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Updating anvil-edge README for edge-24-11-07-18-17-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-11-07-18-17-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "7": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-07-18-17-1/results.html", | ||
| "date1": "Thu Nov 07 18:38:42 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-07-18-17-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-edge/tool-tests/edge-24-11-07-18-17-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| -t collection_element_identifiers --tool-version d3c07d270a50 | ||
| -t deeptools_plot_correlation --tool-version 32e451def88c | ||
| -t flash --tool-version a27654fc4270 | ||
| -t volcanoplot --tool-version 73b8cb5bddcd | ||
| -t medaka_variant --tool-version 43815fa60f3a | ||
| -t poretools_times --tool-version 960be5e0b47e | ||
| -t sailfish --tool-version a8f343909c17 | ||
| -t samtools_phase --tool-version b5c3b1856370 | ||
| -t samtools_phase --tool-version 1e5880498f52 | ||
| -t samtools_mpileup --tool-version fa7ad9b89f4a | ||
| -t anndata_import --tool-version 55e35e9203cf | ||
| -t anndata_import --tool-version fb9e030ffae4 | ||
| -t raceid_inspecttrajectory --tool-version c8434a623268 | ||
| -t raceid_inspecttrajectory --tool-version df8e4e54d367 | ||
| -t scanpy_normalize --tool-version ab55fe8030b6 | ||
| -t scanpy_scale_data --tool-version 9664a6c00fd1 | ||
| -t scanpy_scale_data --tool-version c6e52529260e | ||
| -t regex_find_replace --tool-version ae8c4b2488e7 | ||
| -t lofreq_call --tool-version e1461b5c52a0 | ||
| -t bcftools_plugin_fixploidy --tool-version 365325116147 | ||
| -t bcftools_stats --tool-version b17394940c7a | ||
| -t vcf2tsv --tool-version 285060661b45 | ||
| -t vcfhethom --tool-version 8254e0fe7358 | ||
| -t snpeff_sars_cov_2 --tool-version 2a3a00c1fa0a |
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45
reports/anvil-edge/tool-tests/edge-24-11-07-18-17-1/errors/1ea6250e6fea2ce1.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "1ea6250e6fea2ce1", | ||
| "history_id": "40a145e958faf34f", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-07T19:12:05.520365", | ||
| "update_time": "2024-11-07T19:12:15.930951", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-5frgn", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/136/registry.xml' '/galaxy/server/database/jobs_directory/000/136/upload_params.json' '173:/galaxy/server/database/objects/0/6/6/dataset_06627cc0-45b9-4450-b754-68ee2fad133b_files:/galaxy/server/database/objects/0/6/6/dataset_06627cc0-45b9-4450-b754-68ee2fad133b.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_yo45vnlf\"", | ||
| "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"out_traject_default.ltree.rdat\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ceinolmi\", \"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": "009ace85ba0aeea3", | ||
| "src": "hda", | ||
| "uuid": "06627cc0-45b9-4450-b754-68ee2fad133b" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-11-07-18-17-1/errors/2bb164a84f2454f1.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "2bb164a84f2454f1", | ||
| "history_id": "40a145e958faf34f", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-07T18:55:31.130341", | ||
| "update_time": "2024-11-07T18:55:40.763906", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-g5zx4", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/67/registry.xml' '/galaxy/server/database/jobs_directory/000/67/upload_params.json' '87:/galaxy/server/database/objects/3/2/b/dataset_32b65f7d-352a-43fb-b9fa-12b711604a46_files:/galaxy/server/database/objects/3/2/b/dataset_32b65f7d-352a-43fb-b9fa-12b711604a46.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_b615ux6c\"", | ||
| "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"samtools_phase_in_1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_53a504k7\", \"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": "255b2756c8449c15", | ||
| "src": "hda", | ||
| "uuid": "32b65f7d-352a-43fb-b9fa-12b711604a46" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
48 changes: 48 additions & 0 deletions
48
