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Updating anvil-edge README for edge-24-09-12-18-17-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/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-24-09-12-18-17-1/results.html", | ||
| "date1": "Thu Sep 12 18:33:11 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/tools.yml" | ||
| } | ||
| } |
24 changes: 24 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/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 |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/168c5019d723e181.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "168c5019d723e181", | ||
| "history_id": "7dbaf9c5b5117ca4", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-12T18:54:22.925011", | ||
| "update_time": "2024-09-12T18:54:34.894706", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-mrl6v", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/75/registry.xml' '/galaxy/server/database/jobs_directory/000/75/upload_params.json' '115:/galaxy/server/database/objects/b/a/9/dataset_ba944c94-4c23-4cb2-b583-438bad477192_files:/galaxy/server/database/objects/b/a/9/dataset_ba944c94-4c23-4cb2-b583-438bad477192.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_f53d6ek4\"", | ||
| "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"mpileup.1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_vnsldwr3\", \"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": "f489600111a88594", | ||
| "src": "hda", | ||
| "uuid": "ba944c94-4c23-4cb2-b583-438bad477192" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
59 changes: 59 additions & 0 deletions
59
reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/2ad1970214efc1f1.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "2ad1970214efc1f1", | ||
| "history_id": "7dbaf9c5b5117ca4", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/raceid_inspecttrajectory/0.2.3+galaxy3", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-12T19:10:15.173436", | ||
| "update_time": "2024-09-12T19:10:35.166467", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-g74vv", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/raceid_inspecttrajectory/a6821f856a1e/raceid_inspecttrajectory/scripts/trajectoryinspect.R' '/galaxy/server/database/jobs_directory/000/134/configs/tmphxv6x5b_' 2> '/galaxy/server/database/objects/7/3/4/dataset_7349095f-5024-4676-bbc7-54bd70cc2b2d.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "trjfid": "{\"basic\": {\"__current_case__\": 1, \"cellsfromz\": \"3,9,2\", \"doit\": \"yes\", \"som\": {\"__current_case__\": 1, \"doit\": \"yes\", \"title\": \"Title\", \"use\": {\"__current_case__\": 0, \"def\": \"yes\"}, \"use_genes\": {\"__current_case__\": 0, \"typer\": \"genelist\", \"use_genes\": \"Clca4,Mki67,Defa24,Ybx1,Vasp,Apoa1\"}, \"use_types\": \"\\\\\\\\_\\\\\\\\d+\"}, \"use\": {\"__current_case__\": 1, \"def\": \"no\", \"filterset_minexpr\": \"1\", \"filterset_minnumber\": \"2\", \"getsom_alpha\": \"0.5\", \"getsom_nb\": \"1000\", \"plotheat_xgrid\": false, \"plotheat_xlab\": false, \"plotheat_ygrid\": true, \"procsom_corthr\": \"0.5\", \"procsom_minsom\": \"5\"}}}", | ||
| "trjsid": "{\"basic\": {\"__current_case__\": 1, \"br\": \"6,5,3\", \"doit\": \"yes\", \"i\": \"5\", \"use\": {\"__current_case__\": 1, \"def\": \"no\", \"ndiffgenes\": \"14\", \"zscore\": true}}}" | ||
| }, | ||
| "inputs": { | ||
| "inputrds": { | ||
| "id": "81d018ec229ef1c2", | ||
| "src": "hda", | ||
| "uuid": "fe43bdf3-5177-45e3-9926-e17393153f0b" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "outpdf": { | ||
| "id": "663a32c8d74e11b0", | ||
| "src": "hda", | ||
| "uuid": "d54ab71e-75c6-46ee-8649-ecf57d24cf03" | ||
| }, | ||
| "outdiffgenes": { | ||
