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Updating anvil-production README for prod-25-01-15-12-34-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "5": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/results.html", | ||
| "date1": "Wed Jan 15 12:51:33 2025", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| -t collection_column_join --tool-version 071084070619 | ||
| -t jq --tool-version 5ff75eb1a893 | ||
| -t fastq_paired_end_interlacer --tool-version 2ccb8dcabddc | ||
| -t sam2interval --tool-version 75557c0908a9 | ||
| -t samtools_flagstat --tool-version 22970df7a40e | ||
| -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 medaka_variant_pipeline --tool-version 336b3def9b2b | ||
| -t poretools_qualdist --tool-version ae9060e764b5 | ||
| -t deeptools_plot_coverage --tool-version 56bce3c82278 | ||
| -t miniasm --tool-version 8dee0218ac7d | ||
| -t ivar_consensus --tool-version 78bbd17d0703 | ||
| -t pygenometracks --tool-version 2824d77cd8f8 |
44 changes: 44 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/errors/057d493e2a2600cc.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "057d493e2a2600cc", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2025-01-15T12:52:48.451541", | ||
| "create_time": "2025-01-15T12:52:07.123940", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "de475d512a0622c4", | ||
| "external_id": "gxy-rgksr", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/2/registry.xml' '/galaxy/server/database/jobs_directory/000/2/upload_params.json' '2:/galaxy/server/database/objects/4/0/a/dataset_40a83d01-eed6-49d0-8c51-335a3325354d_files:/galaxy/server/database/objects/4/0/a/dataset_40a83d01-eed6-49d0-8c51-335a3325354d.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_wdwfvt8e\"", | ||
| "files_metadata": "{\"__current_case__\": 311, \"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_deedwsg9\", \"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": "057d493e2a2600cc", | ||
| "src": "hda", | ||
| "uuid": "40a83d01-eed6-49d0-8c51-335a3325354d" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
53 changes: 53 additions & 0 deletions
53
reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/errors/1ec3d2511a0b9c07.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "1ec3d2511a0b9c07", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2025-01-15T13:05:33.493460", | ||
| "create_time": "2025-01-15T13:05:26.682819", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc3+galaxy0", | ||
| "history_id": "de475d512a0622c4", | ||
| "external_id": "gxy-fphvj", | ||
| "command_line": "ln -s '/galaxy/server/database/objects/8/e/a/dataset_8ea658fe-2d0e-461e-980f-115f45ab5b79.dat' 'localref.fa' && vcfleftalign -r 'localref.fa' -w \"150\" '/galaxy/server/database/objects/e/2/b/dataset_e2bb6b0d-2332-4fd4-9635-1ea5dd92fb1b.dat' > '/galaxy/server/database/objects/c/b/a/dataset_cbae0e55-ca22-4209-b7d4-3cc2dbd182c2.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"vcf\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "window_size": "\"150\"", | ||
| "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 71, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}" | ||
| }, | ||
| "inputs": { | ||
| "input_vcf": { | ||
| "id": "114e5fe9521d3047", | ||
| "src": "hda", | ||
| "uuid": "e2bb6b0d-2332-4fd4-9635-1ea5dd92fb1b" | ||
| }, | ||
| "reference_source|ref_file": { | ||
| "id": "b2c59ee5abc2dfd7", | ||
| "src": "hda", | ||
| "uuid": "8ea658fe-2d0e-461e-980f-115f45ab5b79" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "out_file1": { | ||
| "id": "83551b7b4d55cdaa", | ||
| "src": "hda", | ||
| "uuid": "cbae0e55-ca22-4209-b7d4-3cc2dbd182c2" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
44 changes: 44 additions & 0 deletions
44
reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/errors/49a621472be95af6.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "49a621472be95af6", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2025-01-15T13:02:48.570350", | ||
| "create_time": "2025-01-15T13:02:37.917680", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "de475d512a0622c4", | ||
| "external_id": "gxy-msdcm", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/51/registry.xml' '/galaxy/server/database/jobs_directory/000/51/upload_params.json' '56:/galaxy/server/database/objects/7/8/6/dataset_786b6b23-d341-4673-9282-f4ef0ca2217e_files:/galaxy/server/database/objects/7/8/6/dataset_786b6b23-d341-4673-9282-f4ef0ca2217e.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_06jo05tv\"", | ||
| "files_metadata": "{\"__current_case__\": 311, \"file_type\": \"tabular\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"convert.hls.gt.hap\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_rhv0k4vn\", \"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": "9c99cc871e568a73", | ||
| "src": "hda", | ||
| "uuid": "786b6b23-d341-4673-9282-f4ef0ca2217e" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
44 changes: 44 additions & 0 deletions
44
reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/errors/49b6c66709c788b8.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "49b6c66709c788b8", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2025-01-15T13:09:53.207132", | ||