reports/anvil-edge/tool-tests/edge-24-11-07-18-17-1/errors/2f52f6789084f826.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "2f52f6789084f826", | ||
| "history_id": "40a145e958faf34f", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_import/anndata_import/0.7.5+galaxy1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-07T19:03:20.649527", | ||
| "update_time": "2024-11-07T19:03:27.447184", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-lw4j4", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "mkdir mtx && cat '/galaxy/server/database/jobs_directory/000/102/configs/tmptmsuzap8' && python '/galaxy/server/database/jobs_directory/000/102/configs/tmptmsuzap8' && rm -rf mtx", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "hd5_format": "{\"__current_case__\": 0, \"filetype\": \"anndata\", \"in\": {\"__current_case__\": 3, \"adata_format\": \"mtx\", \"matrix\": {\"values\": [{\"id\": 133, \"src\": \"hda\"}]}, \"tenx\": {\"__current_case__\": 0, \"use\": \"no\"}}}" | ||
| }, | ||
| "inputs": { | ||
| "hd5_format|in|matrix": { | ||
| "id": "ed9025dafefe7577", | ||
| "src": "hda", | ||
| "uuid": "0a875b08-be30-44a4-8d19-1616214c584d" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "anndata": { | ||
| "id": "1d9ddd4537023882", | ||
| "src": "hda", | ||
| "uuid": "4aa477ae-001a-468a-8e86-304806254416" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_mtx(filename='/galaxy/server/database/objects/0/a/8/dataset_0a875b08-be30-44a4-8d19-1616214c584d.dat')\n\nadata.write('anndata.h5ad')\n", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "\n\nimport anndata as ad\n \n \nadata = ad.read_mtx(filename='/galaxy/server/database/objects/0/a/8/dataset_0a875b08-be30-44a4-8d19-1616214c584d.dat')\n\nadata.write('anndata.h5ad')\n", | ||
| "stderr": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-11-07-18-17-1/errors/33645feefa028b7a.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "33645feefa028b7a", | ||
| "history_id": "40a145e958faf34f", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-07T18:56:46.642178", | ||
| "update_time": "2024-11-07T18:56:57.279395", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-dx2z2", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/72/registry.xml' '/galaxy/server/database/jobs_directory/000/72/upload_params.json' '98:/galaxy/server/database/objects/6/e/4/dataset_6e48fb82-35d0-4b8c-a3b7-a4b01f4f942c_files:/galaxy/server/database/objects/6/e/4/dataset_6e48fb82-35d0-4b8c-a3b7-a4b01f4f942c.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_6gbkj4od\"", | ||
| "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"samtools_phase_in_1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_d2ql595o\", \"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": "a50c4d3ea920bac3", | ||
| "src": "hda", | ||
| "uuid": "6e48fb82-35d0-4b8c-a3b7-a4b01f4f942c" | ||
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| "copied_from_job_id": null, | ||
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| "stdout": "", | ||
| "stderr": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-11-07-18-17-1/errors/33766d3d29d6d11c.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "33766d3d29d6d11c", | ||
| "history_id": "40a145e958faf34f", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-07T19:23:18.535752", | ||
| "update_time": "2024-11-07T19:23:28.474255", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-vmttv", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/177/registry.xml' '/galaxy/server/database/jobs_directory/000/177/upload_params.json' '227:/galaxy/server/database/objects/5/d/d/dataset_5dd3f78c-c0b4-4ab0-9d6b-89d92a78c973_files:/galaxy/server/database/objects/5/d/d/dataset_5dd3f78c-c0b4-4ab0-9d6b-89d92a78c973.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_pr3b0fgr\"", | ||
| "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"stats.b.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_o4tvfqly\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"vcf\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "6bcd8dad0aed527b", | ||
| "src": "hda", | ||
| "uuid": "5dd3f78c-c0b4-4ab0-9d6b-89d92a78c973" | ||
| } | ||
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| "copied_from_job_id": null, | ||
