\n Sorting block time: 00:00:00\nReturning block of 64 for bucket 5\n Sorting block time: 00:00:00\nReturning block of 95 for bucket 8\nGetting block 9 of 60\n Reserving size (126) for bucket 9\n Calculating Z arrays for bucket 9\nGetting block 10 of 60\n Reserving size (126) for bucket 10\n Calculating Z arrays for bucket 10\n Entering block accumulator loop for bucket 9:\n bucket 9: 10%\n Entering block accumulator loop for bucket 10:\n bucket 9: 20%\n bucket 10: 10%\n bucket 9: 30%\n bucket 10: 20%\n bucket 9: 40%\n bucket 10: 30%\n bucket 9: 50%\n bucket 10: 40%\n bucket 9: 60%\n bucket 10: 50%\n bucket 9: 70%\n bucket 10: 60%\n bucket 9: 80%\n bucket 9: 90%\n bucket 10: 70%\n bucket 9: 100%\n bucket 10: 80%\n Sorting block of length 124 for bucket 9\n (Using difference cover)\n bucket 10: 90%\n bucket 10: 100%\n Sorting block of length 89 for bucket 10\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 90 for bucket 10\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 9\nGetting block 11 of 60\n Reserving size (126) for bucket 11\n Calculating Z arrays for bucket 11\nGetting block 12 of 60\n Reserving size (126) for bucket 12\n Calculating Z arrays for bucket 12\n Entering block accumulator loop for bucket 11:\n bucket 11: 10%\n Entering block accumulator loop for bucket 12:\n bucket 11: 20%\n bucket 12: 10%\n bucket 11: 30%\n bucket 12: 20%\n bucket 11: 40%\n bucket 12: 30%\n bucket 11: 50%\n bucket 12: 40%\n bucket 11: 60%\n bucket 12: 50%\n bucket 11: 70%\n bucket 12: 60%\n bucket 11: 80%\n bucket 12: 70%\n bucket 11: 90%\n bucket 12: 80%\n bucket 11: 100%\n bucket 12: 90%\n Sorting block of length 95 for bucket 11\n (Using difference cover)\n bucket 12: 100%\n Sorting block of length 82 for bucket 12\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 12\n Sorting block time: 00:00:00\nReturning block of 96 for bucket 11\nGetting block 13 of 60\n Reserving size (126) for bucket 13\n Calculating Z arrays for bucket 13\n Entering block accumulator loop for bucket 13:\n bucket 13: 10%\nGetting block 14 of 60\n bucket 13: 20%\n Reserving size (126) for bucket 14\n Calculating Z arrays for bucket 14\n Entering block accumulator loop for bucket 14:\n bucket 13: 30%\n bucket 14: 10%\n bucket 13: 40%\n bucket 14: 20%\n bucket 13: 50%\n bucket 14: 30%\n bucket 13: 60%\n bucket 14: 40%\n bucket 13: 70%\n bucket 14: 50%\n bucket 13: 80%\n bucket 14: 60%\n bucket 13: 90%\n bucket 14: 70%\n bucket 13: 100%\n Sorting block of length 85 for bucket 13\n (Using difference cover)\n bucket 14: 80%\n bucket 14: 90%\n bucket 14: 100%\n Sorting block of length 82 for bucket 14\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 13\n Sorting block time: 00:00:00\nReturning block of 83 for bucket 14\nGetting block 15 of 60\n Reserving size (126) for bucket 15\n Calculating Z arrays for bucket 15\n Entering block accumulator loop for bucket 15:\n bucket 15: 10%\n bucket 15: 20%\n bucket 15: 30%\n bucket 15: 40%\n bucket 15: 50%\nGetting block 16 of 60\n Reserving size (126) for bucket 16\n Calculating Z arrays for bucket 16\n bucket 15: 60%\n bucket 15: 70%\n bucket 15: 80%\n Entering block accumulator loop for bucket 16:\n bucket 15: 90%\n bucket 16: 10%\n bucket 15: 100%\n Sorting block of length 68 for bucket 15\n (Using difference cover)\n bucket 16: 20%\n bucket 16: 30%\n bucket 16: 40%\n bucket 16: 50%\n bucket 16: 60%\n bucket 16: 70%\n bucket 16: 80%\n bucket 16: 90%\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 15\n bucket 16: 100%\n Sorting block of length 100 for bucket 16\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 101 for bucket 16\nGetting block 17 of 60\n Reserving size (126) for bucket 17\n Calculating Z arrays for bucket 17\n Entering block accumulator loop for bucket 17:\n bucket 17: 10%\n bucket 17: 20%\n bucket 17: 30%\n bucket 17: 40%\n bucket 17: 50%\n bucket 17: 60%\n bucket 17: 70%\n bucket 17: 80%\n bucket 17: 90%\nGetting block 18 of 60\n Reserving size (126) for bucket 18\n Calculating Z arrays for bucket 18\n bucket 17: 100%\n Sorting block of length 39 for bucket 17\n (Using difference cover)\n Entering block accumulator loop for bucket 18:\n bucket 18: 10%\n bucket 18: 20%\n bucket 18: 30%\n bucket 18: 40%\n bucket 18: 50%\n bucket 18: 60%\n bucket 18: 70%\n Sorting block time: 00:00:00\nReturning block of 40 for bucket 17\n bucket 18: 80%\n bucket 18: 90%\n bucket 18: 100%\n Sorting block of length 122 for bucket 18\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 18\nGetting block 19 of 60\n Reserving size (126) for bucket 19\n Calculating Z arrays for bucket 19\nGetting block 21 of 60\n Reserving size (126) for bucket 21\nGetting block 20 of 60\n Entering block accumulator loop for bucket 19:\n Reserving size (126) for bucket 20\n Calculating Z arrays for bucket 20\n Calculating Z arrays for bucket 21\n bucket 19: 10%\n Entering block accumulator loop for bucket 20:\n bucket 19: 20%\n Entering block accumulator loop for bucket 21:\n bucket 20: 10%\n bucket 19: 30%\n bucket 20: 20%\n bucket 19: 40%\n bucket 21: 10%\n bucket 20: 30%\n bucket 19: 50%\n bucket 21: 20%\n bucket 19: 60%\n bucket 20: 40%\n bucket 21: 30%\n bucket 19: 70%\n bucket 20: 50%\n bucket 21: 40%\n bucket 19: 80%\n bucket 21: 50%\n bucket 20: 60%\n bucket 19: 90%\n bucket 21: 60%\n bucket 20: 70%\n bucket 21: 70%\n bucket 21: 80%\n bucket 20: 80%\n bucket 19: 100%\n bucket 21: 90%\n bucket 20: 90%\n Sorting block of length 107 for bucket 19\n bucket 21: 100%\n (Using difference cover)\n bucket 20: 100%\n Sorting block of length 54 for bucket 21\n (Using difference cover)\n Sorting block of length 97 for bucket 20\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 98 for bucket 20\n Sorting block time: 00:00:00\nReturning block of 55 for bucket 21\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 19\nGetting block 22 of 60\n Reserving size (126) for bucket 22\n Calculating Z arrays for bucket 22\n Entering block accumulator loop for bucket 22:\n bucket 22: 10%\nGetting block 23 of 60\n Reserving size (126) for bucket 23\n Calculating Z arrays for bucket 23\n Entering block accumulator loop for bucket 23:\n bucket 22: 20%\n bucket 22: 30%\n bucket 23: 10%\n bucket 22: 40%\n bucket 22: 50%\n bucket 23: 20%\n bucket 22: 60%\n bucket 22: 70%\n bucket 23: 30%\n bucket 22: 80%\n bucket 23: 40%\n bucket 22: 90%\n bucket 22: 100%\n Sorting block of length 80 for bucket 22\n (Using difference cover)\n bucket 23: 50%\n bucket 23: 60%\n bucket 23: 70%\n bucket 23: 80%\n bucket 23: 90%\n bucket 23: 100%\n Sorting block of length 64 for bucket 23\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 81 for bucket 22\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 23\nGetting block 24 of 60\n Reserving size (126) for bucket 24\n Calculating Z arrays for bucket 24\n Entering block accumulator loop for bucket 24:\n bucket 24: 10%\n bucket 24: 20%\nGetting block 25 of 60\n Reserving size (126) for bucket 25\n Calculating Z arrays for bucket 25\n bucket 24: 30%\n bucket 24: 40%\n Entering block accumulator loop for bucket 25:\n bucket 24: 50%\n bucket 25: 10%\n bucket 24: 60%\n bucket 25: 20%\n bucket 24: 70%\n bucket 25: 30%\n bucket 24: 80%\n bucket 25: 40%\nGetting block 26 of 60\n bucket 25: 50%\n Reserving size (126) for bucket 26\n Calculating Z arrays for bucket 26\n bucket 25: 60%\n bucket 25: 70%\n bucket 25: 80%\n Entering block accumulator loop for bucket 26:\n bucket 24: 90%\n bucket 26: 10%\n bucket 25: 90%\n bucket 26: 20%\n bucket 24: 100%\n bucket 26: 30%\n Sorting block of length 68 for bucket 24\n (Using difference cover)\n bucket 25: 100%\n bucket 26: 40%\n Sorting block of length 66 for bucket 25\n (Using difference cover)\n bucket 26: 50%\n bucket 26: 60%\n bucket 26: 70%\n bucket 26: 80%\n bucket 26: 90%\n bucket 26: 100%\n Sorting block of length 107 for bucket 26\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 108 for bucket 26\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 25\n Sorting block time: 00:00:00\nReturning block of 69 for bucket 24\nGetting block 27 of 60\n Reserving size (126) for bucket 27\n Calculating Z arrays for bucket 27\n Entering block accumulator loop for bucket 27:\n bucket 27: 10%\n bucket 27: 20%\n bucket 27: 30%\n bucket 27: 40%\n bucket 27: 50%\n bucket 27: 60%\n bucket 27: 70%\nGetting block 28 of 60\n Reserving size (126) for bucket 28\n Calculating Z arrays for bucket 28\n bucket 27: 80%\n bucket 27: 90%\n Entering block accumulator loop for bucket 28:\n bucket 27: 100%\n Sorting block of length 119 for bucket 27\n (Using difference cover)\n bucket 28: 10%\n bucket 28: 20%\n bucket 28: 30%\n bucket 28: 40%\n bucket 28: 50%\n bucket 28: 60%\n bucket 28: 70%\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 27\n bucket 28: 80%\n bucket 28: 90%\n bucket 28: 100%\n Sorting block of length 106 for bucket 28\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 28\nGetting block 29 of 60\n Reserving size (126) for bucket 29\n Calculating Z arrays for bucket 29\nGetting block 30 of 60\n Entering block accumulator loop for bucket 29:\n Reserving size (126) for bucket 30\n Calculating Z arrays for bucket 30\n bucket 29: 10%\n Entering block accumulator loop for bucket 30:\n bucket 29: 20%\n bucket 30: 10%\n bucket 30: 20%\n bucket 29: 30%\n bucket 30: 30%\n bucket 29: 40%\n bucket 30: 40%\n bucket 30: 50%\n bucket 29: 50%\n bucket 30: 60%\n bucket 30: 70%\n bucket 29: 60%\n bucket 30: 80%\n bucket 30: 90%\n bucket 29: 70%\n bucket 30: 100%\n Sorting block of length 124 for bucket 30\n (Using difference cover)\n bucket 29: 80%\n bucket 29: 90%\n bucket 29: 100%\n Sorting block of length 51 for bucket 29\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 125 for bucket 30\n Sorting block time: 00:00:00\nReturning block of 52 for bucket 29\nGetting block 31 of 60\n Reserving size (126) for bucket 31\n Calculating Z arrays for bucket 31\n Entering block accumulator loop for bucket 31:\n bucket 31: 10%\nGetting block 32 of 60\n Reserving size (126) for bucket 32\n Calculating Z arrays for bucket 32\n bucket 31: 20%\n bucket 31: 30%\n Entering block accumulator loop for bucket 32:\n bucket 31: 40%\n bucket 32: 10%\n bucket 31: 50%\n bucket 32: 20%\n bucket 31: 60%\n bucket 32: 30%\n bucket 31: 70%\n bucket 32: 40%\n bucket 31: 80%\n bucket 32: 50%\n bucket 31: 90%\n bucket 32: 60%\n bucket 31: 100%\n Sorting block of length 110 for bucket 31\n (Using difference cover)\n bucket 32: 70%\n bucket 32: 80%\n bucket 32: 90%\n bucket 32: 100%\n Sorting block of length 125 for bucket 32\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 111 for bucket 31\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 32\nGetting block 33 of 60\n Reserving size (126) for bucket 33\n Calculating Z arrays for bucket 33\n Entering block accumulator loop for bucket 33:\n bucket 33: 10%\n bucket 33: 20%\n bucket 33: 30%\n bucket 33: 40%\n bucket 33: 50%\n bucket 33: 60%\nGetting block 34 of 60\n Reserving size (126) for bucket 34\n Calculating Z arrays for bucket 34\n bucket 33: 70%\n Entering block accumulator loop for bucket 34:\n bucket 33: 80%\n bucket 34: 10%\n bucket 33: 90%\n bucket 34: 20%\n bucket 33: 100%\n Sorting block of length 44 for bucket 33\n (Using difference cover)\n bucket 34: 30%\n bucket 34: 40%\n bucket 34: 50%\nGetting block 35 of 60\n Reserving size (126) for bucket 35\n Calculating Z arrays for bucket 35\n bucket 34: 60%\n bucket 34: 70%\n Entering block accumulator loop for bucket 35:\n bucket 34: 80%\n bucket 35: 10%\n bucket 34: 90%\n bucket 35: 20%\n bucket 34: 100%\n bucket 35: 30%\n Sorting block of length 122 for bucket 34\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 45 for bucket 33\n bucket 35: 40%\n bucket 35: 50%\n bucket 35: 60%\n bucket 35: 70%\n bucket 35: 80%\n bucket 35: 90%\n bucket 35: 100%\n Sorting block of length 112 for bucket 35\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 123 for bucket 34\n Sorting block time: 00:00:00\nReturning block of 113 for bucket 35\nGetting block 36 of 60\n Reserving size (126) for bucket 36\n Calculating Z arrays for bucket 36\n Entering block accumulator loop for bucket 36:\n bucket 36: 10%\nGetting block 37 of 60\n Reserving size (126) for bucket 37\n Calculating Z arrays for bucket 37\n bucket 36: 20%\nGetting block 38 of 60\n bucket 36: 30%\n Reserving size (126) for bucket 38\n Entering block accumulator loop for bucket 37:\n Calculating Z arrays for bucket 38\n bucket 36: 40%\n bucket 37: 10%\n bucket 36: 50%\n bucket 37: 20%\n Entering block accumulator loop for bucket 38:\n bucket 37: 30%\n bucket 36: 60%\n bucket 37: 40%\n bucket 38: 10%\n bucket 37: 50%\n bucket 36: 70%\n bucket 37: 60%\n bucket 38: 20%\n bucket 36: 80%\n bucket 37: 70%\n bucket 36: 90%\n bucket 37: 80%\n bucket 38: 30%\n bucket 36: 100%\n bucket 37: 90%\n Sorting block of length 120 for bucket 36\n (Using difference cover)\n bucket 38: 40%\n bucket 37: 100%\n Sorting block of length 59 for bucket 37\n (Using difference cover)\n bucket 38: 50%\n bucket 38: 60%\n bucket 38: 70%\n bucket 38: 80%\n bucket 38: 90%\n bucket 38: 100%\n Sorting block of length 117 for bucket 38\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 60 for bucket 37\n Sorting block time: 00:00:00\nReturning block of 121 for bucket 36\n Sorting block time: 00:00:00\nReturning block of 118 for bucket 38\nGetting block 39 of 60\n Reserving size (126) for bucket 39\n Calculating Z arrays for bucket 39\nGetting block 40 of 60\n Reserving size (126) for bucket 40\n Calculating Z arrays for bucket 40\n Entering block accumulator loop for bucket 39:\n Entering block accumulator loop for bucket 40:\n bucket 39: 10%\n bucket 40: 10%\n bucket 39: 20%\n bucket 40: 20%\n bucket 39: 30%\n bucket 40: 30%\n bucket 39: 40%\n bucket 40: 40%\n bucket 39: 50%\n bucket 40: 50%\n bucket 39: 60%\n bucket 40: 60%\n bucket 39: 70%\n bucket 40: 70%\n bucket 39: 80%\n bucket 40: 80%\n bucket 39: 90%\n bucket 40: 90%\n bucket 39: 100%\n bucket 40: 100%\n Sorting block of length 41 for bucket 40\n (Using difference cover)\n Sorting block of length 125 for bucket 39\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 42 for bucket 40\n Sorting block time: 00:00:00\nReturning block of 126 for bucket 39\nGetting block 41 of 60\n Reserving size (126) for bucket 41\n Calculating Z arrays for bucket 41\n Entering block accumulator loop for bucket 41:\n bucket 41: 10%\n bucket 41: 20%\n bucket 41: 30%\n bucket 41: 40%\n bucket 41: 50%\n bucket 41: 60%\n bucket 41: 70%\n bucket 41: 80%\n bucket 41: 90%\n bucket 41: 100%\n Sorting block of length 88 for bucket 41\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 89 for bucket 41\nGetting block 42 of 60\n Reserving size (126) for bucket 42\n Calculating Z arrays for bucket 42\nGetting block 43 of 60\n Reserving size (126) for bucket 43\n Calculating Z arrays for bucket 43\n Entering block accumulator loop for bucket 42:\n Entering block accumulator loop for bucket 43:\n bucket 42: 10%\n bucket 43: 10%\n bucket 42: 20%\n bucket 43: 20%\n bucket 42: 30%\n bucket 43: 30%\n bucket 42: 40%\n bucket 43: 40%\n bucket 42: 50%\n bucket 43: 50%\n bucket 42: 60%\n bucket 43: 60%\n bucket 42: 70%\n bucket 43: 70%\n bucket 42: 80%\n bucket 43: 80%\n bucket 42: 90%\n bucket 43: 90%\n bucket 42: 100%\n bucket 43: 100%\n Sorting block of length 119 for bucket 42\n (Using difference cover)\n Sorting block of length 121 for bucket 43\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 122 for bucket 43\n Sorting block time: 00:00:00\nReturning block of 120 for bucket 42\nGetting block 44 of 60\n Reserving size (126) for bucket 44\n Calculating Z arrays for bucket 44\n Entering block accumulator loop for bucket 44:\nGetting block 45 of 60\n Reserving size (126) for bucket 45\n Calculating Z arrays for bucket 45\n bucket 44: 10%\n bucket 44: 20%\n Entering block accumulator loop for bucket 45:\n bucket 45: 10%\n bucket 44: 30%\n bucket 45: 20%\n bucket 44: 40%\n bucket 45: 30%\n bucket 44: 50%\n bucket 45: 40%\n bucket 44: 60%\n bucket 45: 50%\n bucket 44: 70%\n bucket 45: 60%\n bucket 44: 80%\n bucket 45: 70%\n bucket 44: 90%\n bucket 45: 80%\n bucket 44: 100%\n Sorting block of length 66 for bucket 44\n (Using difference cover)\n bucket 45: 90%\n bucket 45: 100%\n Sorting block of length 79 for bucket 45\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 67 for bucket 44\n Sorting block time: 00:00:00\nReturning block of 80 for bucket 45\nGetting block 46 of 60\n Reserving size (126) for bucket 46\n Calculating Z arrays for bucket 46\n Entering block accumulator loop for bucket 46:\n bucket 46: 10%\n bucket 46: 20%\n bucket 46: 30%\n bucket 46: 40%\n bucket 46: 50%\n bucket 46: 60%\n bucket 46: 70%\n bucket 46: 80%\n bucket 46: 90%\n bucket 46: 100%\n Sorting block of length 69 for bucket 46\n (Using difference cover)\nGetting block 47 of 60\nGetting block 48 of 60\n Reserving size (126) for bucket 48\n Calculating Z arrays for bucket 48\n Reserving size (126) for bucket 47\n Calculating Z arrays for bucket 47\n Entering block accumulator loop for bucket 48:\n Entering block accumulator loop for bucket 47:\n Sorting block time: 00:00:00\nReturning block of 70 for bucket 46\n bucket 48: 10%\n bucket 47: 10%\n bucket 48: 20%\n bucket 47: 20%\n bucket 48: 30%\n bucket 47: 30%\n bucket 48: 40%\n bucket 47: 40%\n bucket 48: 50%\n bucket 47: 50%\n bucket 48: 60%\n bucket 47: 60%\n bucket 48: 70%\n bucket 47: 70%\n bucket 48: 80%\n bucket 47: 80%\n bucket 48: 90%\n bucket 47: 90%\n bucket 48: 100%\n bucket 47: 100%\n Sorting block of length 83 for bucket 47\n (Using difference cover)\n Sorting block of length 113 for bucket 48\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 48\n Sorting block time: 00:00:00\nReturning block of 84 for bucket 47\nGetting block 49 of 60\n Reserving size (126) for bucket 49\n Calculating Z arrays for bucket 49\n Entering block accumulator loop for bucket 49:\n bucket 49: 10%\n bucket 49: 20%\n bucket 49: 30%\n bucket 49: 40%\n bucket 49: 50%\n bucket 49: 60%\n bucket 49: 70%\n bucket 49: 80%\n bucket 49: 90%\n bucket 49: 100%\n Sorting block of length 74 for bucket 49\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 75 for bucket 49\nGetting block 50 of 60\n Reserving size (126) for bucket 50\n Calculating Z arrays for bucket 50\n Entering block accumulator loop for bucket 50:\n bucket 50: 10%\n bucket 50: 20%\n bucket 50: 30%\n bucket 50: 40%\n bucket 50: 50%\n bucket 50: 60%\n bucket 50: 70%\n bucket 50: 80%\nGetting block 51 of 60\n Reserving size (126) for bucket 51\n Calculating Z arrays for bucket 51\n bucket 50: 90%\n bucket 50: 100%\n Sorting block of length 108 for bucket 50\n (Using difference cover)\n Entering block accumulator loop for bucket 51:\n bucket 51: 10%\n bucket 51: 20%\n bucket 51: 30%\n bucket 51: 40%\n bucket 51: 50%\n bucket 51: 60%\n Sorting block time: 00:00:00\nReturning block of 109 for bucket 50\n bucket 51: 70%\n bucket 51: 80%\n bucket 51: 90%\n bucket 51: 100%\n Sorting block of length 91 for bucket 51\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 92 for bucket 51\nGetting block 52 of 60\n Reserving size (126) for bucket 52\n Calculating Z arrays for bucket 52\nGetting block 53 of 60\n Reserving size (126) for bucket 53\n Calculating Z arrays for bucket 53\n Entering block accumulator loop for bucket 52:\n bucket 52: 10%\n Entering block accumulator loop for bucket 53:\n bucket 53: 10%\n bucket 52: 20%\n bucket 53: 20%\n bucket 53: 30%\n bucket 52: 30%\n bucket 53: 40%\n bucket 52: 40%\n bucket 53: 50%\n bucket 53: 60%\n bucket 52: 50%\n bucket 53: 70%\nGetting block 54 of 60\n Reserving size (126) for bucket 54\n Calculating Z arrays for bucket 54\n bucket 53: 80%\n bucket 52: 60%\n bucket 53: 90%\n bucket 52: 70%\n bucket 53: 100%\n Entering block accumulator loop for bucket 54:\n Sorting block of length 78 for bucket 53\n (Using difference cover)\n bucket 52: 80%\n bucket 54: 10%\n bucket 52: 90%\n bucket 54: 20%\n bucket 52: 100%\n Sorting block of length 106 for bucket 52\n (Using difference cover)\n bucket 54: 30%\n bucket 54: 40%\n bucket 54: 50%\n bucket 54: 60%\n bucket 54: 70%\n bucket 54: 80%\n bucket 54: 90%\n bucket 54: 100%\n Sorting block of length 64 for bucket 54\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 79 for bucket 53\n Sorting block time: 00:00:00\nReturning block of 107 for bucket 52\n Sorting block time: 00:00:00\nReturning block of 65 for bucket 54\nGetting block 55 of 60\n Reserving size (126) for bucket 55\n Calculating Z arrays for bucket 55\n Entering block accumulator loop for bucket 55:\n bucket 55: 10%\n bucket 55: 20%\n bucket 55: 30%\n bucket 55: 40%\n bucket 55: 50%\n bucket 55: 60%\n bucket 55: 70%\nGetting block 56 of 60\n bucket 55: 80%\n Reserving size (126) for bucket 56\n Calculating Z arrays for bucket 56\n bucket 55: 90%\n bucket 55: 100%\n Sorting block of length 79 for bucket 55\n (Using difference cover)\n Entering block accumulator loop for bucket 56:\n bucket 56: 10%\n bucket 56: 20%\n bucket 56: 30%\n bucket 56: 40%\n bucket 56: 50%\n bucket 56: 60%\n bucket 56: 70%\n bucket 56: 80%\n bucket 56: 90%\n bucket 56: 100%\n Sorting block of length 55 for bucket 56\n Sorting block time: 00:00:00\n (Using difference cover)\nReturning block of 80 for bucket 55\n Sorting block time: 00:00:00\nReturning block of 56 for bucket 56\nGetting block 57 of 60\n Reserving size (126) for bucket 57\n Calculating Z arrays for bucket 57\n Entering block accumulator loop for bucket 57:\n bucket 57: 10%\n bucket 57: 20%\n bucket 57: 30%\n bucket 57: 40%\nGetting block 58 of 60\n Reserving size (126) for bucket 58\n Calculating Z arrays for bucket 58\n bucket 57: 50%\n bucket 57: 60%\n Entering block accumulator loop for bucket 58:\nGetting block 59 of 60\n bucket 58: 10%\n Reserving size (126) for bucket 59\n Calculating Z arrays for bucket 59\n bucket 58: 20%\n bucket 57: 70%\n bucket 58: 30%\n Entering block accumulator loop for bucket 59:\n bucket 58: 40%\n bucket 57: 80%\n bucket 58: 50%\n bucket 59: 10%\n bucket 57: 90%\n bucket 58: 60%\n bucket 59: 20%\n bucket 58: 70%\n bucket 57: 100%\n Sorting block of length 85 for bucket 57\n (Using difference cover)\n bucket 59: 30%\n bucket 58: 80%\n bucket 59: 40%\n bucket 58: 90%\n bucket 59: 50%\n bucket 58: 100%\n Sorting block of length 113 for bucket 58\n (Using difference cover)\n bucket 59: 60%\n bucket 59: 70%\n bucket 59: 80%\n bucket 59: 90%\n bucket 59: 100%\n Sorting block of length 109 for bucket 59\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 86 for bucket 57\n Sorting block time: 00:00:00\nReturning block of 114 for bucket 58\n Sorting block time: 00:00:00\nReturning block of 110 for bucket 59\nGetting block 60 of 60\n Reserving size (126) for bucket 60\n Calculating Z arrays for bucket 60\n Entering block accumulator loop for bucket 60:\n bucket 60: 10%\n bucket 60: 20%\n bucket 60: 30%\n bucket 60: 40%\n bucket 60: 50%\n bucket 60: 60%\n bucket 60: 70%\n bucket 60: 80%\n bucket 60: 90%\n bucket 60: 100%\n Sorting block of length 101 for bucket 60\n (Using difference cover)\n Sorting block time: 00:00:00\nReturning block of 102 for bucket 60\n", "stderr": "Settings:\n Output files: \"genome.*.ht2\"\n Line rate: 6 (line is 64 bytes)\n Lines per side: 1 (side is 64 bytes)\n Offset rate: 4 (one in 16)\n FTable chars: 10\n Strings: unpacked\n Local offset rate: 3 (one in 8)\n Local fTable chars: 6\n Local sequence length: 57344\n Local sequence overlap between two consecutive indexes: 1024\n Endianness: little\n Actual local endianness: little\n Sanity checking: disabled\n Assertions: disabled\n Random seed: 0\n Sizeofs: void*:8, int:4, long:8, size_t:8\nInput files DNA, FASTA:\n genome.fa\nReading reference sizes\n Time reading reference sizes: 00:00:00\nCalculating joined length\nWriting header\nReserving space for joined string\nJoining reference sequences\n Time to join reference sequences: 00:00:00\n Time to read SNPs and splice sites: 00:00:00\nUsing parameters --bmax 126 --dcv 1024\n Doing ahead-of-time memory usage test\n Passed! Constructing with these parameters: --bmax 126 --dcv 1024\nConstructing suffix-array element generator\nConverting suffix-array elements to index image\nAllocating ftab, absorbFtab\nEntering GFM loop\nExited GFM loop\nfchr[A]: 0\nfchr[C]: 1292\nfchr[G]: 2447\nfchr[T]: 3700\nfchr[$]: 5386\nExiting GFM::buildToDisk()\nReturning from initFromVector\nWrote 4196349 bytes to primary GFM file: genome.1.ht2\nWrote 1352 bytes to secondary GFM file: genome.2.ht2\nRe-opening _in1 and _in2 as input streams\nReturning from GFM constructor\nReturning from initFromVector\nWrote 9893 bytes to primary GFM file: genome.5.ht2\nWrote 1352 bytes to secondary GFM file: genome.6.ht2\nRe-opening _in5 and _in5 as input streams\nReturning from HGFM constructor\nHeaders:\n len: 5386\n gbwtLen: 5387\n nodes: 5387\n sz: 1347\n gbwtSz: 1347\n lineRate: 6\n offRate: 4\n offMask: 0xfffffff0\n ftabChars: 10\n eftabLen: 0\n eftabSz: 0\n ftabLen: 1048577\n ftabSz: 4194308\n offsLen: 337\n offsSz: 1348\n lineSz: 64\n sideSz: 64\n sideGbwtSz: 48\n sideGbwtLen: 192\n numSides: 29\n numLines: 29\n gbwtTotLen: 1856\n gbwtTotSz: 1856\n reverse: 0\n linearFM: Yes\nTotal time for call to driver() for forward index: 00:00:00\n10 reads; of these:\n 10 (100.00%) were paired; of these:\n 1 (10.00%) aligned concordantly 0 times\n 9 (90.00%) aligned concordantly exactly 1 time\n 0 (0.00%) aligned concordantly >1 times\n ----\n 1 pairs aligned concordantly 0 times; of these:\n 0 (0.00%) aligned discordantly 1 time\n ----\n 1 pairs aligned 0 times concordantly or discordantly; of these:\n 2 mates make up the pairs; of these:\n 1 (50.00%) aligned 0 times\n 1 (50.00%) aligned exactly 1 time\n 0 (0.00%) aligned >1 times\n95.00% overall alignment rate\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:04:00", "plugin": "core", "name": "end_epoch", "raw_value": "1725001440.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:03:59", "plugin": "core", "name": "start_epoch", "raw_value": "1725001439.0000000"}, {"title": "Memory Allocated (MB)", "value": "21474", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "21474.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "ivar_consensus/1.2.2+galaxy0-0", "has_data": true, "data": {"tool_id": "ivar_consensus", "tool_version": "1.2.2+galaxy0", "test_index": 0, "time_seconds": 38.67888140678406, "inputs": {"input_bam": {"src": "hda", "id": "985d6663d911f90a"}, "gap": true}, "job": {"model_class": "Job", "id": "5637fdc663a90275", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ivar_consensus/ivar_consensus/1.2.2+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T08:20:24.842438", "update_time": "2024-08-30T08:20:41.497899", "galaxy_version": "24.1", "external_id": "gxy-s6wtw", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/9/f/8/dataset_9f8250dd-f0a0-4e6f-b260-ce2b84929477.dat' sorted.bam && samtools mpileup -A -d 0 -Q 0 sorted.bam | ivar consensus -p consensus -q 20 -t 0.0 -m 10 -n N && sed -i \"s|consensus|PC00101P_sub_trimmed_sorted_bam|\" consensus.fa", "user_email": "tests@fake.org", "command_version": "iVar version 1.2.2", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "gap": "true", "filter_depth": "false", "min_depth": "\"10\"", "min_freq": "\"0.0\"", "min_qual": "\"20\""}, "inputs": {"input_bam": {"id": "985d6663d911f90a", "src": "hda", "uuid": "9f8250dd-f0a0-4e6f-b260-ce2b84929477"}}, "outputs": {"consensus": {"id": "ece41ba611a6282f", "src": "hda", "uuid": "ecab68d3-7835-42a9-90e1-e9def8c7f547"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "Minimum Quality: 20\nThreshold: 0\nMinimum depth: 10\nRegions with depth less than minimum depth covered by: N\nReference length: 29790\nPositions with 0 depth: 0\nPositions with depth below 10: 921\n", "tool_stderr": "[mpileup] 1 samples in 1 input files\n[mpileup] Max depth set to maximum value (2147483647)\n", "job_stdout": "", "job_stderr": "", "stdout": "Minimum Quality: 20\nThreshold: 0\nMinimum depth: 10\nRegions with depth less than minimum depth covered by: N\nReference length: 29790\nPositions with 0 depth: 0\nPositions with depth below 10: 921\n", "stderr": "[mpileup] 1 samples in 1 input files\n[mpileup] Max depth set to maximum value (2147483647)\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 08:20:29", "plugin": "core", "name": "end_epoch", "raw_value": "1725006029.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 08:20:28", "plugin": "core", "name": "start_epoch", "raw_value": "1725006028.0000000"}, {"title": "Memory Allocated (MB)", "value": "32641", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "32641.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "lofreq_viterbi/2.1.5+galaxy0-0", "has_data": true, "data": {"tool_id": "lofreq_viterbi", "tool_version": "2.1.5+galaxy0", "test_index": 0, "time_seconds": 31.955985069274902, "inputs": {"reads": {"src": "hda", "id": "e2df7eb2735479d5"}, "reference_source|ref": {"src": "hda", "id": "4524c3857055ff8a"}, "reference_source|ref_selector": "history"}, "job": {"model_class": "Job", "id": "b05101e16344c673", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0", "state": "error", "exit_code": null, "create_time": "2024-08-30T08:14:56.028466", "update_time": "2024-08-30T08:15:07.093029", "galaxy_version": "24.1", "external_id": "gxy-mxx4r", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/1/4/7/dataset_147b9d98-7c47-4639-9741-93de3e07aa31.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && lofreq viterbi --ref 'reference.fa' --defqual 2 --out tmp.bam '/galaxy/server/database/objects/c/2/4/dataset_c249f127-0c77-4e45-b325-b1943a1d8603.dat' && samtools sort --no-PG -T \"${TMPDIR:-.}\" -@ ${GALAXY_SLOTS:-1} -O BAM -o '/galaxy/server/database/objects/f/a/e/dataset_fae0696e-1915-48ba-a79d-695a0d7647c8.dat' tmp.bam", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "adv_options": "{\"bq2_handling\": {\"__current_case__\": 0, \"defqual\": \"2\", \"replace_bq2\": \"keep\"}, \"keepflags\": false}", "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 597, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}"}, "inputs": {"reference_source|ref": {"id": "4524c3857055ff8a", "src": "hda", "uuid": "147b9d98-7c47-4639-9741-93de3e07aa31"}, "reads": {"id": "e2df7eb2735479d5", "src": "hda", "uuid": "c249f127-0c77-4e45-b325-b1943a1d8603"}}, "outputs": {"realigned": {"id": "07fa4861902ecd27", "src": "hda", "uuid": "fae0696e-1915-48ba-a79d-695a0d7647c8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "[bam_sort_core] merging from 0 files and 4 in-memory blocks...\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, exit_code: None, stderr: [bam_sort_core] merging from 0 files and 4 in-memory blocks...\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0, exit_code: None, stderr: [bam_sort_core] merging from 0 files and 4 in-memory blocks...\n."], "status": "failure"}}, {"id": "lofreq_viterbi/2.1.5+galaxy0-1", "has_data": true, "data": {"tool_id": "lofreq_viterbi", "tool_version": "2.1.5+galaxy0", "test_index": 1, "time_seconds": 19.780973434448242, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "minimap2/2.17+galaxy4-0", "has_data": true, "data": {"tool_id": "minimap2", "tool_version": "2.17+galaxy4", "test_index": 0, "time_seconds": 34.85319519042969, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "49ad7011cc545b7a"}, "reference_source|reference_source_selector": "history", "fastq_input|fastq_input1": {"src": "hda", "id": "cb5945baa322dbbe"}, "fastq_input|analysis_type_selector": "sr", "fastq_input|fastq_input_selector": "single"}, "job": {"model_class": "Job", "id": "6dad6b28f2e9d99e", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:37:25.094626", "update_time": "2024-08-30T06:37:40.222370", "galaxy_version": "24.1", "external_id": "gxy-sbknh", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/e/f/7/dataset_ef715652-f344-4b79-8551-30bdfd9f1f4e.dat' reference.fa && minimap2 -x sr -t ${GALAXY_SLOTS:-4} reference.fa '/galaxy/server/database/objects/d/a/1/dataset_da1e98a9-4a7d-4fda-88d0-1ad71c1c61c8.dat' -a | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O BAM -o '/galaxy/server/database/objects/f/b/1/dataset_fb1e1f11-67e0-455c-a0cc-66270e337b22.dat'", "user_email": "tests@fake.org", "command_version": "2.17-r941", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "io_options": "{\"K\": \"\", \"L\": false, \"Q\": false, \"Y\": false, \"c\": false, \"cs\": null, \"eqx\": false, \"output_format\": \"BAM\"}", "alignment_options": "{\"A\": \"\", \"B\": \"\", \"E\": \"\", \"E2\": \"\", \"O\": \"\", \"O2\": \"\", \"no_end_flt\": true, \"s\": \"\", \"splicing\": {\"__current_case__\": 0, \"splice_mode\": \"preset\"}, \"z\": \"\", \"z2\": \"\"}", "mapping_options": "{\"F\": \"\", \"N\": \"\", \"X\": false, \"f\": \"\", \"g\": \"\", \"m\": \"\", \"max_chain_iter\": \"\", \"max_chain_skip\": \"\", \"min_occ_floor\": \"\", \"n\": \"\", \"p\": \"\", \"r\": \"\"}", "indexing_options": "{\"H\": false, \"I\": \"\", \"k\": \"\", \"w\": \"\"}", "fastq_input": "{\"__current_case__\": 0, \"analysis_type_selector\": \"sr\", \"fastq_input1\": {\"values\": [{\"id\": 65, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"single\"}", "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 64, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"fastq_input|fastq_input1": {"id": "cb5945baa322dbbe", "src": "hda", "uuid": "da1e98a9-4a7d-4fda-88d0-1ad71c1c61c8"}, "reference_source|ref_file": {"id": "49ad7011cc545b7a", "src": "hda", "uuid": "ef715652-f344-4b79-8551-30bdfd9f1f4e"}}, "outputs": {"alignment_output": {"id": "84d1b775e9099f9d", "src": "hda", "uuid": "fb1e1f11-67e0-455c-a0cc-66270e337b22"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[M::mm_idx_gen::0.004*0.98] collected minimizers\n[M::mm_idx_gen::0.006*1.91] sorted minimizers\n[M::main::0.006*1.90] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.006*1.90] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.006*1.87] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967\n[M::worker_pipeline::0.010*1.76] mapped 100 sequences\n[M::main] Version: 2.17-r941\n[M::main] CMD: minimap2 -x sr -t 8 -a reference.fa /galaxy/server/database/objects/d/a/1/dataset_da1e98a9-4a7d-4fda-88d0-1ad71c1c61c8.dat\n[M::main] Real time: 0.012 sec; CPU: 0.019 sec; Peak RSS: 0.004 GB\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[M::mm_idx_gen::0.004*0.98] collected minimizers\n[M::mm_idx_gen::0.006*1.91] sorted minimizers\n[M::main::0.006*1.90] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.006*1.90] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.006*1.87] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967\n[M::worker_pipeline::0.010*1.76] mapped 100 sequences\n[M::main] Version: 2.17-r941\n[M::main] CMD: minimap2 -x sr -t 8 -a reference.fa /galaxy/server/database/objects/d/a/1/dataset_da1e98a9-4a7d-4fda-88d0-1ad71c1c61c8.dat\n[M::main] Real time: 0.012 sec; CPU: 0.019 sec; Peak RSS: 0.004 GB\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:37:29", "plugin": "core", "name": "end_epoch", "raw_value": "1724999849.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:37:29", "plugin": "core", "name": "start_epoch", "raw_value": "1724999849.0000000"}, {"title": "Memory Allocated (MB)", "value": "34359", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "34359.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "output_problems": ["Output alignment_output: different than expected, difference (using diff):\n( /tmp/local_bam_converted_to_sam_l5b7inhj.sam v. /tmp/history_bam_converted_to_sam_6la1p67i.sam )\n--- local_file\n+++ history_data\n@@ -1,171 +1,171 @@\n-@HD\tVN:1.3\tSO:coordinate\n+@HD\tVN:1.6\tSO:coordinate\n @SQ\tSN:gi|251831106|ref|NC_012920.1|\tLN:16569\n-@PG\tID:minimap2\tPN:minimap2\tVN:2.5-r572\tCL:minimap2 -a -x sr -t 1 reference.fa /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpChsAAk/files/000/dataset_19.dat\n-M01368:8:000000000-A3GHV:1:1101:6911:8255/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t71S180M\t*\t0\t0\tATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\t*\tNM:i:1\tms:i:350\tAS:i:350\tnn:i:0\ttp:A:P\tcm:i:26\ts1:i:169\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16499,+,71M180S,12,2;\n-M01368:8:000000000-A3GHV:1:1101:18422:19051/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t80S171M\t*\t0\t0\tGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\t*\tNM:i:1\tms:i:332\tAS:i:332\tnn:i:0\ttp:A:P\tcm:i:24\ts1:i:160\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16490,+,80M171S,50,1;\n-M01368:8:000000000-A3GHV:1:1102:10403:6021/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t121S130M\t*\t0\t0\tCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\t*\tNM:i:1\tms:i:250\tAS:i:250\tnn:i:0\ttp:A:P\tcm:i:16\ts1:i:123\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16449,+,121M130S,60,1;\n-M01368:8:000000000-A3GHV:1:1102:10677:23253/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t22S213M16S\t*\t0\t0\tCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTGTCTCTTATACACA\t*\tNM:i:1\tms:i:416\tAS:i:416\tnn:i:0\ttp:A:P\tcm:i:32\ts1:i:200\ts2:i:0\n-M01368:8:000000000-A3GHV:1:1102:18842:24844/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t105S146M\t*\t0\t0\tCACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCT\t*\tNM:i:1\tms:i:282\tAS:i:282\tnn:i:0\ttp:A:P\tcm:i:19\ts1:i:137\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16465,+,105M146S,60,1;\n-M01368:8:000000000-A3GHV:1:1102:21788:11027/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t35S213M3S\t*\t0\t0\tGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTG\t*\tNM:i:1\tms:i:416\tAS:i:416\tnn:i:0\ttp:A:P\tcm:i:32\ts1:i:200\ts2:i:0\n-M01368:8:000000000-A3GHV:1:1102:5983:21093/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t80S171M\t*\t0\t0\tGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\t*\tNM:i:1\tms:i:332\tAS:i:332\tnn:i:0\ttp:A:P\tcm:i:24\ts1:i:160\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16490,+,80M171S,50,1;\n-M01368:8:000000000-A3GHV:1:1102:7765:18353/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t119S132M\t*\t0\t0\tCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTC\t*\tNM:i:1\tms:i:254\tAS:i:254\tnn:i:0\ttp:A:P\tcm:i:16\ts1:i:123\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16451,+,119M132S,60,1;\n-M01368:8:000000000-A3GHV:1:1103:10405:17879/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t80S171M\t*\t0\t0\tGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\t*\tNM:i:1\tms:i:332\tAS:i:332\tnn:i:0\ttp:A:P\tcm:i:24\ts1:i:160\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16490,+,80M171S,50,1;\n-M01368:8:000000000-A3GHV:1:1103:13493:8205/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t96S155M\t*\t0\t0\tGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATT\t*\tNM:i:1\tms:i:300\tAS:i:300\tnn:i:0\ttp:A:P\tcm:i:20\ts1:i:142\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16474,+,96M155S,60,1;\n-M01368:8:000000000-A3GHV:1:1103:14060:21273/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t80S156M15S\t*\t0\t0\tGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTACTGTCTCTTATACAC\t*\tNM:i:1\tms:i:302\tAS:i:302\tnn:i:0\ttp:A:P\tcm:i:22\ts1:i:150\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16490,+,80M171S,50,1;\n-M01368:8:000000000-A3GHV:1:1103:14528:12993/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t113S138M\t*\t0\t0\tGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGAT\t*\tNM:i:1\tms:i:266\tAS:i:266\tnn:i:0\ttp:A:P\tcm:i:17\ts1:i:130\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16457,+,113M138S,60,1;\n-M01368:8:000000000-A3GHV:1:1103:17657:20856/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t90S161M\t*\t0\t0\tAAAGCGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTAT\t*\tNM:i:1\tms:i:312\tAS:i:312\tnn:i:0\ttp:A:P\tcm:i:22\ts1:i:150\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16480,+,90M161S,60,2;\n-M01368:8:000000000-A3GHV:1:1103:25519:6301/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t18S184M49S\t*\t0\t0\tAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGCATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATTTCGT\t*\tNM:i:2\tms:i:348\tAS:i:348\tnn:i:0\ttp:A:P\tcm:i:21\ts1:i:157\ts2:i:0\n-M01368:8:000000000-A3GHV:1:1103:6074:6549/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t108S143M\t*\t0\t0\tTAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTG\t*\tNM:i:1\tms:i:276\tAS:i:276\tnn:i:0\ttp:A:P\tcm:i:19\ts1:i:137\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16462,+,108M143S,60,1;\n-M01368:8:000000000-A3GHV:1:1104:11572:8264/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t80S171M\t*\t0\t0\tGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\t*\tNM:i:1\tms:i:332\tAS:i:332\tnn:i:0\ttp:A:P\tcm:i:24\ts1:i:160\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16490,+,80M171S,50,1;\n-M01368:8:000000000-A3GHV:1:1104:12288:20635/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t105S146M\t*\t0\t0\tCACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGCCGCAGCATCTGTCTTTGATTCCTGCCT\t*\tNM:i:3\tms:i:262\tAS:i:262\tnn:i:0\ttp:A:P\tcm:i:14\ts1:i:109\ts2:i:0\tSA:Z:gi|251831106|ref|NC_012920.1|,16465,+,105M146S,60,1;\n-M01368:8:000000000-A3GHV:1:1104:13832:4398/1\t0\tgi|251831106|ref|NC_012920.1|\t1\t60\t7S132M112S\t*\t0\t0\tCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGACAAAAAAAAACACACAACAACCAACACCCAGTAGACTAGTGCGTC\t*\tNM:i:1\tms:i:254\tAS:i:254\tnn:i:0\ttp:A:P\tcm:i:16\ts1:i:123\ts2:i:0\n********\n*SNIP 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AGACATCACGATG\t*\tNM:i:1\tms:i:92\tAS:i:92\tnn:i:0\ttp:A:P\tcm:i:3\ts1:i:34\ts2:i:0\tde:f:0.0196\tSA:Z:gi|251831106|ref|NC_012920.1|,1,-,51S200M,60,1;\trl:i:0\n+M01368:8:000000000-A3GHV:1:1105:13575:19255/1\t2064\tgi|251831106|ref|NC_012920.1|\t16520\t11\t50M201H\t*\t0\t0\tCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\t*\tNM:i:1\tms:i:90\tAS:i:90\tnn:i:0\ttp:A:P\tcm:i:3\ts1:i:34\ts2:i:0\tde:f:0.02\tSA:Z:gi|251831106|ref|NC_012920.1|,1,-,50S201M,60,3;\trl:i:0\n+M01368:8:000000000-A3GHV:1:1108:16350:22621/1\t2064\tgi|251831106|ref|NC_012920.1|\t16520\t11\t50M201H\t*\t0\t0\tCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\t*\tNM:i:1\tms:i:90\tAS:i:90\tnn:i:0\ttp:A:P\tcm:i:3\ts1:i:34\ts2:i:0\tde:f:0.02\tSA:Z:gi|251831106|ref|NC_012920.1|,1,-,50S201M,60,1;\trl:i:0\n+M01368:8:000000000-A3GHV:1:1108:21791:23272/1\t2064\tgi|251831106|ref|NC_012920.1|\t16522\t11\t48M203H\t*\t0\t0\tTAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\t*\tNM:i:1\tms:i:86\tAS:i:86\tnn:i:0\ttp:A:P\tcm:i:3\ts1:i:34\ts2:i:0\tde:f:0.0208\tSA:Z:gi|251831106|ref|NC_012920.1|,1,-,48S203M,60,1;\trl:i:0\n+M01368:8:000000000-A3GHV:1:1105:7169:17145/1\t2048\tgi|251831106|ref|NC_012920.1|\t16525\t11\t45M206H\t*\t0\t0\tAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\t*\tNM:i:1\tms:i:86\tAS:i:86\tnn:i:0\ttp:A:P\tcm:i:3\ts1:i:34\ts2:i:0\tde:f:0.0222\tSA:Z:gi|251831106|ref|NC_012920.1|,1,+,45S206M,60,1;\trl:i:0\n+M01368:8:000000000-A3GHV:1:1114:16639:15258/1\t2048\tgi|251831106|ref|NC_012920.1|\t16527\t11\t43M208H\t*\t0\t0\tCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\t*\tNM:i:0\tms:i:86\tAS:i:86\tnn:i:0\ttp:A:P\tcm:i:3\ts1:i:34\ts2:i:0\tde:f:0\tSA:Z:gi|251831106|ref|NC_012920.1|,1,+,43S208M,60,4;\trl:i:0\n+M01368:8:000000000-A3GHV:1:1103:25465:20010/1\t2064\tgi|251831106|ref|NC_012920.1|\t16527\t11\t88H43M120H\t*\t0\t0\tCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\t*\tNM:i:0\tms:i:86\tAS:i:86\tnn:i:0\ttp:A:P\tcm:i:3\ts1:i:34\ts2:i:0\tde:f:0\tSA:Z:gi|251831106|ref|NC_012920.1|,1,-,131S120M,60,2;\trl:i:0\n+M01368:8:000000000-A3GHV:1:1106:15481:16176/1\t2064\tgi|251831106|ref|NC_012920.1|\t16527\t11\t5H43M203H\t*\t0\t0\tCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\t*\tNM:i:0\tms:i:86\tAS:i:86\tnn:i:0\ttp:A:P\tcm:i:3\ts1:i:34\ts2:i:0\tde:f:0\tSA:Z:gi|251831106|ref|NC_012920.1|,1,-,48S203M,60,1;\trl:i:0\n+M01368:8:000000000-A3GHV:1:1108:7626:10048/1\t2064\tgi|251831106|ref|NC_012920.1|\t16527\t11\t70H43M138H\t*\t0\t0\tCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\t*\tNM:i:0\tms:i:86\tAS:i:86\tnn:i:0\ttp:A:P\tcm:i:3\ts1:i:34\ts2:i:0\tde:f:0\tSA:Z:gi|251831106|ref|NC_012920.1|,1,-,113S138M,60,1;\trl:i:0\n+M01368:8:000000000-A3GHV:1:1109:19224:11655/1\t2048\tgi|251831106|ref|NC_012920.1|\t16530\t11\t40M211H\t*\t0\t0\tAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\t*\tNM:i:0\tms:i:80\tAS:i:80\tnn:i:0\ttp:A:P\tcm:i:3\ts1:i:34\ts2:i:0\tde:f:0\tSA:Z:gi|251831106|ref|NC_012920.1|,1,+,40S186M25S,60,2;\trl:i:0\n"], "status": "failure"}}, {"id": "minimap2/2.17+galaxy4-1", "has_data": true, "data": {"tool_id": "minimap2", "tool_version": "2.17+galaxy4", "test_index": 1, "time_seconds": 33.98173189163208, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "5ff83bf4b24d9fa8"}, "reference_source|reference_source_selector": "history", "fastq_input|fastq_input1": {"src": "hda", "id": "b1425eef57bb8f78"}, "fastq_input|analysis_type_selector": "sr", "fastq_input|fastq_input_selector": "single", "io_options|output_format": "CRAM"}, "job": {"model_class": "Job", "id": "0586d4449e970e5d", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:38:00.280652", "update_time": "2024-08-30T06:38:13.806463", "galaxy_version": "24.1", "external_id": "gxy-lxgk7", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/1/6/2/dataset_16296260-be80-406b-9dfb-729872ab7de4.dat' reference.fa && minimap2 -x sr -t ${GALAXY_SLOTS:-4} reference.fa '/galaxy/server/database/objects/b/9/1/dataset_b915ccf6-2605-4bdb-9e6d-1e7c67a0ce75.dat' -a | samtools sort -T \"${TMPDIR:-.