| "id": "64f324641a66e464", | ||
| "src": "hda", | ||
| "uuid": "22218adb-5292-411f-b25d-e7fc28bfa5fc" | ||
| }, | ||
| "outlog": { | ||
| "id": "731a0f6c2e09e1b3", | ||
| "src": "hda", | ||
| "uuid": "7349095f-5024-4676-bbc7-54bd70cc2b2d" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "NULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\nNULL\nNULL\nNULL\nnull device \n 1 \n", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "NULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\n[1] 1\nNULL\nNULL\nNULL\nNULL\nnull device \n 1 \n", | ||
| "stderr": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
57 changes: 57 additions & 0 deletions
57
reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/3c9b9a9b19ed1b5d.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "3c9b9a9b19ed1b5d", | ||
| "history_id": "7dbaf9c5b5117ca4", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy2", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-12T19:20:00.208909", | ||
| "update_time": "2024-09-12T19:20:14.171223", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-96x7v", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "ln -s '/galaxy/server/database/objects/2/e/f/dataset_2efde3d5-4472-4a87-8ac7-b7632b2f7ae8.dat' reference.fa && lofreq faidx reference.fa 2>&1 || echo \"Error running samtools faidx for indexing fasta reference for lofreq\" >&2 && ln -s '/galaxy/server/database/objects/b/2/4/dataset_b24dbd0f-6326-451b-8e67-3caac826cba8.dat' reads.bam && ln -s -f '/galaxy/server/database/objects/_metadata_files/0/f/6/metadata_0f6bc320-32d1-42ce-8213-fe7581a6f465.dat' reads.bam.bai && lofreq call-parallel --pp-threads ${GALAXY_SLOTS:-1} --verbose --ref 'reference.fa' --out variants.vcf --sig 0.01 --bonf dynamic reads.bam 2>&1 || (tool_exit_code=$? && cat \"$TMPDIR/lofreq2_call_parallel*/*.log\" 1>&2 && exit $tool_exit_code) && echo set_lofreq_standard", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "filter_control": "{\"__current_case__\": 2, \"bonf\": \"dynamic\", \"filter_type\": \"set_lofreq_standard\", \"others\": \"\", \"sig\": \"0.01\"}", | ||
| "call_control": "{\"__current_case__\": 0, \"set_call_options\": \"no\"}", | ||
| "variant_types": "\"\"", | ||
| "regions": "{\"__current_case__\": 0, \"restrict_to_region\": \"genome\"}", | ||
| "reference_source": "{\"__current_case__\": 1, \"ref\": {\"values\": [{\"id\": 218, \"src\": \"hda\"}]}, \"ref_selector\": \"history\"}" | ||
| }, | ||
| "inputs": { | ||
| "reference_source|ref": { | ||
| "id": "7299715a3323e0c8", | ||
| "src": "hda", | ||
| "uuid": "2efde3d5-4472-4a87-8ac7-b7632b2f7ae8" | ||
| }, | ||
| "reads": { | ||
| "id": "097c9c86ae789649", | ||
| "src": "hda", | ||
| "uuid": "b24dbd0f-6326-451b-8e67-3caac826cba8" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "variants": { | ||
| "id": "cebde5ad27a14bc1", | ||
| "src": "hda", | ||
| "uuid": "8e2a573c-380f-45b3-bd7e-39628de603c4" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "INFO [2024-09-12 19:20:07,645]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 19:20:07,656]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:20:09,439]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/159/tmp/lofreq2_call_parallel3do47ktx/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "INFO [2024-09-12 19:20:07,645]: Using 2 threads with following basic args: lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic reads.bam\n\nINFO [2024-09-12 19:20:07,656]: Adding 5 commands to mp-pool\nNumber of substitution tests performed: 66\nNumber of indel tests performed: 0\nINFO [2024-09-12 19:20:09,439]: Executing lofreq filter -i /galaxy/server/database/jobs_directory/000/159/tmp/lofreq2_call_parallel3do47ktx/concat.vcf.gz -o variants.vcf --snvqual-thresh 38 --indelqual-thresh 20\n\nset_lofreq_standard\n", | ||
