Updating anvil-production README for prod-24-09-03-00-32-1

anvilproject · Sep 3, 2024 · bf771f9 · bf771f9
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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
@@ -42,11 +42,11 @@
         "date2": "Mon Aug 26 12:48:20 2024"
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-        "date1": "Tue Aug 27 00:46:45 2024",
-        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-27-00-31-1/tools.yml",
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-        "date2": "Tue Aug 20 00:46:51 2024"
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/results.html",
+        "date1": "Tue Sep 03 00:47:25 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/tools.yml",
+        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-08-27-00-31-1/results.html",
+        "date2": "Tue Aug 27 00:46:45 2024"
     },
     "9": {
         "run1": "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",

diff --git a/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/chunk.json b/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/chunk.json
@@ -0,0 +1,7 @@
+{
+    "2": {
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/results.html",
+        "date1": "Tue Sep 03 00:47:25 2024",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/tools.yml"
+    }
+}
diff --git a/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/chunk.txt b/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/chunk.txt
@@ -0,0 +1,15 @@
+-t collapse_collections --tool-version 90981f86000f
+-t text_processing --tool-version ddf54b12c295
+-t fastq_manipulation --tool-version 5b87038565bb
+-t sam_pileup --tool-version a3b4ad6858ff
+-t samtools_calmd --tool-version 06dc50b7b711
+-t bcftools_consensus --tool-version d6dc477167f8
+-t bcftools_plugin_impute_info --tool-version 776ad0b21536
+-t bcftools_query --tool-version c9c5718edc19
+-t vcfgeno2haplo --tool-version a3dea556218d
+-t medaka_variant --tool-version 43815fa60f3a
+-t poretools_times --tool-version 960be5e0b47e
+-t deeptools_multi_bam_summary --tool-version 78f405266706
+-t lastz --tool-version e7f19d6a9af8
+-t ivar_trim --tool-version db536ad45f28
+-t sailfish --tool-version a8f343909c17
diff --git a/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/errors/13e694cc470506f3.json b/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/errors/13e694cc470506f3.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "13e694cc470506f3",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-03T00:50:53.728755",
+    "create_time": "2024-09-03T00:50:45.310003",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "5cea9815ef649afa",
+    "external_id": "gxy-pqjgk",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/10/registry.xml' '/galaxy/server/database/jobs_directory/000/10/upload_params.json' '10:/galaxy/server/database/objects/e/b/3/dataset_eb3e7104-48a3-4694-bc94-777ba5fff0a0_files:/galaxy/server/database/objects/e/b/3/dataset_eb3e7104-48a3-4694-bc94-777ba5fff0a0.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_f211ez0i\"",
+        "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}",
+        "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_myf5a43p\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+        "file_count": "\"auto\"",
+        "file_type": "\"fastqsanger\""
+    },
+    "inputs": {},
+    "outputs": {
+        "output0": {
+            "id": "13e694cc470506f3",
+            "src": "hda",
+            "uuid": "eb3e7104-48a3-4694-bc94-777ba5fff0a0"
+        }
+    },
+    "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-24-09-03-00-32-1/errors/2016ff1e950e9a83.json b/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/errors/2016ff1e950e9a83.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "2016ff1e950e9a83",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-03T01:06:02.176908",
+    "create_time": "2024-09-03T01:05:53.151142",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "5cea9815ef649afa",
+    "external_id": "gxy-gt8kj",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/82/registry.xml' '/galaxy/server/database/jobs_directory/000/82/upload_params.json' '85:/galaxy/server/database/objects/1/4/b/dataset_14b9df78-3cf8-47ac-993c-6b0ad28550b6_files:/galaxy/server/database/objects/1/4/b/dataset_14b9df78-3cf8-47ac-993c-6b0ad28550b6.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_ylxnk825\"",