}\" -@${GALAXY_SLOTS:-2} -O CRAM --reference reference.fa --output-fmt-option no_ref -o '/galaxy/server/database/objects/d/6/a/dataset_d6a7badf-7d7c-4b13-9c85-350228f18c6c.dat'", "user_email": "tests@fake.org", "command_version": "2.17-r941", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "io_options": "{\"K\": \"\", \"L\": false, \"Q\": false, \"Y\": false, \"c\": false, \"cs\": null, \"eqx\": false, \"output_format\": \"CRAM\"}", "alignment_options": "{\"A\": \"\", \"B\": \"\", \"E\": \"\", \"E2\": \"\", \"O\": \"\", \"O2\": \"\", \"no_end_flt\": true, \"s\": \"\", \"splicing\": {\"__current_case__\": 0, \"splice_mode\": \"preset\"}, \"z\": \"\", \"z2\": \"\"}", "mapping_options": "{\"F\": \"\", \"N\": \"\", \"X\": false, \"f\": \"\", \"g\": \"\", \"m\": \"\", \"max_chain_iter\": \"\", \"max_chain_skip\": \"\", \"min_occ_floor\": \"\", \"n\": \"\", \"p\": \"\", \"r\": \"\"}", "indexing_options": "{\"H\": false, \"I\": \"\", \"k\": \"\", \"w\": \"\"}", "fastq_input": "{\"__current_case__\": 0, \"analysis_type_selector\": \"sr\", \"fastq_input1\": {\"values\": [{\"id\": 68, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"single\"}", "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 67, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"fastq_input|fastq_input1": {"id": "b1425eef57bb8f78", "src": "hda", "uuid": "b915ccf6-2605-4bdb-9e6d-1e7c67a0ce75"}, "reference_source|ref_file": {"id": "5ff83bf4b24d9fa8", "src": "hda", "uuid": "16296260-be80-406b-9dfb-729872ab7de4"}}, "outputs": {"alignment_output": {"id": "24386a768384a20a", "src": "hda", "uuid": "d6a7badf-7d7c-4b13-9c85-350228f18c6c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[M::mm_idx_gen::0.004*1.05] collected minimizers\n[M::mm_idx_gen::0.006*2.20] sorted minimizers\n[M::main::0.006*2.19] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.006*2.19] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.006*2.15] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967\n[M::worker_pipeline::0.009*2.04] mapped 100 sequences\n[M::main] Version: 2.17-r941\n[M::main] CMD: minimap2 -x sr -t 8 -a reference.fa /galaxy/server/database/objects/b/9/1/dataset_b915ccf6-2605-4bdb-9e6d-1e7c67a0ce75.dat\n[M::main] Real time: 0.011 sec; CPU: 0.020 sec; Peak RSS: 0.004 GB\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[M::mm_idx_gen::0.004*1.05] collected minimizers\n[M::mm_idx_gen::0.006*2.20] sorted minimizers\n[M::main::0.006*2.19] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.006*2.19] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.006*2.15] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967\n[M::worker_pipeline::0.009*2.04] mapped 100 sequences\n[M::main] Version: 2.17-r941\n[M::main] CMD: minimap2 -x sr -t 8 -a reference.fa /galaxy/server/database/objects/b/9/1/dataset_b915ccf6-2605-4bdb-9e6d-1e7c67a0ce75.dat\n[M::main] Real time: 0.011 sec; CPU: 0.020 sec; Peak RSS: 0.004 GB\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:38:02", "plugin": "core", "name": "end_epoch", "raw_value": "1724999882.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:38:02", "plugin": "core", "name": "start_epoch", "raw_value": "1724999882.0000000"}, {"title": "Memory Allocated (MB)", "value": "34359", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "34359.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "minimap2/2.17+galaxy4-2", "has_data": true, "data": {"tool_id": "minimap2", "tool_version": "2.17+galaxy4", "test_index": 2, "time_seconds": 11.632200479507446, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "minimap2/2.17+galaxy4-3", "has_data": true, "data": {"tool_id": "minimap2", "tool_version": "2.17+galaxy4", "test_index": 3, "time_seconds": 11.657412052154541, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "minimap2/2.17+galaxy4-4", "has_data": true, "data": {"tool_id": "minimap2", "tool_version": "2.17+galaxy4", "test_index": 4, "time_seconds": 12.04873514175415, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "minimap2/2.17+galaxy4-5", "has_data": true, "data": {"tool_id": "minimap2", "tool_version": "2.17+galaxy4", "test_index": 5, "status": "skip"}}, {"id": "minimap2/2.17+galaxy4-6", "has_data": true, "data": {"tool_id": "minimap2", "tool_version": "2.17+galaxy4", "test_index": 6, "status": "skip"}}, {"id": "minimap2/2.17+galaxy4-7", "has_data": true, "data": {"tool_id": "minimap2", "tool_version": "2.17+galaxy4", "test_index": 7, "time_seconds": 33.03546094894409, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "26aeea36ae88f410"}, "reference_source|reference_source_selector": "history", "fastq_input|fastq_input1": {"src": "hda", "id": "26aeea36ae88f410"}, "fastq_input|analysis_type_selector": "ava-ont", "fastq_input|fastq_input_selector": "single", "io_options|output_format": "paf"}, "job": {"model_class": "Job", "id": "8fe67bcff76f53cb", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:39:09.971872", "update_time": "2024-08-30T06:39:22.651792", "galaxy_version": "24.1", "external_id": "gxy-xpmww", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/3/2/7/dataset_32706fef-eece-4fc1-836c-b3dc17d0bfc4.dat' reference.fa && minimap2 -x ava-ont -t ${GALAXY_SLOTS:-4} reference.fa '/galaxy/server/database/objects/3/2/7/dataset_32706fef-eece-4fc1-836c-b3dc17d0bfc4.dat' > '/galaxy/server/database/objects/a/f/b/dataset_afbe13c3-0e18-40c4-8541-0ff2d37d18ea.dat'", "user_email": "tests@fake.org", "command_version": "2.17-r941", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "io_options": "{\"K\": \"\", \"L\": false, \"Q\": false, \"Y\": false, \"c\": false, \"cs\": null, \"eqx\": false, \"output_format\": \"paf\"}", "alignment_options": "{\"A\": \"\", \"B\": \"\", \"E\": \"\", \"E2\": \"\", \"O\": \"\", \"O2\": \"\", \"no_end_flt\": true, \"s\": \"\", \"splicing\": {\"__current_case__\": 0, \"splice_mode\": \"preset\"}, \"z\": \"\", \"z2\": \"\"}", "mapping_options": "{\"F\": \"\", \"N\": \"\", \"X\": false, \"f\": \"\", \"g\": \"\", \"m\": \"\", \"max_chain_iter\": \"\", \"max_chain_skip\": \"\", \"min_occ_floor\": \"\", \"n\": \"\", \"p\": \"\", \"r\": \"\"}", "indexing_options": "{\"H\": false, \"I\": \"\", \"k\": \"\", \"w\": \"\"}", "fastq_input": "{\"__current_case__\": 0, \"analysis_type_selector\": \"ava-ont\", \"fastq_input1\": {\"values\": [{\"id\": 79, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"single\"}", "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 79, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "26aeea36ae88f410", "src": "hda", "uuid": "32706fef-eece-4fc1-836c-b3dc17d0bfc4"}, "fastq_input|fastq_input1": {"id": "26aeea36ae88f410", "src": "hda", "uuid": "32706fef-eece-4fc1-836c-b3dc17d0bfc4"}}, "outputs": {"alignment_output": {"id": "3925f521cb40181f", "src": "hda", "uuid": "afbe13c3-0e18-40c4-8541-0ff2d37d18ea"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[M::mm_idx_gen::0.015*0.90] collected minimizers\n[M::mm_idx_gen::0.028*2.65] sorted minimizers\n[M::main::0.028*2.65] loaded/built the index for 25 target sequence(s)\n[M::mm_mapopt_update::0.030*2.54] mid_occ = 3\n[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 25\n[M::mm_idx_stat::0.032*2.47] distinct minimizers: 80111 (99.87% are singletons); average occurrences: 1.002; average spacing: 2.935\n[M::worker_pipeline::0.041*2.73] mapped 25 sequences\n[M::main] Version: 2.17-r941\n[M::main] CMD: minimap2 -x ava-ont -t 8 reference.fa /galaxy/server/database/objects/3/2/7/dataset_32706fef-eece-4fc1-836c-b3dc17d0bfc4.dat\n[M::main] Real time: 0.047 sec; CPU: 0.117 sec; Peak RSS: 0.012 GB\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[M::mm_idx_gen::0.015*0.90] collected minimizers\n[M::mm_idx_gen::0.028*2.65] sorted minimizers\n[M::main::0.028*2.65] loaded/built the index for 25 target sequence(s)\n[M::mm_mapopt_update::0.030*2.54] mid_occ = 3\n[M::mm_idx_stat] kmer size: 15; skip: 5; is_hpc: 0; #seq: 25\n[M::mm_idx_stat::0.032*2.47] distinct minimizers: 80111 (99.87% are singletons); average occurrences: 1.002; average spacing: 2.935\n[M::worker_pipeline::0.041*2.73] mapped 25 sequences\n[M::main] Version: 2.17-r941\n[M::main] CMD: minimap2 -x ava-ont -t 8 reference.fa /galaxy/server/database/objects/3/2/7/dataset_32706fef-eece-4fc1-836c-b3dc17d0bfc4.dat\n[M::main] Real time: 0.047 sec; CPU: 0.117 sec; Peak RSS: 0.012 GB\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:39:12", "plugin": "core", "name": "end_epoch", "raw_value": "1724999952.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:39:11", "plugin": "core", "name": "start_epoch", "raw_value": "1724999951.0000000"}, {"title": "Memory Allocated (MB)", "value": "34359", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "34359.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": "8.0000000"}]}, "status": "success"}}, {"id": "minimap2/2.17+galaxy4-8", "has_data": true, "data": {"tool_id": "minimap2", "tool_version": "2.17+galaxy4", "test_index": 8, "time_seconds": 32.32361936569214, "inputs": {"reference_source|ref_file": {"src": "hda", "id": "11fe53cbfa2ecb95"}, "reference_source|reference_source_selector": "history", "fastq_input|fastq_input1": {"src": "hda", "id": "11fe53cbfa2ecb95"}, "fastq_input|analysis_type_selector": "self-homology", "fastq_input|fastq_input_selector": "single"}, "job": {"model_class": "Job", "id": "225b6b2bd98a75f9", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy4", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:39:42.301110", "update_time": "2024-08-30T06:39:54.969375", "galaxy_version": "24.1", "external_id": "gxy-b9cp4", "handler": null, "job_runner_name": null, "command_line": "ln -f -s '/galaxy/server/database/objects/3/f/3/dataset_3f39ad3c-eb67-43c4-b0e3-3f7749445f5d.dat' reference.fa && minimap2 -DP -k19 -w19 -m200 -t ${GALAXY_SLOTS:-4} reference.fa '/galaxy/server/database/objects/3/f/3/dataset_3f39ad3c-eb67-43c4-b0e3-3f7749445f5d.dat' -a | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O BAM -o '/galaxy/server/database/objects/1/a/0/dataset_1a0c94a5-69f3-4a56-8604-bd933f1360c0.dat'", "user_email": "tests@fake.org", "command_version": "2.17-r941", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "io_options": "{\"K\": \"\", \"L\": false, \"Q\": false, \"Y\": false, \"c\": false, \"cs\": null, \"eqx\": false, \"output_format\": \"BAM\"}", "alignment_options": "{\"A\": \"\", \"B\": \"\", \"E\": \"\", \"E2\": \"\", \"O\": \"\", \"O2\": \"\", \"no_end_flt\": true, \"s\": \"\", \"splicing\": {\"__current_case__\": 0, \"splice_mode\": \"preset\"}, \"z\": \"\", \"z2\": \"\"}", "mapping_options": "{\"F\": \"\", \"N\": \"\", \"X\": false, \"f\": \"\", \"g\": \"\", \"m\": \"\", \"max_chain_iter\": \"\", \"max_chain_skip\": \"\", \"min_occ_floor\": \"\", \"n\": \"\", \"p\": \"\", \"r\": \"\"}", "indexing_options": "{\"H\": false, \"I\": \"\", \"k\": \"\", \"w\": \"\"}", "fastq_input": "{\"__current_case__\": 0, \"analysis_type_selector\": \"self-homology\", \"fastq_input1\": {\"values\": [{\"id\": 81, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"single\"}", "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 81, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"}, "inputs": {"reference_source|ref_file": {"id": "11fe53cbfa2ecb95", "src": "hda", "uuid": "3f39ad3c-eb67-43c4-b0e3-3f7749445f5d"}, "fastq_input|fastq_input1": {"id": "11fe53cbfa2ecb95", "src": "hda", "uuid": "3f39ad3c-eb67-43c4-b0e3-3f7749445f5d"}}, "outputs": {"alignment_output": {"id": "4c4a43e5488d989e", "src": "hda", "uuid": "1a0c94a5-69f3-4a56-8604-bd933f1360c0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[M::mm_idx_gen::0.005*0.84] collected minimizers\n[M::mm_idx_gen::0.007*1.61] sorted minimizers\n[M::main::0.007*1.60] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.007*1.57] mid_occ = 9\n[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.008*1.56] distinct minimizers: 2920 (98.42% are singletons); average occurrences: 1.022; average spacing: 10.057\n[M::worker_pipeline::0.036*1.09] mapped 1 sequences\n[M::main] Version: 2.17-r941\n[M::main] CMD: minimap2 -DP -k19 -w19 -m200 -t 8 -a reference.fa /galaxy/server/database/objects/3/f/3/dataset_3f39ad3c-eb67-43c4-b0e3-3f7749445f5d.dat\n[M::main] Real time: 0.038 sec; CPU: 0.041 sec; Peak RSS: 0.011 GB\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[M::mm_idx_gen::0.005*0.84] collected minimizers\n[M::mm_idx_gen::0.007*1.61] sorted minimizers\n[M::main::0.007*1.60] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.007*1.57] mid_occ = 9\n[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.008*1.56] distinct minimizers: 2920 (98.42% are singletons); average occurrences: 1.022; average spacing: 10.057\n[M::worker_pipeline::0.036*1.09] mapped 1 sequences\n[M::main] Version: 2.17-r941\n[M::main] CMD: minimap2 -DP -k19 -w19 -m200 -t 8 -a reference.fa /galaxy/server/database/objects/3/f/3/dataset_3f39ad3c-eb67-43c4-b0e3-3f7749445f5d.dat\n[M::main] Real time: 0.038 sec; CPU: 0.041 sec; Peak RSS: 0.011 GB\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:39:43", "plugin": "core", "name": "end_epoch", "raw_value": "1724999983.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:39:43", "plugin": "core", "name": "start_epoch", "raw_value": "1724999983.0000000"}, {"title": "Memory Allocated (MB)", "value": "34359", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "34359.0000000"}, {"title": "Cores Allocated", "value": "8", "plugin": "core", "name": "galaxy_slots", "raw_value": 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"uuid": "8f603424-c8c7-4e36-9a74-7b2b25b07bfd"}}, "outputs": {"output": {"id": "8becb61cdaf1d973", "src": "hda", "uuid": "928ca242-2c31-47e8-a13b-8171e0433503"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 07:10:44", "plugin": "core", "name": "end_epoch", "raw_value": "1725001844.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:10:44", "plugin": "core", "name": "start_epoch", "raw_value": "1725001844.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_merge/1.9-3", "has_data": true, "data": {"tool_id": "samtools_merge", "tool_version": "1.9", "test_index": 3, "time_seconds": 35.51538300514221, "inputs": {"bamfiles": [{"src": "hda", "id": "2f77b5b427f883a8"}, {"src": "hda", "id": "7be2ee106e0855b4"}], "idrg": true, "idpg": true}, "job": {"model_class": "Job", "id": "0875251307385fa4", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:09:30.545762", "update_time": "2024-08-30T07:09:43.954619", "galaxy_version": "24.1", "external_id": "gxy-r2mhf", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/b/7/9/dataset_b7966f03-a0e7-4e14-9e40-b215096d001a.dat' 0.sam && ln -s '/galaxy/server/database/objects/8/b/8/dataset_8b8328be-5f74-4286-b149-d4336b7ecd0a.dat' 1.sam && samtools merge -@ $addthreads -s 1 -f -c -p /galaxy/server/database/objects/7/0/c/dataset_70cbdc2c-a319-4044-a2c4-09e18bcd8e7e.dat 0.sam 1.sam", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"1\"", "idpg": "true", "idrg": "true", "headerbam": null, "region": null}, "inputs": {"bamfiles": {"id": "2f77b5b427f883a8", "src": "hda", "uuid": "b7966f03-a0e7-4e14-9e40-b215096d001a"}, "bamfiles1": {"id": "2f77b5b427f883a8", "src": "hda", "uuid": "b7966f03-a0e7-4e14-9e40-b215096d001a"}, "bamfiles2": {"id": "7be2ee106e0855b4", "src": "hda", "uuid": "8b8328be-5f74-4286-b149-d4336b7ecd0a"}}, "outputs": {"output": {"id": "6a8e2e23745f6c0d", "src": "hda", "uuid": "70cbdc2c-a319-4044-a2c4-09e18bcd8e7e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bam_translate] PG tag \"colt\" on read \"r001\" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[bam_translate] PG tag \"colt\" on read \"r001\" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 07:09:32", "plugin": "core", "name": "end_epoch", "raw_value": "1725001772.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:09:32", "plugin": "core", "name": "start_epoch", "raw_value": "1725001772.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_merge/1.9-3", "has_data": true, "data": {"tool_id": "samtools_merge", "tool_version": "1.9", "test_index": 3, "time_seconds": 35.39013075828552, "inputs": {"bamfiles": [{"src": "hda", "id": "ebfe298ca7673843"}, {"src": "hda", "id": "5ea88fc908404cc1"}], "idrg": true, "idpg": true}, "job": {"model_class": "Job", "id": "99f189e7e8c10e7f", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:11:16.938374", "update_time": "2024-08-30T07:11:30.705242", "galaxy_version": "24.1", "external_id": "gxy-pbrq9", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/c/6/b/dataset_c6bc6eff-bf84-4f3e-8509-7e67aa53313e.dat' 0.sam && ln -s '/galaxy/server/database/objects/4/6/3/dataset_4636d592-a755-4b84-bb14-51fd14b63f2d.dat' 1.sam && samtools merge -@ $addthreads -s 1 -f -c -p /galaxy/server/database/objects/7/c/a/dataset_7caa53d4-048b-43cd-b2bb-41b64fa0bf9e.dat 0.sam 1.sam", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"bam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"1\"", "idpg": "true", "idrg": "true", "headerbam": null, "region": null}, "inputs": {"bamfiles": {"id": "ebfe298ca7673843", "src": "hda", "uuid": "c6bc6eff-bf84-4f3e-8509-7e67aa53313e"}, "bamfiles1": {"id": "ebfe298ca7673843", "src": "hda", "uuid": "c6bc6eff-bf84-4f3e-8509-7e67aa53313e"}, "bamfiles2": {"id": "5ea88fc908404cc1", "src": "hda", "uuid": "4636d592-a755-4b84-bb14-51fd14b63f2d"}}, "outputs": {"output": {"id": "8d1efb7cd327b8fe", "src": "hda", "uuid": "7caa53d4-048b-43cd-b2bb-41b64fa0bf9e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bam_translate] PG tag \"colt\" on read \"r001\" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[bam_translate] PG tag \"colt\" on read \"r001\" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 07:11:19", "plugin": "core", "name": "end_epoch", "raw_value": "1725001879.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:11:19", "plugin": "core", "name": "start_epoch", "raw_value": "1725001879.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "samtools_merge/1.9-4", "has_data": true, "data": {"tool_id": "samtools_merge", "tool_version": "1.9", "test_index": 4, "time_seconds": 11.87742018699646, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "samtools_merge/1.9-4", "has_data": true, "data": {"tool_id": "samtools_merge", "tool_version": "1.9", "test_index": 4, "time_seconds": 34.57085943222046, "inputs": {"bamfiles": [{"src": "hda", "id": "1ea5da098f90d41d"}, {"src": "hda", "id": "8e847d9dfbfeb264"}]}, "job": {"model_class": "Job", "id": "5a36e3f3b94568a8", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/samtools_merge/samtools_merge/1.9", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:11:51.665638", "update_time": "2024-08-30T07:12:05.514248", "galaxy_version": "24.1", "external_id": "gxy-gdmqm", "handler": null, "job_runner_name": null, "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -O sam -o 0.sam '/galaxy/server/database/objects/e/a/6/dataset_ea6f5ffa-8b74-4850-a6a3-ec0304ac7d28.dat' && samtools sort -@ $addthreads -m ${GALAXY_MEMORY_MB:-768}M -T sorttemp -O sam -o 1.sam '/galaxy/server/database/objects/c/f/8/dataset_cf881e55-8bab-452a-92c6-6a3536da420a.dat' && samtools merge -@ $addthreads -s 1 -f /galaxy/server/database/objects/d/3/7/dataset_d3769a2c-a2fa-4656-8657-7ae5f6d6fb15.dat 0.sam 1.sam", "user_email": "tests@fake.org", "command_version": "Version: 1.9 (using htslib 1.9)", "params": {"__input_ext": "\"sam\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "seed": "\"1\"", "idpg": "false", "idrg": "false", "headerbam": null, "region": null}, "inputs": {"bamfiles": {"id": "1ea5da098f90d41d", "src": "hda", "uuid": "ea6f5ffa-8b74-4850-a6a3-ec0304ac7d28"}, "bamfiles1": {"id": "1ea5da098f90d41d", "src": "hda", "uuid": "ea6f5ffa-8b74-4850-a6a3-ec0304ac7d28"}, "bamfiles2": {"id": "8e847d9dfbfeb264", "src": "hda", "uuid": "cf881e55-8bab-452a-92c6-6a3536da420a"}}, "outputs": {"output": {"id": "e80412c71a16da9b", "src": "hda", "uuid": "d3769a2c-a2fa-4656-8657-7ae5f6d6fb15"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "[bam_translate] PG tag \"colt\" on read \"r001\" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "[bam_translate] PG tag \"colt\" on read \"r001\" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 07:11:53", "plugin": "core", "name": "end_epoch", "raw_value": "1725001913.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:11:53", "plugin": "core", "name": "start_epoch", "raw_value": "1725001913.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-0", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 0, "time_seconds": 56.08265447616577, "inputs": {"adata": {"src": "hda", "id": "84f146f22d18641a"}, "format": "png", "method|type|basis": "umap", "method|type|color": "HES4", "method|type|type": "basis", "method|use_raw": true, "method|sort_order": true, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|color_map": "inferno", "method|plot|palette": "inferno", "method|plot|frameon": true, "method|plot|size": "1", "method|method": "pl.scatter", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "7b7320d72f9e293c", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:20:08.350354", "update_time": "2024-08-30T07:20:44.581517", "galaxy_version": "24.1", "external_id": "gxy-7xk7s", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/c/f/0/dataset_cf0ad3c2-7cbd-49f1-8331-5c0c196f1cff.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/263/configs/tmpn2gpxabo' > '/galaxy/server/database/objects/c/0/6/dataset_c067c807-39a6-4eec-851a-401652598aa1.dat' && python '/galaxy/server/database/jobs_directory/000/263/configs/tmpn2gpxabo' >> '/galaxy/server/database/objects/c/0/6/dataset_c067c807-39a6-4eec-851a-401652598aa1.dat' && ls . >> '/galaxy/server/database/objects/c/0/6/dataset_c067c807-39a6-4eec-851a-401652598aa1.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"groups\": \"\", \"method\": \"pl.scatter\", \"plot\": {\"color_map\": \"inferno\", \"components\": [], \"frameon\": true, \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"palette\": \"inferno\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\"}, \"sort_order\": true, \"type\": {\"__current_case__\": 1, \"basis\": \"umap\", \"color\": \"HES4\", \"type\": \"basis\"}, \"use_raw\": true}", "format": "\"png\""}, "inputs": {"adata": {"id": "84f146f22d18641a", "src": "hda", "uuid": "cf0ad3c2-7cbd-49f1-8331-5c0c196f1cff"}}, "outputs": {"hidden_output": {"id": "df55a8436b219c37", "src": "hda", "uuid": "c067c807-39a6-4eec-851a-401652598aa1"}, "out_png": {"id": "081a75b2a91db55b", "src": "hda", "uuid": "077337ce-506f-43e3-8844-fd072618ba53"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file umap.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: saving figure to file umap.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:20:28", "plugin": "core", "name": "end_epoch", "raw_value": "1725002428.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:20:24", "plugin": "core", "name": "start_epoch", "raw_value": "1725002424.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-0", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 0, "time_seconds": 36.27288031578064, "inputs": {"adata": {"src": "hda", "id": "a5f5c45115dba622"}, "format": "png", "method|type|basis": "umap", "method|type|color": "HES4", "method|type|type": "basis", "method|use_raw": true, "method|sort_order": true, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|color_map": "inferno", "method|plot|palette": "inferno", "method|plot|frameon": true, "method|plot|size": "1", "method|method": "pl.scatter", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "6c555ae15f749b36", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:37:10.742126", "update_time": "2024-08-30T07:37:27.374774", "galaxy_version": "24.1", "external_id": "gxy-kz4g9", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/b/5/2/dataset_b52e5347-c77f-4e7b-814f-e4d7d815474d.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/316/configs/tmprxlvy98d' > '/galaxy/server/database/objects/a/8/1/dataset_a816cdfe-225d-4713-b392-29a31bd2a559.dat' && python '/galaxy/server/database/jobs_directory/000/316/configs/tmprxlvy98d' >> '/galaxy/server/database/objects/a/8/1/dataset_a816cdfe-225d-4713-b392-29a31bd2a559.dat' && ls . >> '/galaxy/server/database/objects/a/8/1/dataset_a816cdfe-225d-4713-b392-29a31bd2a559.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"groups\": \"\", \"method\": \"pl.scatter\", \"plot\": {\"color_map\": \"inferno\", \"components\": [], \"frameon\": true, \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"palette\": \"inferno\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\"}, \"sort_order\": true, \"type\": {\"__current_case__\": 1, \"basis\": \"umap\", \"color\": \"HES4\", \"type\": \"basis\"}, \"use_raw\": true}", "format": "\"png\""}, "inputs": {"adata": {"id": "a5f5c45115dba622", "src": "hda", "uuid": "b52e5347-c77f-4e7b-814f-e4d7d815474d"}}, "outputs": {"hidden_output": {"id": "f9a8b4f25730c270", "src": "hda", "uuid": "a816cdfe-225d-4713-b392-29a31bd2a559"}, "out_png": {"id": "c4d9b441562f57b0", "src": "hda", "uuid": "8eeb13b4-ef26-4a3e-bfb3-89d9610c5429"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file umap.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: saving figure to file umap.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "3 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "3.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:37:16", "plugin": "core", "name": "end_epoch", "raw_value": "1725003436.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:37:13", "plugin": "core", "name": "start_epoch", "raw_value": "1725003433.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-1", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 1, "time_seconds": 37.74851155281067, "inputs": {"adata": {"src": "hda", "id": "5507db5e67553442"}, "format": "png", "method|type|x": "EKLF", "method|type|y": "Cebpa", "method|type|layers|use_layers": "false", "method|type|type": "xy", "method|use_raw": false, "method|sort_order": true, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|palette": "bwr", "method|plot|frameon": false, "method|plot|size": "1", "method|plot|title": "A title", "method|method": "pl.scatter", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "4da2065af1ae5859", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:21:05.183432", "update_time": "2024-08-30T07:21:22.505407", "galaxy_version": "24.1", "external_id": "gxy-c549c", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/a/7/0/dataset_a7074b0f-0a86-4a00-80a6-5a65b9a3ae31.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/265/configs/tmptud2rqqn' > '/galaxy/server/database/objects/4/9/6/dataset_4962f993-e05f-4776-bbdb-eb460eb9522e.dat' && python '/galaxy/server/database/jobs_directory/000/265/configs/tmptud2rqqn' >> '/galaxy/server/database/objects/4/9/6/dataset_4962f993-e05f-4776-bbdb-eb460eb9522e.dat' && ls . >> '/galaxy/server/database/objects/4/9/6/dataset_4962f993-e05f-4776-bbdb-eb460eb9522e.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"groups\": \"\", \"method\": \"pl.scatter\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": false, \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"palette\": \"bwr\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"A title\"}, \"sort_order\": true, \"type\": {\"__current_case__\": 0, \"color\": \"\", \"layers\": {\"__current_case__\": 1, \"use_layers\": \"false\"}, \"type\": \"xy\", \"x\": \"EKLF\", \"y\": \"Cebpa\"}, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "5507db5e67553442", "src": "hda", "uuid": "a7074b0f-0a86-4a00-80a6-5a65b9a3ae31"}}, "outputs": {"hidden_output": {"id": "a69a8c4c5f5ce6f7", "src": "hda", "uuid": "4962f993-e05f-4776-bbdb-eb460eb9522e"}, "out_png": {"id": "e10f48a01acb1fb7", "src": "hda", "uuid": "c80045d4-8d51-4b3b-ad29-8d24d205d7a5"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file scatter.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file scatter.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:21:11", "plugin": "core", "name": "end_epoch", "raw_value": "1725002471.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:21:07", "plugin": "core", "name": "start_epoch", "raw_value": "1725002467.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-1", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 1, "time_seconds": 36.74175310134888, "inputs": {"adata": {"src": "hda", "id": "92fd4852d93afd95"}, "format": "png", "method|type|x": "EKLF", "method|type|y": "Cebpa", "method|type|layers|use_layers": "false", "method|type|type": "xy", "method|use_raw": false, "method|sort_order": true, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|palette": "bwr", "method|plot|frameon": false, "method|plot|size": "1", "method|plot|title": "A title", "method|method": "pl.scatter", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "9e66f7e372adc5d1", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:37:46.927103", "update_time": "2024-08-30T07:38:04.082042", "galaxy_version": "24.1", "external_id": "gxy-vmcpf", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/8/f/dataset_08f37036-62e7-441a-8df3-b99709775a9f.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/318/configs/tmpy8sd2hds' > '/galaxy/server/database/objects/8/a/b/dataset_8ab16a25-7695-4b5c-adac-fd14d310ca68.dat' && python '/galaxy/server/database/jobs_directory/000/318/configs/tmpy8sd2hds' >> '/galaxy/server/database/objects/8/a/b/dataset_8ab16a25-7695-4b5c-adac-fd14d310ca68.dat' && ls . >> '/galaxy/server/database/objects/8/a/b/dataset_8ab16a25-7695-4b5c-adac-fd14d310ca68.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 0, \"groups\": \"\", \"method\": \"pl.scatter\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": false, \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"palette\": \"bwr\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"A title\"}, \"sort_order\": true, \"type\": {\"__current_case__\": 0, \"color\": \"\", \"layers\": {\"__current_case__\": 1, \"use_layers\": \"false\"}, \"type\": \"xy\", \"x\": \"EKLF\", \"y\": \"Cebpa\"}, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "92fd4852d93afd95", "src": "hda", "uuid": "08f37036-62e7-441a-8df3-b99709775a9f"}}, "outputs": {"hidden_output": {"id": "37d28cf59216b1e3", "src": "hda", "uuid": "8ab16a25-7695-4b5c-adac-fd14d310ca68"}, "out_png": {"id": "eebd119805197a6a", "src": "hda", "uuid": "47af0fa9-e848-4d20-b869-389a863748f0"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file scatter.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file scatter.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:37:52", "plugin": "core", "name": "end_epoch", "raw_value": "1725003472.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:37:48", "plugin": "core", "name": "start_epoch", "raw_value": "1725003468.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-10", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 10, "time_seconds": 36.16132998466492, "inputs": {"adata": {"src": "hda", "id": "8c5bffdd5d6b3479"}, "format": "png", "method|var_names|var_names": "Fog1,EKLF,SCL", "method|var_names|type": "custom", "method|groupby": "cell_type", "method|num_categories": "7", "method|gene_symbols": "symbol", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|figsize|width": "10", "method|figsize|height": "3", "method|figsize|test": "yes", "method|swap_axes": false, "method|method": "pl.matrixplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "dc0a06c42acc497a", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:26:05.914212", "update_time": "2024-08-30T07:26:22.668832", "galaxy_version": "24.1", "external_id": "gxy-5mlrc", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/e/8/e/dataset_e8e23bae-0353-4c64-b8a9-3217fc7b31df.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/282/configs/tmp8ohxoy1j' > '/galaxy/server/database/objects/d/d/4/dataset_dd4c1a7c-c9f3-4e78-8fc1-0ef8be87727f.dat' && python '/galaxy/server/database/jobs_directory/000/282/configs/tmp8ohxoy1j' >> '/galaxy/server/database/objects/d/d/4/dataset_dd4c1a7c-c9f3-4e78-8fc1-0ef8be87727f.dat' && ls . >> '/galaxy/server/database/objects/d/d/4/dataset_dd4c1a7c-c9f3-4e78-8fc1-0ef8be87727f.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 5, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 0, \"height\": \"3\", \"test\": \"yes\", \"width\": \"10\"}, \"gene_symbols\": \"symbol\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_pcolor\": {\"alpha\": \"\", \"cmap\": \"Accent\", \"edgecolors\": \"face\", \"snap\": false, \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.matrixplot\", \"num_categories\": \"7\", \"swap_axes\": false, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 1, \"type\": \"custom\", \"var_names\": \"Fog1,EKLF,SCL\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "8c5bffdd5d6b3479", "src": "hda", "uuid": "e8e23bae-0353-4c64-b8a9-3217fc7b31df"}}, "outputs": {"hidden_output": {"id": "48928f7b4a2c5971", "src": "hda", "uuid": "dd4c1a7c-c9f3-4e78-8fc1-0ef8be87727f"}, "out_png": {"id": "2927dab2dcad0b1a", "src": "hda", "uuid": "750bc46f-2009-4b86-9bf5-1c20869d5408"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:26:11", "plugin": "core", "name": "end_epoch", "raw_value": "1725002771.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:26:07", "plugin": "core", "name": "start_epoch", "raw_value": "1725002767.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-10", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 10, "time_seconds": 27.320890426635742, "inputs": {"adata": {"src": "hda", "id": "3c04a6000b1da1cb"}, "format": "png", "method|var_names|var_names": "Fog1,EKLF,SCL", "method|var_names|type": "custom", "method|groupby": "cell_type", "method|num_categories": "7", "method|gene_symbols": "symbol", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|figsize|width": "10", "method|figsize|height": "3", "method|figsize|test": "yes", "method|swap_axes": false, "method|method": "pl.matrixplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "5fcfe86f7ffa46b0", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:43:17.443377", "update_time": "2024-08-30T07:43:26.000334", "galaxy_version": "24.1", "external_id": "gxy-t72mg", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/f/f/dataset_0fff1026-5e52-4116-813a-f8fa32fb486b.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/336/configs/tmplolqd15_' > '/galaxy/server/database/objects/6/0/5/dataset_605abc07-b52e-4a1f-b241-a307f90fdbc7.dat' && python '/galaxy/server/database/jobs_directory/000/336/configs/tmplolqd15_' >> '/galaxy/server/database/objects/6/0/5/dataset_605abc07-b52e-4a1f-b241-a307f90fdbc7.dat' && ls . >> '/galaxy/server/database/objects/6/0/5/dataset_605abc07-b52e-4a1f-b241-a307f90fdbc7.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 5, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 0, \"height\": \"3\", \"test\": \"yes\", \"width\": \"10\"}, \"gene_symbols\": \"symbol\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_pcolor\": {\"alpha\": \"\", \"cmap\": \"Accent\", \"edgecolors\": \"face\", \"snap\": false, \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.matrixplot\", \"num_categories\": \"7\", \"swap_axes\": false, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 1, \"type\": \"custom\", \"var_names\": \"Fog1,EKLF,SCL\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "3c04a6000b1da1cb", "src": "hda", "uuid": "0fff1026-5e52-4116-813a-f8fa32fb486b"}}, "outputs": {"hidden_output": {"id": "14756a0451bf8376", "src": "hda", "uuid": "605abc07-b52e-4a1f-b241-a307f90fdbc7"}, "out_png": {"id": "46da947090ba3225", "src": "hda", "uuid": "eb3a0c42-824c-44f6-9b05-4d7ba8bbccf2"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n."], "status": "failure"}}, {"id": "scanpy_plot/1.7.1+galaxy1-11", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 11, "time_seconds": 10.488723993301392, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "scanpy_plot/1.7.1+galaxy1-11", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 11, "time_seconds": 36.15645623207092, "inputs": {"adata": {"src": "hda", "id": "8fac05969f299686"}, "format": "png", "method|use_raw": false, "method|seaborn_clustermap|method": "single", "method|seaborn_clustermap|metric": "euclidean", "method|seaborn_clustermap|z_score": "None", "method|seaborn_clustermap|standard_scale": "None", "method|seaborn_clustermap|col_cluster": false, "method|seaborn_clustermap|row_cluster": false, "method|method": "pl.clustermap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "30c4be037d80c86f", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:43:45.189054", "update_time": "2024-08-30T07:44:01.801975", "galaxy_version": "24.1", "external_id": "gxy-78wzh", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/a/8/b/dataset_a8bd9326-0328-47f5-846f-fafd545d5dd8.