Updating anvil-production README for prod-24-09-13-12-33-1

anvilproject · Sep 13, 2024 · 033bb5a · 033bb5a
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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
@@ -49,11 +49,11 @@
         "date2": "Tue Sep 03 00:47:25 2024"
     },
     "9": {
-        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-06-12-32-1/results.html",
-        "date1": "Fri Sep 06 12:48:21 2024",
-        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-06-12-32-1/tools.yml",
-        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-30-12-32-1/results.html",
-        "date2": "Fri Aug 30 12:48:09 2024"
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/results.html",
+        "date1": "Fri Sep 13 12:48:35 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/tools.yml",
+        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-06-12-32-1/results.html",
+        "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",

diff --git a/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/chunk.json b/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/chunk.json
@@ -0,0 +1,7 @@
+{
+    "9": {
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/results.html",
+        "date1": "Fri Sep 13 12:48:35 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/tools.yml"
+    }
+}
diff --git a/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/chunk.txt b/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/chunk.txt
@@ -0,0 +1,15 @@
+-t sqlite_to_tabular --tool-version bce29ec10b78
+-t replace_column_by_key_value_file --tool-version d533e4b75800
+-t fastqc --tool-version e7b2202befea
+-t samtools_markdup --tool-version 83b8e36e9cbe
+-t bamtools_filter --tool-version cb20f99fd45b
+-t bcftools_cnv --tool-version 01d6b7d6365e
+-t bcftools_roh --tool-version b76adb2f1c51
+-t vcfbedintersect --tool-version aea8e90ad788
+-t vcfvcfintersect --tool-version 166c4f50525f
+-t poretools_hist --tool-version 5a82eb9e1b89
+-t deeptools_compute_matrix --tool-version 514fa53b5efb
+-t deeptools_bam_coverage --tool-version bb1e4f63e0e6
+-t lofreq_indelqual --tool-version 426d707dfc47
+-t snpsift --tool-version 2e497a770bca
+-t mummer_nucmer --tool-version 636b049e6141
diff --git a/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/errors/1ee5301288f20bcd.json b/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/errors/1ee5301288f20bcd.json
@@ -0,0 +1,61 @@
+{
+    "model_class": "Job",
+    "id": "1ee5301288f20bcd",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-13T12:51:53.517812",
+    "create_time": "2024-09-13T12:51:46.277706",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy1",
+    "history_id": "57401f7398b62ea4",
+    "external_id": "gxy-bf9t5",
+    "command_line": "ln -s '/galaxy/server/database/objects/3/a/7/dataset_3a73a641-51b6-474a-9658-0d42978e3f07.dat' '1000trimmed_fastq' && mkdir -p '/galaxy/server/database/objects/3/4/e/dataset_34ee147c-19e1-459f-a60e-ad004bd34bf9_files' && fastqc --outdir '/galaxy/server/database/objects/3/4/e/dataset_34ee147c-19e1-459f-a60e-ad004bd34bf9_files' --contaminants '/galaxy/server/database/objects/2/9/4/dataset_294903b9-7871-4e93-9c8e-4bdf33f4e3ad.dat'   --threads ${GALAXY_SLOTS:-2} --dir ${TEMP:-$_GALAXY_JOB_TMP_DIR} --quiet --extract  --kmers 7 -f 'fastq' '1000trimmed_fastq'  && cp '/galaxy/server/database/objects/3/4/e/dataset_34ee147c-19e1-459f-a60e-ad004bd34bf9_files'/*/fastqc_data.txt output.txt && cp '/galaxy/server/database/objects/3/4/e/dataset_34ee147c-19e1-459f-a60e-ad004bd34bf9_files'/*\\.html output.html",
+    "traceback": null,
+    "params": {
+        "__input_ext": "\"input\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "kmers": "\"7\"",
+        "min_length": "\"\"",
+        "nogroup": "false",
+        "limits": null,
+        "adapters": null
+    },
+    "inputs": {
+        "input_file": {
+            "id": "a3205355fea834a1",
+            "src": "hda",
+            "uuid": "3a73a641-51b6-474a-9658-0d42978e3f07"
+        },
+        "contaminants": {
+            "id": "1ee5301288f20bcd",
+            "src": "hda",
+            "uuid": "294903b9-7871-4e93-9c8e-4bdf33f4e3ad"
+        }
+    },
+    "outputs": {
+        "text_file": {
+            "id": "23956ed43f4202a0",
+            "src": "hda",
+            "uuid": "9afc0ae2-e52f-464c-a552-b2a3c5e0bea1"
+        },
+        "html_file": {
+            "id": "bec8baf85e485800",
+            "src": "hda",
+            "uuid": "34ee147c-19e1-459f-a60e-ad004bd34bf9"
+        }
+    },
+    "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-24-09-13-12-33-1/errors/7f799bd510a28136.json b/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/errors/7f799bd510a28136.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "7f799bd510a28136",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-13T12:52:40.756000",
+    "create_time": "2024-09-13T12:52:30.803451",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "57401f7398b62ea4",
+    "external_id": "gxy-cl469",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/11/registry.xml' '/galaxy/server/database/jobs_directory/000/11/upload_params.json' '14:/galaxy/server/database/objects/3/9/6/dataset_396cad9f-4228-417f-8538-fde65ff3e63f_files:/galaxy/server/database/objects/3/9/6/dataset_396cad9f-4228-417f-8538-fde65ff3e63f.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_3uiw_22t\"",
