Updating anvil-production README for prod-24-10-21-12-36-1

anvilproject · Oct 21, 2024 · 4932866 · 4932866
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diff --git a/reports/anvil-production/README.md b/reports/anvil-production/README.md
diff --git a/reports/anvil-production/tool-tests/chunks.json b/reports/anvil-production/tool-tests/chunks.json
@@ -35,11 +35,11 @@
         "date2": "Tue Oct 08 12:49:39 2024"
     },
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-        "date1": "Mon Oct 14 12:52:38 2024",
-        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-10-14-12-36-1/tools.yml",
-        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-10-07-12-36-1/results.html",
-        "date2": "Mon Oct 07 12:52:44 2024"
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/results.html",
+        "date1": "Mon Oct 21 12:53:09 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/tools.yml",
+        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-10-14-12-36-1/results.html",
+        "date2": "Mon Oct 14 12:52:38 2024"
     },
     "2": {
         "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-10-15-00-35-1/results.html",

diff --git a/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/chunk.json b/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/chunk.json
@@ -0,0 +1,7 @@
+{
+    "1": {
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/results.html",
+        "date1": "Mon Oct 21 12:53:09 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/tools.yml"
+    }
+}
diff --git a/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/chunk.txt b/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/chunk.txt
@@ -0,0 +1,15 @@
+-t ncbi_acc_download --tool-version 1c58de56d587
+-t add_input_name_as_column --tool-version 3284b72eef56
+-t fastq_groomer --tool-version 47e5dbc3e790
+-t samtools_reheader --tool-version 30388d878f81
+-t samtools_bedcov --tool-version 9149ad20699a
+-t bedtools --tool-version ce3c7f062223
+-t bcftools_convert_from_vcf --tool-version b8e9da766b0f
+-t bcftools_plugin_dosage --tool-version 5c232a738c74
+-t vcfflatten --tool-version f285aa6bdcfb
+-t vcftools_slice --tool-version 1363e5d4a8b8
+-t poretools_winner --tool-version 79c1ac92f31b
+-t deeptools_correct_gc_bias --tool-version 2c37ce318bc3
+-t bwameth --tool-version 29bdbc353f20
+-t snpeff --tool-version 74aebe30fb52
+-t edger --tool-version 334ce9b1bac5
diff --git a/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/0b10f64ac497f8e3.json b/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/0b10f64ac497f8e3.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "0b10f64ac497f8e3",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-10-21T13:17:34.845314",
+    "create_time": "2024-10-21T13:17:21.832306",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "0085f6e78400ca37",
+    "external_id": "gxy-hwr55",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/86/registry.xml' '/galaxy/server/database/jobs_directory/000/86/upload_params.json' '105:/galaxy/server/database/objects/9/c/7/dataset_9c7dffb2-8140-4381-93de-855d16356744_files:/galaxy/server/database/objects/9/c/7/dataset_9c7dffb2-8140-4381-93de-855d16356744.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_vl193zxc\"",
+        "files_metadata": "{\"__current_case__\": 36, \"file_type\": \"bam\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"reheader_input_file.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_lmsjpa1m\", \"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": "4b9f95dc8f687645",
+            "src": "hda",
+            "uuid": "9c7dffb2-8140-4381-93de-855d16356744"
+        }
+    },
+    "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": []
+}
diff --git a/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/1779c611de5c35a2.json b/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/1779c611de5c35a2.json
@@ -0,0 +1,58 @@
+{
+    "model_class": "Job",
+    "id": "1779c611de5c35a2",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-10-21T13:37:41.957439",
+    "create_time": "2024-10-21T13:37:31.353062",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5",
+    "history_id": "0085f6e78400ca37",
+    "external_id": "gxy-k84nh",