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/338/configs/tmp7yp8xpbs' > '/galaxy/server/database/objects/0/3/c/dataset_03cb9c72-a51e-47d0-ba09-cf277f36ab0b.dat' && python '/galaxy/server/database/jobs_directory/000/338/configs/tmp7yp8xpbs' >> '/galaxy/server/database/objects/0/3/c/dataset_03cb9c72-a51e-47d0-ba09-cf277f36ab0b.dat' && ls . >> '/galaxy/server/database/objects/0/3/c/dataset_03cb9c72-a51e-47d0-ba09-cf277f36ab0b.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 6, \"method\": \"pl.clustermap\", \"obs_keys\": \"\", \"seaborn_clustermap\": {\"col_cluster\": false, \"method\": \"single\", \"metric\": \"euclidean\", \"row_cluster\": false, \"standard_scale\": \"None\", \"z_score\": \"None\"}, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "8fac05969f299686", "src": "hda", "uuid": "a8bd9326-0328-47f5-846f-fafd545d5dd8"}}, "outputs": {"hidden_output": {"id": "e68a0bdb017d2b32", "src": "hda", "uuid": "03cb9c72-a51e-47d0-ba09-cf277f36ab0b"}, "out_png": {"id": "ded499747d400639", "src": "hda", "uuid": "31bd24f0-1844-4d8b-a84a-3d88661ca650"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:43:51", "plugin": "core", "name": "end_epoch", "raw_value": "1725003831.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:43:46", "plugin": "core", "name": "start_epoch", "raw_value": "1725003826.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-12", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 12, "time_seconds": 38.63929867744446, "inputs": {"adata": {"src": "hda", "id": "f415d86b8f68fb48"}, "format": "png", "method|n_top": "30", "method|gene_symbols": "means", "method|setseaborn_boxplot|color": "blue", "method|setseaborn_boxplot|saturation": "0.5", "method|method": "pl.highest_expr_genes", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "005c3fb317fece93", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:26:53.376536", "update_time": "2024-08-30T07:27:11.469981", "galaxy_version": "24.1", "external_id": "gxy-fhcqn", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/9/e/e/dataset_9eedb72c-b99c-4116-aba1-026bb706c278.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/285/configs/tmpuhjc9r3r' > '/galaxy/server/database/objects/e/b/9/dataset_eb9ff0ce-9305-4ad3-9ac8-e4ed4ebdeb40.dat' && python '/galaxy/server/database/jobs_directory/000/285/configs/tmpuhjc9r3r' >> '/galaxy/server/database/objects/e/b/9/dataset_eb9ff0ce-9305-4ad3-9ac8-e4ed4ebdeb40.dat' && ls . >> '/galaxy/server/database/objects/e/b/9/dataset_eb9ff0ce-9305-4ad3-9ac8-e4ed4ebdeb40.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 8, \"gene_symbols\": \"means\", \"method\": \"pl.highest_expr_genes\", \"n_top\": \"30\", \"setseaborn_boxplot\": {\"color\": \"blue\", \"palette\": null, \"saturation\": \"0.5\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "f415d86b8f68fb48", "src": "hda", "uuid": "9eedb72c-b99c-4116-aba1-026bb706c278"}}, "outputs": {"hidden_output": {"id": "8a56163087831f03", "src": "hda", "uuid": "eb9ff0ce-9305-4ad3-9ac8-e4ed4ebdeb40"}, "out_png": {"id": "161aa0dfa6b909ab", "src": "hda", "uuid": "1a508a76-f000-4ec8-b765-baf8aa6e2b82"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file highest_expr_genes.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file highest_expr_genes.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:27:00", "plugin": "core", "name": "end_epoch", "raw_value": "1725002820.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:26:56", "plugin": "core", "name": "start_epoch", "raw_value": "1725002816.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-12", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 12, "time_seconds": 36.65406894683838, "inputs": {"adata": {"src": "hda", "id": "ea365538d0103c79"}, "format": "png", "method|n_top": "30", "method|gene_symbols": "means", "method|setseaborn_boxplot|color": "blue", "method|setseaborn_boxplot|saturation": "0.5", "method|method": "pl.highest_expr_genes", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "7aa45690986c8ca7", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:44:22.245512", "update_time": "2024-08-30T07:44:38.272907", "galaxy_version": "24.1", "external_id": "gxy-f4t6q", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/c/9/dataset_1c9baf82-17b9-48cd-b28d-5e780cde7505.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/340/configs/tmp_lyzcy69' > '/galaxy/server/database/objects/0/5/5/dataset_0552bb9d-0d95-49cc-976b-905f0002de75.dat' && python '/galaxy/server/database/jobs_directory/000/340/configs/tmp_lyzcy69' >> '/galaxy/server/database/objects/0/5/5/dataset_0552bb9d-0d95-49cc-976b-905f0002de75.dat' && ls . >> '/galaxy/server/database/objects/0/5/5/dataset_0552bb9d-0d95-49cc-976b-905f0002de75.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 8, \"gene_symbols\": \"means\", \"method\": \"pl.highest_expr_genes\", \"n_top\": \"30\", \"setseaborn_boxplot\": {\"color\": \"blue\", \"palette\": null, \"saturation\": \"0.5\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "ea365538d0103c79", "src": "hda", "uuid": "1c9baf82-17b9-48cd-b28d-5e780cde7505"}}, "outputs": {"hidden_output": {"id": "b11fc81f954767e9", "src": "hda", "uuid": "0552bb9d-0d95-49cc-976b-905f0002de75"}, "out_png": {"id": "226048439f6a4a32", "src": "hda", "uuid": "7e443a1f-18d0-4a4b-bed1-00be612435b9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file highest_expr_genes.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file highest_expr_genes.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:44:27", "plugin": "core", "name": "end_epoch", "raw_value": "1725003867.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:44:23", "plugin": "core", "name": "start_epoch", "raw_value": "1725003863.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-13", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 13, "time_seconds": 37.61434721946716, "inputs": {"adata": {"src": "hda", "id": "46776bb661fa2c92"}, "format": "png", "method|log": false, "method|highly_variable_genes": true, "method|method": "pl.highly_variable_genes", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "ba9aa0c87b6e4cac", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:27:31.208929", "update_time": "2024-08-30T07:27:48.966086", "galaxy_version": "24.1", "external_id": "gxy-s4nr2", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/8/0/5/dataset_80545304-4cff-4a9c-9725-326ebbdb4c67.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/287/configs/tmpvvoprogs' > '/galaxy/server/database/objects/6/d/b/dataset_6db37f6c-2e7c-4379-b7b7-2a7f8a3e6342.dat' && python '/galaxy/server/database/jobs_directory/000/287/configs/tmpvvoprogs' >> '/galaxy/server/database/objects/6/d/b/dataset_6db37f6c-2e7c-4379-b7b7-2a7f8a3e6342.dat' && ls . >> '/galaxy/server/database/objects/6/d/b/dataset_6db37f6c-2e7c-4379-b7b7-2a7f8a3e6342.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 7, \"highly_variable_genes\": true, \"log\": false, \"method\": \"pl.highly_variable_genes\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "46776bb661fa2c92", "src": "hda", "uuid": "80545304-4cff-4a9c-9725-326ebbdb4c67"}}, "outputs": {"hidden_output": {"id": "1259572d12086e25", "src": "hda", "uuid": "6db37f6c-2e7c-4379-b7b7-2a7f8a3e6342"}, "out_png": {"id": "985e61b0cd94c736", "src": "hda", "uuid": "97b3dc32-e720-4390-ae24-6ce6c845f679"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file filter_genes_dispersion.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: saving figure to file filter_genes_dispersion.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:27:37", "plugin": "core", "name": "end_epoch", "raw_value": "1725002857.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:27:33", "plugin": "core", "name": "start_epoch", "raw_value": "1725002853.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-13", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 13, "time_seconds": 29.47061252593994, "inputs": {"adata": {"src": "hda", "id": "86d5a32cd72d8f1f"}, "format": "png", "method|log": false, "method|highly_variable_genes": true, "method|method": "pl.highly_variable_genes", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "3d7c835c180678a2", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:44:59.336865", "update_time": "2024-08-30T07:45:08.277328", "galaxy_version": "24.1", "external_id": "gxy-dvjvq", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/4/3/1/dataset_431cd7d3-482b-4484-8e61-6f19e0d801c7.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/342/configs/tmp753tuud7' > '/galaxy/server/database/objects/1/e/a/dataset_1eadb9f6-ba74-4228-9017-a1d3f92184e2.dat' && python '/galaxy/server/database/jobs_directory/000/342/configs/tmp753tuud7' >> '/galaxy/server/database/objects/1/e/a/dataset_1eadb9f6-ba74-4228-9017-a1d3f92184e2.dat' && ls . >> '/galaxy/server/database/objects/1/e/a/dataset_1eadb9f6-ba74-4228-9017-a1d3f92184e2.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 7, \"highly_variable_genes\": true, \"log\": false, \"method\": \"pl.highly_variable_genes\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "86d5a32cd72d8f1f", "src": "hda", "uuid": "431cd7d3-482b-4484-8e61-6f19e0d801c7"}}, "outputs": {"hidden_output": {"id": "038608c16b6b728c", "src": "hda", "uuid": "1eadb9f6-ba74-4228-9017-a1d3f92184e2"}, "out_png": {"id": "3fd2877a377cc9dd", "src": "hda", "uuid": "f49059eb-0e91-4d98-8d4a-f5fc3d6f4b86"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file filter_genes_dispersion.png\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "WARNING: saving figure to file filter_genes_dispersion.png\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: WARNING: saving figure to file filter_genes_dispersion.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: WARNING: saving figure to file filter_genes_dispersion.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: WARNING: saving figure to file filter_genes_dispersion.png\n."], "status": "failure"}}, {"id": "scanpy_plot/1.7.1+galaxy1-14", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 14, "time_seconds": 10.869374990463257, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "scanpy_plot/1.7.1+galaxy1-14", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 14, "time_seconds": 37.43578743934631, "inputs": {"adata": {"src": "hda", "id": "d7e4f48f7206f731"}, "format": "pdf", "method|color": "CD3D,CD79A", "method|use_raw": false, "method|sort_order": true, "method|plot|components_0|axis1": "1", "method|plot|components_0|axis2": "2", "method|plot|components_1|axis1": "1", "method|plot|components_1|axis2": "3", "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|size": "1", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "2", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.pca", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "809be3818664cddc", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:45:28.487235", "update_time": "2024-08-30T07:45:45.253201", "galaxy_version": "24.1", "external_id": "gxy-m6htl", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/8/1/5/dataset_815e4884-c134-42cb-8dcb-b5359f26fb2f.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/344/configs/tmp1ko43vnf' > '/galaxy/server/database/objects/e/c/6/dataset_ec6aaf89-6ee5-4c53-ac26-9585fe406212.dat' && python '/galaxy/server/database/jobs_directory/000/344/configs/tmp1ko43vnf' >> '/galaxy/server/database/objects/e/c/6/dataset_ec6aaf89-6ee5-4c53-ac26-9585fe406212.dat' && ls . >> '/galaxy/server/database/objects/e/c/6/dataset_ec6aaf89-6ee5-4c53-ac26-9585fe406212.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 9, \"color\": \"CD3D,CD79A\", \"groups\": \"\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.pca\", \"plot\": {\"color_map\": \"None\", \"components\": [{\"__index__\": 0, \"axis1\": \"1\", \"axis2\": \"2\"}, {\"__index__\": 1, \"axis1\": \"1\", \"axis2\": \"3\"}], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"2\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": true, \"use_raw\": false}", "format": "\"pdf\""}, "inputs": {"adata": {"id": "d7e4f48f7206f731", "src": "hda", "uuid": "815e4884-c134-42cb-8dcb-b5359f26fb2f"}}, "outputs": {"hidden_output": {"id": "e269fa308e3ffb15", "src": "hda", "uuid": "ec6aaf89-6ee5-4c53-ac26-9585fe406212"}, "out_pdf": {"id": "5637fdc663a90275", "src": "hda", "uuid": "20eb3465-e26b-4572-a881-f6ce07276ed8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file pca.pdf\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: saving figure to file pca.pdf\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:45:34", "plugin": "core", "name": "end_epoch", "raw_value": "1725003934.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:45:30", "plugin": "core", "name": "start_epoch", "raw_value": "1725003930.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-15", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 15, "time_seconds": 57.25415563583374, "inputs": {"adata": {"src": "hda", "id": "efa1e8c94d75feec"}, "format": "png", "method|components": "1,2,3", "method|method": "pl.pca_loadings", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "ecb83fdf9dcb6c26", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:28:19.720693", "update_time": "2024-08-30T07:28:57.474536", "galaxy_version": "24.1", "external_id": "gxy-wccwm", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/0/c/dataset_10ce026a-26b0-4f59-af77-12f99828de75.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/290/configs/tmpzv2kzyhb' > '/galaxy/server/database/objects/9/5/4/dataset_954e3301-7a54-4919-b8b1-69893d5e01be.dat' && python '/galaxy/server/database/jobs_directory/000/290/configs/tmpzv2kzyhb' >> '/galaxy/server/database/objects/9/5/4/dataset_954e3301-7a54-4919-b8b1-69893d5e01be.dat' && ls . >> '/galaxy/server/database/objects/9/5/4/dataset_954e3301-7a54-4919-b8b1-69893d5e01be.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 10, \"components\": \"1,2,3\", \"method\": \"pl.pca_loadings\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "efa1e8c94d75feec", "src": "hda", "uuid": "10ce026a-26b0-4f59-af77-12f99828de75"}}, "outputs": {"hidden_output": {"id": "586af48babe4309d", "src": "hda", "uuid": "954e3301-7a54-4919-b8b1-69893d5e01be"}, "out_png": {"id": "39e2989d2360ed37", "src": "hda", "uuid": "a17e896b-b7dc-4a23-be60-224498a9b827"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_loadings.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_loadings.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:28:47", "plugin": "core", "name": "end_epoch", "raw_value": "1725002927.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:28:43", "plugin": "core", "name": "start_epoch", "raw_value": "1725002923.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-15", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 15, "time_seconds": 37.1742467880249, "inputs": {"adata": {"src": "hda", "id": "b8fe6aeda43b398f"}, "format": "png", "method|components": "1,2,3", "method|method": "pl.pca_loadings", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "8e4662dca1bc59a1", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:46:05.539529", "update_time": "2024-08-30T07:46:22.652590", "galaxy_version": "24.1", "external_id": "gxy-26nfp", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/5/7/dataset_057efefb-b2a9-44a1-ad4f-2009035fac8d.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/346/configs/tmp_g6i83gk' > '/galaxy/server/database/objects/d/6/4/dataset_d64c3248-a6f2-4633-aeb3-377ecf34bbe3.dat' && python '/galaxy/server/database/jobs_directory/000/346/configs/tmp_g6i83gk' >> '/galaxy/server/database/objects/d/6/4/dataset_d64c3248-a6f2-4633-aeb3-377ecf34bbe3.dat' && ls . >> '/galaxy/server/database/objects/d/6/4/dataset_d64c3248-a6f2-4633-aeb3-377ecf34bbe3.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 10, \"components\": \"1,2,3\", \"method\": \"pl.pca_loadings\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "b8fe6aeda43b398f", "src": "hda", "uuid": "057efefb-b2a9-44a1-ad4f-2009035fac8d"}}, "outputs": {"hidden_output": {"id": "f7a471425c29dd47", "src": "hda", "uuid": "d64c3248-a6f2-4633-aeb3-377ecf34bbe3"}, "out_png": {"id": "97b4c4492bb7bc55", "src": "hda", "uuid": "0c869b2e-dcd0-4247-bc89-5b902992b101"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_loadings.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_loadings.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:46:11", "plugin": "core", "name": "end_epoch", "raw_value": "1725003971.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:46:07", "plugin": "core", "name": "start_epoch", "raw_value": "1725003967.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-16", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 16, "time_seconds": 36.80986309051514, "inputs": {"adata": {"src": "hda", "id": "a12d2bf7f281d615"}, "format": "png", "method|n_pcs": "5", "method|log": false, "method|method": "pl.pca_variance_ratio", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "af80223b2b724185", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:29:16.961928", "update_time": "2024-08-30T07:29:34.253064", "galaxy_version": "24.1", "external_id": "gxy-z8ktm", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/5/0/dataset_3500ee42-8303-440f-b1fa-27f4f2407277.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/292/configs/tmpn2pyydhj' > '/galaxy/server/database/objects/2/8/4/dataset_284297f0-a548-41f5-9ad1-9f303868ff13.dat' && python '/galaxy/server/database/jobs_directory/000/292/configs/tmpn2pyydhj' >> '/galaxy/server/database/objects/2/8/4/dataset_284297f0-a548-41f5-9ad1-9f303868ff13.dat' && ls . >> '/galaxy/server/database/objects/2/8/4/dataset_284297f0-a548-41f5-9ad1-9f303868ff13.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 11, \"log\": false, \"method\": \"pl.pca_variance_ratio\", \"n_pcs\": \"5\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "a12d2bf7f281d615", "src": "hda", "uuid": "3500ee42-8303-440f-b1fa-27f4f2407277"}}, "outputs": {"hidden_output": {"id": "e3c5d80305f891b8", "src": "hda", "uuid": "284297f0-a548-41f5-9ad1-9f303868ff13"}, "out_png": {"id": "359f65ffc3abb465", "src": "hda", "uuid": "734b2ed0-808f-4727-a9d0-56321e39ff3e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:29:22", "plugin": "core", "name": "end_epoch", "raw_value": "1725002962.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:29:18", "plugin": "core", "name": "start_epoch", "raw_value": "1725002958.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-16", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 16, "time_seconds": 27.67914366722107, "inputs": {"adata": {"src": "hda", "id": "c948ff00108a577e"}, "format": "png", "method|n_pcs": "5", "method|log": false, "method|method": "pl.pca_variance_ratio", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "21b4b2693acea78a", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:46:42.485838", "update_time": "2024-08-30T07:46:50.637279", "galaxy_version": "24.1", "external_id": "gxy-tkf98", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/2/8/dataset_028d334c-30f9-4a11-bf97-1c28532bdb15.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/348/configs/tmpm3gqvmnt' > '/galaxy/server/database/objects/4/f/f/dataset_4ff53f62-2edd-4994-9b63-8c6fdba8fa14.dat' && python '/galaxy/server/database/jobs_directory/000/348/configs/tmpm3gqvmnt' >> '/galaxy/server/database/objects/4/f/f/dataset_4ff53f62-2edd-4994-9b63-8c6fdba8fa14.dat' && ls . >> '/galaxy/server/database/objects/4/f/f/dataset_4ff53f62-2edd-4994-9b63-8c6fdba8fa14.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 11, \"log\": false, \"method\": \"pl.pca_variance_ratio\", \"n_pcs\": \"5\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "c948ff00108a577e", "src": "hda", "uuid": "028d334c-30f9-4a11-bf97-1c28532bdb15"}}, "outputs": {"hidden_output": {"id": "4503b172d2db2f67", "src": "hda", "uuid": "4ff53f62-2edd-4994-9b63-8c6fdba8fa14"}, "out_png": {"id": "ede55d2d793e0163", "src": "hda", "uuid": "01f05daa-b8de-4d7b-9289-78fff472829d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca_variance_ratio.png\n."], "status": "failure"}}, {"id": "scanpy_plot/1.7.1+galaxy1-17", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 17, "time_seconds": 38.60452175140381, "inputs": {"adata": {"src": "hda", "id": "f7a314d327c4f3c9"}, "format": "png", "method|use_raw": false, "method|sort_order": true, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|size": "1", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "4", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|method": "pl.pca_overview", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "1aa19454e64c7484", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:29:54.581224", "update_time": "2024-08-30T07:30:12.858852", "galaxy_version": "24.1", "external_id": "gxy-x2rv5", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/f/3/2/dataset_f32a06ee-b605-4738-8efc-ce99e2567a16.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/294/configs/tmpqpb3ccp3' > '/galaxy/server/database/objects/8/0/9/dataset_8094cb42-b642-4b08-82a7-cfd3044126ba.dat' && python '/galaxy/server/database/jobs_directory/000/294/configs/tmpqpb3ccp3' >> '/galaxy/server/database/objects/8/0/9/dataset_8094cb42-b642-4b08-82a7-cfd3044126ba.dat' && ls . >> '/galaxy/server/database/objects/8/0/9/dataset_8094cb42-b642-4b08-82a7-cfd3044126ba.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 12, \"color\": \"\", \"groups\": \"\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.pca_overview\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": true, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "f7a314d327c4f3c9", "src": "hda", "uuid": "f32a06ee-b605-4738-8efc-ce99e2567a16"}}, "outputs": {"hidden_output": {"id": "bf4d76c7d385e253", "src": "hda", "uuid": "8094cb42-b642-4b08-82a7-cfd3044126ba"}, "out_png": {"id": "97c88111acc05e91", "src": "hda", "uuid": "c2b99f6d-353b-4429-ab4c-9bb2302f2edf"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:30:00", "plugin": "core", "name": "end_epoch", "raw_value": "1725003000.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:29:56", "plugin": "core", "name": "start_epoch", "raw_value": "1725002996.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-17", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 17, "time_seconds": 36.10667395591736, "inputs": {"adata": {"src": "hda", "id": "19c05f53a7c6f8a5"}, "format": "png", "method|use_raw": false, "method|sort_order": true, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|size": "1", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "4", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|method": "pl.pca_overview", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "9a7b950bd7b252ef", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:47:09.813743", "update_time": "2024-08-30T07:47:26.533595", "galaxy_version": "24.1", "external_id": "gxy-6gqwm", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/8/b/dataset_18b2f021-7865-4c26-b3c9-3be4635b7c81.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/350/configs/tmp6mea7ukc' > '/galaxy/server/database/objects/f/9/9/dataset_f99ead92-8100-41cf-9d69-0648e40b2869.dat' && python '/galaxy/server/database/jobs_directory/000/350/configs/tmp6mea7ukc' >> '/galaxy/server/database/objects/f/9/9/dataset_f99ead92-8100-41cf-9d69-0648e40b2869.dat' && ls . >> '/galaxy/server/database/objects/f/9/9/dataset_f99ead92-8100-41cf-9d69-0648e40b2869.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 12, \"color\": \"\", \"groups\": \"\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.pca_overview\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": true, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "19c05f53a7c6f8a5", "src": "hda", "uuid": "18b2f021-7865-4c26-b3c9-3be4635b7c81"}}, "outputs": {"hidden_output": {"id": "0d2fa063aa533721", "src": "hda", "uuid": "f99ead92-8100-41cf-9d69-0648e40b2869"}, "out_png": {"id": "b2792ca9e022a4ee", "src": "hda", "uuid": "c1d2c290-423e-4686-923f-4ad5dbb89f38"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file pca.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:47:15", "plugin": "core", "name": "end_epoch", "raw_value": "1725004035.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:47:11", "plugin": "core", "name": "start_epoch", "raw_value": "1725004031.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-18", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 18, "time_seconds": 36.418299198150635, "inputs": {"adata": {"src": "hda", "id": "893909f55c99d392"}, "format": "png", "method|use_raw": false, "method|edges|edges": "False", "method|arrows": false, "method|sort_order": true, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|size": "1", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "4", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.tsne", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "8931930f797580d2", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:30:33.278646", "update_time": "2024-08-30T07:30:49.347530", "galaxy_version": "24.1", "external_id": "gxy-lbxnk", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/f/f/5/dataset_ff5efad1-5e28-4c1a-bd91-a3c8a88c4b4d.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/296/configs/tmp5z7jm9fp' > '/galaxy/server/database/objects/f/d/6/dataset_fd6d3fba-9deb-4b77-b563-572371a557c8.dat' && python '/galaxy/server/database/jobs_directory/000/296/configs/tmp5z7jm9fp' >> '/galaxy/server/database/objects/f/d/6/dataset_fd6d3fba-9deb-4b77-b563-572371a557c8.dat' && ls . >> '/galaxy/server/database/objects/f/d/6/dataset_fd6d3fba-9deb-4b77-b563-572371a557c8.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 13, \"arrows\": false, \"color\": \"\", \"edges\": {\"__current_case__\": 1, \"edges\": \"False\"}, \"groups\": \"\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.tsne\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": true, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "893909f55c99d392", "src": "hda", "uuid": "ff5efad1-5e28-4c1a-bd91-a3c8a88c4b4d"}}, "outputs": {"hidden_output": {"id": "140bdeafc8bc350e", "src": "hda", "uuid": "fd6d3fba-9deb-4b77-b563-572371a557c8"}, "out_png": {"id": "506daac2429afce1", "src": "hda", "uuid": "91800e1c-61eb-4535-b98e-732d364a9681"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file tsne.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file tsne.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:30:38", "plugin": "core", "name": "end_epoch", "raw_value": "1725003038.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:30:34", "plugin": "core", "name": "start_epoch", "raw_value": "1725003034.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-18", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 18, "time_seconds": 36.73835802078247, "inputs": {"adata": {"src": "hda", "id": "f0a9d7a3c9c1e5ec"}, "format": "png", "method|use_raw": false, "method|edges|edges": "False", "method|arrows": false, "method|sort_order": true, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|size": "1", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "4", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.tsne", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "fe996e4549e22ea0", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:47:47.033103", "update_time": "2024-08-30T07:48:03.388063", "galaxy_version": "24.1", "external_id": "gxy-p4tdm", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/6/7/dataset_1671dbec-4db4-49c2-a851-d337e3216cd0.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/352/configs/tmpox1zlgry' > '/galaxy/server/database/objects/1/0/3/dataset_103adab7-6087-4f9e-a196-5be5e1a070a8.dat' && python '/galaxy/server/database/jobs_directory/000/352/configs/tmpox1zlgry' >> '/galaxy/server/database/objects/1/0/3/dataset_103adab7-6087-4f9e-a196-5be5e1a070a8.dat' && ls . >> '/galaxy/server/database/objects/1/0/3/dataset_103adab7-6087-4f9e-a196-5be5e1a070a8.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 13, \"arrows\": false, \"color\": \"\", \"edges\": {\"__current_case__\": 1, \"edges\": \"False\"}, \"groups\": \"\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.tsne\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": true, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "f0a9d7a3c9c1e5ec", "src": "hda", "uuid": "1671dbec-4db4-49c2-a851-d337e3216cd0"}}, "outputs": {"hidden_output": {"id": "073a4cbadaad5d5c", "src": "hda", "uuid": "103adab7-6087-4f9e-a196-5be5e1a070a8"}, "out_png": {"id": "615c6f481a5e3c9e", "src": "hda", "uuid": "a943a6bf-d851-4fc6-9760-c699ffa50ed8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file tsne.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file tsne.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:47:52", "plugin": "core", "name": "end_epoch", "raw_value": "1725004072.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:47:48", "plugin": "core", "name": "start_epoch", "raw_value": "1725004068.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-19", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 19, "time_seconds": 37.322179317474365, "inputs": {"adata": {"src": "hda", "id": "4567c73677a0bfbd"}, "format": "png", "method|color": "paul15_clusters", "method|use_raw": false, "method|edges|edges_width": "0.1", "method|edges|edges_color": "AliceBlue", "method|edges|edges": "True", "method|arrows": false, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|size": "1", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "4", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.umap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "b1ea0f569f8c6a70", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:31:08.988748", "update_time": "2024-08-30T07:31:26.555666", "galaxy_version": "24.1", "external_id": "gxy-5mbd8", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/d/4/4/dataset_d440a617-9259-481b-b553-180995cfe604.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/298/configs/tmptrl__omj' > '/galaxy/server/database/objects/1/f/5/dataset_1f5adf1f-3925-467e-b984-16f4bd1e081e.dat' && python '/galaxy/server/database/jobs_directory/000/298/configs/tmptrl__omj' >> '/galaxy/server/database/objects/1/f/5/dataset_1f5adf1f-3925-467e-b984-16f4bd1e081e.dat' && ls . >> '/galaxy/server/database/objects/1/f/5/dataset_1f5adf1f-3925-467e-b984-16f4bd1e081e.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 14, \"arrows\": false, \"color\": \"paul15_clusters\", \"edges\": {\"__current_case__\": 0, \"edges\": \"True\", \"edges_color\": \"AliceBlue\", \"edges_width\": \"0.1\"}, \"groups\": \"\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.umap\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": true, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "4567c73677a0bfbd", "src": "hda", "uuid": "d440a617-9259-481b-b553-180995cfe604"}}, "outputs": {"hidden_output": {"id": "6812660d00d3caa4", "src": "hda", "uuid": "1f5adf1f-3925-467e-b984-16f4bd1e081e"}, "out_png": {"id": "cd4d9b408497044a", "src": "hda", "uuid": "f9e60199-4141-46e5-9cb3-50c7d1ecd1e7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file umap.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: saving figure to file umap.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:31:15", "plugin": "core", "name": "end_epoch", "raw_value": "1725003075.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:31:11", "plugin": "core", "name": "start_epoch", "raw_value": "1725003071.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-19", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 19, "time_seconds": 30.31559944152832, "inputs": {"adata": {"src": "hda", "id": "11b59b2c17e03455"}, "format": "png", "method|color": "paul15_clusters", "method|use_raw": false, "method|edges|edges_width": "0.1", "method|edges|edges_color": "AliceBlue", "method|edges|edges": "True", "method|arrows": false, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|size": "1", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "4", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.umap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "7037a4c267c5edd7", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:48:24.546670", "update_time": "2024-08-30T07:48:34.008567", "galaxy_version": "24.1", "external_id": "gxy-zfbtm", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/e/7/8/dataset_e789b880-5a55-444c-9de0-f8669cb1d20b.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/354/configs/tmpjx966dm_' > '/galaxy/server/database/objects/5/0/3/dataset_503a0a8a-bc5c-44ed-9989-2bd133af09b7.dat' && python '/galaxy/server/database/jobs_directory/000/354/configs/tmpjx966dm_' >> '/galaxy/server/database/objects/5/0/3/dataset_503a0a8a-bc5c-44ed-9989-2bd133af09b7.dat' && ls . >> '/galaxy/server/database/objects/5/0/3/dataset_503a0a8a-bc5c-44ed-9989-2bd133af09b7.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 14, \"arrows\": false, \"color\": \"paul15_clusters\", \"edges\": {\"__current_case__\": 0, \"edges\": \"True\", \"edges_color\": \"AliceBlue\", \"edges_width\": \"0.1\"}, \"groups\": \"\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.umap\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": true, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "11b59b2c17e03455", "src": "hda", "uuid": "e789b880-5a55-444c-9de0-f8669cb1d20b"}}, "outputs": {"hidden_output": {"id": "3717c512ea73d94f", "src": "hda", "uuid": "503a0a8a-bc5c-44ed-9989-2bd133af09b7"}, "out_png": {"id": "72b2436f04e95d20", "src": "hda", "uuid": "8448e2d6-a0d8-46c9-8710-690c3176a608"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file umap.png\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "WARNING: saving figure to file umap.png\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: WARNING: saving figure to file umap.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: WARNING: saving figure to file umap.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: WARNING: saving figure to file umap.png\n."], "status": "failure"}}, {"id": "scanpy_plot/1.7.1+galaxy1-2", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 2, "time_seconds": 37.55925989151001, "inputs": {"adata": {"src": "hda", "id": "5df604999d9d724d"}, "format": "png", "method|var_names|type": "all", "method|groupby": "cell_type", "method|num_categories": "7", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|figsize|width": "10", "method|figsize|height": "3", "method|figsize|test": "yes", "method|swap_axes": true, "method|show_gene_labels": false, "method|matplotlib_pyplot_imshow|cmap": "YlGnBu", "method|matplotlib_pyplot_imshow|interpolation": "None", "method|matplotlib_pyplot_imshow|origin": "upper", "method|method": "pl.heatmap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "49010eaead7e729e", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:21:42.892040", "update_time": "2024-08-30T07:21:59.965394", "galaxy_version": "24.1", "external_id": "gxy-tk96h", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/6/c/9/dataset_6c9a08fb-3030-4b61-862c-b4d31ffba9f7.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/267/configs/tmpxjm9lis8' > '/galaxy/server/database/objects/8/c/2/dataset_8c22c9ce-cab8-43d9-bdb1-caa866d6b946.dat' && python '/galaxy/server/database/jobs_directory/000/267/configs/tmpxjm9lis8' >> '/galaxy/server/database/objects/8/c/2/dataset_8c22c9ce-cab8-43d9-bdb1-caa866d6b946.dat' && ls . >> '/galaxy/server/database/objects/8/c/2/dataset_8c22c9ce-cab8-43d9-bdb1-caa866d6b946.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 1, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 0, \"height\": \"3\", \"test\": \"yes\", \"width\": \"10\"}, \"gene_symbols\": \"\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_imshow\": {\"alpha\": \"\", \"cmap\": \"YlGnBu\", \"interpolation\": \"None\", \"origin\": \"upper\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.heatmap\", \"num_categories\": \"7\", \"show_gene_labels\": false, \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 0, \"type\": \"all\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "5df604999d9d724d", "src": "hda", "uuid": "6c9a08fb-3030-4b61-862c-b4d31ffba9f7"}}, "outputs": {"hidden_output": {"id": "af76f5d0aabc68bc", "src": "hda", "uuid": "8c22c9ce-cab8-43d9-bdb1-caa866d6b946"}, "out_png": {"id": "88d248b9632a3b3c", "src": "hda", "uuid": "4125db0e-2b39-4e68-a8fa-d1c40a43ef03"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:21:48", "plugin": "core", "name": "end_epoch", "raw_value": "1725002508.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:21:44", "plugin": "core", "name": "start_epoch", "raw_value": "1725002504.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-2", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 2, "time_seconds": 28.305840015411377, "inputs": {"adata": {"src": "hda", "id": "1d8f058f735ff10d"}, "format": "png", "method|var_names|type": "all", "method|groupby": "cell_type", "method|num_categories": "7", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|figsize|width": "10", "method|figsize|height": "3", "method|figsize|test": "yes", "method|swap_axes": true, "method|show_gene_labels": false, "method|matplotlib_pyplot_imshow|cmap": "YlGnBu", "method|matplotlib_pyplot_imshow|interpolation": "None", "method|matplotlib_pyplot_imshow|origin": "upper", "method|method": "pl.heatmap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "ef008abdd885cd3a", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:38:24.567114", "update_time": "2024-08-30T07:38:32.877832", "galaxy_version": "24.1", "external_id": "gxy-ws2hs", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/f/e/3/dataset_fe3ffb95-001a-4a55-b79a-4f4072b4ef6a.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/320/configs/tmps3r7mftg' > '/galaxy/server/database/objects/2/2/c/dataset_22ce5b42-d8a4-4170-b761-77f189e3767c.dat' && python '/galaxy/server/database/jobs_directory/000/320/configs/tmps3r7mftg' >> '/galaxy/server/database/objects/2/2/c/dataset_22ce5b42-d8a4-4170-b761-77f189e3767c.dat' && ls . >> '/galaxy/server/database/objects/2/2/c/dataset_22ce5b42-d8a4-4170-b761-77f189e3767c.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 1, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 0, \"height\": \"3\", \"test\": \"yes\", \"width\": \"10\"}, \"gene_symbols\": \"\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_imshow\": {\"alpha\": \"\", \"cmap\": \"YlGnBu\", \"interpolation\": \"None\", \"origin\": \"upper\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.heatmap\", \"num_categories\": \"7\", \"show_gene_labels\": false, \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 0, \"type\": \"all\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "1d8f058f735ff10d", "src": "hda", "uuid": "fe3ffb95-001a-4a55-b79a-4f4072b4ef6a"}}, "outputs": {"hidden_output": {"id": "72a670fdd9745f64", "src": "hda", "uuid": "22ce5b42-d8a4-4170-b761-77f189e3767c"}, "out_png": {"id": "8997e7210843ec1f", "src": "hda", "uuid": "667c1706-7673-489d-a10b-68ba33924306"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n."], "status": "failure"}}, {"id": "scanpy_plot/1.7.1+galaxy1-20", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 20, "time_seconds": 37.527873277664185, "inputs": {"adata": {"src": "hda", "id": "3dd78a2da23386b4"}, "format": "png", "method|color": "paul15_clusters", "method|use_raw": false, "method|sort_order": true, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|size": "1", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "4", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.diffmap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "d8e603da1c3f291d", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:31:46.989752", "update_time": "2024-08-30T07:32:04.298122", "galaxy_version": "24.1", "external_id": "gxy-2nc8v", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/a/c/dataset_0ac3c2f0-e58b-473e-b5a7-8f5d7c2766e4.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/300/configs/tmpja9gbge1' > '/galaxy/server/database/objects/f/7/0/dataset_f70f99ad-1d26-433e-a345-6d1b66f5bb00.dat' && python '/galaxy/server/database/jobs_directory/000/300/configs/tmpja9gbge1' >> '/galaxy/server/database/objects/f/7/0/dataset_f70f99ad-1d26-433e-a345-6d1b66f5bb00.dat' && ls . >> '/galaxy/server/database/objects/f/7/0/dataset_f70f99ad-1d26-433e-a345-6d1b66f5bb00.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 15, \"color\": \"paul15_clusters\", \"groups\": \"\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.diffmap\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": true, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "3dd78a2da23386b4", "src": "hda", "uuid": "0ac3c2f0-e58b-473e-b5a7-8f5d7c2766e4"}}, "outputs": {"hidden_output": {"id": "dcffa1e60d33a406", "src": "hda", "uuid": "f70f99ad-1d26-433e-a345-6d1b66f5bb00"}, "out_png": {"id": "da32f7721b364e1a", "src": "hda", "uuid": "eb92d4c8-e710-49ec-8b94-e596296056a9"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file diffmap.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: saving figure to file diffmap.