Skip to content

Commit

Permalink
Updating anvil-production README for prod-24-09-15-12-31-1
Browse files Browse the repository at this point in the history
  • Loading branch information
@actions-user
actions-user committed Sep 15, 2024
1 parent 33b9aa2 commit 505cb4f
Show file tree
Hide file tree
Showing 25 changed files with 3,830 additions and 6 deletions.
2 changes: 1 addition & 1 deletion reports/anvil-production/README.md
View file

Large diffs are not rendered by default.

10 changes: 5 additions & 5 deletions reports/anvil-production/tool-tests/chunks.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -56,11 +56,11 @@
"date2": "Fri Sep 06 12:48:21 2024"
},
"13": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-08-12-30-1/results.html",
"date1": "Sun Sep 08 12:46:16 2024",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-08-12-30-1/tools.yml",
"run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-01-12-30-1/results.html",
"date2": "Sun Sep 01 12:46:15 2024"
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/results.html",
"date1": "Sun Sep 15 12:47:00 2024",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/tools.yml",
"run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-08-12-30-1/results.html",
"date2": "Sun Sep 08 12:46:16 2024"
},
"4": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-04-00-32-1/results.html",
Expand Down
7 changes: 7 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/chunk.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
{
"13": {
"run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/results.html",
"date1": "Sun Sep 15 12:47:00 2024",
"tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/tools.yml"
}
}
15 changes: 15 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/chunk.txt
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
-t table_compute --tool-version 60ff16842fcd
-t cutadapt --tool-version 093678460093
-t qualimap_bamqc --tool-version 19ece8afbaab
-t samtools_stats --tool-version 145f6d74ff5e
-t filter_on_md --tool-version ac70bfaf1224
-t bcftools_plugin_mendelian --tool-version bf235558f2cf
-t bcftools_csq --tool-version fdd127bd4a32
-t vcfcommonsamples --tool-version f1852ecef841
-t vcfdistance --tool-version c506b8275b1a
-t poretools_yield_plot --tool-version ca22d8497db5
-t deeptools_bigwig_compare --tool-version 26e7304d6737
-t bowtie2 --tool-version 09b2cdb7ace5
-t snpsift_genesets --tool-version d12a810c837e
-t deseq2 --tool-version 6a3a025714d3
-t mummer_mummer --tool-version 48823c9635a4
62 changes: 62 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/errors/2635ab551e682228.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,62 @@
{
"model_class": "Job",
"id": "2635ab551e682228",
"state": "error",
"exit_code": null,
"update_time": "2024-09-15T13:44:50.517363",
"create_time": "2024-09-15T13:44:45.042805",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.5.3+galaxy1",
"history_id": "8dc7d2120e767ce3",
"external_id": "gxy-mk5tj",
"command_line": "set -o | grep -q pipefail && set -o pipefail; bowtie2-build --threads ${GALAXY_SLOTS:-4} '/galaxy/server/database/objects/6/f/7/dataset_6f78e9ec-445a-4de9-90ea-a13dcbe1a601.dat' genome && ln -s -f '/galaxy/server/database/objects/6/f/7/dataset_6f78e9ec-445a-4de9-90ea-a13dcbe1a601.dat' genome.fa && ln -f -s '/galaxy/server/database/objects/5/d/a/dataset_5da73379-d0c8-4a47-85c9-aaa7fac211b5.dat' input_f.fasta && ln -f -s '/galaxy/server/database/objects/7/d/b/dataset_7db72cdb-0344-4e93-b88d-5eb90723be22.dat' input_r.fasta && THREADS=${GALAXY_SLOTS:-4} && if [ \"$THREADS\" -gt 1 ]; then (( THREADS-- )); fi && bowtie2 -p \"$THREADS\" -x 'genome' -f -1 'input_f.fasta' -2 'input_r.fasta' | samtools sort -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/e/9/d/dataset_e9d0bce6-6d4a-4fee-94e6-82baadac50b0.dat'",
"traceback": null,
"params": {
"__input_ext": "\"input\"",
"dbkey": "\"?\"",
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
"save_mapping_stats": "false",
"sam_options": "{\"__current_case__\": 1, \"sam_options_selector\": \"no\"}",
"analysis_type": "{\"__current_case__\": 0, \"analysis_type_selector\": \"simple\", \"presets\": \"no_presets\"}",