+    "command_line": "Rscript '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/iuc/edger/ae2aad0a6d50/edger/edger.R'  -R '/galaxy/server/database/objects/5/8/2/dataset_582027f4-0341-42b5-b106-e2ae0b16f084.dat' -o '/galaxy/server/database/objects/5/8/2/dataset_582027f4-0341-42b5-b106-e2ae0b16f084_files'  -m '/galaxy/server/database/objects/b/2/6/dataset_b264b679-2059-4555-99f5-1c66d34bfe0b.dat' -i 'Genotype::Mut,Mut,Mut,WT,WT,WT'    -C 'Mut-WT'  -c '1000.0' -s '3'   -l '0.0' -p '0.05' -d 'BH' -n 'TMM' -b  && mkdir ./output_dir  && cp '/galaxy/server/database/objects/5/8/2/dataset_582027f4-0341-42b5-b106-e2ae0b16f084_files'/*.tsv output_dir/",
+    "traceback": null,
+    "params": {
+        "__input_ext": "\"tabular\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "adv": "{\"lfc\": \"0.0\", \"lrtOption\": false, \"normalisationOption\": \"TMM\", \"pAdjust\": \"BH\", \"pVal\": \"0.05\", \"robOption\": true}",
+        "out": "{\"normCounts\": false, \"rdaOption\": false, \"rscript\": false}",
+        "f": "{\"filt\": {\"__current_case__\": 0, \"cformat\": {\"__current_case__\": 0, \"cpmReq\": \"1000.0\", \"cpmSampleReq\": \"3\", \"format_select\": \"cpm\"}, \"filt_select\": \"yes\"}}",
+        "contrasts": "{\"__current_case__\": 0, \"contrastOpt\": \"manual\", \"rep_contrast\": [{\"__index__\": 0, \"contrast\": \"Mut-WT\"}]}",
+        "formula": null,
+        "anno": "{\"__current_case__\": 1, \"annoOpt\": \"no\"}",
+        "input": "{\"__current_case__\": 1, \"counts\": {\"values\": [{\"id\": 220, \"src\": \"hda\"}]}, \"fact\": {\"__current_case__\": 1, \"ffile\": \"no\", \"rep_factor\": [{\"__index__\": 0, \"factorName\": \"Genotype\", \"groupNames\": \"Mut,Mut,Mut,WT,WT,WT\"}]}, \"format\": \"matrix\"}"
+    },
+    "inputs": {
+        "input|counts": {
+            "id": "d90a1e5eac472ab0",
+            "src": "hda",
+            "uuid": "b264b679-2059-4555-99f5-1c66d34bfe0b"
+        }
+    },
+    "outputs": {
+        "outReport": {
+            "id": "7ae46f82f663e8a8",
+            "src": "hda",
+            "uuid": "582027f4-0341-42b5-b106-e2ae0b16f084"
+        }
+    },
+    "output_collections": {
+        "outTables": {
+            "id": "ffc1551f6d488f8d",
+            "src": "hdca"
+        }
+    },
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stderr": "",
+    "stdout": "",
+    "job_messages": null,
+    "dependencies": [],
+    "user_email": "tests@fake.org",
+    "job_metrics": []
+}
diff --git a/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/1c90e89bd7225fd8.json b/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/1c90e89bd7225fd8.json
@@ -0,0 +1,48 @@
+{
+    "model_class": "Job",
+    "id": "1c90e89bd7225fd8",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-10-21T13:15:06.018327",
+    "create_time": "2024-10-21T13:15:00.085275",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.5",
+    "history_id": "0085f6e78400ca37",
+    "external_id": "gxy-czkv6",
+    "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/b/6/f/dataset_b6f8b3e3-d670-4ea0-af25-7616ed3752e9.dat' sanger '/galaxy/server/database/objects/6/b/2/dataset_6b23e6cc-5666-4e50-b3e0-ab560fb44f9c.dat' sanger ascii summarize_input --fix-id",
+    "traceback": null,
+    "params": {
+        "__input_ext": "\"fastq\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "options_type": "{\"__current_case__\": 1, \"fix_id\": true, \"force_quality_encoding\": \"ascii\", \"options_type_selector\": \"advanced\", \"output_type\": \"sanger\", \"summarize_input\": \"summarize_input\"}",
+        "input_type": "\"sanger\""
+    },
+    "inputs": {
+        "input_file": {
+            "id": "a68ca5631f3cd3ec",
+            "src": "hda",
+            "uuid": "b6f8b3e3-d670-4ea0-af25-7616ed3752e9"
+        }
+    },
+    "outputs": {
+        "output_file": {
+            "id": "523d000faeb3f45b",
+            "src": "hda",
+            "uuid": "6b23e6cc-5666-4e50-b3e0-ab560fb44f9c"
+        }
+    },
+    "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": []
+}
diff --git a/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/1cdd0a24aa090b9b.json b/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/1cdd0a24aa090b9b.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "1cdd0a24aa090b9b",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-10-21T13:07:38.147607",
+    "create_time": "2024-10-21T13:07:27.500817",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "0085f6e78400ca37",
+    "external_id": "gxy-96k6j",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/48/registry.xml' '/galaxy/server/database/jobs_directory/000/48/upload_params.json' '67:/galaxy/server/database/objects/9/7/1/dataset_971030e5-9a18-458c-8cb6-fae92e7abc74_files:/galaxy/server/database/objects/9/7/1/dataset_971030e5-9a18-458c-8cb6-fae92e7abc74.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_i804k4t7\"",
