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Updating anvil-edge README for edge-24-11-12-18-17-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "3": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/results.html", | ||
| "date1": "Tue Nov 12 18:33:46 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| -t racon --tool-version a199cd7ac344 | ||
| -t deeptools_compute_gc_bias --tool-version 2bc10a9ca58b | ||
| -t fastq_manipulation --tool-version 5b87038565bb | ||
| -t ncbi_acc_download --tool-version 1c58de56d587 | ||
| -t mummer_show_coords --tool-version 959c1f8dae95 | ||
| -t poretools_squiggle --tool-version 34553d0caa5e | ||
| -t kallisto_quant --tool-version 60f888039fb2 | ||
| -t bamtools --tool-version 4d343c1f606b | ||
| -t samtools_idxstats --tool-version 7a6034296ae9 | ||
| -t samtools_idxstats --tool-version 7def34e6cf4d | ||
| -t music_inspect_eset --tool-version 2fed32b5aa02 | ||
| -t music_inspect_eset --tool-version 7705cc75ac18 | ||
| -t raceid_inspectclusters --tool-version 2b0d3e2f402a | ||
| -t raceid_inspectclusters --tool-version 41f34e925bd5 | ||
| -t scater_plot_pca --tool-version 46fc6751d746 | ||
| -t scater_plot_pca --tool-version c99ba278dfa9 | ||
| -t scanpy_filter_cells --tool-version 4c42e5d8cb7c | ||
| -t scanpy_filter_cells --tool-version ba64b91ed2b9 | ||
| -t column_maker --tool-version 02026300aa45 | ||
| -t column_order_header_sort --tool-version 6ae9724caf4d | ||
| -t sniffles --tool-version 93c4b04a0769 | ||
| -t bcftools_concat --tool-version d40d4bf05718 | ||
| -t bcftools_annotate --tool-version 403553ae19f6 | ||
| -t vcffixup --tool-version 11f62f071125 | ||
| -t vcftools_annotate --tool-version 57a6550df582 |
99 changes: 99 additions & 0 deletions
99
reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/029e02c70d71eef6.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "029e02c70d71eef6", | ||
| "history_id": "aff48f2f86cebb71", | ||
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| "update_time": "2024-11-12T18:51:04.046592", | ||
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| "external_id": "gxy-swbm2", | ||
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| "command_line": "echo 'CP011064,CP0XXXXX,CP021680' | sed -r 's/(\\,|__cn__)/\\n/g' | grep -v \"^[ \\t]*$\" > accessions && mkdir outdir && cd outdir && ignore_errors=0 && while read accession; do echo \"Downloading accession number: \" $accession \" ...\" >> ../error.log && ncbi-acc-download --molecule 'nucleotide' --format 'fasta' --extended-validation all ${accession}; failure=$?; if [ $failure -ne 0 ]; then echo \" failed.\" >> ../error.log; if [ $ignore_errors -ne 0 ]; then echo $accession >> ../failed.txt; else exit 1; fi; else echo \" done.\" >> ../error.log; fi; sleep 2; done < ../accessions 2> >(tee -a ../error.log >&2);", | ||
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| "id": "919ed9e80b102f05" | ||
| } | ||
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| "tool_stdout": "NCBI Entrez returned error code 400, are ID(s) CP0XXXXX valid?\n", | ||
| "tool_stderr": "Failed to download file with id CP0XXXXX from NCBI\n", | ||
| "job_stdout": "", | ||
| "job_stderr": "", | ||
| "stdout": "NCBI Entrez returned error code 400, are ID(s) CP0XXXXX valid?\n", | ||
| "stderr": "Failed to download file with id CP0XXXXX from NCBI\n", | ||
| "job_messages": [ | ||
| { | ||
| "code_desc": "", | ||
| "desc": "Fatal error: Exit code 1 ()", | ||
| "error_level": 3, | ||
| "exit_code": 1, | ||
| "type": "exit_code" | ||
| } | ||
| ], | ||
| "dependencies": [], | ||
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| { | ||
| "title": "Job Runtime (Wall Clock)", | ||
| "value": "4 seconds", | ||
| "plugin": "core", | ||
| "name": "runtime_seconds", | ||
| "raw_value": "4.0000000" | ||
| }, | ||
| { | ||
| "title": "Job End Time", | ||
| "value": "2024-11-12 18:50:51", | ||
| "plugin": "core", | ||
| "name": "end_epoch", | ||
| "raw_value": "1731437451.0000000" | ||
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| { | ||
| "title": "Job Start Time", | ||
| "value": "2024-11-12 18:50:47", | ||
| "plugin": "core", | ||
| "name": "start_epoch", | ||
| "raw_value": "1731437447.0000000" | ||
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| { | ||
| "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" | ||
| } | ||
| ] | ||
| } |
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reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/131fdfbf0346cb1a.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "131fdfbf0346cb1a", | ||