"rg": "{\"__current_case__\": 3, \"rg_selector\": \"do_not_set\"}",
"reference_genome": "{\"__current_case__\": 1, \"own_file\": {\"values\": [{\"id\": 387, \"src\": \"hda\"}]}, \"source\": \"history\"}",
"library": "{\"__current_case__\": 1, \"aligned_file\": false, \"input_1\": {\"values\": [{\"id\": 385, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 386, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 1, \"paired_options_selector\": \"no\"}, \"type\": \"paired\", \"unaligned_file\": false}"
},
"inputs": {
"library|input_1": {
"id": "6c90f6313f69bf03",
"src": "hda",
"uuid": "5da73379-d0c8-4a47-85c9-aaa7fac211b5"
},
"library|input_2": {
"id": "d4ed341c5293401e",
"src": "hda",
"uuid": "7db72cdb-0344-4e93-b88d-5eb90723be22"
},
"reference_genome|own_file": {
"id": "52986156949892f4",
"src": "hda",
"uuid": "6f78e9ec-445a-4de9-90ea-a13dcbe1a601"
}
},
"outputs": {
"output": {
"id": "11fb8b6d7e0f63ee",
"src": "hda",
"uuid": "e9d0bce6-6d4a-4fee-94e6-82baadac50b0"
}
},
"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 reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/errors/286e9de4b25d1b9a.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
{
"model_class": "Job",
"id": "286e9de4b25d1b9a",
"state": "error",
"exit_code": null,
"update_time": "2024-09-15T13:42:56.443687",
"create_time": "2024-09-15T13:42:46.833989",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "upload1",
"history_id": "8dc7d2120e767ce3",
"external_id": "gxy-hmddw",
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/274/registry.xml' '/galaxy/server/database/jobs_directory/000/274/upload_params.json' '373:/galaxy/server/database/objects/d/c/d/dataset_dcdec254-7133-433d-88d4-168078a0f77e_files:/galaxy/server/database/objects/d/c/d/dataset_dcdec254-7133-433d-88d4-168078a0f77e.dat'",
"traceback": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_katrlide\"",
"files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}",
"dbkey": "\"?\"",
"force_composite": "\"false\"",
"files": "[{\"NAME\": \"bowtie2-ref.fasta\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_yekj72w_\", \"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": "c85aa3d1580e0f85",
"src": "hda",
"uuid": "dcdec254-7133-433d-88d4-168078a0f77e"
}
},
"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": []
}
106 changes: 106 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/errors/3eb9767de510deb5.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,106 @@
{
"model_class": "Job",
"id": "3eb9767de510deb5",
"state": "error",
"exit_code": 1,
"update_time": "2024-09-15T13:27:00.634844",
"create_time": "2024-09-15T13:26:49.511959",
"galaxy_version": "23.1",
"command_version": "4.9",
"copied_from_job_id": null,
"tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1",
"history_id": "8dc7d2120e767ce3",
"external_id": "gxy-9pzt5",
"command_line": "ln -f -s '/galaxy/server/database/objects/2/f/2/dataset_2f2a788d-2833-4171-badc-a3ae9df0a6e4.dat' 'bwa-mem-fastq1_fq_gz.fq.gz' && ln -f -s '/galaxy/server/database/objects/9/5/3/dataset_9532760e-5c81-4d94-b8f4-4a144be8258c.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'",
"traceback": null,
"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\": 213, \"src\": \"hda\"}]}, \"input_2\": {\"values\": [{\"id\": 214, \"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_1": {
"id": "0b93eba5cf3093cd",
"src": "hda",
"uuid": "2f2a788d-2833-4171-badc-a3ae9df0a6e4"
},
"library|input_2": {
"id": "0c498463f03571c8",
"src": "hda",
"uuid": "9532760e-5c81-4d94-b8f4-4a144be8258c"
}
},
"outputs": {
"out1": {
"id": "b90049f0a9909974",
"src": "hda",
"uuid": "c8173c4d-e6bf-4b2f-abe0-a838ef15f4c2"
},
"out2": {
"id": "5847934dd1a02478",
"src": "hda",
"uuid": "d0f3f085-15fa-4879-84af-75817fe8555b"
}
},
"output_collections": {},
"tool_stdout": "This is cutadapt 4.9 with Python 3.12.5\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": "",
"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",
"stdout": "This is cutadapt 4.9 with Python 3.12.5\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",
"job_messages": [
{
"code_desc": "",
"desc": "Fatal error: Exit code 1 ()",
"error_level": 3,
"exit_code": 1,