| "create_time": "2025-01-15T13:09:42.496677", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "de475d512a0622c4", | ||
| "external_id": "gxy-pnqkk", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/80/registry.xml' '/galaxy/server/database/jobs_directory/000/80/upload_params.json' '88:/galaxy/server/database/objects/1/4/f/dataset_14f19b65-4c78-4359-bfb2-62ffc31dfe92_files:/galaxy/server/database/objects/1/4/f/dataset_14f19b65-4c78-4359-bfb2-62ffc31dfe92.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_tqd6bggb\"", | ||
| "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"mini_reads.fq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_1ombulrs\", \"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": "e249fcc451c1aaaf", | ||
| "src": "hda", | ||
| "uuid": "14f19b65-4c78-4359-bfb2-62ffc31dfe92" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
44 changes: 44 additions & 0 deletions
44
reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/errors/79dae5742d66f142.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "79dae5742d66f142", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2025-01-15T13:00:28.862129", | ||
| "create_time": "2025-01-15T13:00:18.795044", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "de475d512a0622c4", | ||
| "external_id": "gxy-cs58w", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/40/registry.xml' '/galaxy/server/database/jobs_directory/000/40/upload_params.json' '45:/galaxy/server/database/objects/a/3/c/dataset_a3c92a73-c81b-40bc-8a63-e7ca44db4037_files:/galaxy/server/database/objects/a/3/c/dataset_a3c92a73-c81b-40bc-8a63-e7ca44db4037.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_arg8mvl6\"", | ||
| "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"samtools_flagstat_input1.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_yonj1743\", \"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": "314e2bff28dab941", | ||
| "src": "hda", | ||
| "uuid": "a3c92a73-c81b-40bc-8a63-e7ca44db4037" | ||
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| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
57 changes: 57 additions & 0 deletions
57
reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/errors/89f8e19bff24461e.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "89f8e19bff24461e", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2025-01-15T12:58:41.490452", | ||
| "create_time": "2025-01-15T12:58:36.322791", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1+galaxy0", | ||
| "history_id": "de475d512a0622c4", | ||
| "external_id": "gxy-wnt4g", | ||
| "command_line": "gx-fastq-paired-end-interlacer '/galaxy/server/database/objects/d/2/7/dataset_d27d14dc-c0d1-44a5-8a6f-8ba85f05e99b.dat' sanger '/galaxy/server/database/objects/0/0/0/dataset_00012152-7eaf-4c30-af4d-dd1fa9b3cc99.dat' sanger '/galaxy/server/database/objects/8/a/7/dataset_8a71321e-7259-4aa9-a946-22b5b84f7400.dat' '/galaxy/server/database/objects/1/5/e/dataset_15eaa3e5-9d9a-493b-883a-4845e3b9000f.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"fastqsanger\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "reads": "{\"__current_case__\": 1, \"reads_coll\": {\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}, \"reads_selector\": \"paired_collection\"}" | ||
| }, | ||
| "inputs": { | ||
| "reads|reads_coll1": { | ||
| "id": "cf7b255f74eddf47", | ||
| "src": "hda", | ||
| "uuid": "d27d14dc-c0d1-44a5-8a6f-8ba85f05e99b" | ||
| }, | ||
| "reads|reads_coll2": { | ||
| "id": "48babf3967a0ecd1", | ||
| "src": "hda", | ||
| "uuid": "00012152-7eaf-4c30-af4d-dd1fa9b3cc99" | ||
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| }, | ||
| "outputs": { | ||
| "outfile_pairs_from_coll": { | ||
| "id": "aab10c0a1d896caa", | ||
| "src": "hda", | ||
| "uuid": "8a71321e-7259-4aa9-a946-22b5b84f7400" | ||
| }, | ||
| "outfile_singles_from_coll": { | ||
| "id": "2fd77ff4e499e4a6", | ||
| "src": "hda", | ||
| "uuid": "15eaa3e5-9d9a-493b-883a-4845e3b9000f" | ||
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| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
44 changes: 44 additions & 0 deletions
44
reports/anvil-production/tool-tests/prod-25-01-15-12-34-1/errors/9f9077b56b931bcf.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "9f9077b56b931bcf", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2025-01-15T12:54:19.783616", | ||
| "create_time": "2025-01-15T12:54:08.058341", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "de475d512a0622c4", | ||
| "external_id": "gxy-7hpf2", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/9/registry.xml' '/galaxy/server/database/jobs_directory/000/9/upload_params.json' '9:/galaxy/server/database/objects/e/1/1/dataset_e111a26f-bf84-44f8-947b-e1ef8983e202_files:/galaxy/server/database/objects/e/1/1/dataset_e111a26f-bf84-44f8-947b-e1ef8983e202.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_o2c0ssly\"", | ||
| "files_metadata": "{\"__current_case__\": 311, \"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_jl6a86x1\", \"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": "9f9077b56b931bcf", | ||
| "src": "hda", | ||
| "uuid": "e111a26f-bf84-44f8-947b-e1ef8983e202" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
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