+        "files_metadata": "{\"__current_case__\": 78, \"file_type\": \"fastq\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"solexa_full_range_original_solexa.fastqsolexa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_7fvlg1f8\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+        "file_count": "\"auto\"",
+        "file_type": "\"fastq\""
+    },
+    "inputs": {},
+    "outputs": {
+        "output0": {
+            "id": "c94ad427b28867b1",
+            "src": "hda",
+            "uuid": "971030e5-9a18-458c-8cb6-fae92e7abc74"
+        }
+    },
+    "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": []
+}
diff --git a/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/7aad7ae2b082e337.json b/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/7aad7ae2b082e337.json
@@ -0,0 +1,98 @@
+{
+    "model_class": "Job",
+    "id": "7aad7ae2b082e337",
+    "state": "error",
+    "exit_code": 1,
+    "update_time": "2024-10-21T12:58:03.679999",
+    "create_time": "2024-10-21T12:57:47.300251",
+    "galaxy_version": "23.1",
+    "command_version": "",
+    "copied_from_job_id": null,
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download/0.2.8+galaxy0",
+    "history_id": "0085f6e78400ca37",
+    "external_id": "gxy-72fr4",
+    "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);",
+    "traceback": null,
+    "params": {
+        "__input_ext": "\"data\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "ignore_failed": "\"0\"",
+        "range": null,
+        "molecule": "{\"__current_case__\": 0, \"format\": \"fasta\", \"select\": \"nucleotide\"}",
+        "query_source": "{\"__current_case__\": 1, \"accession_list\": \"CP011064,CP0XXXXX,CP021680\", \"select\": \"accession_list\"}"
+    },
+    "inputs": {},
+    "outputs": {
+        "error_log": {
+            "id": "7ed645558c311f99",
+            "src": "hda",
+            "uuid": "5233d0bb-2771-44b2-a0f1-5800492e57eb"
+        },
+        "__new_primary_file_output|CP011064__": {
+            "id": "ef531acc37f7b724",
+            "src": "hda",
+            "uuid": "6e5cfaa1-c7db-4d1c-ab10-e543fc827389"
+        }
+    },
+    "output_collections": {
+        "output": {
+            "id": "4661815f6c582cbf",
+            "src": "hdca"
+        }
+    },
+    "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": "",
+    "stderr": "Failed to download file with id CP0XXXXX from NCBI\n",
+    "stdout": "NCBI Entrez returned error code 400, are ID(s) CP0XXXXX valid?\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": "4 seconds",
+            "plugin": "core",
+            "name": "runtime_seconds",
+            "raw_value": "4.0000000"
+        },
+        {
+            "title": "Job End Time",
+            "value": "2024-10-21 12:57:52",
+            "plugin": "core",
+            "name": "end_epoch",
+            "raw_value": "1729515472.0000000"
+        },
+        {
+            "title": "Job Start Time",
+            "value": "2024-10-21 12:57:48",
+            "plugin": "core",
+            "name": "start_epoch",
+            "raw_value": "1729515468.0000000"
+        },
+        {
+            "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"
+        }
+    ]
+}
diff --git a/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/8a6c3a75d7a356e8.json b/reports/anvil-production/tool-tests/prod-24-10-21-12-36-1/errors/8a6c3a75d7a356e8.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "8a6c3a75d7a356e8",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-10-21T13:36:38.150712",
+    "create_time": "2024-10-21T13:36:24.950457",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "0085f6e78400ca37",
+    "external_id": "gxy-wjnsd",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/172/registry.xml' '/galaxy/server/database/jobs_directory/000/172/upload_params.json' '209:/galaxy/server/database/objects/7/1/d/dataset_71ddf6a7-aa29-45a9-a35e-3c0dd8fc810f_files:/galaxy/server/database/objects/7/1/d/dataset_71ddf6a7-aa29-45a9-a35e-3c0dd8fc810f.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_l0aklrx_\"",
+        "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"WT3.counts\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_w44488ji\", \"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": "8f78610ed5d14c6d",
+            "src": "hda",
+            "uuid": "71ddf6a7-aa29-45a9-a35e-3c0dd8fc810f"
+        }
+    },
+    "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": []
+}