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:31:52", "plugin": "core", "name": "end_epoch", "raw_value": "1725003112.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:31:48", "plugin": "core", "name": "start_epoch", "raw_value": "1725003108.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-20", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 20, "time_seconds": 36.320199728012085, "inputs": {"adata": {"src": "hda", "id": "6d0cf1bbeebbd767"}, "format": "png", "method|color": "paul15_clusters", "method|use_raw": false, "method|sort_order": true, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontsize": "1", "method|plot|legend_fontweight": "normal", "method|plot|size": "1", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "4", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.diffmap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "e6a4e8500837d9f4", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:48:53.034625", "update_time": "2024-08-30T07:49:10.084857", "galaxy_version": "24.1", "external_id": "gxy-zjk88", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/7/2/dataset_37247db7-5e7e-430c-886f-037da4076429.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/356/configs/tmp62adhwnc' > '/galaxy/server/database/objects/a/9/b/dataset_a9be0d3c-8257-4b91-92d7-a54d6cbbeaf2.dat' && python '/galaxy/server/database/jobs_directory/000/356/configs/tmp62adhwnc' >> '/galaxy/server/database/objects/a/9/b/dataset_a9be0d3c-8257-4b91-92d7-a54d6cbbeaf2.dat' && ls . >> '/galaxy/server/database/objects/a/9/b/dataset_a9be0d3c-8257-4b91-92d7-a54d6cbbeaf2.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 15, \"color\": \"paul15_clusters\", \"groups\": \"\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.diffmap\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"1\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"1.0\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": true, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "6d0cf1bbeebbd767", "src": "hda", "uuid": "37247db7-5e7e-430c-886f-037da4076429"}}, "outputs": {"hidden_output": {"id": "e06ad968dfe0d0b7", "src": "hda", "uuid": "a9be0d3c-8257-4b91-92d7-a54d6cbbeaf2"}, "out_png": {"id": "c0d64fe212eafce8", "src": "hda", "uuid": "9b971d14-4b03-48b9-8e47-68f1ee6b132d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file diffmap.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: saving figure to file diffmap.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:48:58", "plugin": "core", "name": "end_epoch", "raw_value": "1725004138.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:48:54", "plugin": "core", "name": "start_epoch", "raw_value": "1725004134.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-21", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 21, "time_seconds": 37.469560861587524, "inputs": {"adata": {"src": "hda", "id": "2001ff2411c151c6"}, "format": "png", "method|use_raw": false, "method|layout": "fr", "method|edges|edges_width": "0.1", "method|edges|edges_color": "Crimson", "method|edges|edges": "True", "method|arrows": false, "method|sort_order": false, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontweight": "normal", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "4", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.draw_graph", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "6be82dcbc2b5c0e1", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:32:24.477525", "update_time": "2024-08-30T07:32:41.654795", "galaxy_version": "24.1", "external_id": "gxy-7jxkk", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/d/d/dataset_1dd16680-a734-4a7d-82e6-0ed9700bf240.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/302/configs/tmp3ygy17j9' > '/galaxy/server/database/objects/d/d/5/dataset_dd579f06-1fdc-4d50-b0f5-c30c8399b08c.dat' && python '/galaxy/server/database/jobs_directory/000/302/configs/tmp3ygy17j9' >> '/galaxy/server/database/objects/d/d/5/dataset_dd579f06-1fdc-4d50-b0f5-c30c8399b08c.dat' && ls . >> '/galaxy/server/database/objects/d/d/5/dataset_dd579f06-1fdc-4d50-b0f5-c30c8399b08c.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 16, \"arrows\": false, \"color\": \"\", \"edges\": {\"__current_case__\": 0, \"edges\": \"True\", \"edges_color\": \"Crimson\", \"edges_width\": \"0.1\"}, \"gene_symbols\": \"\", \"groups\": \"\", \"layout\": \"fr\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.draw_graph\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": false, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "2001ff2411c151c6", "src": "hda", "uuid": "1dd16680-a734-4a7d-82e6-0ed9700bf240"}}, "outputs": {"hidden_output": {"id": "8850619d4cd07191", "src": "hda", "uuid": "dd579f06-1fdc-4d50-b0f5-c30c8399b08c"}, "out_png": {"id": "20cfe52fc7898bf9", "src": "hda", "uuid": "6ee0d516-05c6-4205-b763-a39997e17cf1"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file draw_graph_fr.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: saving figure to file draw_graph_fr.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:32:30", "plugin": "core", "name": "end_epoch", "raw_value": "1725003150.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:32:26", "plugin": "core", "name": "start_epoch", "raw_value": "1725003146.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-21", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 21, "time_seconds": 38.226569414138794, "inputs": {"adata": {"src": "hda", "id": "0dfd4776286dd863"}, "format": "png", "method|use_raw": false, "method|layout": "fr", "method|edges|edges_width": "0.1", "method|edges|edges_color": "Crimson", "method|edges|edges": "True", "method|arrows": false, "method|sort_order": false, "method|plot|projection": "2d", "method|plot|legend_loc": "right margin", "method|plot|legend_fontweight": "normal", "method|plot|palette": "viridis", "method|plot|frameon": true, "method|plot|ncols": "4", "method|plot|wspace": "0.1", "method|plot|hspace": "0.25", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.draw_graph", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "081a75b2a91db55b", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:49:30.558506", "update_time": "2024-08-30T07:49:48.408908", "galaxy_version": "24.1", "external_id": "gxy-jtztm", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/5/f/a/dataset_5fa7fd31-03dd-473b-8835-494606cb50dd.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/358/configs/tmpgl4lwibc' > '/galaxy/server/database/objects/3/c/d/dataset_3cd348d0-2c46-42aa-99af-8d1d94e307d9.dat' && python '/galaxy/server/database/jobs_directory/000/358/configs/tmpgl4lwibc' >> '/galaxy/server/database/objects/3/c/d/dataset_3cd348d0-2c46-42aa-99af-8d1d94e307d9.dat' && ls . >> '/galaxy/server/database/objects/3/c/d/dataset_3cd348d0-2c46-42aa-99af-8d1d94e307d9.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 16, \"arrows\": false, \"color\": \"\", \"edges\": {\"__current_case__\": 0, \"edges\": \"True\", \"edges_color\": \"Crimson\", \"edges_width\": \"0.1\"}, \"gene_symbols\": \"\", \"groups\": \"\", \"layout\": \"fr\", \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.draw_graph\", \"plot\": {\"color_map\": \"None\", \"components\": [], \"frameon\": true, \"hspace\": \"0.25\", \"legend_fontsize\": \"\", \"legend_fontweight\": \"normal\", \"legend_loc\": \"right margin\", \"ncols\": \"4\", \"palette\": \"viridis\", \"projection\": \"2d\", \"size\": \"\", \"title\": \"\", \"wspace\": \"0.1\"}, \"sort_order\": false, \"use_raw\": false}", "format": "\"png\""}, "inputs": {"adata": {"id": "0dfd4776286dd863", "src": "hda", "uuid": "5fa7fd31-03dd-473b-8835-494606cb50dd"}}, "outputs": {"hidden_output": {"id": "af591120e484a5e0", "src": "hda", "uuid": "3cd348d0-2c46-42aa-99af-8d1d94e307d9"}, "out_png": {"id": "411ebba1473b3c2c", "src": "hda", "uuid": "a4b58327-9d8a-43fa-8d19-d4a9286a39d4"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file draw_graph_fr.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: saving figure to file draw_graph_fr.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:49:36", "plugin": "core", "name": "end_epoch", "raw_value": "1725004176.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:49:32", "plugin": "core", "name": "start_epoch", "raw_value": "1725004172.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-22", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 22, "time_seconds": 55.53962182998657, "inputs": {"adata": {"src": "hda", "id": "c6c6e7114012ff4a"}, "format": "png", "method|heatmap|color_map": "viridis", "method|heatmap|as_heatmap": "True", "method|method": "pl.dpt_timeseries", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "5ac3666d409c110b", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:33:02.332390", "update_time": "2024-08-30T07:33:37.273916", "galaxy_version": "24.1", "external_id": "gxy-9qgpr", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/e/b/5/dataset_eb5da994-8cbf-4053-b7ab-3da353769253.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/304/configs/tmpn1al0zx7' > '/galaxy/server/database/objects/1/8/7/dataset_187c1888-9a20-40f9-9bdc-f9fdfacb7d3d.dat' && python '/galaxy/server/database/jobs_directory/000/304/configs/tmpn1al0zx7' >> '/galaxy/server/database/objects/1/8/7/dataset_187c1888-9a20-40f9-9bdc-f9fdfacb7d3d.dat' && ls . >> '/galaxy/server/database/objects/1/8/7/dataset_187c1888-9a20-40f9-9bdc-f9fdfacb7d3d.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 18, \"heatmap\": {\"__current_case__\": 0, \"as_heatmap\": \"True\", \"color_map\": \"viridis\"}, \"method\": \"pl.dpt_timeseries\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "c6c6e7114012ff4a", "src": "hda", "uuid": "eb5da994-8cbf-4053-b7ab-3da353769253"}}, "outputs": {"hidden_output": {"id": "ce1cbbe8e1a86205", "src": "hda", "uuid": "187c1888-9a20-40f9-9bdc-f9fdfacb7d3d"}, "out_png": {"id": "ba59fb127ab9c9a0", "src": "hda", "uuid": "7b3bc264-eae7-42bc-898b-a29ba2b053b8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: Plotting more than 100 genes might take some while, consider selecting only highly variable genes, for example.\nWARNING: saving figure to file dpt_timeseries.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: Plotting more than 100 genes might take some while, consider selecting only highly variable genes, for example.\nWARNING: saving figure to file dpt_timeseries.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "22 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "22.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:33:26", "plugin": "core", "name": "end_epoch", "raw_value": "1725003206.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:33:04", "plugin": "core", "name": "start_epoch", "raw_value": "1725003184.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-22", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 22, "time_seconds": 53.14589500427246, "inputs": {"adata": {"src": "hda", "id": "a96860ed7ff6a2c3"}, "format": "png", "method|heatmap|color_map": "viridis", "method|heatmap|as_heatmap": "True", "method|method": "pl.dpt_timeseries", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "5507db5e67553442", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:50:07.259192", "update_time": "2024-08-30T07:50:41.448451", "galaxy_version": "24.1", "external_id": "gxy-9l5fp", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/7/4/3/dataset_743ccb6c-3bf7-46aa-8d3b-d71ae4f40b48.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/360/configs/tmpeqjd0q9s' > '/galaxy/server/database/objects/3/7/c/dataset_37ca1308-f769-485e-b653-5d1abb83f295.dat' && python '/galaxy/server/database/jobs_directory/000/360/configs/tmpeqjd0q9s' >> '/galaxy/server/database/objects/3/7/c/dataset_37ca1308-f769-485e-b653-5d1abb83f295.dat' && ls . >> '/galaxy/server/database/objects/3/7/c/dataset_37ca1308-f769-485e-b653-5d1abb83f295.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 18, \"heatmap\": {\"__current_case__\": 0, \"as_heatmap\": \"True\", \"color_map\": \"viridis\"}, \"method\": \"pl.dpt_timeseries\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "a96860ed7ff6a2c3", "src": "hda", "uuid": "743ccb6c-3bf7-46aa-8d3b-d71ae4f40b48"}}, "outputs": {"hidden_output": {"id": "ce921996e1c784f4", "src": "hda", "uuid": "37ca1308-f769-485e-b653-5d1abb83f295"}, "out_png": {"id": "5f5c3cf08ff49e63", "src": "hda", "uuid": "da591238-53eb-4c11-a7eb-df6e3437d52d"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: Plotting more than 100 genes might take some while, consider selecting only highly variable genes, for example.\nWARNING: saving figure to file dpt_timeseries.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: Plotting more than 100 genes might take some while, consider selecting only highly variable genes, for example.\nWARNING: saving figure to file dpt_timeseries.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "21 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "21.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:50:30", "plugin": "core", "name": "end_epoch", "raw_value": "1725004230.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:50:09", "plugin": "core", "name": "start_epoch", "raw_value": "1725004209.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-23", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 23, "time_seconds": 37.30355525016785, "inputs": {"adata": {"src": "hda", "id": "5598805a675b3255"}, "format": "png", "method|n_genes": "10", "method|fontsize": "8", "method|ncols": "4", "method|sharey": true, "method|method": "pl.rank_genes_groups", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "ade34174ea908ec9", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:33:57.733420", "update_time": "2024-08-30T07:34:14.809199", "galaxy_version": "24.1", "external_id": "gxy-v2rpr", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/a/8/dataset_1a859e4b-4ad0-494a-8ada-0354ddbdffe0.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/306/configs/tmpxbokkzgz' > '/galaxy/server/database/objects/f/5/7/dataset_f577085c-ea09-43d4-89d7-f9711e34b014.dat' && python '/galaxy/server/database/jobs_directory/000/306/configs/tmpxbokkzgz' >> '/galaxy/server/database/objects/f/5/7/dataset_f577085c-ea09-43d4-89d7-f9711e34b014.dat' && ls . >> '/galaxy/server/database/objects/f/5/7/dataset_f577085c-ea09-43d4-89d7-f9711e34b014.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 22, \"fontsize\": \"8\", \"gene_symbols\": \"\", \"groups\": \"\", \"method\": \"pl.rank_genes_groups\", \"n_genes\": \"10\", \"ncols\": \"4\", \"sharey\": true}", "format": "\"png\""}, "inputs": {"adata": {"id": "5598805a675b3255", "src": "hda", "uuid": "1a859e4b-4ad0-494a-8ada-0354ddbdffe0"}}, "outputs": {"hidden_output": {"id": "bc7e7c8fb51df1d4", "src": "hda", "uuid": "f577085c-ea09-43d4-89d7-f9711e34b014"}, "out_png": {"id": "898fc6797b7528ac", "src": "hda", "uuid": "327229b7-fd1f-4001-9725-eab721ae3787"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file rank_genes_groups_cell_type.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file rank_genes_groups_cell_type.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:34:03", "plugin": "core", "name": "end_epoch", "raw_value": "1725003243.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:33:59", "plugin": "core", "name": "start_epoch", "raw_value": "1725003239.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-23", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 23, "time_seconds": 37.41058588027954, "inputs": {"adata": {"src": "hda", "id": "0b094eeb7c553073"}, "format": "png", "method|n_genes": "10", "method|fontsize": "8", "method|ncols": "4", "method|sharey": true, "method|method": "pl.rank_genes_groups", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "a69a8c4c5f5ce6f7", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:51:00.969661", "update_time": "2024-08-30T07:51:18.971952", "galaxy_version": "24.1", "external_id": "gxy-zq8tl", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/8/9/f/dataset_89f3acab-adbb-47a9-9fb4-2b5c61e93aa7.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/362/configs/tmpy1td4pso' > '/galaxy/server/database/objects/9/e/9/dataset_9e9f55a0-2292-4f50-8d71-03126ff1e33e.dat' && python '/galaxy/server/database/jobs_directory/000/362/configs/tmpy1td4pso' >> '/galaxy/server/database/objects/9/e/9/dataset_9e9f55a0-2292-4f50-8d71-03126ff1e33e.dat' && ls . >> '/galaxy/server/database/objects/9/e/9/dataset_9e9f55a0-2292-4f50-8d71-03126ff1e33e.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 22, \"fontsize\": \"8\", \"gene_symbols\": \"\", \"groups\": \"\", \"method\": \"pl.rank_genes_groups\", \"n_genes\": \"10\", \"ncols\": \"4\", \"sharey\": true}", "format": "\"png\""}, "inputs": {"adata": {"id": "0b094eeb7c553073", "src": "hda", "uuid": "89f3acab-adbb-47a9-9fb4-2b5c61e93aa7"}}, "outputs": {"hidden_output": {"id": "51f9b87f29fb9a11", "src": "hda", "uuid": "9e9f55a0-2292-4f50-8d71-03126ff1e33e"}, "out_png": {"id": "0daf71a2eca0821b", "src": "hda", "uuid": "74a2efbd-33cc-4bc4-8eae-17dab6c74b6f"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file rank_genes_groups_cell_type.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file rank_genes_groups_cell_type.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:51:07", "plugin": "core", "name": "end_epoch", "raw_value": "1725004267.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:51:03", "plugin": "core", "name": "start_epoch", "raw_value": "1725004263.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-24", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 24, "time_seconds": 37.42212510108948, "inputs": {"adata": {"src": "hda", "id": "321d29551c7dbfce"}, "format": "png", "method|n_genes": "10", "method|log": false, "method|use_raw": false, "method|dendrogram": false, "method|color_map": "viridis", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.rank_genes_groups_dotplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "fda5818e8a5af745", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:34:34.317543", "update_time": "2024-08-30T07:34:52.290080", "galaxy_version": "24.1", "external_id": "gxy-kdm47", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/f/d/0/dataset_fd0593ef-aed7-4068-b6a0-66c13c434027.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/308/configs/tmpmkuqb8zf' > '/galaxy/server/database/objects/8/2/7/dataset_827ce93e-d01f-4be3-b48c-90b407f85ea6.dat' && python '/galaxy/server/database/jobs_directory/000/308/configs/tmpmkuqb8zf' >> '/galaxy/server/database/objects/8/2/7/dataset_827ce93e-d01f-4be3-b48c-90b407f85ea6.dat' && ls . >> '/galaxy/server/database/objects/8/2/7/dataset_827ce93e-d01f-4be3-b48c-90b407f85ea6.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 24, \"color_map\": \"viridis\", \"dendrogram\": false, \"dot_max\": \"\", \"dot_min\": \"\", \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"groups\": \"\", \"key\": \"\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.rank_genes_groups_dotplot\", \"n_genes\": \"10\", \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "321d29551c7dbfce", "src": "hda", "uuid": "fd0593ef-aed7-4068-b6a0-66c13c434027"}}, "outputs": {"hidden_output": {"id": "5af639b8e1ecde0e", "src": "hda", "uuid": "827ce93e-d01f-4be3-b48c-90b407f85ea6"}, "out_png": {"id": "b894019688c3dc49", "src": "hda", "uuid": "682dfad0-c1ff-463f-8415-dce3c7d5b91e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file dotplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file dotplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:34:40", "plugin": "core", "name": "end_epoch", "raw_value": "1725003280.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:34:36", "plugin": "core", "name": "start_epoch", "raw_value": "1725003276.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-24", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 24, "time_seconds": 37.20273184776306, "inputs": {"adata": {"src": "hda", "id": "625acc4e7b1bce7d"}, "format": "png", "method|n_genes": "10", "method|log": false, "method|use_raw": false, "method|dendrogram": false, "method|color_map": "viridis", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.rank_genes_groups_dotplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "88d248b9632a3b3c", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:51:39.098096", "update_time": "2024-08-30T07:51:56.370969", "galaxy_version": "24.1", "external_id": "gxy-8lhw4", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/d/d/b/dataset_ddb708de-f545-4775-a75c-2df80c335fb7.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/364/configs/tmppicyyr9t' > '/galaxy/server/database/objects/5/4/e/dataset_54ea2e0b-4bbe-4232-bc0d-76ae12a1d150.dat' && python '/galaxy/server/database/jobs_directory/000/364/configs/tmppicyyr9t' >> '/galaxy/server/database/objects/5/4/e/dataset_54ea2e0b-4bbe-4232-bc0d-76ae12a1d150.dat' && ls . >> '/galaxy/server/database/objects/5/4/e/dataset_54ea2e0b-4bbe-4232-bc0d-76ae12a1d150.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 24, \"color_map\": \"viridis\", \"dendrogram\": false, \"dot_max\": \"\", \"dot_min\": \"\", \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"groups\": \"\", \"key\": \"\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.rank_genes_groups_dotplot\", \"n_genes\": \"10\", \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "625acc4e7b1bce7d", "src": "hda", "uuid": "ddb708de-f545-4775-a75c-2df80c335fb7"}}, "outputs": {"hidden_output": {"id": "2ffdfafa859b6a24", "src": "hda", "uuid": "54ea2e0b-4bbe-4232-bc0d-76ae12a1d150"}, "out_png": {"id": "c314d6298ad35034", "src": "hda", "uuid": "05598fbc-a1b5-4410-b49d-c97991c3e2b7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file dotplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file dotplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:51:45", "plugin": "core", "name": "end_epoch", "raw_value": "1725004305.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:51:40", "plugin": "core", "name": "start_epoch", "raw_value": "1725004300.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-25", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 25, "time_seconds": 38.581533432006836, "inputs": {"adata": {"src": "hda", "id": "63e29910ffeaaa12"}, "format": "png", "method|n_genes": "10", "method|log": false, "method|use_raw": false, "method|dendrogram": false, "method|swap_axes": false, "method|show_gene_labels": false, "method|matplotlib_pyplot_imshow|cmap": "viridis", "method|matplotlib_pyplot_imshow|interpolation": "None", "method|matplotlib_pyplot_imshow|origin": "upper", "method|method": "pl.rank_genes_groups_heatmap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "c8642ef18f13529c", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:35:13.191307", "update_time": "2024-08-30T07:35:30.947092", "galaxy_version": "24.1", "external_id": "gxy-xffqz", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/d/2/a/dataset_d2ac571e-92ef-4385-a8f1-9543b4085dd5.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/310/configs/tmpfgs2ihdw' > '/galaxy/server/database/objects/9/0/c/dataset_90c4ef8e-3f35-422c-bbd8-27cf4f5f7664.dat' && python '/galaxy/server/database/jobs_directory/000/310/configs/tmpfgs2ihdw' >> '/galaxy/server/database/objects/9/0/c/dataset_90c4ef8e-3f35-422c-bbd8-27cf4f5f7664.dat' && ls . >> '/galaxy/server/database/objects/9/0/c/dataset_90c4ef8e-3f35-422c-bbd8-27cf4f5f7664.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 25, \"dendrogram\": false, \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"groups\": \"\", \"key\": \"\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_imshow\": {\"alpha\": \"\", \"cmap\": \"viridis\", \"interpolation\": \"None\", \"origin\": \"upper\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.rank_genes_groups_heatmap\", \"n_genes\": \"10\", \"show_gene_labels\": false, \"swap_axes\": false, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "63e29910ffeaaa12", "src": "hda", "uuid": "d2ac571e-92ef-4385-a8f1-9543b4085dd5"}}, "outputs": {"hidden_output": {"id": "0c5fa726f67a9d66", "src": "hda", "uuid": "90c4ef8e-3f35-422c-bbd8-27cf4f5f7664"}, "out_png": {"id": "2907c9e51e5e30e7", "src": "hda", "uuid": "5684d4d1-7e0f-495a-9617-e412c6c5d757"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file heatmap.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file heatmap.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:35:19", "plugin": "core", "name": "end_epoch", "raw_value": "1725003319.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:35:15", "plugin": "core", "name": "start_epoch", "raw_value": "1725003315.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-25", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 25, "time_seconds": 35.273040533065796, "inputs": {"adata": {"src": "hda", "id": "1c64024de6e38305"}, "format": "png", "method|n_genes": "10", "method|log": false, "method|use_raw": false, "method|dendrogram": false, "method|swap_axes": false, "method|show_gene_labels": false, "method|matplotlib_pyplot_imshow|cmap": "viridis", "method|matplotlib_pyplot_imshow|interpolation": "None", "method|matplotlib_pyplot_imshow|origin": "upper", "method|method": "pl.rank_genes_groups_heatmap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "79ebb522ac2ecfbe", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:52:15.747636", "update_time": "2024-08-30T07:52:31.757073", "galaxy_version": "24.1", "external_id": "gxy-rcgqw", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/7/a/5/dataset_7a509a27-4632-42f8-8382-b510fbf73fe7.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/366/configs/tmpguls5ftf' > '/galaxy/server/database/objects/4/3/b/dataset_43b318a9-f2c6-4a03-872c-3cca30df55d7.dat' && python '/galaxy/server/database/jobs_directory/000/366/configs/tmpguls5ftf' >> '/galaxy/server/database/objects/4/3/b/dataset_43b318a9-f2c6-4a03-872c-3cca30df55d7.dat' && ls . >> '/galaxy/server/database/objects/4/3/b/dataset_43b318a9-f2c6-4a03-872c-3cca30df55d7.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 25, \"dendrogram\": false, \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"groups\": \"\", \"key\": \"\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_imshow\": {\"alpha\": \"\", \"cmap\": \"viridis\", \"interpolation\": \"None\", \"origin\": \"upper\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.rank_genes_groups_heatmap\", \"n_genes\": \"10\", \"show_gene_labels\": false, \"swap_axes\": false, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "1c64024de6e38305", "src": "hda", "uuid": "7a509a27-4632-42f8-8382-b510fbf73fe7"}}, "outputs": {"hidden_output": {"id": "452e306558188a64", "src": "hda", "uuid": "43b318a9-f2c6-4a03-872c-3cca30df55d7"}, "out_png": {"id": "fe1b23cacd8e2eab", "src": "hda", "uuid": "46f04c85-eebb-417d-9bf5-3853f87508b2"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file heatmap.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file heatmap.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:52:21", "plugin": "core", "name": "end_epoch", "raw_value": "1725004341.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:52:17", "plugin": "core", "name": "start_epoch", "raw_value": "1725004337.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-26", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 26, "time_seconds": 36.05078077316284, "inputs": {"adata": {"src": "hda", "id": "4ce0b3a72d8db0cc"}, "format": "png", "method|n_genes": "10", "method|log": false, "method|use_raw": false, "method|dendrogram": false, "method|swap_axes": false, "method|matplotlib_pyplot_pcolor|cmap": "viridis", "method|matplotlib_pyplot_pcolor|edgecolors": "face", "method|matplotlib_pyplot_pcolor|snap": false, "method|method": "pl.rank_genes_groups_matrixplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "388a4dbdf6225b5e", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:35:50.422700", "update_time": "2024-08-30T07:36:07.133670", "galaxy_version": "24.1", "external_id": "gxy-9t96n", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/9/7/dataset_1971ea97-3cc7-4c2e-9878-86144ffdec52.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/312/configs/tmpdlm73glt' > '/galaxy/server/database/objects/9/4/a/dataset_94a26d64-5b32-425c-a9a1-a1e4b8086df1.dat' && python '/galaxy/server/database/jobs_directory/000/312/configs/tmpdlm73glt' >> '/galaxy/server/database/objects/9/4/a/dataset_94a26d64-5b32-425c-a9a1-a1e4b8086df1.dat' && ls . >> '/galaxy/server/database/objects/9/4/a/dataset_94a26d64-5b32-425c-a9a1-a1e4b8086df1.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 26, \"dendrogram\": false, \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"groups\": \"\", \"key\": \"\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_pcolor\": {\"alpha\": \"\", \"cmap\": \"viridis\", \"edgecolors\": \"face\", \"snap\": false, \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.rank_genes_groups_matrixplot\", \"n_genes\": \"10\", \"swap_axes\": false, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "4ce0b3a72d8db0cc", "src": "hda", "uuid": "1971ea97-3cc7-4c2e-9878-86144ffdec52"}}, "outputs": {"hidden_output": {"id": "7f342ba2fedfc39f", "src": "hda", "uuid": "94a26d64-5b32-425c-a9a1-a1e4b8086df1"}, "out_png": {"id": "f6d1cb77975ebf23", "src": "hda", "uuid": "5e15c313-a60a-4372-98f5-45a9c1257685"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file matrixplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file matrixplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:35:56", "plugin": "core", "name": "end_epoch", "raw_value": "1725003356.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:35:51", "plugin": "core", "name": "start_epoch", "raw_value": "1725003351.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-26", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 26, "time_seconds": 36.34633779525757, "inputs": {"adata": {"src": "hda", "id": "3a7bc74bcd62412a"}, "format": "png", "method|n_genes": "10", "method|log": false, "method|use_raw": false, "method|dendrogram": false, "method|swap_axes": false, "method|matplotlib_pyplot_pcolor|cmap": "viridis", "method|matplotlib_pyplot_pcolor|edgecolors": "face", "method|matplotlib_pyplot_pcolor|snap": false, "method|method": "pl.rank_genes_groups_matrixplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "37c8e51ae9a43513", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:52:51.309427", "update_time": "2024-08-30T07:53:08.201672", "galaxy_version": "24.1", "external_id": "gxy-kp8hr", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/4/7/d/dataset_47d65804-7454-4080-9be2-9549523fbb0a.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/368/configs/tmp37ikh239' > '/galaxy/server/database/objects/4/f/0/dataset_4f07a732-7de5-460a-afad-0f577a3b9c2c.dat' && python '/galaxy/server/database/jobs_directory/000/368/configs/tmp37ikh239' >> '/galaxy/server/database/objects/4/f/0/dataset_4f07a732-7de5-460a-afad-0f577a3b9c2c.dat' && ls . >> '/galaxy/server/database/objects/4/f/0/dataset_4f07a732-7de5-460a-afad-0f577a3b9c2c.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 26, \"dendrogram\": false, \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"groups\": \"\", \"key\": \"\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_pcolor\": {\"alpha\": \"\", \"cmap\": \"viridis\", \"edgecolors\": \"face\", \"snap\": false, \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.rank_genes_groups_matrixplot\", \"n_genes\": \"10\", \"swap_axes\": false, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "3a7bc74bcd62412a", "src": "hda", "uuid": "47d65804-7454-4080-9be2-9549523fbb0a"}}, "outputs": {"hidden_output": {"id": "3c0045496832579b", "src": "hda", "uuid": "4f07a732-7de5-460a-afad-0f577a3b9c2c"}, "out_png": {"id": "90cc78a13b1c9923", "src": "hda", "uuid": "c7a3cb0d-51b9-4c42-a617-3616ea4fb26c"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file matrixplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: saving figure to file matrixplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:52:57", "plugin": "core", "name": "end_epoch", "raw_value": "1725004377.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:52:53", "plugin": "core", "name": "start_epoch", "raw_value": "1725004373.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-27", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 27, "time_seconds": 43.07107949256897, "inputs": {"adata": {"src": "hda", "id": "587daa74c700f387"}, "format": "png", "method|n_genes": "10", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|swap_axes": true, "method|violin_plot|stripplot|stripplot": "True", "method|violin_plot|scale": "width", "method|row_palette": "muted", "method|standard_scale": "None", "method|seaborn_violinplot|bw": "scott", "method|seaborn_violinplot|linewidth": "0", "method|seaborn_violinplot|color": "AliceBlue", "method|seaborn_violinplot|saturation": "0.75", "method|method": "pl.rank_genes_groups_stacked_violin", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "bfc105b661dbaf2b", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:36:27.701041", "update_time": "2024-08-30T07:36:50.208181", "galaxy_version": "24.1", "external_id": "gxy-5rth4", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/f/5/7/dataset_f5768892-63ca-465a-a334-ac93bd3f7679.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/314/configs/tmp1ypg3np7' > '/galaxy/server/database/objects/a/9/7/dataset_a971de46-fadb-4553-88fb-bcb7105de1ea.dat' && python '/galaxy/server/database/jobs_directory/000/314/configs/tmp1ypg3np7' >> '/galaxy/server/database/objects/a/9/7/dataset_a971de46-fadb-4553-88fb-bcb7105de1ea.dat' && ls . >> '/galaxy/server/database/objects/a/9/7/dataset_a971de46-fadb-4553-88fb-bcb7105de1ea.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 27, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"groups\": \"\", \"key\": \"\", \"layer\": \"\", \"log\": false, \"method\": \"pl.rank_genes_groups_stacked_violin\", \"n_genes\": \"10\", \"row_palette\": \"muted\", \"seaborn_violinplot\": {\"bw\": \"scott\", \"color\": \"AliceBlue\", \"linewidth\": \"0.0\", \"orient\": null, \"saturation\": \"0.75\"}, \"standard_scale\": \"None\", \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"violin_plot\": {\"scale\": \"width\", \"stripplot\": {\"__current_case__\": 0, \"jitter\": {\"__current_case__\": 0, \"jitter\": \"True\", \"size\": \"1.0\"}, \"stripplot\": \"True\"}}}", "format": "\"png\""}, "inputs": {"adata": {"id": "587daa74c700f387", "src": "hda", "uuid": "f5768892-63ca-465a-a334-ac93bd3f7679"}}, "outputs": {"hidden_output": {"id": "e72b2281228b4553", "src": "hda", "uuid": "a971de46-fadb-4553-88fb-bcb7105de1ea"}, "out_png": {"id": "b103671a4f13c8f1", "src": "hda", "uuid": "8dc388dc-37eb-490e-aa51-a99cb3f66e63"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file stacked_violin_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file stacked_violin_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "8 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "8.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:36:38", "plugin": "core", "name": "end_epoch", "raw_value": "1725003398.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:36:30", "plugin": "core", "name": "start_epoch", "raw_value": "1725003390.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-27", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 27, "time_seconds": 12.22402572631836, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "scanpy_plot/1.7.1+galaxy1-3", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 3, "time_seconds": 35.56679058074951, "inputs": {"adata": {"src": "hda", "id": "79ebb522ac2ecfbe"}, "format": "png", "method|var_names|var_names": "Fog1,EKLF,SCL", "method|var_names|type": "custom", "method|groupby": "cell_type", "method|num_categories": "7", "method|gene_symbols": "symbol", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|figsize|width": "10", "method|figsize|height": "3", "method|figsize|test": "yes", "method|swap_axes": true, "method|show_gene_labels": true, "method|matplotlib_pyplot_imshow|cmap": "YlGnBu", "method|matplotlib_pyplot_imshow|interpolation": "None", "method|matplotlib_pyplot_imshow|origin": "upper", "method|method": "pl.heatmap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "0e58dc256cff5b8c", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:22:20.547002", "update_time": "2024-08-30T07:22:36.259808", "galaxy_version": "24.1", "external_id": "gxy-zbg8f", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/8/7/6/dataset_876c76ea-9ef1-4167-ac28-67516b774b3b.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/269/configs/tmpwhfhc8g1' > '/galaxy/server/database/objects/0/e/c/dataset_0ecaf889-1bf1-4b91-8d7a-11d7b5962183.dat' && python '/galaxy/server/database/jobs_directory/000/269/configs/tmpwhfhc8g1' >> '/galaxy/server/database/objects/0/e/c/dataset_0ecaf889-1bf1-4b91-8d7a-11d7b5962183.dat' && ls . >> '/galaxy/server/database/objects/0/e/c/dataset_0ecaf889-1bf1-4b91-8d7a-11d7b5962183.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 1, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 0, \"height\": \"3\", \"test\": \"yes\", \"width\": \"10\"}, \"gene_symbols\": \"symbol\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_imshow\": {\"alpha\": \"\", \"cmap\": \"YlGnBu\", \"interpolation\": \"None\", \"origin\": \"upper\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.heatmap\", \"num_categories\": \"7\", \"show_gene_labels\": true, \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 1, \"type\": \"custom\", \"var_names\": \"Fog1,EKLF,SCL\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "79ebb522ac2ecfbe", "src": "hda", "uuid": "876c76ea-9ef1-4167-ac28-67516b774b3b"}}, "outputs": {"hidden_output": {"id": "37c8e51ae9a43513", "src": "hda", "uuid": "0ecaf889-1bf1-4b91-8d7a-11d7b5962183"}, "out_png": {"id": "ac61cc0bf38fcd33", "src": "hda", "uuid": "1c5210b1-6787-4c50-a7af-f3dfbc386846"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:22:25", "plugin": "core", "name": "end_epoch", "raw_value": "1725002545.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:22:21", "plugin": "core", "name": "start_epoch", "raw_value": "1725002541.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-3", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 3, "time_seconds": 37.21701240539551, "inputs": {"adata": {"src": "hda", "id": "09110387a65efcb5"}, "format": "png", "method|var_names|var_names": "Fog1,EKLF,SCL", "method|var_names|type": "custom", "method|groupby": "cell_type", "method|num_categories": "7", "method|gene_symbols": "symbol", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|figsize|width": "10", "method|figsize|height": "3", "method|figsize|test": "yes", "method|swap_axes": true, "method|show_gene_labels": true, "method|matplotlib_pyplot_imshow|cmap": "YlGnBu", "method|matplotlib_pyplot_imshow|interpolation": "None", "method|matplotlib_pyplot_imshow|origin": "upper", "method|method": "pl.heatmap", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "787f20cab39ce662", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:38:52.980750", "update_time": "2024-08-30T07:39:10.115542", "galaxy_version": "24.1", "external_id": "gxy-c776t", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/e/8/e/dataset_e8e6d07e-2b0a-455d-931f-17ad777a65b0.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/322/configs/tmp09xqu6_k' > '/galaxy/server/database/objects/4/7/7/dataset_4776c047-f024-4440-9fb8-5ac66b75e7ae.dat' && python '/galaxy/server/database/jobs_directory/000/322/configs/tmp09xqu6_k' >> '/galaxy/server/database/objects/4/7/7/dataset_4776c047-f024-4440-9fb8-5ac66b75e7ae.dat' && ls . >> '/galaxy/server/database/objects/4/7/7/dataset_4776c047-f024-4440-9fb8-5ac66b75e7ae.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 1, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 0, \"height\": \"3\", \"test\": \"yes\", \"width\": \"10\"}, \"gene_symbols\": \"symbol\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_imshow\": {\"alpha\": \"\", \"cmap\": \"YlGnBu\", \"interpolation\": \"None\", \"origin\": \"upper\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.heatmap\", \"num_categories\": \"7\", \"show_gene_labels\": true, \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 1, \"type\": \"custom\", \"var_names\": \"Fog1,EKLF,SCL\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "09110387a65efcb5", "src": "hda", "uuid": "e8e6d07e-2b0a-455d-931f-17ad777a65b0"}}, "outputs": {"hidden_output": {"id": "4388269e16e5b2ed", "src": "hda", "uuid": "4776c047-f024-4440-9fb8-5ac66b75e7ae"}, "out_png": {"id": "0963fa0ec04b9133", "src": "hda", "uuid": "23db4496-8222-483a-9319-be6388a4e6e7"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file heatmap.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:38:59", "plugin": "core", "name": "end_epoch", "raw_value": "1725003539.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:38:55", "plugin": "core", "name": "start_epoch", "raw_value": "1725003535.