| "stderr": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/6bc47c51ca0fac40.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "6bc47c51ca0fac40", | ||
| "history_id": "7dbaf9c5b5117ca4", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-12T18:40:26.813204", | ||
| "update_time": "2024-09-12T18:40:39.694520", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-dh55v", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/24/registry.xml' '/galaxy/server/database/jobs_directory/000/24/upload_params.json' '46:/galaxy/server/database/objects/4/1/9/dataset_419b779c-07f0-4435-bf5c-7904f2ad0a3a_files:/galaxy/server/database/objects/4/1/9/dataset_419b779c-07f0-4435-bf5c-7904f2ad0a3a.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_ctqvtdoj\"", | ||
| "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"input.tab\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_m58m3k0v\", \"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": "47d8f1eb9c871c1f", | ||
| "src": "hda", | ||
| "uuid": "419b779c-07f0-4435-bf5c-7904f2ad0a3a" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
55 changes: 55 additions & 0 deletions
55
reports/anvil-edge/tool-tests/edge-24-09-12-18-17-1/errors/73e4ef2f2e01965c.json
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Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "73e4ef2f2e01965c", | ||
| "history_id": "7dbaf9c5b5117ca4", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bcftools_stats/bcftools_stats/1.15.1+galaxy4", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-09-12T19:26:40.846878", | ||
| "update_time": "2024-09-12T19:26:45.740636", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-kkhjl", | ||
| "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/8/4/3/dataset_8435d287-38fb-4227-8d9f-8d005c03e930.dat' > input0.vcf.gz && bcftools index input0.vcf.gz && echo 'input0.vcf.gz' >> vcfs_list && bgzip -c '/galaxy/server/database/objects/0/e/8/dataset_0e87e6a5-9e28-4f76-9090-0931695f266f.dat' > input1.vcf.gz && bcftools index input1.vcf.gz && echo 'input1.vcf.gz' >> vcfs_list && bcftools stats --regions-overlap 1 input0.vcf.gz input1.vcf.gz > '/galaxy/server/database/objects/2/3/c/dataset_23c6ce8b-ff0e-4dce-bc53-28f0d930e12c.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "plot_title": "\"\"", | ||
| "sec_default": "{\"af_tag\": \"\", \"afbins\": {\"__current_case__\": 0, \"afbins_select\": \"default\"}, \"depth\": {\"__current_case__\": 0, \"set_depth\": \"no\"}, \"exons_file\": null, \"first_allele_only\": false, \"reference_source\": {\"__current_case__\": 0, \"reference_source_selector\": \"\"}, \"split_by_ID\": false, \"user_tstv\": \"\", \"verbose\": false}", | ||
| "sec_restrict": "{\"apply_filters\": \"\", \"collapse\": null, \"exclude\": null, \"include\": null, \"invert_samples\": false, \"invert_samples_file\": false, \"regions\": {\"__current_case__\": 0, \"regions_src\": \"__none__\"}, \"regions_overlap\": \"1\", \"samples\": \"\", \"samples_file\": null, \"targets\": {\"__current_case__\": 0, \"targets_src\": \"__none__\"}, \"targets_overlap\": null}" | ||
| }, | ||
| "inputs": { | ||
| "input_file": { | ||
| "id": "1df47cc768d658ae", | ||
| "src": "hda", | ||
| "uuid": "8435d287-38fb-4227-8d9f-8d005c03e930" | ||
| }, | ||
| "inputB_file": { | ||
| "id": "36650d18141ad1f9", | ||
| "src": "hda", | ||
| "uuid": "0e87e6a5-9e28-4f76-9090-0931695f266f" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output_file": { | ||
| "id": "f40a8c5d0662968d", | ||
| "src": "hda", | ||
| "uuid": "23c6ce8b-ff0e-4dce-bc53-28f0d930e12c" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
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