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Updating anvil-production README for prod-24-09-12-00-32-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-24-09-12-00-32-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "6": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-12-00-32-1/results.html", | ||
| "date1": "Thu Sep 12 00:49:13 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-12-00-32-1/tools.yml" | ||
| } | ||
| } |
15 changes: 15 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-24-09-12-00-32-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| -t filter_tabular --tool-version 6544e4b87a4f | ||
| -t gff3_rebase --tool-version 238981ed43b7 | ||
| -t flash --tool-version a27654fc4270 | ||
| -t qualimap_multi_bamqc --tool-version e38af83df163 | ||
| -t samtools_sort --tool-version e613c1ad4c4c | ||
| -t bcftools_norm --tool-version c077f71d351f | ||
| -t bcftools_plugin_fill_tags --tool-version bf7d6acd9884 | ||
| -t vcfallelicprimitives --tool-version 57a16b310fe8 | ||
| -t vcfprimers --tool-version 17096387c0e6 | ||
| -t medaka_consensus --tool-version db25ec99c3ea | ||
| -t poretools_nucdist --tool-version a57b6350fd5d | ||
| -t deeptools_plot_enrichment --tool-version e65d16fb2724 | ||
| -t racon --tool-version a199cd7ac344 | ||
| -t ivar_filtervariants --tool-version 7fe36019c073 | ||
| -t circos --tool-version df7356989ac1 |
44 changes: 44 additions & 0 deletions
44
reports/anvil-production/tool-tests/prod-24-09-12-00-32-1/errors/62deecfda358412d.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "62deecfda358412d", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-12T01:03:54.089497", | ||
| "create_time": "2024-09-12T01:03:45.562654", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "a29501d373e152f6", | ||
| "external_id": "gxy-pww6n", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/76/registry.xml' '/galaxy/server/database/jobs_directory/000/76/upload_params.json' '101:/galaxy/server/database/objects/5/7/0/dataset_5709eb8c-7899-419c-9fd9-89eca762af5f_files:/galaxy/server/database/objects/5/7/0/dataset_5709eb8c-7899-419c-9fd9-89eca762af5f.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_eshi9zza\"", | ||
| "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"alignment.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_hennoahl\", \"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": "c497ec2541264b8e", | ||
| "src": "hda", | ||
| "uuid": "5709eb8c-7899-419c-9fd9-89eca762af5f" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
46 changes: 46 additions & 0 deletions
46
reports/anvil-production/tool-tests/prod-24-09-12-00-32-1/errors/ad5395f0e2462a13.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "ad5395f0e2462a13", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-12T01:06:06.875801", | ||
| "create_time": "2024-09-12T01:06:01.344967", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/poretools_nucdist/poretools_nucdist/0.6.1a1.0", | ||
| "history_id": "a29501d373e152f6", | ||
| "external_id": "gxy-bzcd9", | ||
| "command_line": "poretools nucdist '/galaxy/server/database/objects/f/1/6/dataset_f1662c2d-8f4d-4a60-b426-8dfc1ecd4103.dat' > '/galaxy/server/database/objects/a/0/8/dataset_a08756c0-b8fd-4bfd-bc14-8eab2010ef39.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"fast5.tar\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"" | ||
| }, | ||
| "inputs": { | ||
| "input": { | ||
| "id": "0a5dddba80bcae8d", | ||
| "src": "hda", | ||
| "uuid": "f1662c2d-8f4d-4a60-b426-8dfc1ecd4103" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output": { | ||
| "id": "b9766c73044a1d93", | ||
| "src": "hda", | ||
| "uuid": "a08756c0-b8fd-4bfd-bc14-8eab2010ef39" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
47 changes: 47 additions & 0 deletions
47
reports/anvil-production/tool-tests/prod-24-09-12-00-32-1/errors/b856dbbe142dc81f.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "b856dbbe142dc81f", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-12T00:56:29.646355", | ||
| "create_time": "2024-09-12T00:56:24.278949", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.3", | ||
| "history_id": "a29501d373e152f6", | ||
| "external_id": "gxy-rj6xn", | ||
| "command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && addmemory=${GALAXY_MEMORY_MB_PER_SLOT:-768} && ((addmemory=addmemory*75/100)) && samtools sort -@ $addthreads -m $addmemory\"M\" -n -O bam -T sorttmp '/galaxy/server/database/objects/1/1/8/dataset_1180fe71-52eb-4cad-945a-8f29fb31009c.dat' > '/galaxy/server/database/objects/3/a/4/dataset_3a407b1d-2df1-4c19-bf80-c67b47b68b6b.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "prim_key_cond": "{\"__current_case__\": 1, \"prim_key_select\": \"-n\"}" | ||
| }, | ||
| "inputs": { | ||
| "input1": { | ||
| "id": "4b52f109fd891312", | ||
| "src": "hda", | ||
| "uuid": "1180fe71-52eb-4cad-945a-8f29fb31009c" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output1": { | ||
| "id": "7cdc6ac81113b012", | ||
| "src": "hda", | ||
| "uuid": "3a407b1d-2df1-4c19-bf80-c67b47b68b6b" | ||
| } | ||
| }, | ||
| "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-24-09-12-00-32-1/errors/e6072946cad327cd.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "e6072946cad327cd", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-09-12T01:07:49.083457", | ||
| "create_time": "2024-09-12T01:07:39.924410", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "a29501d373e152f6", | ||
| "external_id": "gxy-bvjtp", | ||
| "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' '118:/galaxy/server/database/objects/d/c/7/dataset_dc73f06b-593a-4ad7-8348-a54c1ee7c805_files:/galaxy/server/database/objects/d/c/7/dataset_dc73f06b-593a-4ad7-8348-a54c1ee7c805.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_n46e8qur\"", | ||
| "files_metadata": "{\"__current_case__\": 122, \"file_type\": \"interval\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"sample_overlaps.paf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_s78skdyd\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"interval\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "0301fe1a00fbb883", | ||
| "src": "hda", | ||
| "uuid": "dc73f06b-593a-4ad7-8348-a54c1ee7c805" | ||
| } | ||
| }, | ||
| "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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