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-4", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 4, "time_seconds": 36.925981283187866, "inputs": {"adata": {"src": "hda", "id": "e9af9b83d77bdec3"}, "format": "png", "method|var_names|var_names": "CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402", "method|var_names|type": "custom", "method|groupby": "louvain", "method|num_categories": "7", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|var_group_positions_0|start": "0", "method|var_group_positions_0|end": "1", "method|var_group_positions_0|label": "B cells", "method|var_group_positions_1|start": "11", "method|var_group_positions_1|end": "12", "method|var_group_positions_1|label": "dendritic", "method|figsize|test": "no", "method|color_map": "hot", "method|dot_max": "0.7", "method|dot_min": "0.1", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.dotplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "d7f111b001e819c5", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:22:55.918833", "update_time": "2024-08-30T07:23:12.651038", "galaxy_version": "24.1", "external_id": "gxy-4bl7m", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/c/7/8/dataset_c78ca9e3-3bbb-49ce-b33b-539d0bef81d0.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/271/configs/tmpem037cuy' > '/galaxy/server/database/objects/e/5/7/dataset_e57a6b35-4460-41a4-94e9-61cad9e26652.dat' && python '/galaxy/server/database/jobs_directory/000/271/configs/tmpem037cuy' >> '/galaxy/server/database/objects/e/5/7/dataset_e57a6b35-4460-41a4-94e9-61cad9e26652.dat' && ls . >> '/galaxy/server/database/objects/e/5/7/dataset_e57a6b35-4460-41a4-94e9-61cad9e26652.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 2, \"color_map\": \"hot\", \"dendrogram\": true, \"dot_max\": \"0.7\", \"dot_min\": \"0.1\", \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"gene_symbols\": \"\", \"groupby\": \"louvain\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.dotplot\", \"num_categories\": \"7\", \"use_raw\": false, \"var_group_positions\": [{\"__index__\": 0, \"end\": \"1\", \"label\": \"B cells\", \"start\": \"0\"}, {\"__index__\": 1, \"end\": \"12\", \"label\": \"dendritic\", \"start\": \"11\"}], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 1, \"type\": \"custom\", \"var_names\": \"CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "e9af9b83d77bdec3", "src": "hda", "uuid": "c78ca9e3-3bbb-49ce-b33b-539d0bef81d0"}}, "outputs": {"hidden_output": {"id": "16218136a2e3da41", "src": "hda", "uuid": "e57a6b35-4460-41a4-94e9-61cad9e26652"}, "out_png": {"id": "2761ccccef04f710", "src": "hda", "uuid": "1eb6566a-3fe4-4c38-9799-374a88eedba3"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: dendrogram data not found (using key=dendrogram_louvain). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.\ncategories: 0, 1, 2, etc.\nvar_group_labels: B cells, dendritic\nWARNING: saving figure to file dotplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: dendrogram data not found (using key=dendrogram_louvain). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.\ncategories: 0, 1, 2, etc.\nvar_group_labels: B cells, dendritic\nWARNING: saving figure to file dotplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:23:01", "plugin": "core", "name": "end_epoch", "raw_value": "1725002581.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:22:57", "plugin": "core", "name": "start_epoch", "raw_value": "1725002577.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-4", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 4, "time_seconds": 38.86984896659851, "inputs": {"adata": {"src": "hda", "id": "fe621fd64dce2762"}, "format": "png", "method|var_names|var_names": "CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402", "method|var_names|type": "custom", "method|groupby": "louvain", "method|num_categories": "7", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|var_group_positions_0|start": "0", "method|var_group_positions_0|end": "1", "method|var_group_positions_0|label": "B cells", "method|var_group_positions_1|start": "11", "method|var_group_positions_1|end": "12", "method|var_group_positions_1|label": "dendritic", "method|figsize|test": "no", "method|color_map": "hot", "method|dot_max": "0.7", "method|dot_min": "0.1", "method|matplotlib_pyplot_scatter|linewidths": "0", "method|matplotlib_pyplot_scatter|edgecolors": "face", "method|method": "pl.dotplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "4e3c5faea0b03fb3", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:39:30.768545", "update_time": "2024-08-30T07:39:48.720281", "galaxy_version": "24.1", "external_id": "gxy-8k8gk", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/0/e/0/dataset_0e0b00cc-df0f-4195-ba50-2cb8e61f8ee8.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/324/configs/tmpg05e6x5f' > '/galaxy/server/database/objects/1/7/5/dataset_175484bf-9656-4e45-bec8-266ea1f981ce.dat' && python '/galaxy/server/database/jobs_directory/000/324/configs/tmpg05e6x5f' >> '/galaxy/server/database/objects/1/7/5/dataset_175484bf-9656-4e45-bec8-266ea1f981ce.dat' && ls . >> '/galaxy/server/database/objects/1/7/5/dataset_175484bf-9656-4e45-bec8-266ea1f981ce.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 2, \"color_map\": \"hot\", \"dendrogram\": true, \"dot_max\": \"0.7\", \"dot_min\": \"0.1\", \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"gene_symbols\": \"\", \"groupby\": \"louvain\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.dotplot\", \"num_categories\": \"7\", \"use_raw\": false, \"var_group_positions\": [{\"__index__\": 0, \"end\": \"1\", \"label\": \"B cells\", \"start\": \"0\"}, {\"__index__\": 1, \"end\": \"12\", \"label\": \"dendritic\", \"start\": \"11\"}], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 1, \"type\": \"custom\", \"var_names\": \"CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "fe621fd64dce2762", "src": "hda", "uuid": "0e0b00cc-df0f-4195-ba50-2cb8e61f8ee8"}}, "outputs": {"hidden_output": {"id": "fbfcbe3a7b0bf152", "src": "hda", "uuid": "175484bf-9656-4e45-bec8-266ea1f981ce"}, "out_png": {"id": "6ef983da3bac57eb", "src": "hda", "uuid": "b93e2d39-85df-4ce0-a5c3-af5adc253e90"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: dendrogram data not found (using key=dendrogram_louvain). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.\ncategories: 0, 1, 2, etc.\nvar_group_labels: B cells, dendritic\nWARNING: saving figure to file dotplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: dendrogram data not found (using key=dendrogram_louvain). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: Groups are not reordered because the `groupby` categories and the `var_group_labels` are different.\ncategories: 0, 1, 2, etc.\nvar_group_labels: B cells, dendritic\nWARNING: saving figure to file dotplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:39:36", "plugin": "core", "name": "end_epoch", "raw_value": "1725003576.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:39:32", "plugin": "core", "name": "start_epoch", "raw_value": "1725003572.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-5", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 5, "time_seconds": 38.17630863189697, "inputs": {"adata": {"src": "hda", "id": "9d66ff102ec7d768"}, "format": "png", "method|var_names|var_names": "Fog1,EKLF,SCL", "method|var_names|type": "custom", "method|groupby": "cell_type", "method|num_categories": "7", "method|gene_symbols": "symbol", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|method": "pl.dotplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "d055f39f4ce4ec90", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:23:33.361126", "update_time": "2024-08-30T07:23:51.381065", "galaxy_version": "24.1", "external_id": "gxy-rhk4r", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/d/0/dataset_1d096969-aaa3-4479-b7e5-faff86cd03cb.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/273/configs/tmpseqwvnyc' > '/galaxy/server/database/objects/4/c/c/dataset_4cc3792b-543a-4e3c-a0a4-fce81d68ec48.dat' && python '/galaxy/server/database/jobs_directory/000/273/configs/tmpseqwvnyc' >> '/galaxy/server/database/objects/4/c/c/dataset_4cc3792b-543a-4e3c-a0a4-fce81d68ec48.dat' && ls . >> '/galaxy/server/database/objects/4/c/c/dataset_4cc3792b-543a-4e3c-a0a4-fce81d68ec48.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 2, \"color_map\": \"viridis\", \"dendrogram\": true, \"dot_max\": \"\", \"dot_min\": \"\", \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"gene_symbols\": \"symbol\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.dotplot\", \"num_categories\": \"7\", \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 1, \"type\": \"custom\", \"var_names\": \"Fog1,EKLF,SCL\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "9d66ff102ec7d768", "src": "hda", "uuid": "1d096969-aaa3-4479-b7e5-faff86cd03cb"}}, "outputs": {"hidden_output": {"id": "6e5ce194bdd1086a", "src": "hda", "uuid": "4cc3792b-543a-4e3c-a0a4-fce81d68ec48"}, "out_png": {"id": "dd9c250bd7eccd9e", "src": "hda", "uuid": "8ac62812-f599-4fba-b79f-ad2f6e436906"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file dotplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file dotplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:23:39", "plugin": "core", "name": "end_epoch", "raw_value": "1725002619.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:23:35", "plugin": "core", "name": "start_epoch", "raw_value": "1725002615.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-5", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 5, "time_seconds": 36.708731174468994, "inputs": {"adata": {"src": "hda", "id": "6f7f1c0aaf6e1002"}, "format": "png", "method|var_names|var_names": "Fog1,EKLF,SCL", "method|var_names|type": "custom", "method|groupby": "cell_type", "method|num_categories": "7", "method|gene_symbols": "symbol", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|method": "pl.dotplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "7abcafbf17910b1a", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:40:08.657868", "update_time": "2024-08-30T07:40:26.038228", "galaxy_version": "24.1", "external_id": "gxy-h7rsb", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/2/a/8/dataset_2a81becc-f8b3-41a2-8d72-7afb31b47fdd.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/326/configs/tmpuq5jnki7' > '/galaxy/server/database/objects/7/1/5/dataset_71506253-b4b7-42c9-90d4-15834c17c8b1.dat' && python '/galaxy/server/database/jobs_directory/000/326/configs/tmpuq5jnki7' >> '/galaxy/server/database/objects/7/1/5/dataset_71506253-b4b7-42c9-90d4-15834c17c8b1.dat' && ls . >> '/galaxy/server/database/objects/7/1/5/dataset_71506253-b4b7-42c9-90d4-15834c17c8b1.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 2, \"color_map\": \"viridis\", \"dendrogram\": true, \"dot_max\": \"\", \"dot_min\": \"\", \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"gene_symbols\": \"symbol\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_scatter\": {\"alpha\": \"\", \"edgecolors\": \"face\", \"linewidths\": \"0.0\", \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.dotplot\", \"num_categories\": \"7\", \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 1, \"type\": \"custom\", \"var_names\": \"Fog1,EKLF,SCL\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "6f7f1c0aaf6e1002", "src": "hda", "uuid": "2a81becc-f8b3-41a2-8d72-7afb31b47fdd"}}, "outputs": {"hidden_output": {"id": "8e7ac21428a179b0", "src": "hda", "uuid": "71506253-b4b7-42c9-90d4-15834c17c8b1"}, "out_png": {"id": "b05101e16344c673", "src": "hda", "uuid": "dc42380b-68ba-449f-9540-e75cfa8ed515"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file dotplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file dotplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:40:15", "plugin": "core", "name": "end_epoch", "raw_value": "1725003615.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:40:11", "plugin": "core", "name": "start_epoch", "raw_value": "1725003611.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-6", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 6, "time_seconds": 29.393787145614624, "inputs": {"adata": {"src": "hda", "id": "1325463534297ec8"}, "format": "png", "method|key_variables|keys": "n_genes, percent_mito, n_counts", "method|key_variables|type": "custom", "method|log": false, "method|use_raw": false, "method|violin_plot|stripplot|stripplot": "True", "method|violin_plot|multi_panel|width": "20", "method|violin_plot|multi_panel|height": "20", "method|violin_plot|multi_panel|multi_panel": "True", "method|violin_plot|scale": "width", "method|seaborn_violinplot|bw": "scott", "method|seaborn_violinplot|linewidth": "0", "method|seaborn_violinplot|color": "AliceBlue", "method|seaborn_violinplot|saturation": "0.75", "method|method": "pl.violin", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "47fccb329a775a72", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "error", "exit_code": null, "create_time": "2024-08-30T07:24:12.485692", "update_time": "2024-08-30T07:24:20.888017", "galaxy_version": "24.1", "external_id": "gxy-cb9pp", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/9/4/f/dataset_94f285ad-837d-4681-bf47-c61fe11a2421.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/275/configs/tmpyqdazgx_' > '/galaxy/server/database/objects/b/e/b/dataset_bebe4fa6-8af1-4a63-bf55-18cc062a5e40.dat' && python '/galaxy/server/database/jobs_directory/000/275/configs/tmpyqdazgx_' >> '/galaxy/server/database/objects/b/e/b/dataset_bebe4fa6-8af1-4a63-bf55-18cc062a5e40.dat' && ls . >> '/galaxy/server/database/objects/b/e/b/dataset_bebe4fa6-8af1-4a63-bf55-18cc062a5e40.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": null, "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 3, \"groupby\": \"\", \"key_variables\": {\"__current_case__\": 2, \"keys\": \"n_genes, percent_mito, n_counts\", \"type\": \"custom\"}, \"log\": false, \"method\": \"pl.violin\", \"rotation\": \"\", \"seaborn_violinplot\": {\"bw\": \"scott\", \"color\": \"AliceBlue\", \"linewidth\": \"0.0\", \"orient\": null, \"saturation\": \"0.75\"}, \"use_raw\": false, \"violin_plot\": {\"multi_panel\": {\"__current_case__\": 0, \"height\": \"20\", \"multi_panel\": \"True\", \"width\": \"20\"}, \"scale\": \"width\", \"stripplot\": {\"__current_case__\": 0, \"jitter\": {\"__current_case__\": 0, \"jitter\": \"True\", \"size\": \"1.0\"}, \"stripplot\": \"True\"}}, \"xlabel\": \"\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "1325463534297ec8", "src": "hda", "uuid": "94f285ad-837d-4681-bf47-c61fe11a2421"}}, "outputs": {"hidden_output": {"id": "44f6cd6d9970c8f1", "src": "hda", "uuid": "bebe4fa6-8af1-4a63-bf55-18cc062a5e40"}, "out_png": {"id": "ecfb059196fefc44", "src": "hda", "uuid": "b88d4b8f-0092-479d-a19a-13bd288120bb"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file violin.png\n", "job_stdout": null, "job_stderr": null, "stdout": "", "stderr": "WARNING: saving figure to file violin.png\n", "job_messages": null, "dependencies": [], "job_metrics": []}, "output_problems": ["Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: WARNING: saving figure to file violin.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: WARNING: saving figure to file violin.png\n.", "Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1, exit_code: None, stderr: WARNING: saving figure to file violin.png\n."], "status": "failure"}}, {"id": "scanpy_plot/1.7.1+galaxy1-6", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 6, "time_seconds": 39.1015841960907, "inputs": {"adata": {"src": "hda", "id": "9ab7433e8dc2dd11"}, "format": "png", "method|key_variables|keys": "n_genes, percent_mito, n_counts", "method|key_variables|type": "custom", "method|log": false, "method|use_raw": false, "method|violin_plot|stripplot|stripplot": "True", "method|violin_plot|multi_panel|width": "20", "method|violin_plot|multi_panel|height": "20", "method|violin_plot|multi_panel|multi_panel": "True", "method|violin_plot|scale": "width", "method|seaborn_violinplot|bw": "scott", "method|seaborn_violinplot|linewidth": "0", "method|seaborn_violinplot|color": "AliceBlue", "method|seaborn_violinplot|saturation": "0.75", "method|method": "pl.violin", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "37044600c9a534ea", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:40:46.664463", "update_time": "2024-08-30T07:41:04.544753", "galaxy_version": "24.1", "external_id": "gxy-2g7t8", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/3/c/d/dataset_3cd929f9-168d-4a82-9fa1-c94255c7e992.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/328/configs/tmp93oskny4' > '/galaxy/server/database/objects/d/1/e/dataset_d1e51f1f-aee7-4697-a198-64f7470c1a12.dat' && python '/galaxy/server/database/jobs_directory/000/328/configs/tmp93oskny4' >> '/galaxy/server/database/objects/d/1/e/dataset_d1e51f1f-aee7-4697-a198-64f7470c1a12.dat' && ls . >> '/galaxy/server/database/objects/d/1/e/dataset_d1e51f1f-aee7-4697-a198-64f7470c1a12.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 3, \"groupby\": \"\", \"key_variables\": {\"__current_case__\": 2, \"keys\": \"n_genes, percent_mito, n_counts\", \"type\": \"custom\"}, \"log\": false, \"method\": \"pl.violin\", \"rotation\": \"\", \"seaborn_violinplot\": {\"bw\": \"scott\", \"color\": \"AliceBlue\", \"linewidth\": \"0.0\", \"orient\": null, \"saturation\": \"0.75\"}, \"use_raw\": false, \"violin_plot\": {\"multi_panel\": {\"__current_case__\": 0, \"height\": \"20\", \"multi_panel\": \"True\", \"width\": \"20\"}, \"scale\": \"width\", \"stripplot\": {\"__current_case__\": 0, \"jitter\": {\"__current_case__\": 0, \"jitter\": \"True\", \"size\": \"1.0\"}, \"stripplot\": \"True\"}}, \"xlabel\": \"\"}", "format": "\"png\""}, "inputs": {"adata": {"id": "9ab7433e8dc2dd11", "src": "hda", "uuid": "3cd929f9-168d-4a82-9fa1-c94255c7e992"}}, "outputs": {"hidden_output": {"id": "8260c89c5eeb31c8", "src": "hda", "uuid": "d1e51f1f-aee7-4697-a198-64f7470c1a12"}, "out_png": {"id": "0a3002928b60a638", "src": "hda", "uuid": "60eb0e49-54bf-439a-b116-3d3be498de29"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "WARNING: saving figure to file violin.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "WARNING: saving figure to file violin.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:40:53", "plugin": "core", "name": "end_epoch", "raw_value": "1725003653.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:40:48", "plugin": "core", "name": "start_epoch", "raw_value": "1725003648.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-7", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 7, "time_seconds": 37.63020658493042, "inputs": {"adata": {"src": "hda", "id": "df4746b5f0de4595"}, "format": "png", "method|var_names|type": "all", "method|groupby": "cell_type", "method|num_categories": "7", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|figsize|test": "no", "method|swap_axes": true, "method|violin_plot|stripplot|stripplot": "True", "method|violin_plot|scale": "width", "method|row_palette": "muted", "method|standard_scale": "None", "method|seaborn_violinplot|bw": "scott", "method|seaborn_violinplot|linewidth": "0", "method|seaborn_violinplot|color": "AliceBlue", "method|seaborn_violinplot|saturation": "0.75", "method|method": "pl.stacked_violin", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "54464ef7c0297c1f", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:24:40.174940", "update_time": "2024-08-30T07:24:57.982822", "galaxy_version": "24.1", "external_id": "gxy-bw7tk", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/b/f/9/dataset_bf9eb92f-9909-4426-be5e-34eb08d7c791.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/277/configs/tmprb3p6u2p' > '/galaxy/server/database/objects/9/2/7/dataset_927cee3c-76bc-4359-abed-33b9291bfdba.dat' && python '/galaxy/server/database/jobs_directory/000/277/configs/tmprb3p6u2p' >> '/galaxy/server/database/objects/9/2/7/dataset_927cee3c-76bc-4359-abed-33b9291bfdba.dat' && ls . >> '/galaxy/server/database/objects/9/2/7/dataset_927cee3c-76bc-4359-abed-33b9291bfdba.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 4, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"gene_symbols\": \"\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"method\": \"pl.stacked_violin\", \"num_categories\": \"7\", \"row_palette\": \"muted\", \"seaborn_violinplot\": {\"bw\": \"scott\", \"color\": \"AliceBlue\", \"linewidth\": \"0.0\", \"orient\": null, \"saturation\": \"0.75\"}, \"standard_scale\": \"None\", \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 0, \"type\": \"all\"}, \"violin_plot\": {\"scale\": \"width\", \"stripplot\": {\"__current_case__\": 0, \"jitter\": {\"__current_case__\": 0, \"jitter\": \"True\", \"size\": \"1.0\"}, \"stripplot\": \"True\"}}}", "format": "\"png\""}, "inputs": {"adata": {"id": "df4746b5f0de4595", "src": "hda", "uuid": "bf9eb92f-9909-4426-be5e-34eb08d7c791"}}, "outputs": {"hidden_output": {"id": "6fcfb6eba893b611", "src": "hda", "uuid": "927cee3c-76bc-4359-abed-33b9291bfdba"}, "out_png": {"id": "f888dfd4eddf9ea6", "src": "hda", "uuid": "348ff2b3-07a8-4590-8fe6-766c44a25c77"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file stacked_violin_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file stacked_violin_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:24:46", "plugin": "core", "name": "end_epoch", "raw_value": "1725002686.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:24:42", "plugin": "core", "name": "start_epoch", "raw_value": "1725002682.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-7", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 7, "time_seconds": 37.68809223175049, "inputs": {"adata": {"src": "hda", "id": "d3004320169a031c"}, "format": "png", "method|var_names|type": "all", "method|groupby": "cell_type", "method|num_categories": "7", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|figsize|test": "no", "method|swap_axes": true, "method|violin_plot|stripplot|stripplot": "True", "method|violin_plot|scale": "width", "method|row_palette": "muted", "method|standard_scale": "None", "method|seaborn_violinplot|bw": "scott", "method|seaborn_violinplot|linewidth": "0", "method|seaborn_violinplot|color": "AliceBlue", "method|seaborn_violinplot|saturation": "0.75", "method|method": "pl.stacked_violin", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "dbaa233cd776bf88", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:41:24.485200", "update_time": "2024-08-30T07:41:42.388360", "galaxy_version": "24.1", "external_id": "gxy-2zqld", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/f/3/d/dataset_f3dd12da-2d78-462a-8c09-ea77d21554ed.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/330/configs/tmphd75ukq9' > '/galaxy/server/database/objects/d/d/2/dataset_dd2b9c67-cca6-4ed3-aa2b-6f8ef719ad02.dat' && python '/galaxy/server/database/jobs_directory/000/330/configs/tmphd75ukq9' >> '/galaxy/server/database/objects/d/d/2/dataset_dd2b9c67-cca6-4ed3-aa2b-6f8ef719ad02.dat' && ls . >> '/galaxy/server/database/objects/d/d/2/dataset_dd2b9c67-cca6-4ed3-aa2b-6f8ef719ad02.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 4, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"gene_symbols\": \"\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"method\": \"pl.stacked_violin\", \"num_categories\": \"7\", \"row_palette\": \"muted\", \"seaborn_violinplot\": {\"bw\": \"scott\", \"color\": \"AliceBlue\", \"linewidth\": \"0.0\", \"orient\": null, \"saturation\": \"0.75\"}, \"standard_scale\": \"None\", \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 0, \"type\": \"all\"}, \"violin_plot\": {\"scale\": \"width\", \"stripplot\": {\"__current_case__\": 0, \"jitter\": {\"__current_case__\": 0, \"jitter\": \"True\", \"size\": \"1.0\"}, \"stripplot\": \"True\"}}}", "format": "\"png\""}, "inputs": {"adata": {"id": "d3004320169a031c", "src": "hda", "uuid": "f3dd12da-2d78-462a-8c09-ea77d21554ed"}}, "outputs": {"hidden_output": {"id": "a65ae33bbb8a093e", "src": "hda", "uuid": "dd2b9c67-cca6-4ed3-aa2b-6f8ef719ad02"}, "out_png": {"id": "1bb6bf1feaf2c31c", "src": "hda", "uuid": "8cb36ee9-3054-4f5f-b746-3430ae209105"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file stacked_violin_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file stacked_violin_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "5 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "5.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:41:31", "plugin": "core", "name": "end_epoch", "raw_value": "1725003691.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:41:26", "plugin": "core", "name": "start_epoch", "raw_value": "1725003686.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-8", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 8, "time_seconds": 12.364529609680176, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "scanpy_plot/1.7.1+galaxy1-8", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 8, "time_seconds": 37.865705490112305, "inputs": {"adata": {"src": "hda", "id": "4c631faa67f4435b"}, "format": "png", "method|var_names|var_names": "Fog1,EKLF,SCL", "method|var_names|type": "custom", "method|groupby": "cell_type", "method|num_categories": "7", "method|gene_symbols": "symbol", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|swap_axes": true, "method|method": "pl.stacked_violin", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "9de2ed719293250f", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:42:03.558095", "update_time": "2024-08-30T07:42:20.678254", "galaxy_version": "24.1", "external_id": "gxy-gqhvr", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/5/9/d/dataset_59d8f6fd-e3c5-41cf-bfff-a9afe02dafe0.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/332/configs/tmp5ctxb6x5' > '/galaxy/server/database/objects/c/a/d/dataset_cad916d3-bb6c-48e2-9faf-127d5f8dee8e.dat' && python '/galaxy/server/database/jobs_directory/000/332/configs/tmp5ctxb6x5' >> '/galaxy/server/database/objects/c/a/d/dataset_cad916d3-bb6c-48e2-9faf-127d5f8dee8e.dat' && ls . >> '/galaxy/server/database/objects/c/a/d/dataset_cad916d3-bb6c-48e2-9faf-127d5f8dee8e.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 4, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"gene_symbols\": \"symbol\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"method\": \"pl.stacked_violin\", \"num_categories\": \"7\", \"row_palette\": \"muted\", \"seaborn_violinplot\": {\"bw\": \"scott\", \"color\": \"AliceBlue\", \"linewidth\": \"0.0\", \"orient\": null, \"saturation\": \"0.75\"}, \"standard_scale\": \"None\", \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 1, \"type\": \"custom\", \"var_names\": \"Fog1,EKLF,SCL\"}, \"violin_plot\": {\"scale\": \"width\", \"stripplot\": {\"__current_case__\": 0, \"jitter\": {\"__current_case__\": 0, \"jitter\": \"True\", \"size\": \"1.0\"}, \"stripplot\": \"True\"}}}", "format": "\"png\""}, "inputs": {"adata": {"id": "4c631faa67f4435b", "src": "hda", "uuid": "59d8f6fd-e3c5-41cf-bfff-a9afe02dafe0"}}, "outputs": {"hidden_output": {"id": "06d6bda11c46fb19", "src": "hda", "uuid": "cad916d3-bb6c-48e2-9faf-127d5f8dee8e"}, "out_png": {"id": "a408ede2787f3002", "src": "hda", "uuid": "50d00373-c71d-4e22-bcb3-01a16ad1e48e"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file stacked_violin_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file stacked_violin_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:42:09", "plugin": "core", "name": "end_epoch", "raw_value": "1725003729.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:42:05", "plugin": "core", "name": "start_epoch", "raw_value": "1725003725.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-9", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 9, "time_seconds": 35.325703144073486, "inputs": {"adata": {"src": "hda", "id": "d3a9677d1e16a3d5"}, "format": "png", "method|var_names|type": "all", "method|groupby": "cell_type", "method|num_categories": "7", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|figsize|test": "no", "method|swap_axes": true, "method|matplotlib_pyplot_pcolor|cmap": "viridis", "method|matplotlib_pyplot_pcolor|edgecolors": "face", "method|matplotlib_pyplot_pcolor|snap": false, "method|method": "pl.matrixplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "52c051c290ff1f7a", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:25:30.294129", "update_time": "2024-08-30T07:25:46.006323", "galaxy_version": "24.1", "external_id": "gxy-s9tmz", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/1/f/3/dataset_1f31744c-747b-4884-801c-11d81d647b14.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/280/configs/tmp8las177p' > '/galaxy/server/database/objects/f/5/5/dataset_f554e032-30ec-475b-9509-c612b5f7d939.dat' && python '/galaxy/server/database/jobs_directory/000/280/configs/tmp8las177p' >> '/galaxy/server/database/objects/f/5/5/dataset_f554e032-30ec-475b-9509-c612b5f7d939.dat' && ls . >> '/galaxy/server/database/objects/f/5/5/dataset_f554e032-30ec-475b-9509-c612b5f7d939.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 5, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"gene_symbols\": \"\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_pcolor\": {\"alpha\": \"\", \"cmap\": \"viridis\", \"edgecolors\": \"face\", \"snap\": false, \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.matrixplot\", \"num_categories\": \"7\", \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 0, \"type\": \"all\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "d3a9677d1e16a3d5", "src": "hda", "uuid": "1f31744c-747b-4884-801c-11d81d647b14"}}, "outputs": {"hidden_output": {"id": "1c1690c2df8ccc46", "src": "hda", "uuid": "f554e032-30ec-475b-9509-c612b5f7d939"}, "out_png": {"id": "475c456764bb4a49", "src": "hda", "uuid": "a2959173-9430-4c03-88fc-dd022f5344c8"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:25:35", "plugin": "core", "name": "end_epoch", "raw_value": "1725002735.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:25:31", "plugin": "core", "name": "start_epoch", "raw_value": "1725002731.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_plot/1.7.1+galaxy1-9", "has_data": true, "data": {"tool_id": "scanpy_plot", "tool_version": "1.7.1+galaxy1", "test_index": 9, "time_seconds": 37.71287965774536, "inputs": {"adata": {"src": "hda", "id": "e5b7d3cf9928aacb"}, "format": "png", "method|var_names|type": "all", "method|groupby": "cell_type", "method|num_categories": "7", "method|log": false, "method|use_raw": false, "method|dendrogram": true, "method|figsize|test": "no", "method|swap_axes": true, "method|matplotlib_pyplot_pcolor|cmap": "viridis", "method|matplotlib_pyplot_pcolor|edgecolors": "face", "method|matplotlib_pyplot_pcolor|snap": false, "method|method": "pl.matrixplot", "advanced_common|show_log": true}, "job": {"model_class": "Job", "id": "254446c4c22f43e3", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/scanpy_plot/scanpy_plot/1.7.1+galaxy1", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:42:41.304993", "update_time": "2024-08-30T07:42:58.068320", "galaxy_version": "24.1", "external_id": "gxy-g47zq", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/objects/7/d/b/dataset_7db7290a-93bc-42a3-a727-87831093446e.dat' 'anndata.h5ad' && cat '/galaxy/server/database/jobs_directory/000/334/configs/tmpx34xjd3w' > '/galaxy/server/database/objects/8/4/0/dataset_8407754f-6ec8-4cc4-93b2-6637974f510c.dat' && python '/galaxy/server/database/jobs_directory/000/334/configs/tmpx34xjd3w' >> '/galaxy/server/database/objects/8/4/0/dataset_8407754f-6ec8-4cc4-93b2-6637974f510c.dat' && ls . >> '/galaxy/server/database/objects/8/4/0/dataset_8407754f-6ec8-4cc4-93b2-6637974f510c.dat' && touch 'anndata_info.txt' && cat 'anndata_info.txt' | sed -r '1 s|AnnData object with (.+) = (.*)\\s*|\\1: \\2|g' | sed \"s|'||g\" | sed -r 's|^\\s*(.*):\\s(.*)|[\\1]\\n- \\2|g' | sed 's|, |\\n- |g'", "user_email": "tests@fake.org", "command_version": "scanpy version: 1.7.1", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "advanced_common": "{\"show_log\": true}", "method": "{\"__current_case__\": 5, \"dendrogram\": true, \"figsize\": {\"__current_case__\": 1, \"test\": \"no\"}, \"gene_symbols\": \"\", \"groupby\": \"cell_type\", \"layer\": \"\", \"log\": false, \"matplotlib_pyplot_pcolor\": {\"alpha\": \"\", \"cmap\": \"viridis\", \"edgecolors\": \"face\", \"snap\": false, \"vmax\": \"\", \"vmin\": \"\"}, \"method\": \"pl.matrixplot\", \"num_categories\": \"7\", \"swap_axes\": true, \"use_raw\": false, \"var_group_positions\": [], \"var_group_rotation\": \"\", \"var_names\": {\"__current_case__\": 0, \"type\": \"all\"}}", "format": "\"png\""}, "inputs": {"adata": {"id": "e5b7d3cf9928aacb", "src": "hda", "uuid": "7db7290a-93bc-42a3-a727-87831093446e"}}, "outputs": {"hidden_output": {"id": "5038122632c28f0a", "src": "hda", "uuid": "8407754f-6ec8-4cc4-93b2-6637974f510c"}, "out_png": {"id": "8c9132f0c6a1175e", "src": "hda", "uuid": "9e68d14c-d485-43d9-8f4f-acc03418d40b"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\nWARNING: dendrogram data not found (using key=dendrogram_cell_type). Running `sc.tl.dendrogram` with default parameters. For fine tuning it is recommended to run `sc.tl.dendrogram` independently.\nWARNING: saving figure to file matrixplot_.png\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "4 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "4.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:42:47", "plugin": "core", "name": "end_epoch", "raw_value": "1725003767.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:42:43", "plugin": "core", "name": "start_epoch", "raw_value": "1725003763.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "scanpy_run_pca/1.8.1+3+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_run_pca", "tool_version": "1.8.1+3+galaxy0", "test_index": 0, "time_seconds": 0.15224909782409668, "execution_problem": "Input staging problem: Test input file (scale_data.h5) cannot be found.", "status": "error"}}, {"id": "scanpy_run_pca/1.8.1+3+galaxy0-0", "has_data": true, "data": {"tool_id": "scanpy_run_pca", "tool_version": "1.8.1+3+galaxy0", "test_index": 0, "time_seconds": 0.15477275848388672, "execution_problem": "Input staging problem: Test input file (scale_data.h5) cannot be found.", "status": "error"}}, {"id": "table_compute/1.2.4+galaxy0-0", "has_data": true, "data": {"tool_id": "table_compute", "tool_version": "1.2.4+galaxy0", "test_index": 0, "time_seconds": 41.4585497379303, "inputs": {"singtabop|input": {"src": "hda", "id": "f18ca6e508041cdd"}, "singtabop|user|select_cols_wanted": "2:4,2,2", "singtabop|user|select_rows_wanted": "2:5,3,3", "singtabop|user|select_keepdupe": "select_cols_keepdupe", "singtabop|user|mode": "select", "singtabop|use_type": "single", "precision": "2"}, "job": {"model_class": "Job", "id": "16218136a2e3da41", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:53:44.040379", "update_time": "2024-08-30T07:54:05.268432", "galaxy_version": "24.1", "external_id": "gxy-d8f95", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/jobs_directory/000/371/configs/tmp84bx5d8f' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py", "user_email": "tests@fake.org", "command_version": "0.9.2", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precision": "\"2\"", "out_opts": "[\"ignore_nas\", \"output_headers_col\", \"output_headers_row\"]", "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 517, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 1, \"mode\": \"select\", \"select_cols_wanted\": \"2:4,2,2\", \"select_keepdupe\": \"select_cols_keepdupe\", \"select_rows_wanted\": \"2:5,3,3\"}}"}, "inputs": {"singtabop|input": {"id": "f18ca6e508041cdd", "src": "hda", "uuid": "b1eb6318-a933-494f-afa5-4ef86a8edc39"}}, "outputs": {"table": {"id": "9f0ec53418dfe36c", "src": "hda", "uuid": "a0d6f197-0e62-4096-9bbd-fa2c7be254ab"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "2 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "2.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:53:52", "plugin": "core", "name": "end_epoch", "raw_value": "1725004432.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:53:50", "plugin": "core", "name": "start_epoch", "raw_value": "1725004430.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "table_compute/1.2.4+galaxy0-1", "has_data": true, "data": {"tool_id": "table_compute", "tool_version": "1.2.4+galaxy0", "test_index": 1, "time_seconds": 33.176870822906494, "inputs": {"singtabop|input": {"src": "hda", "id": "341052640f9305e9"}, "singtabop|user|select_cols_wanted": "2:4,2,2", "singtabop|user|select_keepdupe": ["select_cols_keepdupe", "select_rows_keepdupe"], "singtabop|user|mode": "select", "singtabop|use_type": "single", "precision": "2"}, "job": {"model_class": "Job", "id": "dd9c250bd7eccd9e", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:54:24.571086", "update_time": "2024-08-30T07:54:38.609117", "galaxy_version": "24.1", "external_id": "gxy-tmgn2", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/jobs_directory/000/373/configs/tmpp9j2o4a1' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python 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'/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py", "user_email": "tests@fake.org", "command_version": "0.9.2", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precision": "\"6\"", "out_opts": "[\"ignore_nas\", \"output_headers_col\"]", "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 554, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 4, \"general\": {\"__current_case__\": 0, \"use\": \"transpose\"}, \"mode\": \"fulltable\"}}"}, "inputs": {"singtabop|input": {"id": "72e397f8b9e0b93a", "src": "hda", "uuid": "942d32fb-a389-4e37-9b97-1a3cab2cce39"}}, "outputs": 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./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py", "user_email": "tests@fake.org", "command_version": "0.9.2", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precision": "\"6\"", "out_opts": "[\"ignore_nas\", \"output_headers_col\"]", "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 556, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 4, \"general\": {\"__current_case__\": 1, \"id_vars\": 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"cp '/galaxy/server/database/jobs_directory/000/446/configs/tmpo6k33kbx' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py", "user_email": "tests@fake.org", "command_version": "0.9.2", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precision": "\"6\"", "out_opts": "[\"ignore_nas\", \"output_headers_col\", \"output_headers_row\"]", "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 592, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 4, \"general\": {\"__current_case__\": 2, \"aggfunc\": null, \"colfun_map\": [{\"__index__\": 0, \"column\": \"Age\", \"functions\": [{\"__index__\": 0, \"aggfunc\": \"mean\"}]}, {\"__index__\": 1, \"column\": \"Random\", \"functions\": [{\"__index__\": 0, \"aggfunc\": \"mean\"}, {\"__index__\": 1, \"aggfunc\": \"std\"}]}], \"column\": \"\", \"index\": \"Position\", \"use\": \"pivot\", \"values\": \"\"}, \"mode\": \"fulltable\"}}"}, "inputs": {"singtabop|input": {"id": "defd7a1068adcd23", "src": "hda", "uuid": "71465ab7-9567-4006-8f66-6a7807c6e812"}}, "outputs": {"table": {"id": "d597e41cdd610813", "src": "hda", "uuid": "7df624eb-fc9d-4224-bc1a-69a64057fd83"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 08:13:48", "plugin": "core", "name": "end_epoch", "raw_value": "1725005628.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 08:13:47", "plugin": "core", "name": "start_epoch", "raw_value": "1725005627.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "table_compute/1.2.4+galaxy0-42", "has_data": true, "data": {"tool_id": "table_compute", "tool_version": "1.2.4+galaxy0", "test_index": 42, "time_seconds": 34.60102725028992, "inputs": {"singtabop|input": {"src": "hda", "id": "3c55efb5ac0624de"}, "singtabop|col_row_names": "has_col_names", "singtabop|user|general|index": "A", "singtabop|user|general|column": "C", "singtabop|user|general|values": "D", "singtabop|user|general|aggfunc": "max", "singtabop|user|general|use": "pivot", "singtabop|user|mode": "fulltable", "singtabop|use_type": "single"}, "job": {"model_class": "Job", "id": "6ef983da3bac57eb", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T08:14:19.173905", "update_time": "2024-08-30T08:14:34.278276", "galaxy_version": "24.1", "external_id": "gxy-s4pb6", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/jobs_directory/000/448/configs/tmphwnb8g3h' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py", "user_email": "tests@fake.org", "command_version": "0.9.2", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precision": "\"6\"", "out_opts": "[\"ignore_nas\", \"output_headers_col\", \"output_headers_row\"]", "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": \"has_col_names\", \"input\": {\"values\": [{\"id\": 594, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 4, \"general\": {\"__current_case__\": 2, \"aggfunc\": \"max\", \"colfun_map\": [], \"column\": \"C\", \"index\": \"A\", \"use\": \"pivot\", \"values\": \"D\"}, \"mode\": \"fulltable\"}}"}, "inputs": {"singtabop|input": {"id": "3c55efb5ac0624de", "src": "hda", "uuid": "6bc31b45-e820-453b-9652-107e6c8e1fc8"}}, "outputs": {"table": {"id": "e73aefd7c490418f", "src": "hda", "uuid": "9c174e54-171f-4f79-8b82-d4ea65f7e6aa"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 08:14:22", "plugin": "core", "name": "end_epoch", "raw_value": "1725005662.