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Updating anvil-edge README for edge-25-01-13-06-12-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-25-01-13-06-12-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "0": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-13-06-12-1/results.html", | ||
| "date1": "Mon Jan 13 06:28:17 2025", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-13-06-12-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-edge/tool-tests/edge-25-01-13-06-12-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| -t unicycler --tool-version 9e3e80cc4ad4 | ||
| -t deeptools_bam_compare --tool-version e821645ef8fc | ||
| -t cutadapt --tool-version 093678460093 | ||
| -t cutadapt --tool-version 135b80fb1ac2 | ||
| -t fastqc --tool-version 3d0c7bdf12f5 | ||
| -t fastqc --tool-version e7b2202befea | ||
| -t rna_starsolo --tool-version eec9494fdafa | ||
| -t rna_starsolo --tool-version 79b885ce78d7 | ||
| -t poretools_hist --tool-version 5a82eb9e1b89 | ||
| -t picard --tool-version b502c227b5e6 | ||
| -t samtools_view --tool-version b72793637686 | ||
| -t samtools_split --tool-version 135c85f4cfaf | ||
| -t sam_merge --tool-version 1977f1637890 | ||
| -t dropletutils_read_10x --tool-version ca62f52e0d7f | ||
| -t scater_normalize --tool-version 946179ef029c | ||
| -t anndata_ops --tool-version 54f1212d26ac | ||
| -t anndata_ops --tool-version 6aa025ea64d3 | ||
| -t scanpy_plot_embed --tool-version 99dd7baf9e23 | ||
| -t scanpy_plot_embed --tool-version a8ef4bc35839 | ||
| -t jq --tool-version 5ff75eb1a893 | ||
| -t snpsift_dbnsfp --tool-version 4e21e4f2bc48 | ||
| -t bcftools_plugin_counts --tool-version 4813f99d81b7 | ||
| -t bcftools_view --tool-version 23680a42e149 | ||
| -t vcfcheck --tool-version 2968c6916579 | ||
| -t vcfdistance --tool-version 5822b40f3037 |
59 changes: 59 additions & 0 deletions
59
reports/anvil-edge/tool-tests/edge-25-01-13-06-12-1/errors/0e05c64a5f8dc41b.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "0e05c64a5f8dc41b", | ||
| "history_id": "ba138934d9c0e5e1", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/3.5.4+galaxy0", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2025-01-13T06:45:34.348366", | ||
| "update_time": "2025-01-13T06:45:56.358146", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-zxbsm", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "ln -s '/galaxy/server/database/objects/4/c/6/dataset_4c66305d-15c3-4a1f-bc39-aa53d0cd1aa9.dat' one.bam && ln -s '/galaxy/server/database/objects/_metadata_files/9/0/5/metadata_90580d9e-1220-4298-a73b-69010ec1326f.dat' one.bam.bai && ln -s '/galaxy/server/database/objects/4/c/6/dataset_4c66305d-15c3-4a1f-bc39-aa53d0cd1aa9.dat' two.bam && ln -s '/galaxy/server/database/objects/_metadata_files/9/0/5/metadata_90580d9e-1220-4298-a73b-69010ec1326f.dat' two.bam.bai && bamCompare --numberOfProcessors \"${GALAXY_SLOTS:-4}\" --bamfile1 one.bam --bamfile2 two.bam --outFileName '/galaxy/server/database/objects/b/9/e/dataset_b9e222b2-7ea2-45c7-9104-c9656fbee3e9.dat' --outFileFormat 'bedgraph' --binSize 5 --scaleFactorsMethod readCount --operation ratio --pseudocount 1 1", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "advancedOpt": "{\"__current_case__\": 0, \"showAdvancedOpt\": \"no\"}", | ||
| "region": "\"\"", | ||
| "outFileFormat": "\"bedgraph\"", | ||
| "exactScaling": "false", | ||
| "comparison": "{\"__current_case__\": 1, \"pseudocount\": \"1 1\", \"type\": \"ratio\"}", | ||
| "scaling": "{\"__current_case__\": 1, \"method\": \"readCount\"}", | ||
| "binSize": "\"5\"" | ||
| }, | ||
| "inputs": { | ||
| "bamFile2": { | ||
| "id": "aaed783dec58dd79", | ||
| "src": "hda", | ||
| "uuid": "4c66305d-15c3-4a1f-bc39-aa53d0cd1aa9" | ||
| }, | ||
| "bamFile1": { | ||
| "id": "aaed783dec58dd79", | ||
| "src": "hda", | ||
| "uuid": "4c66305d-15c3-4a1f-bc39-aa53d0cd1aa9" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "outFileName": { | ||