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| "stdout": "", | ||
| "stderr": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
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| } |
70 changes: 70 additions & 0 deletions
70
reports/anvil-edge/tool-tests/edge-24-11-07-18-17-1/errors/360a8fe4469d8711.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "360a8fe4469d8711", | ||
| "history_id": "40a145e958faf34f", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/medaka_variant/1.7.2+galaxy1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-07T18:48:54.905027", | ||
| "update_time": "2024-11-07T18:49:05.459520", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-h9p4m", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "gunzip -c '/galaxy/server/database/objects/a/2/5/dataset_a2580d4b-3912-494d-b5bb-45bb2c2c1cdd.dat' > reference.fa && medaka variant --debug --ambig_ref reference.fa '/galaxy/server/database/objects/6/0/6/dataset_606dcc14-c7b1-4eec-afd8-c4c77e216209.dat' raw.vcf 2>&1 | tee '/galaxy/server/database/objects/2/5/3/dataset_25391a94-99ca-4bd0-8577-e2d15d28d8dd.dat' && ln -s '/galaxy/server/database/objects/0/0/9/dataset_00992ed8-fb0a-41e2-8fbd-e9b1a3b883d2.dat' in.bam && ln -s '/galaxy/server/database/objects/_metadata_files/e/5/c/metadata_e5c3412e-bd19-45e9-8af2-fb41f454a965.dat' in.bai && medaka tools annotate --dpsp --pad 25 raw.vcf reference.fa in.bam tmp.vcf && python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/medaka_variant/eb746fa6f514/medaka_variant/convert_VCF_info_fields.py' tmp.vcf '/galaxy/server/database/objects/e/1/c/dataset_e1cde41f-c1d6-4c7e-86cf-2452ccf70b15.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "output_log_bool": "true", | ||
| "output_annotated": "{\"__current_case__\": 0, \"in_bam\": {\"values\": [{\"id\": 54, \"src\": \"hda\"}]}, \"output_annotated_select\": \"true\", \"pad\": \"25\"}", | ||
| "gvcf": "false", | ||
| "ambig_ref": "true", | ||
| "verbose": "false", | ||
| "regions": "\"\"", | ||
| "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 53, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}", | ||
| "pool": "{\"__current_case__\": 1, \"input\": {\"values\": [{\"id\": 52, \"src\": \"hda\"}]}, \"pool_mode\": \"No\"}" | ||
| }, | ||
| "inputs": { | ||
| "pool|input": { | ||
| "id": "348d952fc993e7b6", | ||
| "src": "hda", | ||
| "uuid": "606dcc14-c7b1-4eec-afd8-c4c77e216209" | ||
| }, | ||
| "reference_source|ref_file": { | ||
| "id": "d091a872f90283ac", | ||
| "src": "hda", | ||
| "uuid": "a2580d4b-3912-494d-b5bb-45bb2c2c1cdd" | ||
| }, | ||
| "output_annotated|in_bam": { | ||
| "id": "92a51a42c254f4fa", | ||
| "src": "hda", | ||
| "uuid": "00992ed8-fb0a-41e2-8fbd-e9b1a3b883d2" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "out_variants": { | ||
| "id": "9a7c6b5f53391a2d", | ||
| "src": "hda", | ||
| "uuid": "e1cde41f-c1d6-4c7e-86cf-2452ccf70b15" | ||
| }, | ||
| "out_log": { | ||
| "id": "82f9831b95b2c34f", | ||
| "src": "hda", | ||
| "uuid": "25391a94-99ca-4bd0-8577-e2d15d28d8dd" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "[18:48:59 - DataStre] Loaded sample register.\n[18:48:59 - DataIndx] Loaded 1/1 (100.00%) sample files.\n[18:48:59 - Variants] Label decoding is:\n0: ('*',)\n1: ('A',)\n2: ('C',)\n3: ('G',)\n4: ('T',)\n[18:48:59 - Variants] Processing NC_045512.2:0-.\n", | ||
| "tool_stderr": "[18:49:01 - Annotate] Getting chrom coordinates\n[18:49:01 - Annotate] Processing chunk with coordinates: NC_045512.2:44-1813\n[18:49:01 - BAMFile] Creating pool of 16 BAM file sets.\n", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "[18:48:59 - DataStre] Loaded sample register.\n[18:48:59 - DataIndx] Loaded 1/1 (100.00%) sample files.\n[18:48:59 - Variants] Label decoding is:\n0: ('*',)\n1: ('A',)\n2: ('C',)\n3: ('G',)\n4: ('T',)\n[18:48:59 - Variants] Processing NC_045512.2:0-.\n", | ||
| "stderr": "[18:49:01 - Annotate] Getting chrom coordinates\n[18:49:01 - Annotate] Processing chunk with coordinates: NC_045512.2:44-1813\n[18:49:01 - BAMFile] Creating pool of 16 BAM file sets.\n", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
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