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 08:14:21", "plugin": "core", "name": "start_epoch", "raw_value": "1725005661.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "table_compute/1.2.4+galaxy0-5", "has_data": true, "data": {"tool_id": "table_compute", "tool_version": "1.2.4+galaxy0", "test_index": 5, "time_seconds": 33.52861571311951, "inputs": {"singtabop|input": {"src": "hda", "id": "b2882f065dff4bbb"}, "singtabop|user|axis": "0", "singtabop|user|filtersumval_mode|operation": "sum", "singtabop|user|filtersumval_mode|compare_op": "gt", "singtabop|user|filtersumval_mode|against": "10", "singtabop|user|filtersumval_mode|use": "operation", "singtabop|user|mode": "filtersumval", "singtabop|use_type": "single", "precision": "2"}, "job": {"model_class": "Job", "id": "91460c972fdbcae8", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:56:36.938451", "update_time": "2024-08-30T07:56:50.916666", "galaxy_version": "24.1", "external_id": "gxy-vn4gr", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/jobs_directory/000/381/configs/tmpvotd2abm' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py", "user_email": "tests@fake.org", "command_version": "0.9.2", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precision": "\"2\"", "out_opts": "[\"ignore_nas\", \"output_headers_col\", \"output_headers_row\"]", "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 527, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 2, \"axis\": \"0\", \"filtersumval_mode\": {\"__current_case__\": 0, \"against\": \"10.0\", \"compare_op\": \"gt\", \"operation\": \"sum\", \"use\": \"operation\"}, \"mode\": \"filtersumval\"}}"}, "inputs": {"singtabop|input": {"id": "b2882f065dff4bbb", "src": "hda", "uuid": "e68c2fbd-243e-4688-91a8-bf2921d44da2"}}, "outputs": {"table": {"id": "50f00000b490794b", "src": "hda", "uuid": "7cd19770-27ab-4911-90ca-6f687e7c1d69"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:56:39", "plugin": "core", "name": "end_epoch", "raw_value": "1725004599.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:56:38", "plugin": "core", "name": "start_epoch", "raw_value": "1725004598.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "table_compute/1.2.4+galaxy0-6", "has_data": true, "data": {"tool_id": "table_compute", "tool_version": "1.2.4+galaxy0", "test_index": 6, "time_seconds": 10.574324369430542, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "table_compute/1.2.4+galaxy0-7", "has_data": true, "data": {"tool_id": "table_compute", "tool_version": "1.2.4+galaxy0", "test_index": 7, "time_seconds": 31.922544717788696, "inputs": {"singtabop|input": {"src": "hda", "id": "c2729aada187f501"}, "singtabop|user|axis": "1", "singtabop|user|filtersumval_mode|minmatch": "2", "singtabop|user|filtersumval_mode|operation": "gt", "singtabop|user|filtersumval_mode|against": "2", "singtabop|user|filtersumval_mode|use": "element", "singtabop|user|mode": "filtersumval", "singtabop|use_type": "single", "precision": "5"}, "job": {"model_class": "Job", "id": "1c1690c2df8ccc46", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:57:20.775400", "update_time": "2024-08-30T07:57:33.608307", "galaxy_version": "24.1", "external_id": "gxy-4v24q", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/jobs_directory/000/384/configs/tmp2yg_7q2k' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py", "user_email": "tests@fake.org", "command_version": "0.9.2", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precision": "\"5\"", "out_opts": "[\"ignore_nas\", \"output_headers_col\", \"output_headers_row\"]", "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 530, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 2, \"axis\": \"1\", \"filtersumval_mode\": {\"__current_case__\": 1, \"against\": \"2\", \"minmatch\": \"2\", \"operation\": \"gt\", \"use\": \"element\"}, \"mode\": \"filtersumval\"}}"}, "inputs": {"singtabop|input": {"id": "c2729aada187f501", "src": "hda", "uuid": "0a65ae66-5579-4dfe-8c6f-98d9d5cd47da"}}, "outputs": {"table": {"id": "25d0f2d0837b9774", "src": "hda", "uuid": "e015502a-aae4-416d-84b5-809f7d3ae527"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:57:23", "plugin": "core", "name": "end_epoch", "raw_value": "1725004643.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:57:22", "plugin": "core", "name": "start_epoch", "raw_value": "1725004642.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "table_compute/1.2.4+galaxy0-8", "has_data": true, "data": {"tool_id": "table_compute", "tool_version": "1.2.4+galaxy0", "test_index": 8, "time_seconds": 33.499672651290894, "inputs": {"singtabop|input": {"src": "hda", "id": "c3e9c8db839704bf"}, "singtabop|user|axis": "0", "singtabop|user|filtersumval_mode|minmatch": "4", "singtabop|user|filtersumval_mode|operation": "str_ne", "singtabop|user|filtersumval_mode|against": "0", "singtabop|user|filtersumval_mode|use": "element", "singtabop|user|mode": "filtersumval", "singtabop|use_type": "single", "precision": "3"}, "job": {"model_class": "Job", "id": "2927dab2dcad0b1a", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:57:53.053699", "update_time": "2024-08-30T07:58:06.946958", "galaxy_version": "24.1", "external_id": "gxy-k9pdb", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/jobs_directory/000/386/configs/tmpb4di9vy8' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py", "user_email": "tests@fake.org", "command_version": "0.9.2", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precision": "\"3\"", "out_opts": "[\"ignore_nas\", \"output_headers_col\", \"output_headers_row\"]", "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 532, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 2, \"axis\": \"0\", \"filtersumval_mode\": {\"__current_case__\": 1, \"against\": \"0\", \"minmatch\": \"4\", \"operation\": \"str_ne\", \"use\": \"element\"}, \"mode\": \"filtersumval\"}}"}, "inputs": {"singtabop|input": {"id": "c3e9c8db839704bf", "src": "hda", "uuid": "33169e4e-bb81-4b09-91cc-052dfa5617d5"}}, "outputs": {"table": {"id": "9c6ede7f108b5c6f", "src": "hda", "uuid": "fc6961c7-9e82-43a2-83d6-ac0fb5b471f2"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:57:55", "plugin": "core", "name": "end_epoch", "raw_value": "1725004675.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:57:54", "plugin": "core", "name": "start_epoch", "raw_value": "1725004674.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "table_compute/1.2.4+galaxy0-9", "has_data": true, "data": {"tool_id": "table_compute", "tool_version": "1.2.4+galaxy0", "test_index": 9, "time_seconds": 33.595874071121216, "inputs": {"singtabop|input": {"src": "hda", "id": "3354d9517b77277d"}, "singtabop|user|matrixapply_func|vector_op": "max", "singtabop|user|dimension": "1", "singtabop|user|mode": "matrixapply", "singtabop|use_type": "single", "out_opts": ["ignore_nas", "output_headers_row"], "precision": "0"}, "job": {"model_class": "Job", "id": "4a8a75b94f6b4c18", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute/1.2.4+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T07:58:26.326380", "update_time": "2024-08-30T07:58:40.590880", "galaxy_version": "24.1", "external_id": "gxy-x72g9", "handler": null, "job_runner_name": null, "command_line": "cp '/galaxy/server/database/jobs_directory/000/388/configs/tmp1arztl_v' ./userconfig.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/safety.py' ./safety.py && cp '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/table_compute/3bf5661c0280/table_compute/scripts/table_compute.py' ./table_compute.py && python ./table_compute.py", "user_email": "tests@fake.org", "command_version": "0.9.2", "params": {"__input_ext": "\"tabular\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "precision": "\"0\"", "out_opts": "[\"ignore_nas\", \"output_headers_row\"]", "singtabop": "{\"__current_case__\": 0, \"adv\": {\"header\": \"\", \"nrows\": \"\", \"skip_blank_lines\": true, \"skipfooter\": \"\"}, \"col_row_names\": [\"has_col_names\", \"has_row_names\"], \"input\": {\"values\": [{\"id\": 534, \"src\": \"hda\"}]}, \"use_type\": \"single\", \"user\": {\"__current_case__\": 3, \"dimension\": \"1\", \"matrixapply_func\": {\"__current_case__\": 2, \"vector_op\": \"max\"}, \"mode\": \"matrixapply\"}}"}, "inputs": {"singtabop|input": {"id": "3354d9517b77277d", "src": "hda", "uuid": "dab08e0b-a309-4aee-aebd-64646cc718e9"}}, "outputs": {"table": {"id": "c16a231844980f2e", "src": "hda", "uuid": "ce3f1678-5cd8-43d1-8c12-b6a54d8f0aca"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 07:58:29", "plugin": "core", "name": "end_epoch", "raw_value": "1725004709.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 07:58:28", "plugin": "core", "name": "start_epoch", "raw_value": "1725004708.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "trim_galore/0.6.3-0", "has_data": true, "data": {"tool_id": "trim_galore", "tool_version": "0.6.3", "test_index": 0, "time_seconds": 46.461719036102295, "inputs": {"singlePaired|input_singles": {"src": "hda", "id": "cf63c6079ae7a62b"}, "singlePaired|sPaired": "single", "params|report": true, "params|settingsType": "custom"}, "job": {"model_class": "Job", "id": "7b9e4b2fc7b1fff8", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:32:20.249586", "update_time": "2024-08-30T06:32:46.374994", "galaxy_version": "24.1", "external_id": "gxy-mds6r", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/5/2/f/dataset_52f9fdf9-a7ba-4873-85e6-ab70d1e227b9.dat' input_1.fastq && trim_galore --phred33 --quality 20 --stringency 1 -e 0.1 --length 20 --output_dir ./ input_1.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi && cat ./*_trimming_report.txt > '/galaxy/server/database/objects/e/1/3/dataset_e13e6feb-9cd1-4a29-903b-eb1eaf395062.dat'", "user_email": "tests@fake.org", "command_version": "Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n version 0.6.3\n\n Last update: 21 03 2019", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rrbs": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "params": "{\"__current_case__\": 1, \"clip_R1\": \"\", \"clip_R2\": \"\", \"error_rate\": \"0.1\", \"min_length\": \"20\", \"quality\": \"20\", \"report\": true, \"retain_unpaired\": {\"__current_case__\": 0, \"retain_unpaired_select\": \"no_output\"}, \"settingsType\": \"custom\", \"stringency\": \"1\"}", "singlePaired": "{\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 36, \"src\": \"hda\"}]}, \"sPaired\": \"single\", \"three_prime_clip_R1\": \"\", \"trimming\": {\"__current_case__\": 0, \"trimming_select\": \"\"}}"}, "inputs": {"singlePaired|input_singles": {"id": "cf63c6079ae7a62b", "src": "hda", "uuid": "52f9fdf9-a7ba-4873-85e6-ab70d1e227b9"}}, "outputs": {"trimmed_reads_single": {"id": "3aa19c63876e6d0d", "src": "hda", "uuid": "3d45fc01-a1f7-4c5b-bd96-f0cc1ef998af"}, "report_file": {"id": "fbabe62400066224", "src": "hda", "uuid": "e13e6feb-9cd1-4a29-903b-eb1eaf395062"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/34/working/\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nsmallRNA\t0\tTGGAATTCTCGG\t2\t0.00\nIllumina\t0\tAGATCGGAAGAGC\t2\t0.00\nNextera\t0\tCTGTCTCTTATA\t2\t0.00\nUnable to auto-detect most prominent adapter from the first specified file (count smallRNA: 0, count Illumina: 0)\nDefaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).\n\nWriting report to '/galaxy/server/database/jobs_directory/000/34/working/input_1.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq\nTrimming mode: single-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length before a sequence gets removed: 20 bp\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.00 s (2036 us/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 1 (50.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 188 bp\nQuality-trimmed: 20 bp (10.6%)\nTotal written (filtered): 167 bp (88.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t1\t0.5\t0\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq\n=============================================\n2 sequences processed in total\nSequences removed because they became shorter than the length cutoff of 20 bp:\t0 (0.0%)\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/34/working/\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nsmallRNA\t0\tTGGAATTCTCGG\t2\t0.00\nIllumina\t0\tAGATCGGAAGAGC\t2\t0.00\nNextera\t0\tCTGTCTCTTATA\t2\t0.00\nUnable to auto-detect most prominent adapter from the first specified file (count smallRNA: 0, count Illumina: 0)\nDefaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).\n\nWriting report to '/galaxy/server/database/jobs_directory/000/34/working/input_1.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq\nTrimming mode: single-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length before a sequence gets removed: 20 bp\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.00 s (2036 us/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 1 (50.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 188 bp\nQuality-trimmed: 20 bp (10.6%)\nTotal written (filtered): 167 bp (88.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t1\t0.5\t0\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq\n=============================================\n2 sequences processed in total\nSequences removed because they became shorter than the length cutoff of 20 bp:\t0 (0.0%)\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:32:31", "plugin": "core", "name": "end_epoch", "raw_value": "1724999551.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:32:31", "plugin": "core", "name": "start_epoch", "raw_value": "1724999551.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "trim_galore/0.6.3-1", "has_data": true, "data": {"tool_id": "trim_galore", "tool_version": "0.6.3", "test_index": 1, "time_seconds": 10.960808753967285, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "trim_galore/0.6.3-2", "has_data": true, "data": {"tool_id": "trim_galore", "tool_version": "0.6.3", "test_index": 2, "time_seconds": 32.40316390991211, "inputs": {"singlePaired|input_singles": {"src": "hda", "id": "c5c55061c2d5fc67"}, "singlePaired|trimming|trimming_select": "--illumina", "singlePaired|sPaired": "single"}, "job": {"model_class": "Job", "id": "3aa19c63876e6d0d", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:33:17.198609", "update_time": "2024-08-30T06:33:30.266407", "galaxy_version": "24.1", "external_id": "gxy-rx5mn", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/5/c/3/dataset_5c39f173-d13c-4111-b5bf-701bd7e9b4d2.dat' input_1.fastq && trim_galore --phred33 --output_dir ./ --illumina input_1.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi", "user_email": "tests@fake.org", "command_version": "Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n version 0.6.3\n\n Last update: 21 03 2019", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rrbs": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "params": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "singlePaired": "{\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 40, \"src\": \"hda\"}]}, \"sPaired\": \"single\", \"three_prime_clip_R1\": \"\", \"trimming\": {\"__current_case__\": 1, \"trimming_select\": \"--illumina\"}}"}, "inputs": {"singlePaired|input_singles": {"id": "c5c55061c2d5fc67", "src": "hda", "uuid": "5c39f173-d13c-4111-b5bf-701bd7e9b4d2"}}, "outputs": {"trimmed_reads_single": {"id": "56beb7879a6251d0", "src": "hda", "uuid": "4db7fcd9-69be-4a26-ae48-53076fd4fc79"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/37/working/\nWriting report to '/galaxy/server/database/jobs_directory/000/37/working/input_1.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq\nTrimming mode: single-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length before a sequence gets removed: 20 bp\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.00 s (2165 us/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 1 (50.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 188 bp\nQuality-trimmed: 20 bp (10.6%)\nTotal written (filtered): 167 bp (88.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t1\t0.5\t0\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq\n=============================================\n2 sequences processed in total\nSequences removed because they became shorter than the length cutoff of 20 bp:\t0 (0.0%)\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/37/working/\nWriting report to '/galaxy/server/database/jobs_directory/000/37/working/input_1.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq\nTrimming mode: single-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length before a sequence gets removed: 20 bp\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.00 s (2165 us/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 1 (50.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 188 bp\nQuality-trimmed: 20 bp (10.6%)\nTotal written (filtered): 167 bp (88.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t1\t0.5\t0\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq\n=============================================\n2 sequences processed in total\nSequences removed because they became shorter than the length cutoff of 20 bp:\t0 (0.0%)\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:33:19", "plugin": "core", "name": "end_epoch", "raw_value": "1724999599.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:33:19", "plugin": "core", "name": "start_epoch", "raw_value": "1724999599.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "trim_galore/0.6.3-3", "has_data": true, "data": {"tool_id": "trim_galore", "tool_version": "0.6.3", "test_index": 3, "time_seconds": 31.924254894256592, "inputs": {"singlePaired|input_singles": {"src": "hda", "id": "8c9d1fbd6eb66564"}, "singlePaired|trimming|trimming_select": "--illumina", "singlePaired|sPaired": "single"}, "job": {"model_class": "Job", "id": "146acc7fcb1e613d", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:33:49.579762", "update_time": "2024-08-30T06:34:02.271141", "galaxy_version": "24.1", "external_id": "gxy-r6l7d", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/0/3/c/dataset_03c2928b-6d23-468b-b7bc-172fdf4c0869.dat' input_1.fastq.gz && trim_galore --phred33 --output_dir ./ --illumina input_1.fastq.gz && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi", "user_email": "tests@fake.org", "command_version": "Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n version 0.6.3\n\n Last update: 21 03 2019", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rrbs": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "params": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "singlePaired": "{\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 42, \"src\": \"hda\"}]}, \"sPaired\": \"single\", \"three_prime_clip_R1\": \"\", \"trimming\": {\"__current_case__\": 1, \"trimming_select\": \"--illumina\"}}"}, "inputs": {"singlePaired|input_singles": {"id": "8c9d1fbd6eb66564", "src": "hda", "uuid": "03c2928b-6d23-468b-b7bc-172fdf4c0869"}}, "outputs": {"trimmed_reads_single": {"id": "cac0eb9cbbbf4c51", "src": "hda", "uuid": "717429c3-fc56-458d-b54d-e3eb9df80f24"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/39/working/\nWriting report to '/galaxy/server/database/jobs_directory/000/39/working/input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: single-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length before a sequence gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.02 s (7946 us/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 1 (50.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 188 bp\nQuality-trimmed: 20 bp (10.6%)\nTotal written (filtered): 167 bp (88.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t1\t0.5\t0\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n2 sequences processed in total\nSequences removed because they became shorter than the length cutoff of 20 bp:\t0 (0.0%)\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/39/working/\nWriting report to '/galaxy/server/database/jobs_directory/000/39/working/input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: single-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length before a sequence gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.02 s (7946 us/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 1 (50.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 188 bp\nQuality-trimmed: 20 bp (10.6%)\nTotal written (filtered): 167 bp (88.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t1\t0.5\t0\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n2 sequences processed in total\nSequences removed because they became shorter than the length cutoff of 20 bp:\t0 (0.0%)\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "1 second", "plugin": "core", "name": "runtime_seconds", "raw_value": "1.0000000"}, {"title": "Job End Time", "value": "2024-08-30 06:33:51", "plugin": "core", "name": "end_epoch", "raw_value": "1724999631.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:33:50", "plugin": "core", "name": "start_epoch", "raw_value": "1724999630.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "trim_galore/0.6.3-4", "has_data": true, "data": {"tool_id": "trim_galore", "tool_version": "0.6.3", "test_index": 4, "time_seconds": 32.256720542907715, "inputs": {"singlePaired|input_singles": {"src": "hda", "id": "c44f77758a9ec877"}, "singlePaired|sPaired": "single"}, "job": {"model_class": "Job", "id": "56beb7879a6251d0", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:34:21.870279", "update_time": "2024-08-30T06:34:34.678664", "galaxy_version": "24.1", "external_id": "gxy-xh97j", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/b/e/1/dataset_be11ff6e-f42e-440b-80bd-403717f17d6b.dat' input_1.fastq && trim_galore --phred33 --output_dir ./ input_1.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi", "user_email": "tests@fake.org", "command_version": "Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n version 0.6.3\n\n Last update: 21 03 2019", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rrbs": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "params": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "singlePaired": "{\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 44, \"src\": \"hda\"}]}, \"sPaired\": \"single\", \"three_prime_clip_R1\": \"\", \"trimming\": {\"__current_case__\": 0, \"trimming_select\": \"\"}}"}, "inputs": {"singlePaired|input_singles": {"id": "c44f77758a9ec877", "src": "hda", "uuid": "be11ff6e-f42e-440b-80bd-403717f17d6b"}}, "outputs": {"trimmed_reads_single": {"id": "db1462c67ec46ff4", "src": "hda", "uuid": "9d73c6b9-be97-46c8-b7ee-b0d84af04a03"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/41/working/\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t0\tAGATCGGAAGAGC\t2\t0.00\nNextera\t0\tCTGTCTCTTATA\t2\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t2\t0.00\nUnable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count Nextera: 0)\nDefaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).\n\nWriting report to '/galaxy/server/database/jobs_directory/000/41/working/input_1.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq\nTrimming mode: single-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length before a sequence gets removed: 20 bp\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.00 s (1824 us/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 1 (50.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 188 bp\nQuality-trimmed: 20 bp (10.6%)\nTotal written (filtered): 167 bp (88.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t1\t0.5\t0\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq\n=============================================\n2 sequences processed in total\nSequences removed because they became shorter than the length cutoff of 20 bp:\t0 (0.0%)\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/41/working/\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t0\tAGATCGGAAGAGC\t2\t0.00\nNextera\t0\tCTGTCTCTTATA\t2\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t2\t0.00\nUnable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count Nextera: 0)\nDefaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).\n\nWriting report to '/galaxy/server/database/jobs_directory/000/41/working/input_1.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq\nTrimming mode: single-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length before a sequence gets removed: 20 bp\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.00 s (1824 us/read; 0.03 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 1 (50.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 188 bp\nQuality-trimmed: 20 bp (10.6%)\nTotal written (filtered): 167 bp (88.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t1\t0.5\t0\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq\n=============================================\n2 sequences processed in total\nSequences removed because they became shorter than the length cutoff of 20 bp:\t0 (0.0%)\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:34:23", "plugin": "core", "name": "end_epoch", "raw_value": "1724999663.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:34:23", "plugin": "core", "name": "start_epoch", "raw_value": "1724999663.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "trim_galore/0.6.3-5", "has_data": true, "data": {"tool_id": "trim_galore", "tool_version": "0.6.3", "test_index": 5, "time_seconds": 32.6671416759491, "inputs": {"singlePaired|input_singles": {"src": "hda", "id": "a1c6e2bddc25c128"}, "singlePaired|sPaired": "single"}, "job": {"model_class": "Job", "id": "cac0eb9cbbbf4c51", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:34:53.251143", "update_time": "2024-08-30T06:35:07.369677", "galaxy_version": "24.1", "external_id": "gxy-gwbnt", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/b/f/d/dataset_bfd474bc-a14d-49ca-ab07-69d6fdb554e7.dat' input_1.fastq.gz && trim_galore --phred33 --output_dir ./ input_1.fastq.gz && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi", "user_email": "tests@fake.org", "command_version": "Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n version 0.6.3\n\n Last update: 21 03 2019", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rrbs": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "params": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "singlePaired": "{\"__current_case__\": 0, \"input_singles\": {\"values\": [{\"id\": 46, \"src\": \"hda\"}]}, \"sPaired\": \"single\", \"three_prime_clip_R1\": \"\", \"trimming\": {\"__current_case__\": 0, \"trimming_select\": \"\"}}"}, "inputs": {"singlePaired|input_singles": {"id": "a1c6e2bddc25c128", "src": "hda", "uuid": "bfd474bc-a14d-49ca-ab07-69d6fdb554e7"}}, "outputs": {"trimmed_reads_single": {"id": "cac58447170d8679", "src": "hda", "uuid": "e1474cdd-5abc-49e9-8299-00223c9c1617"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/43/working/\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t0\tAGATCGGAAGAGC\t2\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t2\t0.00\nNextera\t0\tCTGTCTCTTATA\t2\t0.00\nUnable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count smallRNA: 0)\nDefaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).\n\nWriting report to '/galaxy/server/database/jobs_directory/000/43/working/input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: single-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length before a sequence gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.02 s (8292 us/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 1 (50.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 188 bp\nQuality-trimmed: 20 bp (10.6%)\nTotal written (filtered): 167 bp (88.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t1\t0.5\t0\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n2 sequences processed in total\nSequences removed because they became shorter than the length cutoff of 20 bp:\t0 (0.0%)\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/43/working/\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq.gz <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nIllumina\t0\tAGATCGGAAGAGC\t2\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t2\t0.00\nNextera\t0\tCTGTCTCTTATA\t2\t0.00\nUnable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count smallRNA: 0)\nDefaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).\n\nWriting report to '/galaxy/server/database/jobs_directory/000/43/working/input_1.fastq.gz_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq.gz\nTrimming mode: single-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length before a sequence gets removed: 20 bp\nOutput file(s) will be GZIP compressed\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq.gz\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.02 s (8292 us/read; 0.01 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 2\nReads with adapters: 1 (50.0%)\nReads written (passing filters): 2 (100.0%)\n\nTotal basepairs processed: 188 bp\nQuality-trimmed: 20 bp (10.6%)\nTotal written (filtered): 167 bp (88.8%)\n\n=== Adapter 1 ===\n\nSequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-13 bp: 1\n\nBases preceding removed adapters:\n A: 0.0%\n C: 100.0%\n G: 0.0%\n T: 0.0%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t1\t0.5\t0\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq.gz\n=============================================\n2 sequences processed in total\nSequences removed because they became shorter than the length cutoff of 20 bp:\t0 (0.0%)\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:34:55", "plugin": "core", "name": "end_epoch", "raw_value": "1724999695.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:34:55", "plugin": "core", "name": "start_epoch", "raw_value": "1724999695.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "trim_galore/0.6.3-6", "has_data": true, "data": {"tool_id": "trim_galore", "tool_version": "0.6.3", "test_index": 6, "time_seconds": 39.54944038391113, "inputs": {"singlePaired|input_mate1": {"src": "hda", "id": "8f0e3ed7f9185b2e"}, "singlePaired|input_mate2": {"src": "hda", "id": "fdb4cb76fd53a0dd"}, "singlePaired|sPaired": "paired", "params|report": true, "params|settingsType": "custom"}, "job": {"model_class": "Job", "id": "a1c6e2bddc25c128", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:35:32.472567", "update_time": "2024-08-30T06:35:46.036097", "galaxy_version": "24.1", "external_id": "gxy-xc2gp", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/c/1/b/dataset_c1bdada7-f941-4cd6-8638-d3a4606892a7.dat' input_1.fastq && ln -s '/galaxy/server/database/objects/e/d/c/dataset_edc81050-0095-4da9-9af6-1167a6e76249.dat' input_2.fastq && trim_galore --phred33 --quality 20 --stringency 1 -e 0.1 --length 20 --output_dir ./ --paired input_1.fastq input_2.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi && cat ./*_trimming_report.txt > '/galaxy/server/database/objects/f/f/5/dataset_ff58856c-59a0-49fb-9644-622f04518c86.dat'", "user_email": "tests@fake.org", "command_version": "Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n version 0.6.3\n\n Last update: 21 03 2019", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rrbs": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "params": "{\"__current_case__\": 1, \"clip_R1\": \"\", \"clip_R2\": \"\", \"error_rate\": \"0.1\", \"min_length\": \"20\", \"quality\": \"20\", \"report\": true, \"retain_unpaired\": {\"__current_case__\": 0, \"retain_unpaired_select\": \"no_output\"}, \"settingsType\": \"custom\", \"stringency\": \"1\"}", "singlePaired": "{\"__current_case__\": 1, \"input_mate1\": {\"values\": [{\"id\": 48, \"src\": \"hda\"}]}, \"input_mate2\": {\"values\": [{\"id\": 49, \"src\": \"hda\"}]}, \"sPaired\": \"paired\", \"three_prime_clip_R1\": \"\", \"three_prime_clip_R2\": \"\", \"trim1\": false, \"trimming\": {\"__current_case__\": 0, \"trimming_select\": \"\"}}"}, "inputs": {"singlePaired|input_mate1": {"id": "8f0e3ed7f9185b2e", "src": "hda", "uuid": "c1bdada7-f941-4cd6-8638-d3a4606892a7"}, "singlePaired|input_mate2": {"id": "fdb4cb76fd53a0dd", "src": "hda", "uuid": "edc81050-0095-4da9-9af6-1167a6e76249"}}, "outputs": {"trimmed_reads_pair1": {"id": "8a07dd31a303e923", "src": "hda", "uuid": "0c59babe-21c0-4d68-a8b5-daaa0e781dcb"}, "trimmed_reads_pair2": {"id": "91ec9d61b8f03d66", "src": "hda", "uuid": "2f328e73-6885-4153-83bc-5986796d7794"}, "report_file": {"id": "e05e374c00c9c88a", "src": "hda", "uuid": "ff58856c-59a0-49fb-9644-622f04518c86"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/46/working/\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nNextera\t29\tCTGTCTCTTATA\t99\t29.29\nIllumina\t0\tAGATCGGAAGAGC\t99\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t99\t0.00\nUsing Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)\n\nWriting report to '/galaxy/server/database/jobs_directory/000/46/working/input_1.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq\nTrimming mode: paired-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_1.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.01 s (55 us/read; 1.10 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 52 (52.5%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 205 bp (0.8%)\nTotal written (filtered): 23,339 bp (93.9%)\n\n=== Adapter 1 ===\n\nSequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 9.6%\n C: 38.5%\n G: 23.1%\n T: 28.8%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t11\t24.8\t0\t11\n2\t5\t6.2\t0\t5\n3\t3\t1.5\t0\t3\n4\t3\t0.4\t0\t3\n12\t1\t0.0\t1\t1\n13\t2\t0.0\t1\t2\n14\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t1\n17\t1\t0.0\t1\t0 1\n20\t2\t0.0\t1\t2\n21\t1\t0.0\t1\t1\n24\t1\t0.0\t1\t1\n26\t2\t0.0\t1\t2\n31\t1\t0.0\t1\t1\n33\t1\t0.0\t1\t1\n41\t2\t0.0\t1\t2\n49\t1\t0.0\t1\t1\n50\t1\t0.0\t1\t1\n54\t1\t0.0\t1\t1\n56\t1\t0.0\t1\t1\n58\t2\t0.0\t1\t2\n60\t1\t0.0\t1\t1\n67\t2\t0.0\t1\t2\n68\t1\t0.0\t1\t1\n69\t1\t0.0\t1\t1\n73\t1\t0.0\t1\t1\n80\t1\t0.0\t1\t1\n86\t1\t0.0\t1\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq\n=============================================\n99 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to '/galaxy/server/database/jobs_directory/000/46/working/input_2.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq\nTrimming mode: paired-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j -j 1\nWriting final adapter and quality trimmed output to input_2_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_2.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.01 s (67 us/read; 0.90 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 58 (58.6%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 745 bp (3.0%)\nTotal written (filtered): 23,035 bp (92.7%)\n\n=== Adapter 1 ===\n\nSequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 12.1%\n C: 37.9%\n G: 8.6%\n T: 41.4%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t16\t24.8\t0\t16\n2\t7\t6.2\t0\t7\n3\t1\t1.5\t0\t1\n4\t2\t0.4\t0\t2\n6\t2\t0.0\t0\t2\n9\t1\t0.0\t0\t1\n10\t1\t0.0\t1\t1\n13\t1\t0.0\t1\t1\n14\t2\t0.0\t1\t2\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t1\n17\t1\t0.0\t1\t1\n19\t2\t0.0\t1\t2\n21\t1\t0.0\t1\t1\n25\t1\t0.0\t1\t1\n30\t1\t0.0\t1\t1\n32\t2\t0.0\t1\t2\n34\t1\t0.0\t1\t1\n36\t2\t0.0\t1\t2\n38\t1\t0.0\t1\t1\n40\t1\t0.0\t1\t1\n41\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t1\n43\t1\t0.0\t1\t1\n49\t1\t0.0\t1\t1\n51\t1\t0.0\t1\t1\n56\t1\t0.0\t1\t1\n57\t1\t0.0\t1\t1\n60\t1\t0.0\t1\t1\n67\t1\t0.0\t1\t1\n80\t1\t0.0\t1\t1\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq\n=============================================\n99 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq and input_2_trimmed.fq\nfile_1: input_1_trimmed.fq, file_2: input_2_trimmed.fq\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq and input_2_trimmed.fq <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq\nWriting validated paired-end read 2 reads to input_2_val_2.fq\n\nTotal number of sequences analysed: 99\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)\n\nDeleting both intermediate output files input_1_trimmed.fq and input_2_trimmed.fq\n\n====================================================================================================\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/46/working/\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nNextera\t29\tCTGTCTCTTATA\t99\t29.29\nIllumina\t0\tAGATCGGAAGAGC\t99\t0.00\nsmallRNA\t0\tTGGAATTCTCGG\t99\t0.00\nUsing Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)\n\nWriting report to '/galaxy/server/database/jobs_directory/000/46/working/input_1.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq\nTrimming mode: paired-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_1.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.01 s (55 us/read; 1.10 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 52 (52.5%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 205 bp (0.8%)\nTotal written (filtered): 23,339 bp (93.9%)\n\n=== Adapter 1 ===\n\nSequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 9.6%\n C: 38.5%\n G: 23.1%\n T: 28.8%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t11\t24.8\t0\t11\n2\t5\t6.2\t0\t5\n3\t3\t1.5\t0\t3\n4\t3\t0.4\t0\t3\n12\t1\t0.0\t1\t1\n13\t2\t0.0\t1\t2\n14\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t1\n17\t1\t0.0\t1\t0 1\n20\t2\t0.0\t1\t2\n21\t1\t0.0\t1\t1\n24\t1\t0.0\t1\t1\n26\t2\t0.0\t1\t2\n31\t1\t0.0\t1\t1\n33\t1\t0.0\t1\t1\n41\t2\t0.0\t1\t2\n49\t1\t0.0\t1\t1\n50\t1\t0.0\t1\t1\n54\t1\t0.0\t1\t1\n56\t1\t0.0\t1\t1\n58\t2\t0.0\t1\t2\n60\t1\t0.0\t1\t1\n67\t2\t0.0\t1\t2\n68\t1\t0.0\t1\t1\n69\t1\t0.0\t1\t1\n73\t1\t0.0\t1\t1\n80\t1\t0.0\t1\t1\n86\t1\t0.0\t1\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq\n=============================================\n99 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to '/galaxy/server/database/jobs_directory/000/46/working/input_2.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq\nTrimming mode: paired-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j -j 1\nWriting final adapter and quality trimmed output to input_2_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_2.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.01 s (67 us/read; 0.90 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 58 (58.6%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 745 bp (3.0%)\nTotal written (filtered): 23,035 bp (92.7%)\n\n=== Adapter 1 ===\n\nSequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 12.1%\n C: 37.9%\n G: 8.6%\n T: 41.4%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t16\t24.8\t0\t16\n2\t7\t6.2\t0\t7\n3\t1\t1.5\t0\t1\n4\t2\t0.4\t0\t2\n6\t2\t0.0\t0\t2\n9\t1\t0.0\t0\t1\n10\t1\t0.0\t1\t1\n13\t1\t0.0\t1\t1\n14\t2\t0.0\t1\t2\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t1\n17\t1\t0.0\t1\t1\n19\t2\t0.0\t1\t2\n21\t1\t0.0\t1\t1\n25\t1\t0.0\t1\t1\n30\t1\t0.0\t1\t1\n32\t2\t0.0\t1\t2\n34\t1\t0.0\t1\t1\n36\t2\t0.0\t1\t2\n38\t1\t0.0\t1\t1\n40\t1\t0.0\t1\t1\n41\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t1\n43\t1\t0.0\t1\t1\n49\t1\t0.0\t1\t1\n51\t1\t0.0\t1\t1\n56\t1\t0.0\t1\t1\n57\t1\t0.0\t1\t1\n60\t1\t0.0\t1\t1\n67\t1\t0.0\t1\t1\n80\t1\t0.0\t1\t1\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq\n=============================================\n99 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq and input_2_trimmed.fq\nfile_1: input_1_trimmed.fq, file_2: input_2_trimmed.fq\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq and input_2_trimmed.fq <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq\nWriting validated paired-end read 2 reads to input_2_val_2.fq\n\nTotal number of sequences analysed: 99\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)\n\nDeleting both intermediate output files input_1_trimmed.fq and input_2_trimmed.fq\n\n====================================================================================================\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:35:34", "plugin": "core", "name": "end_epoch", "raw_value": "1724999734.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:35:34", "plugin": "core", "name": "start_epoch", "raw_value": "1724999734.