Updating anvil-production README for prod-24-09-02-12-34-1

anvilproject · Sep 2, 2024 · 734eb5d · 734eb5d
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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 Aug 20 12:48:20 2024"
     },
     "1": {
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-        "date1": "Mon Aug 26 12:48:20 2024",
-        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-26-12-32-1/tools.yml",
-        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-19-12-32-1/results.html",
-        "date2": "Mon Aug 19 12:47:26 2024"
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/results.html",
+        "date1": "Mon Sep 02 12:49:25 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/tools.yml",
+        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-26-12-32-1/results.html",
+        "date2": "Mon Aug 26 12:48:20 2024"
     },
     "2": {
         "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-27-00-31-1/results.html",

diff --git a/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/chunk.json b/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/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-24-09-02-12-34-1/results.html",
+        "date1": "Mon Sep 02 12:49:25 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/tools.yml"
+    }
+}
diff --git a/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/chunk.txt b/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/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-24-09-02-12-34-1/errors/12681b9a3ceebc02.json b/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/errors/12681b9a3ceebc02.json
@@ -0,0 +1,48 @@
+{
+    "model_class": "Job",
+    "id": "12681b9a3ceebc02",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-02T13:00:31.227755",
+    "create_time": "2024-09-02T13:00:25.925995",
+    "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": "23978eb40fac2e5c",
+    "external_id": "gxy-sf4nm",
+    "command_line": "gx-fastq-groomer '/galaxy/server/database/objects/3/6/2/dataset_36297608-92b6-4ad1-af38-92324c641133.dat' solexa '/galaxy/server/database/objects/6/1/0/dataset_610f7637-dd21-4642-a56f-19f62ac3ddff.dat' solexa None 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\": \"None\", \"options_type_selector\": \"advanced\", \"output_type\": \"solexa\", \"summarize_input\": \"summarize_input\"}",
+        "input_type": "\"solexa\""
+    },
+    "inputs": {
+        "input_file": {
+            "id": "9168252f8aad37e5",
+            "src": "hda",
+            "uuid": "36297608-92b6-4ad1-af38-92324c641133"
+        }
+    },
+    "outputs": {
+        "output_file": {
+            "id": "7a0283391e8686d0",
+            "src": "hda",
+            "uuid": "610f7637-dd21-4642-a56f-19f62ac3ddff"
+        }
+    },
+    "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-24-09-02-12-34-1/errors/30ba8669a56c4e06.json b/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/errors/30ba8669a56c4e06.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "30ba8669a56c4e06",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-02T12:56:49.552406",
+    "create_time": "2024-09-02T12:56:41.435958",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "23978eb40fac2e5c",
+    "external_id": "gxy-qq5hq",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/26/registry.xml' '/galaxy/server/database/jobs_directory/000/26/upload_params.json' '42:/galaxy/server/database/objects/a/4/1/dataset_a41933fd-f7aa-4ef4-a5bc-b00a0326f2b3_files:/galaxy/server/database/objects/a/4/1/dataset_a41933fd-f7aa-4ef4-a5bc-b00a0326f2b3.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_frzy421h\"",
+        "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_n74m86pn\", \"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": "39c39aa7d5d6beff",
+            "src": "hda",
+            "uuid": "a41933fd-f7aa-4ef4-a5bc-b00a0326f2b3"
+        }
+    },
+    "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-24-09-02-12-34-1/errors/39c39aa7d5d6beff.json b/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/errors/39c39aa7d5d6beff.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "39c39aa7d5d6beff",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-02T13:00:11.124590",
+    "create_time": "2024-09-02T13:00:03.232987",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "23978eb40fac2e5c",
+    "external_id": "gxy-gn8bc",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/42/registry.xml' '/galaxy/server/database/jobs_directory/000/42/upload_params.json' '58:/galaxy/server/database/objects/9/e/1/dataset_9e15c63c-d1cf-4727-9244-891ef012eea5_files:/galaxy/server/database/objects/9/e/1/dataset_9e15c63c-d1cf-4727-9244-891ef012eea5.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_3dxsjxol\"",
+        "files_metadata": "{\"__current_case__\": 78, \"file_type\": \"fastq\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"sanger_full_range_original_sanger.fastqsanger\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_ncl4m4b8\", \"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": "78c8de430e5f50a8",
+            "src": "hda",
+            "uuid": "9e15c63c-d1cf-4727-9244-891ef012eea5"
+        }
+    },
+    "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-24-09-02-12-34-1/errors/47a1d5dd6efea740.json b/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/errors/47a1d5dd6efea740.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "47a1d5dd6efea740",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-02T13:24:23.894685",