+        "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"1000trimmed.fastq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_lhf5zxm0\", \"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": "22a3a53eec4dc684",
+            "src": "hda",
+            "uuid": "396cad9f-4228-417f-8538-fde65ff3e63f"
+        }
+    },
+    "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-24-09-13-12-33-1/errors/ae9d1c8a286997a4.json b/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/errors/ae9d1c8a286997a4.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "ae9d1c8a286997a4",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-13T13:03:34.388771",
+    "create_time": "2024-09-13T13:03:24.742047",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "57401f7398b62ea4",
+    "external_id": "gxy-vvrp2",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/54/registry.xml' '/galaxy/server/database/jobs_directory/000/54/upload_params.json' '70:/galaxy/server/database/objects/2/5/4/dataset_2543075c-2295-4edc-9456-e722c4ac657e_files:/galaxy/server/database/objects/2/5/4/dataset_2543075c-2295-4edc-9456-e722c4ac657e.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_l5s535sp\"",
+        "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"vcflib-test-genome-phix.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_xkdbbw1p\", \"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": "4e852b4933785fed",
+            "src": "hda",
+            "uuid": "2543075c-2295-4edc-9456-e722c4ac657e"
+        }
+    },
+    "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-24-09-13-12-33-1/errors/c1b25d7d928c3338.json b/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/errors/c1b25d7d928c3338.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "c1b25d7d928c3338",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-13T13:02:47.184868",
+    "create_time": "2024-09-13T13:02:37.020586",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "57401f7398b62ea4",
+    "external_id": "gxy-ngwzf",
+    "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' '64:/galaxy/server/database/objects/d/0/c/dataset_d0c57a36-2700-48ea-9e7e-0d918debc846_files:/galaxy/server/database/objects/d/0/c/dataset_d0c57a36-2700-48ea-9e7e-0d918debc846.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_4yzf94_4\"",
+        "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"vcflib.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_m3aw5fl7\", \"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": "94e988f24a2940c3",
+            "src": "hda",
+            "uuid": "d0c57a36-2700-48ea-9e7e-0d918debc846"
+        }
+    },
+    "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-24-09-13-12-33-1/errors/dbdc826e649e374e.json b/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/errors/dbdc826e649e374e.json
@@ -0,0 +1,47 @@
+{
+    "model_class": "Job",
+    "id": "dbdc826e649e374e",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-13T13:13:14.850311",
+    "create_time": "2024-09-13T13:13:09.751212",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy1",
+    "history_id": "57401f7398b62ea4",
+    "external_id": "gxy-6kvjn",
+    "command_line": "lofreq indelqual --uniform 20 -o output.bam /galaxy/server/database/objects/c/2/5/dataset_c253d643-255a-4ac3-9490-8a4e356076da.dat",
+    "traceback": null,
+    "params": {
+        "__input_ext": "\"input\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "strategy": "{\"__current_case__\": 0, \"deletions\": \"\", \"insertions\": \"20\", \"selector\": \"uniform\"}"
+    },
+    "inputs": {
+        "reads": {
+            "id": "cf2071ea82745af9",
+            "src": "hda",
+            "uuid": "c253d643-255a-4ac3-9490-8a4e356076da"
+        }
+    },
+    "outputs": {
+        "output": {
+            "id": "a083bdfdd75782eb",
+            "src": "hda",
+            "uuid": "fd317dac-31c1-43a1-980e-010cad45b415"
+        }
+    },
+    "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-24-09-13-12-33-1/errors/f2289033cdf645a6.json b/reports/anvil-production/tool-tests/prod-24-09-13-12-33-1/errors/f2289033cdf645a6.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "f2289033cdf645a6",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-13T13:12:43.469271",
+    "create_time": "2024-09-13T13:12:33.237332",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "57401f7398b62ea4",
+    "external_id": "gxy-52frq",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/91/registry.xml' '/galaxy/server/database/jobs_directory/000/91/upload_params.json' '107:/galaxy/server/database/objects/0/b/0/dataset_0b001f7a-be72-4ad2-97f9-ebb1c0c6e8b5_files:/galaxy/server/database/objects/0/b/0/dataset_0b001f7a-be72-4ad2-97f9-ebb1c0c6e8b5.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_kj6wauet\"",
+        "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"pBR322.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_jyxsh01_\", \"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": "63f2d075265fe0ec",
+            "src": "hda",
+            "uuid": "0b001f7a-be72-4ad2-97f9-ebb1c0c6e8b5"
+        }
+    },
+    "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": []
+}