"type": "exit_code"
}
],
"dependencies": [],
"user_email": "tests@fake.org",
"job_metrics": [
{
"title": "Job Runtime (Wall Clock)",
"value": "1 second",
"plugin": "core",
"name": "runtime_seconds",
"raw_value": "1.0000000"
},
{
"title": "Job End Time",
"value": "2024-09-15 13:26:52",
"plugin": "core",
"name": "end_epoch",
"raw_value": "1726406812.0000000"
},
{
"title": "Job Start Time",
"value": "2024-09-15 13:26:51",
"plugin": "core",
"name": "start_epoch",
"raw_value": "1726406811.0000000"
},
{
"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"
}
]
}
66 changes: 66 additions & 0 deletions reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/errors/5f9f44d67cda1375.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,66 @@
{
"model_class": "Job",
"id": "5f9f44d67cda1375",
"state": "error",
"exit_code": null,
"update_time": "2024-09-15T13:31:38.656773",
"create_time": "2024-09-15T13:31:33.360216",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5",
"history_id": "8dc7d2120e767ce3",
"external_id": "gxy-gdc89",
"command_line": "addthreads=${GALAXY_SLOTS:-1} && (( addthreads-- )) && ln -s '/galaxy/server/database/objects/3/6/5/dataset_3653046f-956b-4f37-8fcd-a59499819d32.dat' infile && reffa=\"reference.fa\" && ln -s '/galaxy/server/database/objects/0/5/8/dataset_0582d9ad-0e16-455b-95e2-4ef32bdd03ad.dat' $reffa && samtools faidx $reffa && reffai=$reffa.fai && samtools stats --insert-size 0 --ref-seq \"$reffa\" -@ $addthreads infile > '/galaxy/server/database/objects/9/4/6/dataset_946e5c7e-b0e6-4396-92b0-2e52a3c0ec0e.dat'",
"traceback": null,
"params": {
"__input_ext": "\"input\"",
"dbkey": "\"?\"",
"chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
"cov_threshold": "\"\"",
"remove_overlaps": "false",
"sparse": "false",
"cond_region": "{\"__current_case__\": 0, \"select_region\": \"no\"}",
"addref_cond": "{\"__current_case__\": 1, \"addref_select\": \"history\", \"ref\": {\"values\": [{\"id\": 305, \"src\": \"hda\"}]}}",
"trim_quality": "\"\"",
"most_inserts": "\"\"",
"read_length": "\"\"",
"read_group": null,
"insert_size": "\"0\"",
"gc_depth": "\"\"",
"filter_by_flags": "{\"__current_case__\": 1, \"filter_flags\": \"nofilter\"}",
"split_output_cond": "{\"__current_case__\": 0, \"split_output_selector\": \"no\"}",
"remove_dups": "false",
"coverage_cond": "{\"__current_case__\": 0, \"coverage_select\": \"no\"}"
},
"inputs": {
"input": {
"id": "4676469627fdcfe8",
"src": "hda",
"uuid": "3653046f-956b-4f37-8fcd-a59499819d32"
},
"addref_cond|ref": {
"id": "80dbf36c1afde1c7",
"src": "hda",
"uuid": "0582d9ad-0e16-455b-95e2-4ef32bdd03ad"
}
},
"outputs": {
"output": {
"id": "edc9d7b6bfb001c9",
"src": "hda",
"uuid": "946e5c7e-b0e6-4396-92b0-2e52a3c0ec0e"
}
},
"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 reports/anvil-production/tool-tests/prod-24-09-15-12-31-1/errors/671cfe54a939492d.json
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
{
"model_class": "Job",
"id": "671cfe54a939492d",
"state": "error",
"exit_code": null,
"update_time": "2024-09-15T13:23:54.610738",
"create_time": "2024-09-15T13:23:46.632216",
"galaxy_version": "23.1",
"command_version": null,
"copied_from_job_id": null,
"tool_id": "upload1",
"history_id": "8dc7d2120e767ce3",
"external_id": "gxy-wxtxs",
"command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/174/registry.xml' '/galaxy/server/database/jobs_directory/000/174/upload_params.json' '198:/galaxy/server/database/objects/8/3/3/dataset_833f3488-1807-402b-8208-6f28ad4eea29_files:/galaxy/server/database/objects/8/3/3/dataset_833f3488-1807-402b-8208-6f28ad4eea29.dat'",
"traceback": null,
"params": {
"paramfile": "\"/galaxy/server/database/tmp/upload_params_fa4lnl28\"",
"files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
"dbkey": "\"?\"",
"force_composite": "\"false\"",
"files": "[{\"NAME\": \"polya.1.fasta\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_2s7g189h\", \"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": "490b136d2fa5088e",
"src": "hda",
"uuid": "833f3488-1807-402b-8208-6f28ad4eea29"
}
},
"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": []
}
Loading

0 comments on commit 505cb4f

Please sign in to comment.