+    "create_time": "2024-09-02T13:24:14.213455",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "23978eb40fac2e5c",
+    "external_id": "gxy-5pds5",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/169/registry.xml' '/galaxy/server/database/jobs_directory/000/169/upload_params.json' '203:/galaxy/server/database/objects/b/d/f/dataset_bdf0eca2-43e8-4b2a-9f23-79334f528318_files:/galaxy/server/database/objects/b/d/f/dataset_bdf0eca2-43e8-4b2a-9f23-79334f528318.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_ltu4krh2\"",
+        "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"matrix.txt\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_5s52m7lq\", \"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": "50d53ea8a8192de0",
+            "src": "hda",
+            "uuid": "bdf0eca2-43e8-4b2a-9f23-79334f528318"
+        }
+    },
+    "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-24-09-02-12-34-1/errors/5749c0e6df9a7ebd.json b/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/errors/5749c0e6df9a7ebd.json
@@ -0,0 +1,87 @@
+{
+    "model_class": "Job",
+    "id": "5749c0e6df9a7ebd",
+    "state": "error",
+    "exit_code": 0,
+    "update_time": "2024-09-02T13:14:18.163366",
+    "create_time": "2024-09-02T13:14:04.632944",
+    "galaxy_version": "23.1",
+    "command_version": "",
+    "copied_from_job_id": null,
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/vcftools_slice/vcftools_slice/0.1",
+    "history_id": "23978eb40fac2e5c",
+    "external_id": "gxy-kvfq4",
+    "command_line": "vcf-sort /galaxy/server/database/objects/c/7/7/dataset_c77b8c7c-2427-4383-832e-6a406465cf30.dat > sorted.vcf  ; echo '#dummy header' | cat - /galaxy/server/database/objects/8/1/c/dataset_81cd49af-141c-4705-9406-a5d23c335629.dat > regions.bed  ; vcftools --vcf sorted.vcf --out output --bed regions.bed --recode",
+    "traceback": null,
+    "params": {
+        "__input_ext": "\"vcf\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\""
+    },
+    "inputs": {
+        "regions": {
+            "id": "adfb05b1c09dcc79",
+            "src": "hda",
+            "uuid": "81cd49af-141c-4705-9406-a5d23c335629"
+        },
+        "input": {
+            "id": "543e429489ccb417",
+            "src": "hda",
+            "uuid": "c77b8c7c-2427-4383-832e-6a406465cf30"
+        }
+    },
+    "outputs": {
+        "output": {
+            "id": "45fd9bd910a5de5e",
+            "src": "hda",
+            "uuid": "1f1a3e62-3ff7-45a4-aea3-36f6b821d24e"
+        }
+    },
+    "output_collections": {},
+    "tool_stdout": "\nVCFtools - v0.1.11\n(C) Adam Auton 2009\n\nParameters as interpreted:\n\t--vcf sorted.vcf\n\t--out output\n\t--recode\n\t--bed regions.bed\n\nIndex file is older than variant file. Will regenerate.\nBuilding new index file.\nError:No header or meta information. Invalid file: sorted.vcf\n",
+    "tool_stderr": "/galaxy/server/database/jobs_directory/000/114/tool_script.sh: line 22: vcf-sort: command not found\n",
+    "job_stdout": "",
+    "job_stderr": "",
+    "stderr": "/galaxy/server/database/jobs_directory/000/114/tool_script.sh: line 22: vcf-sort: command not found\n",
+    "stdout": "\nVCFtools - v0.1.11\n(C) Adam Auton 2009\n\nParameters as interpreted:\n\t--vcf sorted.vcf\n\t--out output\n\t--recode\n\t--bed regions.bed\n\nIndex file is older than variant file. Will regenerate.\nBuilding new index file.\nError:No header or meta information. Invalid file: sorted.vcf\n",
+    "job_messages": [],
+    "dependencies": [],
+    "user_email": "tests@fake.org",
+    "job_metrics": [
+        {
+            "title": "Job Runtime (Wall Clock)",
+            "value": "0 seconds",
+            "plugin": "core",
+            "name": "runtime_seconds",
+            "raw_value": "0E-7"
+        },
+        {
+            "title": "Job End Time",
+            "value": "2024-09-02 13:14:09",
+            "plugin": "core",
+            "name": "end_epoch",
+            "raw_value": "1725282849.0000000"
+        },
+        {
+            "title": "Job Start Time",
+            "value": "2024-09-02 13:14:09",
+            "plugin": "core",
+            "name": "start_epoch",
+            "raw_value": "1725282849.0000000"
+        },
+        {
+            "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-24-09-02-12-34-1/errors/5c3a0426b896d3cf.json b/reports/anvil-production/tool-tests/prod-24-09-02-12-34-1/errors/5c3a0426b896d3cf.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "5c3a0426b896d3cf",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-02T12:51:54.267744",
+    "create_time": "2024-09-02T12:51:45.310577",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "23978eb40fac2e5c",
+    "external_id": "gxy-fndrs",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/5/registry.xml' '/galaxy/server/database/jobs_directory/000/5/upload_params.json' '9:/galaxy/server/database/objects/a/8/4/dataset_a84f6a37-581b-4e59-957e-f0906792b507_files:/galaxy/server/database/objects/a/8/4/dataset_a84f6a37-581b-4e59-957e-f0906792b507.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_xrobmqq7\"",
+        "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"accessions_1.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9w82kh2p\", \"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": "a8e290ed65b9f81f",
+            "src": "hda",
+            "uuid": "a84f6a37-581b-4e59-957e-f0906792b507"
+        }
+    },
+    "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": []
+}