| "id": "52e41da1db8f184a", | ||
| "src": "hda", | ||
| "uuid": "b9e222b2-7ea2-45c7-9104-c9656fbee3e9" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "bamFilesList: ['one.bam', 'two.bam']\nbinLength: 5\nnumberOfSamples: 0\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 5\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "", | ||
| "stderr": "bamFilesList: ['one.bam', 'two.bam']\nbinLength: 5\nnumberOfSamples: 0\nblackListFileName: None\nskipZeroOverZero: False\nbed_and_bin: False\ngenomeChunkSize: None\ndefaultFragmentLength: read length\nnumberOfProcessors: 8\nverbose: False\nregion: None\nbedFile: None\nminMappingQuality: None\nignoreDuplicates: False\nchrsToSkip: []\nstepSize: 5\ncenter_read: False\nsamFlag_include: None\nsamFlag_exclude: None\nminFragmentLength: 0\nmaxFragmentLength: 0\nzerosToNans: False\nsmoothLength: None\nsave_data: False\nout_file_for_raw_data: None\nmaxPairedFragmentLength: 1000\n", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-25-01-13-06-12-1/errors/0e7cd2f000b1cff9.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "0e7cd2f000b1cff9", | ||
| "history_id": "ba138934d9c0e5e1", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2025-01-13T06:32:22.931505", | ||
| "update_time": "2025-01-13T06:32:38.297650", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-d2njl", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/6/registry.xml' '/galaxy/server/database/jobs_directory/000/6/upload_params.json' '7:/galaxy/server/database/objects/e/1/1/dataset_e11930d7-385a-4d7f-ac84-3a7bf7216bf1_files:/galaxy/server/database/objects/e/1/1/dataset_e11930d7-385a-4d7f-ac84-3a7bf7216bf1.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_0pn_yywf\"", | ||
| "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"onp.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_h5acrblf\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"fasta\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "6f742401f335b0c6", | ||
| "src": "hda", | ||
| "uuid": "e11930d7-385a-4d7f-ac84-3a7bf7216bf1" | ||
| } | ||
| }, | ||
| "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": [] | ||
| } |
107 changes: 107 additions & 0 deletions
107
reports/anvil-edge/tool-tests/edge-25-01-13-06-12-1/errors/17b56c8276be0fce.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "17b56c8276be0fce", | ||
| "history_id": "ba138934d9c0e5e1", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", | ||
| "state": "error", | ||
| "exit_code": 1, | ||
| "create_time": "2025-01-13T07:31:59.306013", | ||
| "update_time": "2025-01-13T07:32:11.906734", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-rh4tr", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "ln -f -s '/galaxy/server/database/objects/5/f/8/dataset_5f86c425-f283-4fb6-ba82-2f2760a71625.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/e/b/5/dataset_eb55abc1-41da-48f6-8218-af68dc1c3ed4.dat' 'bwa-mem-fastq_mispaired2_fq_gz.fq.gz' && cutadapt -j=${GALAXY_SLOTS:-4} -a 'AGATCGGAAGAGC' -A 'AGATCGGAAGAGC' --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o 'out1.fq.gz' -p 'out2.fq.gz' 'bwa-mem-fastq1_fq_gz.fq.gz' 'bwa-mem-fastq_mispaired2_fq_gz.fq.gz'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": "4.9", | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "output_selector": null, | ||
| "read_mod_options": "{\"length_tag\": null, \"rename\": null, \"strip_suffix\": null, \"zero_cap\": false}", | ||
| "filter_options": "{\"discard_casava\": false, \"discard_trimmed\": false, \"discard_untrimmed\": false, \"max_average_error_rate\": \"\", \"max_expected_errors\": \"\", \"max_n\": \"\", \"maximum_length\": \"\", \"maximum_length2\": \"\", \"minimum_length\": \"1\", \"minimum_length2\": \"\", \"pair_filter\": \"any\"}", | ||