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "trim_galore/0.6.3-7", "has_data": true, "data": {"tool_id": "trim_galore", "tool_version": "0.6.3", "test_index": 7, "time_seconds": 20.298912048339844, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "trim_galore/0.6.3-8", "has_data": true, "data": {"tool_id": "trim_galore", "tool_version": "0.6.3", "test_index": 8, "time_seconds": 36.256853103637695, "inputs": {"singlePaired|input_mate_pairs": {"src": "hdca", "id": "436da20d1fd8461d"}, "singlePaired|sPaired": "paired_collection", "params|report": true, "params|retain_unpaired|retain_unpaired_select": "retain_unpaired_output", "params|settingsType": "custom"}, "job": {"model_class": "Job", "id": "91ec9d61b8f03d66", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.6.3", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T06:36:27.868398", "update_time": "2024-08-30T06:36:42.618766", "galaxy_version": "24.1", "external_id": "gxy-kwkvd", "handler": null, "job_runner_name": null, "command_line": "ln -s '/galaxy/server/database/objects/7/6/7/dataset_76751eb2-f9a3-450a-9607-470f4ad321dc.dat' input_1.fastq && ln -s '/galaxy/server/database/objects/e/b/d/dataset_ebdb8457-e755-4260-a484-103bb976966f.dat' input_2.fastq && trim_galore --phred33 --quality 20 --stringency 1 -e 0.1 --length 20 --retain_unpaired --length_1 35 --length_2 35 --output_dir ./ --paired input_1.fastq input_2.fastq --dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi && cat ./*_trimming_report.txt > '/galaxy/server/database/objects/d/3/a/dataset_d3a7f5a0-b05c-49c9-9395-05076ec29d60.dat'", "user_email": "tests@fake.org", "command_version": "Quality-/Adapter-/RRBS-/Speciality-Trimming\n [powered by Cutadapt]\n version 0.6.3\n\n Last update: 21 03 2019", "params": {"__input_ext": "\"input\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", "rrbs": "{\"__current_case__\": 0, \"settingsType\": \"default\"}", "params": "{\"__current_case__\": 1, \"clip_R1\": \"\", \"clip_R2\": \"\", \"error_rate\": \"0.1\", \"min_length\": \"20\", \"quality\": \"20\", \"report\": true, \"retain_unpaired\": {\"__current_case__\": 1, \"length_1\": \"35\", \"length_2\": \"35\", \"retain_unpaired_select\": \"retain_unpaired_output\"}, \"settingsType\": \"custom\", \"stringency\": \"1\"}", "singlePaired": "{\"__current_case__\": 2, \"input_mate_pairs\": {\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}, \"sPaired\": \"paired_collection\", \"three_prime_clip_R1\": \"\", \"three_prime_clip_R2\": \"\", \"trim1\": false, \"trimming\": {\"__current_case__\": 0, \"trimming_select\": \"\"}}"}, "inputs": {"singlePaired|input_mate_pairs2": {"id": "6dad6b28f2e9d99e", "src": "hda", "uuid": "ebdb8457-e755-4260-a484-103bb976966f"}, "singlePaired|input_mate_pairs1": {"id": "8a63c73e85e54e58", "src": "hda", "uuid": "76751eb2-f9a3-450a-9607-470f4ad321dc"}}, "outputs": {"trimmed_reads_paired_collection|__part__|forward": {"id": "5a48f5525fc2000c", "src": "hda", "uuid": "ca985e1f-c4e8-43d3-a16c-85f835678e9a"}, "trimmed_reads_paired_collection|__part__|reverse": {"id": "153a5eb3be4368e2", "src": "hda", "uuid": "64295152-27bd-4e2a-8b3f-045e483b5eb8"}, "trimmed_reads_unpaired_collection|__part__|forward": {"id": "0586d4449e970e5d", "src": "hda", "uuid": "8334f286-75bd-486f-a682-0fd51f7f0a6b"}, "trimmed_reads_unpaired_collection|__part__|reverse": {"id": "22f19ad876838d6e", "src": "hda", "uuid": "77544b85-79d3-4660-8a60-7617a38667bd"}, "report_file": {"id": "2e620655b7d5d6f2", "src": "hda", "uuid": "d3a7f5a0-b05c-49c9-9395-05076ec29d60"}}, "copied_from_job_id": null, "output_collections": {"trimmed_reads_unpaired_collection": {"src": "hdca", "id": "efa4958f6a453fa0"}, "trimmed_reads_paired_collection": {"src": "hdca", "id": "686e0a29bc0973eb"}}, "tool_stdout": "", "tool_stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/51/working/\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nNextera\t29\tCTGTCTCTTATA\t99\t29.29\nsmallRNA\t0\tTGGAATTCTCGG\t99\t0.00\nIllumina\t0\tAGATCGGAAGAGC\t99\t0.00\nUsing Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)\n\nWriting report to '/galaxy/server/database/jobs_directory/000/51/working/input_1.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq\nTrimming mode: paired-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nLength cut-off for read 1: 35 bp (default)\nLength cut-off for read 2: 35 bb (default)\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_1.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.01 s (54 us/read; 1.11 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 52 (52.5%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 205 bp (0.8%)\nTotal written (filtered): 23,339 bp (93.9%)\n\n=== Adapter 1 ===\n\nSequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 9.6%\n C: 38.5%\n G: 23.1%\n T: 28.8%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t11\t24.8\t0\t11\n2\t5\t6.2\t0\t5\n3\t3\t1.5\t0\t3\n4\t3\t0.4\t0\t3\n12\t1\t0.0\t1\t1\n13\t2\t0.0\t1\t2\n14\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t1\n17\t1\t0.0\t1\t0 1\n20\t2\t0.0\t1\t2\n21\t1\t0.0\t1\t1\n24\t1\t0.0\t1\t1\n26\t2\t0.0\t1\t2\n31\t1\t0.0\t1\t1\n33\t1\t0.0\t1\t1\n41\t2\t0.0\t1\t2\n49\t1\t0.0\t1\t1\n50\t1\t0.0\t1\t1\n54\t1\t0.0\t1\t1\n56\t1\t0.0\t1\t1\n58\t2\t0.0\t1\t2\n60\t1\t0.0\t1\t1\n67\t2\t0.0\t1\t2\n68\t1\t0.0\t1\t1\n69\t1\t0.0\t1\t1\n73\t1\t0.0\t1\t1\n80\t1\t0.0\t1\t1\n86\t1\t0.0\t1\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq\n=============================================\n99 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to '/galaxy/server/database/jobs_directory/000/51/working/input_2.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq\nTrimming mode: paired-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nLength cut-off for read 1: 35 bp (default)\nLength cut-off for read 2: 35 bb (default)\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j -j 1\nWriting final adapter and quality trimmed output to input_2_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_2.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.01 s (63 us/read; 0.95 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 58 (58.6%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 745 bp (3.0%)\nTotal written (filtered): 23,035 bp (92.7%)\n\n=== Adapter 1 ===\n\nSequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 12.1%\n C: 37.9%\n G: 8.6%\n T: 41.4%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t16\t24.8\t0\t16\n2\t7\t6.2\t0\t7\n3\t1\t1.5\t0\t1\n4\t2\t0.4\t0\t2\n6\t2\t0.0\t0\t2\n9\t1\t0.0\t0\t1\n10\t1\t0.0\t1\t1\n13\t1\t0.0\t1\t1\n14\t2\t0.0\t1\t2\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t1\n17\t1\t0.0\t1\t1\n19\t2\t0.0\t1\t2\n21\t1\t0.0\t1\t1\n25\t1\t0.0\t1\t1\n30\t1\t0.0\t1\t1\n32\t2\t0.0\t1\t2\n34\t1\t0.0\t1\t1\n36\t2\t0.0\t1\t2\n38\t1\t0.0\t1\t1\n40\t1\t0.0\t1\t1\n41\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t1\n43\t1\t0.0\t1\t1\n49\t1\t0.0\t1\t1\n51\t1\t0.0\t1\t1\n56\t1\t0.0\t1\t1\n57\t1\t0.0\t1\t1\n60\t1\t0.0\t1\t1\n67\t1\t0.0\t1\t1\n80\t1\t0.0\t1\t1\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq\n=============================================\n99 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq and input_2_trimmed.fq\nfile_1: input_1_trimmed.fq, file_2: input_2_trimmed.fq\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq and input_2_trimmed.fq <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq\nWriting validated paired-end read 2 reads to input_2_val_2.fq\n\nWriting unpaired read 1 reads to input_1_unpaired_1.fq\nWriting unpaired read 2 reads to input_2_unpaired_2.fq\n\nTotal number of sequences analysed: 99\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)\n\nDeleting both intermediate output files input_1_trimmed.fq and input_2_trimmed.fq\n\n====================================================================================================\n\n", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "Multicore support not enabled. Proceeding with single-core trimming.\nPath to Cutadapt set as: 'cutadapt' (default)\nCutadapt seems to be working fine (tested command 'cutadapt --version')\nCutadapt version: 2.3\nsingle-core operation.\nOutput will be written into the directory: /galaxy/server/database/jobs_directory/000/51/working/\n\n\nAUTO-DETECTING ADAPTER TYPE\n===========================\nAttempting to auto-detect adapter type from the first 1 million sequences of the first file (>> input_1.fastq <<)\n\nFound perfect matches for the following adapter sequences:\nAdapter type\tCount\tSequence\tSequences analysed\tPercentage\nNextera\t29\tCTGTCTCTTATA\t99\t29.29\nsmallRNA\t0\tTGGAATTCTCGG\t99\t0.00\nIllumina\t0\tAGATCGGAAGAGC\t99\t0.00\nUsing Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)\n\nWriting report to '/galaxy/server/database/jobs_directory/000/51/working/input_1.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_1.fastq\nTrimming mode: paired-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nLength cut-off for read 1: 35 bp (default)\nLength cut-off for read 2: 35 bb (default)\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1\nWriting final adapter and quality trimmed output to input_1_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_1.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.01 s (54 us/read; 1.11 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 52 (52.5%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 205 bp (0.8%)\nTotal written (filtered): 23,339 bp (93.9%)\n\n=== Adapter 1 ===\n\nSequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 9.6%\n C: 38.5%\n G: 23.1%\n T: 28.8%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t11\t24.8\t0\t11\n2\t5\t6.2\t0\t5\n3\t3\t1.5\t0\t3\n4\t3\t0.4\t0\t3\n12\t1\t0.0\t1\t1\n13\t2\t0.0\t1\t2\n14\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t1\n17\t1\t0.0\t1\t0 1\n20\t2\t0.0\t1\t2\n21\t1\t0.0\t1\t1\n24\t1\t0.0\t1\t1\n26\t2\t0.0\t1\t2\n31\t1\t0.0\t1\t1\n33\t1\t0.0\t1\t1\n41\t2\t0.0\t1\t2\n49\t1\t0.0\t1\t1\n50\t1\t0.0\t1\t1\n54\t1\t0.0\t1\t1\n56\t1\t0.0\t1\t1\n58\t2\t0.0\t1\t2\n60\t1\t0.0\t1\t1\n67\t2\t0.0\t1\t2\n68\t1\t0.0\t1\t1\n69\t1\t0.0\t1\t1\n73\t1\t0.0\t1\t1\n80\t1\t0.0\t1\t1\n86\t1\t0.0\t1\t1\n\nRUN STATISTICS FOR INPUT FILE: input_1.fastq\n=============================================\n99 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nWriting report to '/galaxy/server/database/jobs_directory/000/51/working/input_2.fastq_trimming_report.txt'\n\nSUMMARISING RUN PARAMETERS\n==========================\nInput filename: input_2.fastq\nTrimming mode: paired-end\nTrim Galore version: 0.6.3\nCutadapt version: 2.3\nNumber of cores used for trimming: 1\nQuality Phred score cutoff: 20\nQuality encoding type selected: ASCII+33\nAdapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)\nMaximum trimming error rate: 0.1 (default)\nMinimum required adapter overlap (stringency): 1 bp\nMinimum required sequence length for both reads before a sequence pair gets removed: 20 bp\nLength cut-off for read 1: 35 bp (default)\nLength cut-off for read 2: 35 bb (default)\n\nCutadapt seems to be fairly up-to-date (version 2.3). Setting -j -j 1\nWriting final adapter and quality trimmed output to input_2_trimmed.fq\n\n\n >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_2.fastq <<< \nThis is cutadapt 2.3 with Python 3.7.3\nCommand line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq\nProcessing reads on 1 core in single-end mode ...\nFinished in 0.01 s (63 us/read; 0.95 M reads/minute).\n\n=== Summary ===\n\nTotal reads processed: 99\nReads with adapters: 58 (58.6%)\nReads written (passing filters): 99 (100.0%)\n\nTotal basepairs processed: 24,849 bp\nQuality-trimmed: 745 bp (3.0%)\nTotal written (filtered): 23,035 bp (92.7%)\n\n=== Adapter 1 ===\n\nSequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.\n\nNo. of allowed errors:\n0-9 bp: 0; 10-12 bp: 1\n\nBases preceding removed adapters:\n A: 12.1%\n C: 37.9%\n G: 8.6%\n T: 41.4%\n none/other: 0.0%\n\nOverview of removed sequences\nlength\tcount\texpect\tmax.err\terror counts\n1\t16\t24.8\t0\t16\n2\t7\t6.2\t0\t7\n3\t1\t1.5\t0\t1\n4\t2\t0.4\t0\t2\n6\t2\t0.0\t0\t2\n9\t1\t0.0\t0\t1\n10\t1\t0.0\t1\t1\n13\t1\t0.0\t1\t1\n14\t2\t0.0\t1\t2\n15\t1\t0.0\t1\t1\n16\t1\t0.0\t1\t1\n17\t1\t0.0\t1\t1\n19\t2\t0.0\t1\t2\n21\t1\t0.0\t1\t1\n25\t1\t0.0\t1\t1\n30\t1\t0.0\t1\t1\n32\t2\t0.0\t1\t2\n34\t1\t0.0\t1\t1\n36\t2\t0.0\t1\t2\n38\t1\t0.0\t1\t1\n40\t1\t0.0\t1\t1\n41\t1\t0.0\t1\t1\n42\t1\t0.0\t1\t1\n43\t1\t0.0\t1\t1\n49\t1\t0.0\t1\t1\n51\t1\t0.0\t1\t1\n56\t1\t0.0\t1\t1\n57\t1\t0.0\t1\t1\n60\t1\t0.0\t1\t1\n67\t1\t0.0\t1\t1\n80\t1\t0.0\t1\t1\n\nRUN STATISTICS FOR INPUT FILE: input_2.fastq\n=============================================\n99 sequences processed in total\nThe length threshold of paired-end sequences gets evaluated later on (in the validation step)\n\nValidate paired-end files input_1_trimmed.fq and input_2_trimmed.fq\nfile_1: input_1_trimmed.fq, file_2: input_2_trimmed.fq\n\n\n>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq and input_2_trimmed.fq <<<<<\nWriting validated paired-end read 1 reads to input_1_val_1.fq\nWriting validated paired-end read 2 reads to input_2_val_2.fq\n\nWriting unpaired read 1 reads to input_1_unpaired_1.fq\nWriting unpaired read 2 reads to input_2_unpaired_2.fq\n\nTotal number of sequences analysed: 99\n\nNumber of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%)\n\nDeleting both intermediate output files input_1_trimmed.fq and input_2_trimmed.fq\n\n====================================================================================================\n\n", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 06:36:30", "plugin": "core", "name": "end_epoch", "raw_value": "1724999790.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 06:36:30", "plugin": "core", "name": "start_epoch", "raw_value": "1724999790.0000000"}, {"title": "Memory Allocated (MB)", "value": "20401", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "20401.0000000"}, {"title": "Cores Allocated", "value": "5", "plugin": "core", "name": "galaxy_slots", "raw_value": "5.0000000"}]}, "status": "success"}}, {"id": "trim_galore/0.6.3-9", "has_data": true, "data": {"tool_id": "trim_galore", "tool_version": "0.6.3", "test_index": 9, "time_seconds": 20.527000188827515, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}, {"id": "vcfaddinfo/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfaddinfo", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 38.44857120513916, "inputs": {"input1": {"src": "hda", "id": "ef99d5bf47fca212"}, "input2": {"src": "hda", "id": "c5fe5f73b7ee06d8"}}, "job": {"model_class": "Job", "id": "86d5a32cd72d8f1f", "history_id": "436da20d1fd8461d", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfaddinfo/vcfaddinfo/1.0.0_rc3+galaxy0", "state": "ok", "exit_code": 0, "create_time": "2024-08-30T08:19:32.018924", "update_time": "2024-08-30T08:19:50.143489", "galaxy_version": "24.1", "external_id": "gxy-h55m9", "handler": null, "job_runner_name": null, "command_line": "vcfaddinfo '/galaxy/server/database/objects/6/f/4/dataset_6f4427cd-7587-4ec7-886f-ada57e9bc406.dat' '/galaxy/server/database/objects/2/e/7/dataset_2e7d9743-c686-4456-a29e-597ef15665b1.dat' > '/galaxy/server/database/objects/4/f/7/dataset_4f7c2485-fbe2-464d-9576-8f0433e22090.dat'", "user_email": "tests@fake.org", "command_version": "", "params": {"__input_ext": "\"vcf\"", "dbkey": "\"?\"", "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""}, "inputs": {"input2": {"id": "c5fe5f73b7ee06d8", "src": "hda", "uuid": "2e7d9743-c686-4456-a29e-597ef15665b1"}, "input1": {"id": "ef99d5bf47fca212", "src": "hda", "uuid": "6f4427cd-7587-4ec7-886f-ada57e9bc406"}}, "outputs": {"out_file1": {"id": "f3e231b4375b1160", "src": "hda", "uuid": "4f7c2485-fbe2-464d-9576-8f0433e22090"}}, "copied_from_job_id": null, "output_collections": {}, "tool_stdout": "", "tool_stderr": "", "job_stdout": "", "job_stderr": "", "stdout": "", "stderr": "", "job_messages": [], "dependencies": [], "job_metrics": [{"title": "Job Runtime (Wall Clock)", "value": "0 seconds", "plugin": "core", "name": "runtime_seconds", "raw_value": "0E-7"}, {"title": "Job End Time", "value": "2024-08-30 08:19:37", "plugin": "core", "name": "end_epoch", "raw_value": "1725005977.0000000"}, {"title": "Job Start Time", "value": "2024-08-30 08:19:37", "plugin": "core", "name": "start_epoch", "raw_value": "1725005977.0000000"}, {"title": "Memory Allocated (MB)", "value": "4080", "plugin": "core", "name": "galaxy_memory_mb", "raw_value": "4080.0000000"}, {"title": "Cores Allocated", "value": "1", "plugin": "core", "name": "galaxy_slots", "raw_value": "1.0000000"}]}, "status": "success"}}, {"id": "vcfleftalign/1.0.0_rc3+galaxy0-0", "has_data": true, "data": {"tool_id": "vcfleftalign", "tool_version": "1.0.0_rc3+galaxy0", "test_index": 0, "time_seconds": 10.822591781616211, "execution_problem": "Input staging problem: Job in error state.. tool_id: upload1, exit_code: None, stderr: .", "status": "error"}}], "galaxy_url": "http://34.73.121.129:8000/galaxy/"}
\ No newline at end of file
diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.xunit b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/results.xunit
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@@ -0,0 +1,2416 @@
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+ 1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0contig count: 1412 element count: 235270 complex nodes: 8# of ones in rank vector: 1411[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.[2024-08-30 07:19:02.343] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./indexsize = 235270-----------------------------------------| Loading contigs | Time = 1.333 ms-----------------------------------------size = 235270-----------------------------------------| Loading contig boundaries | Time = 878.1 us-----------------------------------------Number of ones: 1411Number of ones per inventory item: 512Inventory entries filled: 31411[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.[2024-08-30 07:19:02.346] [puff::index::jointLog] [info] contig count for validation: 1411[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of Contigs : 1411[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Total # of contig vec entries: 6088[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] bits per offset entry 13[2024-08-30 07:19:02.348] [puff::index::jointLog] [info] Done constructing the contig vector. 1412[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] # segments = 1411[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] total length = 235270[2024-08-30 07:19:02.365] [puff::index::jointLog] [info] Reading the reference files ...[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] positional integer width = 18[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] seqSize = 235270[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] rankSize = 235270[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] edgeVecSize = 0[2024-08-30 07:19:02.383] [puff::index::jointLog] [info] num keys = 192940[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.37 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.37 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.59 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.59 % elapsed: 0 min 0 sec remaining: 0 min 0 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elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97.2 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97.2 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97.5 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97.5 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97.9 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 97.9 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 98.1 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 98.1 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 98.4 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 98.4 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] mphf size = 0.121223 MB[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk size = 117635[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 0 = [0, 117644)[2024-08-30 07:19:02.512] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] finished populating pos vector[2024-08-30 07:19:02.525] [puff::index::jointLog] [info] writing index components[2024-08-30 07:19:02.549] [puff::index::jointLog] [info] finished writing dense pufferfish index[2024-08-30 07:19:02.556] [jLog] [info] done building indexVersion Info: ### PLEASE UPGRADE SALMON ###### A newer version of salmon with important bug fixes and improvements is available. #######The newest version, available at https://github.com/COMBINE-lab/salmon/releasescontains new features, improvements, and bug fixes; please upgrade at yourearliest convenience.###Sign up for the salmon mailing list to hear about new versions, features and updates at:https://oceangenomics.com/subscribe###[2024-08-30 07:19:03.265] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipelineLogs will be written to ./output/logs[2024-08-30 07:19:03.295] [jointLog] [info] setting maxHashResizeThreads to 8[2024-08-30 07:19:03.295] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.[2024-08-30 07:19:03.295] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.[2024-08-30 07:19:03.295] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65[2024-08-30 07:19:03.295] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. [2024-08-30 07:19:03.295] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.[2024-08-30 07:19:03.295] [jointLog] [info] Using default value of 0.87 for minScoreFraction in AlevinUsing default value of 0.6 for consensusSlack in Alevin### alevin (dscRNA-seq quantification) v1.5.1### [ program ] => salmon ### [ command ] => alevin ### [ libType ] => { A }### [ index ] => { ./index }### [ mates1 ] => { ./mate1.fastq }### [ mates2 ] => { ./mate2.fastq }### [ output ] => { ./output }### [ threads ] => { 8 }### [ chromium ] => { }### [ tgMap ] => { ./alevinmap.tsv }### [ keepCBFraction ] => { 1.0 }### [ dumpFeatures ] => { }### [ dumpMtx ] => { }### [ freqThreshold ] => { 5 }[2024-08-30 07:19:03.299] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)[2024-08-30 07:19:03.300] [alevinLog] [info] Filled with 322 txp to gene entries [2024-08-30 07:19:03.300] [alevinLog] [info] Found all transcripts to gene mappings[2024-08-30 07:19:03.310] [alevinLog] [info] Processing barcodes files (if Present) [2024-08-30 07:19:03.363] [alevinLog] [info] Done barcode density calculation.[2024-08-30 07:19:03.363] [alevinLog] [info] # Barcodes Used: [32m125000[0m / [31m125000[0m.[2024-08-30 07:19:03.366] [alevinLog] [info] Forcing to use 15126 cells[2024-08-30 07:19:03.388] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads[2024-08-30 07:19:03.408] [alevinLog] [info] Total [32m5104[0m(has [32m501[0m low confidence) barcodes[2024-08-30 07:19:03.446] [alevinLog] [info] Done True Barcode Sampling[2024-08-30 07:19:03.449] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.[2024-08-30 07:19:03.576] [alevinLog] [info] Done populating Z matrix[2024-08-30 07:19:03.576] [alevinLog] [info] Total 0 CB got sequence corrected[2024-08-30 07:19:03.576] [alevinLog] [info] Done indexing Barcodes[2024-08-30 07:19:03.576] [alevinLog] [info] Total Unique barcodes found: 15126[2024-08-30 07:19:03.576] [alevinLog] [info] Used Barcodes except Whitelist: 0[2024-08-30 07:19:03.597] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify[2024-08-30 07:19:03.597] [alevinLog] [info] parsing read library format-----------------------------------------| Loading contig table | Time = 1.2347 ms-----------------------------------------size = 1412-----------------------------------------| Loading contig offsets | Time = 1.089 ms----------------------------------------------------------------------------------| Loading reference lengths | Time = 8.44 us----------------------------------------------------------------------------------| Loading mphf table | Time = 806.25 us-----------------------------------------size = 235270Number of ones: 1411Number of ones per inventory item: 512Inventory entries filled: 3-----------------------------------------| Loading contig boundaries | Time = 1.6259 ms-----------------------------------------size = 235270-----------------------------------------| Loading sequence | Time = 1.2949 ms-----------------------------------------size = 192940-----------------------------------------| Loading positions | Time = 1.7425 ms-----------------------------------------size = 570828-----------------------------------------| Loading reference sequence | Time = 1.2667 ms----------------------------------------------------------------------------------| Loading reference accumulative lengths | Time = 18.15 us-----------------------------------------[2024-08-30 07:19:03.597] [jointLog] [info] There is 1 library.[2024-08-30 07:19:03.713] [jointLog] [info] Loading pufferfish index[2024-08-30 07:19:03.714] [jointLog] [info] Loading dense pufferfish index.[2024-08-30 07:19:03.726] [jointLog] [info] done[2024-08-30 07:19:03.726] [jointLog] [info] Index contained 322 targets[2024-08-30 07:19:03.726] [jointLog] [info] Number of decoys : 0[2024-08-30 07:19:04.660] [jointLog] [info] Computed 41 rich equivalence classes for further processing[2024-08-30 07:19:04.660] [jointLog] [info] Counted 96 total reads in the equivalence classes [2024-08-30 07:19:04.661] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0[2024-08-30 07:19:04.661] [jointLog] [info] Mapping rate = 0.0768%[2024-08-30 07:19:04.661] [jointLog] [info] finished quantifyLibrary()[2024-08-30 07:19:04.681] [alevinLog] [info] Starting optimizer[2024-08-30 07:19:04.827] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting[2024-08-30 07:19:04.827] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting[A[32mAnalyzed 36 cells ([31m1%[32m of all).[0m[A[32mAnalyzed 42 cells ([31m1%[32m of all).[0m[A[32mAnalyzed 46 cells ([31m1%[32m of all).[0m[A[32mAnalyzed 47 cells ([31m1%[32m of all).[0m[A[32mAnalyzed 47 cells ([31m1%[32m of all).[0m[A[32mAnalyzed 93 cells ([31m2%[32m of all).[0m[A[32mAnalyzed 95 cells ([31m2%[32m of all).[0m[A[32mAnalyzed 95 cells ([31m2%[32m of all).[0m[A[32mAnalyzed 231 cells ([31m5%[32m of all).[0m[A[32mAnalyzed 231 cells ([31m5%[32m of all).[0m[A[32mAnalyzed 262 cells ([31m5%[32m of all).[0m[A[32mAnalyzed 276 cells ([31m5%[32m of all).[0m[A[32mAnalyzed 285 cells ([31m6%[32m of all).[0m[A[32mAnalyzed 285 cells ([31m6%[32m of all).[0m[A[32mAnalyzed 328 cells ([31m6%[32m of all).[0m[A[32mAnalyzed 328 cells ([31m6%[32m of all).[0m[A[32mAnalyzed 385 cells ([31m8%[32m of all).[0m[A[32mAnalyzed 403 cells ([31m8%[32m of all).[0m[A[32mAnalyzed 409 cells ([31m8%[32m of all).[0m[A[32mAnalyzed 436 cells ([31m9%[32m of all).[0m[A[32mAnalyzed 409 cells ([31m8%[32m of all).[0m[A[32mAnalyzed 519 cells ([31m10%[32m of all).[0m[A[32mAnalyzed 520 cells ([31m10%[32m of all).[0m[A[32mAnalyzed 575 cells ([31m11%[32m of all).[0m[A[32mAnalyzed 609 cells ([31m12%[32m of all).[0m[A[32mAnalyzed 609 cells ([31m12%[32m of all).[0m[A[32mAnalyzed 614 cells ([31m12%[32m of all).[0m[A[32mAnalyzed 614 cells ([31m12%[32m of all).[0m[A[32mAnalyzed 702 cells ([31m14%[32m of all).[0m[A[32mAnalyzed 740 cells ([31m15%[32m of all).[0m[A[32mAnalyzed 780 cells ([31m15%[32m of all).[0m[A[32mAnalyzed 789 cells ([31m15%[32m of all).[0m[A[32mAnalyzed 789 cells ([31m15%[32m of all).[0m[A[32mAnalyzed 802 cells ([31m16%[32m of all).[0m[A[32mAnalyzed 805 cells ([31m16%[32m of all).[0m[A[32mAnalyzed 805 cells ([31m16%[32m of all).[0m[A[32mAnalyzed 937 cells ([31m18%[32m of all).[0m[A[32mAnalyzed 937 cells ([31m18%[32m of all).[0m[A[32mAnalyzed 960 cells ([31m19%[32m of all).[0m[A[32mAnalyzed 1036 cells ([31m20%[32m of all).[0m[A[32mAnalyzed 1036 cells ([31m20%[32m of all).[0m[A[32mAnalyzed 1101 cells ([31m22%[32m of all).[0m[A[32mAnalyzed 1119 cells ([31m22%[32m of all).[0m[A[32mAnalyzed 1119 cells ([31m22%[32m of all).[0m[A[32mAnalyzed 1156 cells ([31m23%[32m of all).[0m[A[32mAnalyzed 1156 cells ([31m23%[32m of all).[0m[A[32mAnalyzed 1156 cells ([31m23%[32m of all).[0m[A[32mAnalyzed 1392 cells ([31m27%[32m of all).[0m[A[32mAnalyzed 1393 cells ([31m27%[32m of all).[0m[A[32mAnalyzed 1444 cells ([31m28%[32m of all).[0m[A[32mAnalyzed 1528 cells ([31m30%[32m of all).[0m[A[32mAnalyzed 1570 cells ([31m31%[32m of all).[0m[A[32mAnalyzed 1721 cells ([31m34%[32m of all).[0m[A[32mAnalyzed 1771 cells ([31m35%[32m of all).[0m[A[32mAnalyzed 1803 cells ([31m35%[32m of all).[0m[A[32mAnalyzed 1820 cells ([31m36%[32m of all).[0m[A[32mAnalyzed 1842 cells ([31m36%[32m of all).[0m[A[32mAnalyzed 1878 cells ([31m37%[32m of all).[0m[A[32mAnalyzed 1898 cells ([31m37%[32m of all).[0m[A[32mAnalyzed 1922 cells ([31m38%[32m of all).[0m[A[32mAnalyzed 1957 cells ([31m38%[32m of all).[0m[A[32mAnalyzed 1957 cells ([31m38%[32m of all).[0m[A[32mAnalyzed 2064 cells ([31m40%[32m of all).[0m[A[32mAnalyzed 2210 cells ([31m43%[32m of all).[0m[A[32mAnalyzed 2229 cells ([31m44%[32m of all).[0m[A[32mAnalyzed 2266 cells ([31m44%[32m of all).[0m[A[32mAnalyzed 2336 cells ([31m46%[32m of all).[0m[A[32mAnalyzed 2455 cells ([31m48%[32m of all).[0m[A[32mAnalyzed 2757 cells ([31m54%[32m of all).[0m[A[32mAnalyzed 2769 cells ([31m54%[32m of all).[0m[A[32mAnalyzed 2775 cells ([31m54%[32m of all).[0m[A[32mAnalyzed 2781 cells ([31m54%[32m of all).[0m[A[32mAnalyzed 2849 cells ([31m56%[32m of all).[0m[A[32mAnalyzed 3004 cells ([31m59%[32m of all).[0m[A[32mAnalyzed 3021 cells ([31m59%[32m of all).[0m[A[32mAnalyzed 3087 cells ([31m60%[32m of all).[0m[A[32mAnalyzed 3087 cells ([31m60%[32m of all).[0m[A[32mAnalyzed 3319 cells ([31m65%[32m of all).[0m[A[32mAnalyzed 3603 cells ([31m71%[32m of all).[0m[A[32mAnalyzed 3799 cells ([31m74%[32m of all).[0m[A[32mAnalyzed 3927 cells ([31m77%[32m of all).[0m[A[32mAnalyzed 4019 cells ([31m79%[32m of all).[0m[A[32mAnalyzed 4089 cells ([31m80%[32m of all).[0m[A[32mAnalyzed 4127 cells ([31m81%[32m of all).[0m[A[32mAnalyzed 4133 cells ([31m81%[32m of all).[0m[A[32mAnalyzed 4158 cells ([31m81%[32m of all).[0m[A[32mAnalyzed 4220 cells ([31m83%[32m of all).[0m[A[32mAnalyzed 4267 cells ([31m84%[32m of all).[0m[A[32mAnalyzed 4220 cells ([31m83%[32m of all).[0m[A[32mAnalyzed 4267 cells ([31m84%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[2024-08-30 07:19:04.835] [alevinLog] [info] Total 96.00 UMI after deduplicating.[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 BiDirected Edges.[2024-08-30 07:19:04.835] [alevinLog] [info] Total 0 UniDirected Edges.[2024-08-30 07:19:04.835] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read[2024-08-30 07:19:04.861] [alevinLog] [info] Clearing EqMap; Might take some time.[2024-08-30 07:19:04.864] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping[2024-08-30 07:19:04.864] [alevinLog] [info] Starting dumping cell v gene counts in mtx format[2024-08-30 07:19:04.872] [alevinLog] [info] Finished dumping counts into mtx[2024-08-30 07:19:04.872] [alevinLog] [info] Finished optimizer[2024-08-30 07:19:04.893] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :Found no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details
+ ]]>
+
+
+
+
+
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+
+ 1 & succ>1)=5 | (succ>1 & isStart)=2 | (prec>1 & isEnd)=1 | (isStart & isEnd)=0contig count: 1412 element count: 235270 complex nodes: 8# of ones in rank vector: 1411[2024-08-30 07:19:40.925] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.[2024-08-30 07:19:40.926] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./indexsize = 235270-----------------------------------------| Loading contigs | Time = 1.7824 ms-----------------------------------------size = 235270-----------------------------------------| Loading contig boundaries | Time = 1.37 ms-----------------------------------------Number of ones: 1411Number of ones per inventory item: 512Inventory entries filled: 31411[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.[2024-08-30 07:19:40.929] [puff::index::jointLog] [info] contig count for validation: 1411[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of Contigs : 1411[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of numerical Contigs : 1411[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Total # of contig vec entries: 6088[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] bits per offset entry 13[2024-08-30 07:19:40.931] [puff::index::jointLog] [info] Done constructing the contig vector. 1412[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] # segments = 1411[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] total length = 235270[2024-08-30 07:19:40.951] [puff::index::jointLog] [info] Reading the reference files ...[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] positional integer width = 18[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] seqSize = 235270[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] rankSize = 235270[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] edgeVecSize = 0[2024-08-30 07:19:40.973] [puff::index::jointLog] [info] num keys = 192940[Building BooPHF] 0.228% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.455% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.683% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 0.911% elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.14 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.37 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.37 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.59 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 1.59 % elapsed: 0 min 0 sec remaining: 0 min 0 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min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[Building BooPHF] 100 % elapsed: 0 min 0 sec remaining: 0 min 0 sec[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] mphf size = 0.121223 MB[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk size = 117635[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 0 = [0, 117644)[2024-08-30 07:19:41.110] [puff::index::jointLog] [info] chunk 1 = [117644, 235240)[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] finished populating pos vector[2024-08-30 07:19:41.123] [puff::index::jointLog] [info] writing index components[2024-08-30 07:19:41.148] [puff::index::jointLog] [info] finished writing dense pufferfish index[2024-08-30 07:19:41.156] [jLog] [info] done building indexVersion Info: ### PLEASE UPGRADE SALMON ###### A newer version of salmon with important bug fixes and improvements is available. #######The newest version, available at https://github.com/COMBINE-lab/salmon/releasescontains new features, improvements, and bug fixes; please upgrade at yourearliest convenience.###Sign up for the salmon mailing list to hear about new versions, features and updates at:https://oceangenomics.com/subscribe###Logs will be written to ./output/logs[2024-08-30 07:19:41.893] [alevinLog] [warning] Force Cells to 1 fraction of All possible CB.This is not recommended way to run the pipeline,and it might slow the pipeline[2024-08-30 07:19:41.924] [jointLog] [info] setting maxHashResizeThreads to 8[2024-08-30 07:19:41.924] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.[2024-08-30 07:19:41.924] [jointLog] [info] The --mimicBT2, --mimicStrictBT2 and --hardFilter flags imply mapping validation (--validateMappings). Enabling mapping validation.[2024-08-30 07:19:41.924] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65[2024-08-30 07:19:41.924] [jointLog] [info] The use of range-factorized equivalence classes does not make sense in conjunction with --hardFilter. Disabling range-factorized equivalence classes. [2024-08-30 07:19:41.924] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.[2024-08-30 07:19:41.924] [jointLog] [info] Using default value of 0.87 for minScoreFraction in AlevinUsing default value of 0.6 for consensusSlack in Alevin### alevin (dscRNA-seq quantification) v1.5.1### [ program ] => salmon ### [ command ] => alevin ### [ libType ] => { A }### [ index ] => { ./index }### [ mates1 ] => { ./mate1.fastq }### [ mates2 ] => { ./mate2.fastq }### [ output ] => { ./output }### [ threads ] => { 8 }### [ chromium ] => { }### [ tgMap ] => { ./alevinmap.tsv }### [ numCellBootstraps ] => { 2 }### [ keepCBFraction ] => { 1.0 }### [ dumpFeatures ] => { }### [ dumpMtx ] => { }### [ freqThreshold ] => { 5 }[2024-08-30 07:19:41.929] [alevinLog] [info] Found 322 transcripts(+0 decoys, +0 short and +0 duplicate names in the index)[2024-08-30 07:19:41.931] [alevinLog] [info] Filled with 322 txp to gene entries [2024-08-30 07:19:41.931] [alevinLog] [info] Found all transcripts to gene mappings[2024-08-30 07:19:41.942] [alevinLog] [info] Processing barcodes files (if Present) [2024-08-30 07:19:41.997] [alevinLog] [info] Done barcode density calculation.[2024-08-30 07:19:41.997] [alevinLog] [info] # Barcodes Used: [32m125000[0m / [31m125000[0m.[2024-08-30 07:19:42.001] [alevinLog] [info] Forcing to use 15126 cells[2024-08-30 07:19:42.022] [alevinLog] [info] Throwing 10524 barcodes with < 5 reads[2024-08-30 07:19:42.043] [alevinLog] [info] Total [32m5104[0m(has [32m501[0m low confidence) barcodes[2024-08-30 07:19:42.081] [alevinLog] [info] Done True Barcode Sampling[2024-08-30 07:19:42.084] [alevinLog] [info] Total 8.0184% reads will be thrown away because of noisy Cellular barcodes.[2024-08-30 07:19:42.213] [alevinLog] [info] Done populating Z matrix[2024-08-30 07:19:42.213] [alevinLog] [info] Total 0 CB got sequence corrected[2024-08-30 07:19:42.213] [alevinLog] [info] Done indexing Barcodes[2024-08-30 07:19:42.213] [alevinLog] [info] Total Unique barcodes found: 15126[2024-08-30 07:19:42.213] [alevinLog] [info] Used Barcodes except Whitelist: 0[2024-08-30 07:19:42.234] [alevinLog] [info] Done with Barcode Processing; Moving to Quantify[2024-08-30 07:19:42.234] [alevinLog] [info] parsing read library format-----------------------------------------| Loading contig table | Time = 1.4834 ms-----------------------------------------size = 1412-----------------------------------------| Loading contig offsets | Time = 1.2083 ms----------------------------------------------------------------------------------| Loading reference lengths | Time = 11.98 us----------------------------------------------------------------------------------| Loading mphf table | Time = 930.92 us-----------------------------------------size = 235270Number of ones: 1411Number of ones per inventory item: 512Inventory entries filled: 3-----------------------------------------| Loading contig boundaries | Time = 1.8072 ms-----------------------------------------size = 235270-----------------------------------------| Loading sequence | Time = 1.2416 ms-----------------------------------------size = 192940-----------------------------------------| Loading positions | Time = 1.3634 ms-----------------------------------------size = 570828-----------------------------------------| Loading reference sequence | Time = 1.2181 ms----------------------------------------------------------------------------------| Loading reference accumulative lengths | Time = 9.31 us-----------------------------------------[2024-08-30 07:19:42.234] [jointLog] [info] There is 1 library.[2024-08-30 07:19:42.351] [jointLog] [info] Loading pufferfish index[2024-08-30 07:19:42.352] [jointLog] [info] Loading dense pufferfish index.[2024-08-30 07:19:42.365] [jointLog] [info] done[2024-08-30 07:19:42.366] [jointLog] [info] Index contained 322 targets[2024-08-30 07:19:42.366] [jointLog] [info] Number of decoys : 0[2024-08-30 07:19:43.302] [jointLog] [info] Computed 41 rich equivalence classes for further processing[2024-08-30 07:19:43.302] [jointLog] [info] Counted 96 total reads in the equivalence classes [2024-08-30 07:19:43.302] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0[2024-08-30 07:19:43.303] [jointLog] [info] Mapping rate = 0.0768%[2024-08-30 07:19:43.303] [jointLog] [info] finished quantifyLibrary()[2024-08-30 07:19:43.314] [alevinLog] [info] Starting optimizer[A[32mAnalyzed 36 cells ([31m1%[32m of all).[0m[A[32mAnalyzed 42 cells ([31m1%[32m of all).[0m[A[32mAnalyzed 42 cells ([31m1%[32m of all).[0m[A[32mAnalyzed 47 cells ([31m1%[32m of all).[0m[A[32mAnalyzed 86 cells ([31m2%[32m of all).[0m[A[32mAnalyzed 93 cells ([31m2%[32m of all).[0m[A[32mAnalyzed 95 cells ([31m2%[32m of all).[0m[A[32mAnalyzed 140 cells ([31m3%[32m of all).[0m[A[32mAnalyzed 231 cells ([31m5%[32m of all).[0m[A[32mAnalyzed 231 cells ([31m5%[32m of all).[0m[A[32mAnalyzed 262 cells ([31m5%[32m of all).[0m[A[32mAnalyzed 276 cells ([31m5%[32m of all).[0m[A[32mAnalyzed 285 cells ([31m6%[32m of all).[0m[A[32mAnalyzed 297 cells ([31m6%[32m of all).[0m[A[32mAnalyzed 297 cells ([31m6%[32m of all).[0m[A[32mAnalyzed 331 cells ([31m6%[32m of all).[0m[A[32mAnalyzed 385 cells ([31m8%[32m of all).[0m[A[32mAnalyzed 403 cells ([31m8%[32m of all).[0m[A[32mAnalyzed 409 cells ([31m8%[32m of all).[0m[A[32mAnalyzed 436 cells ([31m9%[32m of all).[0m[A[32mAnalyzed 491 cells ([31m10%[32m of all).[0m[A[32mAnalyzed 519 cells ([31m10%[32m of all).[0m[A[32mAnalyzed 519 cells ([31m10%[32m of all).[0m[A[32mAnalyzed 575 cells ([31m11%[32m of all).[0m[A[32mAnalyzed 609 cells ([31m12%[32m of all).[0m[A[32mAnalyzed 614 cells ([31m12%[32m of all).[0m[A[32mAnalyzed 614 cells ([31m12%[32m of all).[0m[A[32mAnalyzed 673 cells ([31m13%[32m of all).[0m[A[32mAnalyzed 702 cells ([31m14%[32m of all).[0m[A[32mAnalyzed 702 cells ([31m14%[32m of all).[0m[A[32mAnalyzed 780 cells ([31m15%[32m of all).[0m[A[32mAnalyzed 789 cells ([31m15%[32m of all).[0m[A[32mAnalyzed 799 cells ([31m16%[32m of all).[0m[A[32mAnalyzed 802 cells ([31m16%[32m of all).[0m[A[32mAnalyzed 805 cells ([31m16%[32m of all).[0m[A[32mAnalyzed 886 cells ([31m17%[32m of all).[0m[A[32mAnalyzed 937 cells ([31m18%[32m of all).[0m[A[32mAnalyzed 944 cells ([31m18%[32m of all).[0m[A[32mAnalyzed 960 cells ([31m19%[32m of all).[0m[A[32mAnalyzed 1036 cells ([31m20%[32m of all).[0m[A[32mAnalyzed 1042 cells ([31m20%[32m of all).[0m[A[32mAnalyzed 1101 cells ([31m22%[32m of all).[0m[A[32mAnalyzed 1119 cells ([31m22%[32m of all).[0m[A[32mAnalyzed 1153 cells ([31m23%[32m of all).[0m[A[32mAnalyzed 1156 cells ([31m23%[32m of all).[0m[A[32mAnalyzed 1156 cells ([31m23%[32m of all).[0m[A[32mAnalyzed 1205 cells ([31m24%[32m of all).[0m[A[32mAnalyzed 1156 cells ([31m23%[32m of all).[0m[A[32mAnalyzed 1393 cells ([31m27%[32m of all).[0m[A[32mAnalyzed 1444 cells ([31m28%[32m of all).[0m[A[32mAnalyzed 1528 cells ([31m30%[32m of all).[0m[A[32mAnalyzed 1570 cells ([31m31%[32m of all).[0m[A[32mAnalyzed 1721 cells ([31m34%[32m of all).[0m[A[32mAnalyzed 1771 cells ([31m35%[32m of all).[0m[A[32mAnalyzed 1803 cells ([31m35%[32m of all).[0m[A[32mAnalyzed 1820 cells ([31m36%[32m of all).[0m[A[32mAnalyzed 1842 cells ([31m36%[32m of all).[0m[A[32mAnalyzed 1820 cells ([31m36%[32m of all).[0m[A[32mAnalyzed 1898 cells ([31m37%[32m of all).[0m[A[32mAnalyzed 1922 cells ([31m38%[32m of all).[0m[A[32mAnalyzed 1957 cells ([31m38%[32m of all).[0m[A[32mAnalyzed 2044 cells ([31m40%[32m of all).[0m[A[32mAnalyzed 2064 cells ([31m40%[32m of all).[0m[A[32mAnalyzed 2210 cells ([31m43%[32m of all).[0m[A[32mAnalyzed 2229 cells ([31m44%[32m of all).[0m[A[32mAnalyzed 2266 cells ([31m44%[32m of all).[0m[A[32mAnalyzed 2336 cells ([31m46%[32m of all).[0m[A[32mAnalyzed 2660 cells ([31m52%[32m of all).[0m[A[32mAnalyzed 2660 cells ([31m52%[32m of all).[0m[A[32mAnalyzed 2769 cells ([31m54%[32m of all).[0m[A[32mAnalyzed 2775 cells ([31m54%[32m of all).[0m[A[32mAnalyzed 2781 cells ([31m54%[32m of all).[0m[A[32mAnalyzed 2775 cells ([31m54%[32m of all).[0m[A[32mAnalyzed 3004 cells ([31m59%[32m of all).[0m[A[32mAnalyzed 3021 cells ([31m59%[32m of all).[0m[A[32mAnalyzed 3087 cells ([31m60%[32m of all).[0m[A[32mAnalyzed 3181 cells ([31m62%[32m of all).[0m[A[32mAnalyzed 3319 cells ([31m65%[32m of all).[0m[A[32mAnalyzed 3603 cells ([31m71%[32m of all).[0m[A[32mAnalyzed 3799 cells ([31m74%[32m of all).[0m[A[32mAnalyzed 3927 cells ([31m77%[32m of all).[0m[A[32mAnalyzed 3927 cells ([31m77%[32m of all).[0m[A[32mAnalyzed 4089 cells ([31m80%[32m of all).[0m[A[32mAnalyzed 4127 cells ([31m81%[32m of all).[0m[A[32mAnalyzed 4133 cells ([31m81%[32m of all).[0m[A[32mAnalyzed 4134 cells ([31m81%[32m of all).[0m[A[32mAnalyzed 4220 cells ([31m83%[32m of all).[0m[A[32mAnalyzed 4267 cells ([31m84%[32m of all).[0m[A[32mAnalyzed 4362 cells ([31m85%[32m of all).[0m[A[32mAnalyzed 4790 cells ([31m94%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[A[32mAnalyzed 5103 cells ([31m100%[32m of all).[0m[2024-08-30 07:19:43.460] [alevinLog] [warning] mrna file not provided; using is 1 less feature for whitelisting[2024-08-30 07:19:43.460] [alevinLog] [warning] rrna file not provided; using is 1 less feature for whitelisting[2024-08-30 07:19:43.477] [alevinLog] [info] Total 96.00 UMI after deduplicating.[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 BiDirected Edges.[2024-08-30 07:19:43.477] [alevinLog] [info] Total 0 UniDirected Edges.[2024-08-30 07:19:43.477] [alevinLog] [warning] Skipped 5007 barcodes due to No mapped read[2024-08-30 07:19:43.522] [alevinLog] [info] Clearing EqMap; Might take some time.[2024-08-30 07:19:43.525] [alevinLog] [warning] Num Low confidence barcodes too less 2 < 200.Can't performing whitelisting; Skipping[2024-08-30 07:19:43.526] [alevinLog] [info] Starting dumping cell v gene counts in mtx format[2024-08-30 07:19:43.532] [alevinLog] [info] Finished dumping counts into mtx[2024-08-30 07:19:43.532] [alevinLog] [info] Finished optimizer[2024-08-30 07:19:43.553] [jointLog] [warning] NOTE: Read Lib [[ ./mate1.fastq, ./mate2.fastq]] :Found no concordant and consistent mappings. If this is a paired-end library, are you sure the reads are properly paired? check the file: ./output/lib_format_counts.json for details