| "history_id": "aff48f2f86cebb71", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-12T19:07:16.762776", | ||
| "update_time": "2024-11-12T19:07:28.176788", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-856zs", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/119/registry.xml' '/galaxy/server/database/jobs_directory/000/119/upload_params.json' '153:/galaxy/server/database/objects/8/b/7/dataset_8b7fe276-8679-4951-937e-81609e469184_files:/galaxy/server/database/objects/8/b/7/dataset_8b7fe276-8679-4951-937e-81609e469184.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_sre65yyk\"", | ||
| "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"EMTABesethealthy.subset.rds\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_vxhejdzk\", \"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": {}, | ||
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| "id": "3afdcc1316e79fd7", | ||
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| "stderr": "", | ||
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| "dependencies": [], | ||
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| } |
47 changes: 47 additions & 0 deletions
47
reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/22517353a62337da.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "22517353a62337da", | ||
| "history_id": "aff48f2f86cebb71", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc3+galaxy0", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-11-12T19:32:39.003959", | ||
| "update_time": "2024-11-12T19:32:51.328111", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-rcxxp", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "vcffixup '/galaxy/server/database/objects/4/3/8/dataset_4388fc55-f87a-4119-a927-a2b62cec447f.dat' > '/galaxy/server/database/objects/5/0/7/dataset_5074dd1a-a586-4e2b-a282-669b9f6fe7eb.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"vcf\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"" | ||
| }, | ||
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| "id": "1e5b4154869d2527", | ||
| "src": "hda", | ||
| "uuid": "4388fc55-f87a-4119-a927-a2b62cec447f" | ||
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| "src": "hda", | ||
| "uuid": "5074dd1a-a586-4e2b-a282-669b9f6fe7eb" | ||
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45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/2e4c4b2409f06dfd.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
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| "create_time": "2024-11-12T18:44:48.697434", | ||
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| "galaxy_version": "24.1", | ||
| "external_id": "gxy-dl2rp", | ||
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| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/38/registry.xml' '/galaxy/server/database/jobs_directory/000/38/upload_params.json' '38:/galaxy/server/database/objects/f/a/d/dataset_fadefed9-046c-4ace-9377-f4481496eec8_files:/galaxy/server/database/objects/f/a/d/dataset_fadefed9-046c-4ace-9377-f4481496eec8.dat'", | ||
| "user_email": "tests@fake.org", | ||
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| "dbkey": "\"?\"", | ||
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| "file_count": "\"auto\"", | ||
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45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/300354dbb5b5c093.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
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| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/139/registry.xml' '/galaxy/server/database/jobs_directory/000/139/upload_params.json' '181:/galaxy/server/database/objects/8/8/9/dataset_889f1d4f-ddd2-46c7-9057-fe70783e328f_files:/galaxy/server/database/objects/8/8/9/dataset_889f1d4f-ddd2-46c7-9057-fe70783e328f.dat'", | ||
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45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-11-12-18-17-1/errors/361b9c563cfcdddf.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
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| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/112/registry.xml' '/galaxy/server/database/jobs_directory/000/112/upload_params.json' '146:/galaxy/server/database/objects/1/a/d/dataset_1ad23151-e666-462a-b325-262dc19294a9_files:/galaxy/server/database/objects/1/a/d/dataset_1ad23151-e666-462a-b325-262dc19294a9.dat'", | ||
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