| "other_trimming_options": "{\"cut\": \"0\", \"cut2\": \"0\", \"nextseq_trim\": \"0\", \"poly_a\": false, \"quality_cutoff\": \"0\", \"quality_cutoff2\": \"\", \"shorten_options\": {\"__current_case__\": 1, \"shorten_values\": \"False\"}, \"shorten_options_r2\": {\"__current_case__\": 1, \"shorten_values_r2\": \"False\"}, \"trim_n\": false}", | ||
| "adapter_options": "{\"action\": \"trim\", \"error_rate\": \"0.1\", \"match_read_wildcards\": false, \"no_indels\": false, \"no_match_adapter_wildcards\": true, \"overlap\": \"3\", \"revcomp\": false, \"times\": \"1\"}", | ||
| "library": "{\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 306, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 307, \"src\": \"hda\"}]}, \"pair_adapters\": false, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters\": [], \"front_adapters\": []}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source\": {\"__current_case__\": 0, \"adapter\": \"AGATCGGAAGAGC\", \"adapter_name\": \"\", \"adapter_source_list\": \"user\"}, \"single_noindels\": false}], \"anywhere_adapters2\": [], \"front_adapters2\": []}, \"type\": \"paired\"}" | ||
| }, | ||
| "inputs": { | ||
| "library|input_2": { | ||
| "id": "4b6a0029cde0702e", | ||
| "src": "hda", | ||
| "uuid": "eb55abc1-41da-48f6-8218-af68dc1c3ed4" | ||
| }, | ||
| "library|input_1": { | ||
| "id": "91f080166144152d", | ||
| "src": "hda", | ||
| "uuid": "5f86c425-f283-4fb6-ba82-2f2760a71625" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "out2": { | ||
| "id": "c382a1458a5b7e7b", | ||
| "src": "hda", | ||
| "uuid": "3831e944-0a95-47c0-84b6-0c013a5bee7a" | ||
| }, | ||
| "out1": { | ||
| "id": "d7e224701a5c260f", | ||
| "src": "hda", | ||
| "uuid": "fc3d670c-08ec-4415-ac8b-a7048a28001f" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "This is cutadapt 4.9 with Python 3.12.8\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq_mispaired2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\n", | ||
| "tool_stderr": "Error in sequence file at unknown line: Reads are improperly paired. Read name 'M01368:8:000000000-A3GHV:1:1101:6911:8255/1' in file 1 does not match 'M01368:8:000000000-A3GHV:1:1101:14518:9998/2' in file 2.\n", | ||
| "job_stdout": "", | ||
| "job_stderr": "", | ||
| "stdout": "This is cutadapt 4.9 with Python 3.12.8\nCommand line parameters: -j=5 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --error-rate=0.1 --times=1 --overlap=3 --action=trim --minimum-length=1 -o out1.fq.gz -p out2.fq.gz bwa-mem-fastq1_fq_gz.fq.gz bwa-mem-fastq_mispaired2_fq_gz.fq.gz\nProcessing paired-end reads on 5 cores ...\n", | ||
| "stderr": "Error in sequence file at unknown line: Reads are improperly paired. Read name 'M01368:8:000000000-A3GHV:1:1101:6911:8255/1' in file 1 does not match 'M01368:8:000000000-A3GHV:1:1101:14518:9998/2' in file 2.\n", | ||
| "job_messages": [ | ||
| { | ||
| "code_desc": "", | ||
| "desc": "Fatal error: Exit code 1 ()", | ||
| "error_level": 3, | ||
| "exit_code": 1, | ||
| "type": "exit_code" | ||
| } | ||
| ], | ||
| "dependencies": [], | ||
| "job_metrics": [ | ||
| { | ||
| "title": "Job Runtime (Wall Clock)", | ||
| "value": "1 second", | ||
| "plugin": "core", | ||
| "name": "runtime_seconds", | ||
| "raw_value": "1.0000000" | ||
| }, | ||
| { | ||
| "title": "Job End Time", | ||
| "value": "2025-01-13 07:32:01", | ||
| "plugin": "core", | ||
| "name": "end_epoch", | ||
| "raw_value": "1736753521.0000000" | ||
| }, | ||
| { | ||
| "title": "Job Start Time", | ||
| "value": "2025-01-13 07:32:00", | ||
| "plugin": "core", | ||
| "name": "start_epoch", | ||
| "raw_value": "1736753520.0000000" | ||
| }, | ||
| { | ||
| "title": "Memory Allocated (MB)", | ||
| "value": "20401", | ||
| "plugin": "core", | ||
| "name": "galaxy_memory_mb", | ||
| "raw_value": "20401.0000000" | ||
| }, | ||
| { | ||
| "title": "Cores Allocated", | ||
| "value": "5", | ||
| "plugin": "core", | ||
| "name": "galaxy_slots", | ||
| "raw_value": "5.0000000" | ||
| } | ||
| ] | ||
| } |
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