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+ >>STAGE: configure[2024-08-30 06:40:23] INFO: Configuring run[2024-08-30 06:40:23] INFO: Total read length: 1466260[2024-08-30 06:40:23] INFO: Input genome size: 10000[2024-08-30 06:40:23] INFO: Estimated coverage: 146[2024-08-30 06:40:23] INFO: Reads N50/N90: 9054 / 4697[2024-08-30 06:40:23] INFO: Minimum overlap set to 5000[2024-08-30 06:40:23] INFO: Selected k-mer size: 15[2024-08-30 06:40:23] INFO: >>>STAGE: assembly[2024-08-30 06:40:23] INFO: Assembling disjointigs[2024-08-30 06:40:23] INFO: Reading sequences[2024-08-30 06:40:23] INFO: Generating solid k-mer index[2024-08-30 06:40:45] INFO: Counting k-mers (1/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:40:45] INFO: Counting k-mers (2/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:40:45] INFO: Filling index table0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:40:49] INFO: Extending reads[2024-08-30 06:40:52] INFO: Overlap-based coverage: 25[2024-08-30 06:40:52] INFO: Median overlap divergence: 0.1690630% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:40:52] INFO: Assembled 1 disjointigs[2024-08-30 06:40:52] INFO: Generating sequence10% 20% 40% 50% 70% 80% 100% [2024-08-30 06:40:52] INFO: >>>STAGE: consensus[2024-08-30 06:40:52] INFO: Running Minimap2[2024-08-30 06:40:53] INFO: Computing consensus[2024-08-30 06:40:54] INFO: Alignment error rate: 0.158711[2024-08-30 06:40:54] INFO: >>>STAGE: repeat[2024-08-30 06:40:54] INFO: Building and resolving repeat graph[2024-08-30 06:40:54] INFO: Reading sequences[2024-08-30 06:40:54] INFO: Building repeat graph50% 100% [2024-08-30 06:41:16] INFO: Median overlap divergence: 0[2024-08-30 06:41:16] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:41:38] INFO: Aligned read sequence: 1184568 / 1313105 (0.902112)[2024-08-30 06:41:38] INFO: Median overlap divergence: 0.0607255[2024-08-30 06:41:38] INFO: Mean edge coverage: 29[2024-08-30 06:41:38] INFO: Resolving repeats[2024-08-30 06:41:38] INFO: >>>STAGE: trestleTraceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000b25aad00000073'[2024-08-30 06:41:38] INFO: Simple unbridged repeats: 0[2024-08-30 06:41:38] INFO: Resolved: 0[2024-08-30 06:41:38] INFO: >>>STAGE: contigger[2024-08-30 06:41:38] INFO: Generating contigs[2024-08-30 06:41:38] INFO: Reading sequences[2024-08-30 06:41:38] INFO: Generated 1 contigs[2024-08-30 06:41:38] INFO: Added 0 scaffold connections[2024-08-30 06:41:39] INFO: >>>STAGE: polishing[2024-08-30 06:41:39] INFO: Polishing genome (1/1)[2024-08-30 06:41:39] INFO: Running minimap2[2024-08-30 06:41:39] INFO: Separating alignment into bubbles[2024-08-30 06:41:40] INFO: Alignment error rate: 0.101562[2024-08-30 06:41:40] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000b25ac700000074'[2024-08-30 06:41:41] INFO: >>>STAGE: finalize[2024-08-30 06:41:41] INFO: Assembly statistics:Total length:39948Fragments:1Fragments N50:39948Largest frg:39948Scaffolds:0Mean coverage:28[2024-08-30 06:41:41] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/74/working/out_dir/assembly.fasta
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+
+
+ >>STAGE: configure[2024-08-30 06:42:15] INFO: Configuring run[2024-08-30 06:42:15] INFO: Total read length: 1466260[2024-08-30 06:42:15] INFO: Input genome size: 10000[2024-08-30 06:42:15] INFO: Estimated coverage: 146[2024-08-30 06:42:15] INFO: Reads N50/N90: 9054 / 4697[2024-08-30 06:42:15] INFO: Minimum overlap set to 5000[2024-08-30 06:42:15] INFO: Selected k-mer size: 15[2024-08-30 06:42:15] INFO: >>>STAGE: assembly[2024-08-30 06:42:15] INFO: Assembling disjointigs[2024-08-30 06:42:15] INFO: Reading sequences[2024-08-30 06:42:15] INFO: Generating solid k-mer index[2024-08-30 06:42:37] INFO: Counting k-mers (1/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:42:37] INFO: Counting k-mers (2/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:42:37] INFO: Filling index table0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:42:41] INFO: Extending reads[2024-08-30 06:42:44] INFO: Overlap-based coverage: 25[2024-08-30 06:42:44] INFO: Median overlap divergence: 0.1691080% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:42:44] INFO: Assembled 1 disjointigs[2024-08-30 06:42:44] INFO: Generating sequence10% 20% 40% 50% 70% 80% 100% [2024-08-30 06:42:44] INFO: >>>STAGE: consensus[2024-08-30 06:42:44] INFO: Running Minimap2[2024-08-30 06:42:44] INFO: Computing consensus[2024-08-30 06:42:45] INFO: Alignment error rate: 0.156815[2024-08-30 06:42:45] INFO: >>>STAGE: repeat[2024-08-30 06:42:45] INFO: Building and resolving repeat graph[2024-08-30 06:42:45] INFO: Reading sequences[2024-08-30 06:42:45] INFO: Building repeat graph50% 100% [2024-08-30 06:43:08] INFO: Median overlap divergence: 0[2024-08-30 06:43:08] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:43:30] INFO: Aligned read sequence: 1184563 / 1313105 (0.902108)[2024-08-30 06:43:30] INFO: Median overlap divergence: 0.0610287[2024-08-30 06:43:30] INFO: Mean edge coverage: 29[2024-08-30 06:43:30] INFO: Resolving repeats[2024-08-30 06:43:30] INFO: >>>STAGE: trestleTraceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b1c00000076'[2024-08-30 06:43:30] INFO: Simple unbridged repeats: 0[2024-08-30 06:43:30] INFO: Resolved: 0[2024-08-30 06:43:30] INFO: >>>STAGE: contigger[2024-08-30 06:43:30] INFO: Generating contigs[2024-08-30 06:43:30] INFO: Reading sequences[2024-08-30 06:43:30] INFO: Generated 1 contigs[2024-08-30 06:43:30] INFO: Added 0 scaffold connections[2024-08-30 06:43:30] INFO: >>>STAGE: polishing[2024-08-30 06:43:30] INFO: Polishing genome (1/1)[2024-08-30 06:43:30] INFO: Running minimap2[2024-08-30 06:43:30] INFO: Separating alignment into bubbles[2024-08-30 06:43:32] INFO: Alignment error rate: 0.101979[2024-08-30 06:43:32] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b3300000077'[2024-08-30 06:43:32] INFO: >>>STAGE: finalize[2024-08-30 06:43:32] INFO: Assembly statistics:Total length:40422Fragments:1Fragments N50:40422Largest frg:40422Scaffolds:0Mean coverage:27[2024-08-30 06:43:32] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/76/working/out_dir/assembly.fasta
+ ]]>
+
+
+
+
+
+ >>STAGE: configure[2024-08-30 06:44:07] INFO: Configuring run[2024-08-30 06:44:07] INFO: Total read length: 1466260[2024-08-30 06:44:07] INFO: Input genome size: 10000[2024-08-30 06:44:07] INFO: Estimated coverage: 146[2024-08-30 06:44:07] INFO: Reads N50/N90: 9054 / 4697[2024-08-30 06:44:07] INFO: Minimum overlap set to 5000[2024-08-30 06:44:07] INFO: Selected k-mer size: 17[2024-08-30 06:44:07] INFO: Using longest 40x reads for contig assembly[2024-08-30 06:44:07] INFO: >>>STAGE: assembly[2024-08-30 06:44:07] INFO: Assembling disjointigs[2024-08-30 06:44:07] INFO: Reading sequences[2024-08-30 06:44:07] INFO: Generating solid k-mer index[2024-08-30 06:44:29] INFO: Counting k-mers (1/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:44:29] INFO: Counting k-mers (2/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:44:29] INFO: Filling index table0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:44:33] INFO: Extending reads[2024-08-30 06:44:33] INFO: Overlap-based coverage: 3[2024-08-30 06:44:33] INFO: Median overlap divergence: 0.1734680% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:44:33] INFO: Assembled 1 disjointigs[2024-08-30 06:44:33] INFO: Generating sequence10% 20% 40% 50% 70% 80% 100% [2024-08-30 06:44:33] INFO: >>>STAGE: consensus[2024-08-30 06:44:33] INFO: Running Minimap2[2024-08-30 06:44:33] INFO: Computing consensus[2024-08-30 06:44:34] INFO: Alignment error rate: 0.146313[2024-08-30 06:44:34] INFO: >>>STAGE: repeat[2024-08-30 06:44:34] INFO: Building and resolving repeat graph[2024-08-30 06:44:34] INFO: Reading sequences[2024-08-30 06:44:34] INFO: Building repeat graph50% 100% [2024-08-30 06:44:57] INFO: Median overlap divergence: 0[2024-08-30 06:44:57] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:45:19] INFO: Aligned read sequence: 1174263 / 1313105 (0.894264)[2024-08-30 06:45:19] INFO: Median overlap divergence: 0.0589391[2024-08-30 06:45:19] INFO: Mean edge coverage: 29[2024-08-30 06:45:19] INFO: Resolving repeats[2024-08-30 06:45:19] INFO: >>>STAGE: contigger[2024-08-30 06:45:19] INFO: Generating contigs[2024-08-30 06:45:19] INFO: Reading sequences[2024-08-30 06:45:19] INFO: Generated 1 contigs[2024-08-30 06:45:19] INFO: Added 0 scaffold connectionsTraceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b8900000079'[2024-08-30 06:45:19] INFO: >>>STAGE: polishing[2024-08-30 06:45:19] INFO: Polishing genome (1/2)[2024-08-30 06:45:19] INFO: Running minimap2[2024-08-30 06:45:19] INFO: Separating alignment into bubbles[2024-08-30 06:45:20] INFO: Alignment error rate: 0.099017[2024-08-30 06:45:20] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b9a0000007a'[2024-08-30 06:45:21] INFO: Polishing genome (2/2)[2024-08-30 06:45:21] INFO: Running minimap2[2024-08-30 06:45:21] INFO: Separating alignment into bubbles[2024-08-30 06:45:22] INFO: Alignment error rate: 0.094400[2024-08-30 06:45:22] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:45:23] INFO: >>>STAGE: finalize[2024-08-30 06:45:23] INFO: Assembly statistics:Total length:40414Fragments:1Fragments N50:40414Largest frg:40414Scaffolds:0Mean coverage:27[2024-08-30 06:45:23] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/78/working/out_dir/assembly.fastaTraceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000b25b9c0000007c'
+ ]]>
+
+
+
+
+
+ >>STAGE: configure[2024-08-30 06:46:00] INFO: Configuring run[2024-08-30 06:46:00] INFO: Total read length: 1466260[2024-08-30 06:46:00] INFO: Input genome size: 10000[2024-08-30 06:46:00] INFO: Estimated coverage: 146[2024-08-30 06:46:00] INFO: Reads N50/N90: 9054 / 4697[2024-08-30 06:46:00] INFO: Minimum overlap set to 5000[2024-08-30 06:46:00] INFO: Selected k-mer size: 15[2024-08-30 06:46:00] INFO: >>>STAGE: assembly[2024-08-30 06:46:00] INFO: Assembling disjointigs[2024-08-30 06:46:00] INFO: Reading sequences[2024-08-30 06:46:00] INFO: Generating solid k-mer index[2024-08-30 06:46:22] INFO: Counting k-mers (1/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:46:22] INFO: Counting k-mers (2/2):0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:46:22] INFO: Filling index table (1/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:46:22] INFO: Filling index table (2/2)0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:46:26] INFO: Extending reads[2024-08-30 06:46:28] INFO: Overlap-based coverage: 24[2024-08-30 06:46:28] INFO: Median overlap divergence: 0.1844920% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:46:29] INFO: Assembled 1 disjointigs[2024-08-30 06:46:29] INFO: Generating sequence10% 20% 30% 40% 50% 60% 70% 80% 100% [2024-08-30 06:46:29] INFO: >>>STAGE: consensus[2024-08-30 06:46:29] INFO: Running Minimap2[2024-08-30 06:46:29] INFO: Computing consensus[2024-08-30 06:46:30] INFO: Alignment error rate: 0.182990[2024-08-30 06:46:30] INFO: >>>STAGE: repeat[2024-08-30 06:46:30] INFO: Building and resolving repeat graph[2024-08-30 06:46:30] INFO: Reading sequences[2024-08-30 06:46:30] INFO: Building repeat graph50% 100% [2024-08-30 06:46:53] INFO: Median overlap divergence: 0[2024-08-30 06:46:53] INFO: Aligning reads to the graph0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% [2024-08-30 06:47:15] INFO: Aligned read sequence: 1158758 / 1313105 (0.882456)[2024-08-30 06:47:15] INFO: Median overlap divergence: 0.0639983[2024-08-30 06:47:15] INFO: Mean edge coverage: 32[2024-08-30 06:47:15] INFO: Resolving repeats[2024-08-30 06:47:15] INFO: >>>STAGE: plasmids[2024-08-30 06:47:15] INFO: Recovering short unassembled sequencesTraceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000b25bef0000007e'[2024-08-30 06:47:15] INFO: Added 0 extra contigs[2024-08-30 06:47:15] INFO: >>>STAGE: contigger[2024-08-30 06:47:15] INFO: Generating contigs[2024-08-30 06:47:15] INFO: Reading sequences[2024-08-30 06:47:15] INFO: Generated 1 contigs[2024-08-30 06:47:15] INFO: Added 0 scaffold connections[2024-08-30 06:47:15] INFO: >>>STAGE: polishing[2024-08-30 06:47:15] INFO: Polishing genome (1/1)[2024-08-30 06:47:15] INFO: Running minimap2[2024-08-30 06:47:16] INFO: Separating alignment into bubbles[2024-08-30 06:47:17] INFO: Alignment error rate: 0.115118[2024-08-30 06:47:17] INFO: Correcting bubbles0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000b25bff0000007f'Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap self.run() File "/usr/local/lib/python3.7/multiprocessing/process.py", line 99, in run self._target(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 577, in _run_server server.serve_forever() File "/usr/local/lib/python3.7/multiprocessing/managers.py", line 173, in serve_forever sys.exit(0)SystemExit: 0During handling of the above exception, another exception occurred:Traceback (most recent call last): File "/usr/local/lib/python3.7/multiprocessing/util.py", line 265, in _run_finalizers finalizer() File "/usr/local/lib/python3.7/multiprocessing/util.py", line 189, in __call__ res = self._callback(*self._args, **self._kwargs) File "/usr/local/lib/python3.7/shutil.py", line 491, in rmtree _rmtree_safe_fd(fd, path, onerror) File "/usr/local/lib/python3.7/shutil.py", line 449, in _rmtree_safe_fd onerror(os.unlink, fullname, sys.exc_info()) File "/usr/local/lib/python3.7/shutil.py", line 447, in _rmtree_safe_fd os.unlink(entry.name, dir_fd=topfd)OSError: [Errno 16] Device or resource busy: '.nfs0000000000b25c0b00000080'[2024-08-30 06:47:18] INFO: >>>STAGE: finalize[2024-08-30 06:47:18] INFO: Assembly statistics:Total length:35687Fragments:1Fragments N50:35687Largest frg:35687Scaffolds:0Mean coverage:35[2024-08-30 06:47:18] INFO: Final assembly: /galaxy/server/database/jobs_directory/000/80/working/out_dir/assembly.fasta
+ ]]>
+
+
+
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times: 0 (0.00%)Overall alignment rate: 100.00%
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 3 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 3 pairs aligned 0 times concordantly or discordantly; of these: 6 mates make up the pairs; of these: 3 (50.00%) aligned 0 times 3 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times85.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 3 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 3 pairs aligned 0 times concordantly or discordantly; of these: 6 mates make up the pairs; of these: 3 (50.00%) aligned 0 times 3 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times85.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times100.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times100.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 10 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 10 pairs aligned 0 times concordantly or discordantly; of these: 20 mates make up the pairs; of these: 20 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times0.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 1 times ---- 71 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 71 pairs aligned 0 times concordantly or discordantly; of these: 142 mates make up the pairs; of these: 74 (52.11%) aligned 0 times 68 (47.89%) aligned exactly 1 time 0 (0.00%) aligned >1 times92.60% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times85.80% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times85.80% overall alignment rate
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 1 times ---- 3 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 3 pairs aligned 0 times concordantly or discordantly; of these: 6 mates make up the pairs; of these: 6 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times0.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 3 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 3 pairs aligned 0 times concordantly or discordantly; of these: 6 mates make up the pairs; of these: 6 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times0.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times85.80% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times85.80% overall alignment rate
+ ]]>
+
+
+
+
+
+
+
+
+
+
+ 1 times85.80% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
+
+
+
+
+
+ 1 times ---- 1 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 1 pairs aligned 0 times concordantly or discordantly; of these: 2 mates make up the pairs; of these: 1 (50.00%) aligned 0 times 1 (50.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times95.00% overall alignment rate
+ ]]>
+
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+
+ > input_1.fastq <<)Found perfect matches for the following adapter sequences:Adapter typeCountSequenceSequences analysedPercentagesmallRNA0TGGAATTCTCGG20.00Illumina0AGATCGGAAGAGC20.00Nextera0CTGTCTCTTATA20.00Unable to auto-detect most prominent adapter from the first specified file (count smallRNA: 0, count Illumina: 0)Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).Writing report to '/galaxy/server/database/jobs_directory/000/34/working/input_1.fastq_trimming_report.txt'SUMMARISING RUN PARAMETERS==========================Input filename: input_1.fastqTrimming mode: single-endTrim Galore version: 0.6.3Cutadapt version: 2.3Number of cores used for trimming: 1Quality Phred score cutoff: 20Quality encoding type selected: ASCII+33Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))Maximum trimming error rate: 0.1 (default)Minimum required adapter overlap (stringency): 1 bpMinimum required sequence length before a sequence gets removed: 20 bpCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1Writing final adapter and quality trimmed output to input_1_trimmed.fq >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< This is cutadapt 2.3 with Python 3.7.3Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastqProcessing reads on 1 core in single-end mode ...Finished in 0.00 s (2036 us/read; 0.03 M reads/minute).=== Summary ===Total reads processed: 2Reads with adapters: 1 (50.0%)Reads written (passing filters): 2 (100.0%)Total basepairs processed: 188 bpQuality-trimmed: 20 bp (10.6%)Total written (filtered): 167 bp (88.8%)=== Adapter 1 ===Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.No. of allowed errors:0-9 bp: 0; 10-13 bp: 1Bases preceding removed adapters: A: 0.0% C: 100.0% G: 0.0% T: 0.0% none/other: 0.0%Overview of removed sequenceslengthcountexpectmax.errerror counts110.501RUN STATISTICS FOR INPUT FILE: input_1.fastq=============================================2 sequences processed in totalSequences removed because they became shorter than the length cutoff of 20 bp:0 (0.0%)
+ ]]>
+
+
+
+
+
+
+
+
+
+
+ >> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< This is cutadapt 2.3 with Python 3.7.3Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastqProcessing reads on 1 core in single-end mode ...Finished in 0.00 s (2165 us/read; 0.03 M reads/minute).=== Summary ===Total reads processed: 2Reads with adapters: 1 (50.0%)Reads written (passing filters): 2 (100.0%)Total basepairs processed: 188 bpQuality-trimmed: 20 bp (10.6%)Total written (filtered): 167 bp (88.8%)=== Adapter 1 ===Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.No. of allowed errors:0-9 bp: 0; 10-13 bp: 1Bases preceding removed adapters: A: 0.0% C: 100.0% G: 0.0% T: 0.0% none/other: 0.0%Overview of removed sequenceslengthcountexpectmax.errerror counts110.501RUN STATISTICS FOR INPUT FILE: input_1.fastq=============================================2 sequences processed in totalSequences removed because they became shorter than the length cutoff of 20 bp:0 (0.0%)
+ ]]>
+
+
+
+
+
+
+ >> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< This is cutadapt 2.3 with Python 3.7.3Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gzProcessing reads on 1 core in single-end mode ...Finished in 0.02 s (7946 us/read; 0.01 M reads/minute).=== Summary ===Total reads processed: 2Reads with adapters: 1 (50.0%)Reads written (passing filters): 2 (100.0%)Total basepairs processed: 188 bpQuality-trimmed: 20 bp (10.6%)Total written (filtered): 167 bp (88.8%)=== Adapter 1 ===Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.No. of allowed errors:0-9 bp: 0; 10-13 bp: 1Bases preceding removed adapters: A: 0.0% C: 100.0% G: 0.0% T: 0.0% none/other: 0.0%Overview of removed sequenceslengthcountexpectmax.errerror counts110.501RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz=============================================2 sequences processed in totalSequences removed because they became shorter than the length cutoff of 20 bp:0 (0.0%)
+ ]]>
+
+
+
+
+
+
+ > input_1.fastq <<)Found perfect matches for the following adapter sequences:Adapter typeCountSequenceSequences analysedPercentageIllumina0AGATCGGAAGAGC20.00Nextera0CTGTCTCTTATA20.00smallRNA0TGGAATTCTCGG20.00Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count Nextera: 0)Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).Writing report to '/galaxy/server/database/jobs_directory/000/41/working/input_1.fastq_trimming_report.txt'SUMMARISING RUN PARAMETERS==========================Input filename: input_1.fastqTrimming mode: single-endTrim Galore version: 0.6.3Cutadapt version: 2.3Number of cores used for trimming: 1Quality Phred score cutoff: 20Quality encoding type selected: ASCII+33Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))Maximum trimming error rate: 0.1 (default)Minimum required adapter overlap (stringency): 1 bpMinimum required sequence length before a sequence gets removed: 20 bpCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1Writing final adapter and quality trimmed output to input_1_trimmed.fq >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq <<< This is cutadapt 2.3 with Python 3.7.3Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastqProcessing reads on 1 core in single-end mode ...Finished in 0.00 s (1824 us/read; 0.03 M reads/minute).=== Summary ===Total reads processed: 2Reads with adapters: 1 (50.0%)Reads written (passing filters): 2 (100.0%)Total basepairs processed: 188 bpQuality-trimmed: 20 bp (10.6%)Total written (filtered): 167 bp (88.8%)=== Adapter 1 ===Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.No. of allowed errors:0-9 bp: 0; 10-13 bp: 1Bases preceding removed adapters: A: 0.0% C: 100.0% G: 0.0% T: 0.0% none/other: 0.0%Overview of removed sequenceslengthcountexpectmax.errerror counts110.501RUN STATISTICS FOR INPUT FILE: input_1.fastq=============================================2 sequences processed in totalSequences removed because they became shorter than the length cutoff of 20 bp:0 (0.0%)
+ ]]>
+
+
+
+
+
+
+ > input_1.fastq.gz <<)Found perfect matches for the following adapter sequences:Adapter typeCountSequenceSequences analysedPercentageIllumina0AGATCGGAAGAGC20.00smallRNA0TGGAATTCTCGG20.00Nextera0CTGTCTCTTATA20.00Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count smallRNA: 0)Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior).Writing report to '/galaxy/server/database/jobs_directory/000/43/working/input_1.fastq.gz_trimming_report.txt'SUMMARISING RUN PARAMETERS==========================Input filename: input_1.fastq.gzTrimming mode: single-endTrim Galore version: 0.6.3Cutadapt version: 2.3Number of cores used for trimming: 1Quality Phred score cutoff: 20Quality encoding type selected: ASCII+33Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection))Maximum trimming error rate: 0.1 (default)Minimum required adapter overlap (stringency): 1 bpMinimum required sequence length before a sequence gets removed: 20 bpOutput file(s) will be GZIP compressedCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1Writing final adapter and quality trimmed output to input_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file input_1.fastq.gz <<< This is cutadapt 2.3 with Python 3.7.3Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gzProcessing reads on 1 core in single-end mode ...Finished in 0.02 s (8292 us/read; 0.01 M reads/minute).=== Summary ===Total reads processed: 2Reads with adapters: 1 (50.0%)Reads written (passing filters): 2 (100.0%)Total basepairs processed: 188 bpQuality-trimmed: 20 bp (10.6%)Total written (filtered): 167 bp (88.8%)=== Adapter 1 ===Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times.No. of allowed errors:0-9 bp: 0; 10-13 bp: 1Bases preceding removed adapters: A: 0.0% C: 100.0% G: 0.0% T: 0.0% none/other: 0.0%Overview of removed sequenceslengthcountexpectmax.errerror counts110.501RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz=============================================2 sequences processed in totalSequences removed because they became shorter than the length cutoff of 20 bp:0 (0.0%)
+ ]]>
+
+
+
+
+
+
+ > input_1.fastq <<)Found perfect matches for the following adapter sequences:Adapter typeCountSequenceSequences analysedPercentageNextera29CTGTCTCTTATA9929.29Illumina0AGATCGGAAGAGC990.00smallRNA0TGGAATTCTCGG990.00Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0)Writing report to '/galaxy/server/database/jobs_directory/000/46/working/input_1.fastq_trimming_report.txt'SUMMARISING RUN PARAMETERS==========================Input filename: input_1.fastqTrimming mode: paired-endTrim Galore version: 0.6.3Cutadapt version: 2.3Number of cores used for trimming: 1Quality Phred score cutoff: 20Quality encoding type selected: ASCII+33Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)Maximum trimming error rate: 0.1 (default)Minimum required adapter overlap (stringency): 1 bpMinimum required sequence length for both reads before a sequence pair gets removed: 20 bpCutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1Writing final adapter and quality trimmed output to input_1_trimmed.fq >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_1.fastq <<< This is cutadapt 2.3 with Python 3.7.3Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastqProcessing reads on 1 core in single-end mode ...Finished in 0.01 s (55 us/read; 1.10 M reads/minute).=== Summary ===Total reads processed: 99Reads with adapters: 52 (52.5%)Reads written (passing filters): 99 (100.0%)Total basepairs processed: 24,849 bpQuality-trimmed: 205 bp (0.8%)Total written (filtered): 23,339 bp (93.9%)=== Adapter 1 ===Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.No. of allowed errors:0-9 bp: 0; 10-12 bp: 1Bases preceding removed adapters: A: 9.6% C: 38.5% G: 23.1% T: 28.8% none/other: 0.0%Overview of removed sequenceslengthcountexpectmax.errerror counts11124.8011256.205331.503430.4031210.0111320.0121410.0111610.0111710.010 12020.0122110.0112410.0112620.0123110.0113310.0114120.0124910.0115010.0115410.0115610.0115820.0126010.0116720.0126810.0116910.0117310.0118010.0118610.011RUN STATISTICS FOR INPUT FILE: input_1.fastq=============================================99 sequences processed in totalThe length threshold of paired-end sequences gets evaluated later on (in the validation step)Writing report to '/galaxy/server/database/jobs_directory/000/46/working/input_2.fastq_trimming_report.txt'SUMMARISING RUN PARAMETERS==========================Input filename: input_2.fastqTrimming mode: paired-endTrim Galore version: 0.6.3Cutadapt version: 2.3Number of cores used for trimming: 1Quality Phred score cutoff: 20Quality encoding type selected: ASCII+33Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)Maximum trimming error rate: 0.1 (default)Minimum required adapter overlap (stringency): 1 bpMinimum required sequence length for both reads before a sequence pair gets removed: 20 bpCutadapt seems to be fairly up-to-date (version 2.3). Setting -j -j 1Writing final adapter and quality trimmed output to input_2_trimmed.fq >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_2.fastq <<< This is cutadapt 2.3 with Python 3.7.3Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastqProcessing reads on 1 core in single-end mode ...Finished in 0.01 s (67 us/read; 0.90 M reads/minute).=== Summary ===Total reads processed: 99Reads with adapters: 58 (58.6%)Reads written (passing filters): 99 (100.0%)Total basepairs processed: 24,849 bpQuality-trimmed: 745 bp (3.0%)Total written (filtered): 23,035 bp (92.7%)=== Adapter 1 ===Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.No. of allowed errors:0-9 bp: 0; 10-12 bp: 1Bases preceding removed adapters: A: 12.1% C: 37.9% G: 8.6% T: 41.4% none/other: 0.0%Overview of removed sequenceslengthcountexpectmax.errerror counts11624.8016276.207311.501420.402620.002910.0011010.0111310.0111420.0121510.0111610.0111710.0111920.0122110.0112510.0113010.0113220.0123410.0113620.0123810.0114010.0114110.0114210.0114310.0114910.0115110.0115610.0115710.0116010.0116710.0118010.011RUN STATISTICS FOR INPUT FILE: input_2.fastq=============================================99 sequences processed in totalThe length threshold of paired-end sequences gets evaluated later on (in the validation step)Validate paired-end files input_1_trimmed.fq and input_2_trimmed.fqfile_1: input_1_trimmed.fq, file_2: input_2_trimmed.fq>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq and input_2_trimmed.fq <<<<
+
+
+
+
+
+
+
+
+
+
+ > input_1.fastq <<)Found perfect matches for the following adapter sequences:Adapter typeCountSequenceSequences analysedPercentageNextera29CTGTCTCTTATA9929.29smallRNA0TGGAATTCTCGG990.00Illumina0AGATCGGAAGAGC990.00Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0)Writing report to '/galaxy/server/database/jobs_directory/000/51/working/input_1.fastq_trimming_report.txt'SUMMARISING RUN PARAMETERS==========================Input filename: input_1.fastqTrimming mode: paired-endTrim Galore version: 0.6.3Cutadapt version: 2.3Number of cores used for trimming: 1Quality Phred score cutoff: 20Quality encoding type selected: ASCII+33Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)Maximum trimming error rate: 0.1 (default)Minimum required adapter overlap (stringency): 1 bpMinimum required sequence length for both reads before a sequence pair gets removed: 20 bpLength cut-off for read 1: 35 bp (default)Length cut-off for read 2: 35 bb (default)Cutadapt seems to be fairly up-to-date (version 2.3). Setting -j 1Writing final adapter and quality trimmed output to input_1_trimmed.fq >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_1.fastq <<< This is cutadapt 2.3 with Python 3.7.3Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastqProcessing reads on 1 core in single-end mode ...Finished in 0.01 s (54 us/read; 1.11 M reads/minute).=== Summary ===Total reads processed: 99Reads with adapters: 52 (52.5%)Reads written (passing filters): 99 (100.0%)Total basepairs processed: 24,849 bpQuality-trimmed: 205 bp (0.8%)Total written (filtered): 23,339 bp (93.9%)=== Adapter 1 ===Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times.No. of allowed errors:0-9 bp: 0; 10-12 bp: 1Bases preceding removed adapters: A: 9.6% C: 38.5% G: 23.1% T: 28.8% none/other: 0.0%Overview of removed sequenceslengthcountexpectmax.errerror counts11124.8011256.205331.503430.4031210.0111320.0121410.0111610.0111710.010 12020.0122110.0112410.0112620.0123110.0113310.0114120.0124910.0115010.0115410.0115610.0115820.0126010.0116720.0126810.0116910.0117310.0118010.0118610.011RUN STATISTICS FOR INPUT FILE: input_1.fastq=============================================99 sequences processed in totalThe length threshold of paired-end sequences gets evaluated later on (in the validation step)Writing report to '/galaxy/server/database/jobs_directory/000/51/working/input_2.fastq_trimming_report.txt'SUMMARISING RUN PARAMETERS==========================Input filename: input_2.fastqTrimming mode: paired-endTrim Galore version: 0.6.3Cutadapt version: 2.3Number of cores used for trimming: 1Quality Phred score cutoff: 20Quality encoding type selected: ASCII+33Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)Maximum trimming error rate: 0.1 (default)Minimum required adapter overlap (stringency): 1 bpMinimum required sequence length for both reads before a sequence pair gets removed: 20 bpLength cut-off for read 1: 35 bp (default)Length cut-off for read 2: 35 bb (default)Cutadapt seems to be fairly up-to-date (version 2.3). Setting -j -j 1Writing final adapter and quality trimmed output to input_2_trimmed.fq >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file input_2.fastq <<< This is cutadapt 2.3 with Python 3.7.3Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastqProcessing reads on 1 core in single-end mode ...Finished in 0.01 s (63 us/read; 0.95 M reads/minute).=== Summary ===Total reads processed: 99Reads with adapters: 58 (58.6%)Reads written (passing filters): 99 (100.0%)Total basepairs processed: 24,849 bpQuality-trimmed: 745 bp (3.0%)Total written (filtered): 23,035 bp (92.7%)=== Adapter 1 ===Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times.No. of allowed errors:0-9 bp: 0; 10-12 bp: 1Bases preceding removed adapters: A: 12.1% C: 37.9% G: 8.6% T: 41.4% none/other: 0.0%Overview of removed sequenceslengthcountexpectmax.errerror counts11624.8016276.207311.501420.402620.002910.0011010.0111310.0111420.0121510.0111610.0111710.0111920.0122110.0112510.0113010.0113220.0123410.0113620.0123810.0114010.0114110.0114210.0114310.0114910.0115110.0115610.0115710.0116010.0116710.0118010.011RUN STATISTICS FOR INPUT FILE: input_2.fastq=============================================99 sequences processed in totalThe length threshold of paired-end sequences gets evaluated later on (in the validation step)Validate paired-end files input_1_trimmed.fq and input_2_trimmed.fqfile_1: input_1_trimmed.fq, file_2: input_2_trimmed.fq>>>>> Now validing the length of the 2 paired-end infiles: input_1_trimmed.fq and input_2_trimmed.fq <<<<
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diff --git a/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/tools.yml b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/tools.yml
new file mode 100644
index 000000000..8b3131b96
--- /dev/null
+++ b/reports/anvil-edge/tool-tests/edge-24-08-30-06-10-1/tools.yml
@@ -0,0 +1,129 @@
+chunk: 8
+tools:
+- name: collection_column_join
+ owner: iuc
+ revisions:
+ - 071084070619
+ - 58228a4d58fe
+ tool_panel_section_id: collection_operations
+ tool_panel_section_label: Collection Operations
+- name: deeptools_plot_coverage
+ owner: bgruening
+ revisions:
+ - 56bce3c82278
+ tool_panel_section_id: deeptools
+ tool_panel_section_label: deepTools
+- name: trim_galore
+ owner: bgruening
+ revisions:
+ - 084bbd8ba7b8
+ tool_panel_section_id: fasta_fastq
+ tool_panel_section_label: FASTA/FASTQ
+- name: minimap2
+ owner: iuc
+ revisions:
+ - f54f5baedfdd
+ tool_panel_section_id: mapping
+ tool_panel_section_label: Mapping
+- name: flye
+ owner: bgruening
+ revisions:
+ - 3ee0ef312022
+ tool_panel_section_id: nanopore
+ tool_panel_section_label: Nanopore
+- name: poretools_tabular
+ owner: iuc
+ revisions:
+ - 2cb2feb94f0e
+ tool_panel_section_id: nanopore
+ tool_panel_section_label: Nanopore
+- name: hisat2
+ owner: iuc
+ revisions:
+ - 26371a1df031
+ - f4af63aaf57a
+ tool_panel_section_id: rna_seq
+ tool_panel_section_label: RNA-seq
+- name: samtools_merge
+ owner: iuc
+ revisions:
+ - 740ce0a18f0d
+ - 36677f429310
+ tool_panel_section_id: sam_bam
+ tool_panel_section_label: SAM/BAM
+- name: bam_to_sam
+ owner: devteam
+ revisions:
+ - 88eedb4abea0
+ tool_panel_section_id: sam_bam
+ tool_panel_section_label: SAM/BAM
+- name: anndata_export
+ owner: iuc
+ revisions:
+ - 707023fa62fe
+ - 0cb889db0910
+ tool_panel_section_id: single_cell
+ tool_panel_section_label: Single-cell
+- name: alevin
+ owner: bgruening
+ revisions:
+ - 04b494623f8e
+ - e4c01dcece8b
+ tool_panel_section_id: single_cell
+ tool_panel_section_label: Single-cell
+- name: scanpy_plot
+ owner: iuc
+ revisions:
+ - aa0c474463c2
+ - a8f865950ac4
+ tool_panel_section_id: single_cell
+ tool_panel_section_label: Single-cell
+- name: scanpy_run_pca
+ owner: ebi-gxa
+ revisions:
+ - 988edd5fa902
+ - ce93e630b55a
+ tool_panel_section_id: single_cell
+ tool_panel_section_label: Single-cell
+- name: table_compute
+ owner: iuc
+ revisions:
+ - 60ff16842fcd
+ tool_panel_section_id: text_manipulation
+ tool_panel_section_label: Text Manipulation
+- name: lofreq_viterbi
+ owner: iuc
+ revisions:
+ - aa35ee7f3ab2
+ tool_panel_section_id: variant_calling
+ tool_panel_section_label: Variant Calling
+- name: bcftools_convert_to_vcf
+ owner: iuc
+ revisions:
+ - fec517907949
+ tool_panel_section_id: vcf_bcf
+ tool_panel_section_label: VCF/BCF
+- name: bcftools_plugin_fill_an_ac
+ owner: iuc
+ revisions:
+ - 582f8b13873d
+ tool_panel_section_id: vcf_bcf
+ tool_panel_section_label: VCF/BCF
+- name: vcfaddinfo
+ owner: devteam
+ revisions:
+ - 6ea73d6151ec
+ tool_panel_section_id: vcf_bcf
+ tool_panel_section_label: VCF/BCF
+- name: vcfleftalign
+ owner: devteam
+ revisions:
+ - 29f9b782727e
+ tool_panel_section_id: vcf_bcf
+ tool_panel_section_label: VCF/BCF
+- name: ivar_consensus
+ owner: iuc
+ revisions:
+ - 78bbd17d0703
+ tool_panel_section_id: virology
+ tool_panel_section_label: Virology