+        "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"ARTIC-V1-bad.bed\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_qyn9fkes\", \"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": "4a974719d1cb6a8b",
+            "src": "hda",
+            "uuid": "14b9df78-3cf8-47ac-993c-6b0ad28550b6"
+        }
+    },
+    "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-24-09-03-00-32-1/errors/25322fb1e4f09432.json b/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/errors/25322fb1e4f09432.json
@@ -0,0 +1,84 @@
+{
+    "model_class": "Job",
+    "id": "25322fb1e4f09432",
+    "state": "error",
+    "exit_code": 1,
+    "update_time": "2024-09-03T00:49:48.755565",
+    "create_time": "2024-09-03T00:49:38.110359",
+    "galaxy_version": "23.1",
+    "command_version": "",
+    "copied_from_job_id": null,
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5",
+    "history_id": "5cea9815ef649afa",
+    "external_id": "gxy-45nx4",
+    "command_line": "gx-fastq-manipulation '/galaxy/server/database/objects/5/3/b/dataset_53b69ecb-ce01-4dfa-adbb-b6fa292dcfd8.dat' '/galaxy/server/database/jobs_directory/000/5/configs/tmp39g705iy' '/galaxy/server/database/objects/e/9/3/dataset_e9319a7e-c009-4d71-9ebd-6b5f45f8b7e6.dat' '/galaxy/server/database/objects/e/9/3/dataset_e9319a7e-c009-4d71-9ebd-6b5f45f8b7e6_files' 'sanger'",
+    "traceback": null,
+    "params": {
+        "__input_ext": "\"fastqsanger\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "manipulate_blocks": "[{\"__index__\": 0, \"manipulation_type\": {\"__current_case__\": 3, \"manipulation\": {\"__current_case__\": 0, \"manipulation_selector\": \"remove\"}, \"manipulation_type_selector\": \"miscellaneous\"}}]",
+        "match_blocks": "[{\"__index__\": 0, \"match_type\": {\"__current_case__\": 0, \"match\": {\"__current_case__\": 0, \"match_by\": \".*\", \"match_selector\": \"regex\"}, \"match_type_selector\": \"identifier\"}}]"
+    },
+    "inputs": {
+        "input_file": {
+            "id": "a6980d35911d564f",
+            "src": "hda",
+            "uuid": "53b69ecb-ce01-4dfa-adbb-b6fa292dcfd8"
+        }
+    },
+    "outputs": {
+        "output_file": {
+            "id": "25322fb1e4f09432",
+            "src": "hda",
+            "uuid": "e9319a7e-c009-4d71-9ebd-6b5f45f8b7e6"
+        }
+    },
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "Traceback (most recent call last):\n  File \"/usr/local/bin/gx-fastq-manipulation\", line 6, in <module>\n    from galaxy_utils.sequence.scripts.fastq_manipulation import main\n  File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_manipulation.py\", line 5, in <module>\n    import imp\nModuleNotFoundError: No module named 'imp'\n",
+    "job_stdout": "",
+    "job_stderr": "",
+    "stderr": "Traceback (most recent call last):\n  File \"/usr/local/bin/gx-fastq-manipulation\", line 6, in <module>\n    from galaxy_utils.sequence.scripts.fastq_manipulation import main\n  File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_manipulation.py\", line 5, in <module>\n    import imp\nModuleNotFoundError: No module named 'imp'\n",
+    "stdout": "",
+    "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": "2024-09-03 00:49:40",
+            "plugin": "core",
+            "name": "end_epoch",
+            "raw_value": "1725324580.0000000"
+        },
+        {
+            "title": "Job Start Time",
+            "value": "2024-09-03 00:49:40",
+            "plugin": "core",
+            "name": "start_epoch",
+            "raw_value": "1725324580.0000000"
+        },
+        {
+            "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-24-09-03-00-32-1/errors/2a9f1f58f7f505ab.json b/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/errors/2a9f1f58f7f505ab.json
@@ -0,0 +1,44 @@
+{
+    "model_class": "Job",
+    "id": "2a9f1f58f7f505ab",
+    "state": "error",
+    "exit_code": null,
+    "update_time": "2024-09-03T01:00:38.641949",
+    "create_time": "2024-09-03T01:00:28.830379",
+    "galaxy_version": "23.1",
+    "command_version": null,
+    "copied_from_job_id": null,
+    "tool_id": "upload1",
+    "history_id": "5cea9815ef649afa",
+    "external_id": "gxy-dtcld",
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/60/registry.xml' '/galaxy/server/database/jobs_directory/000/60/upload_params.json' '63:/galaxy/server/database/objects/a/7/d/dataset_a7dfd2b2-410d-4873-9807-4ac9304c45be_files:/galaxy/server/database/objects/a/7/d/dataset_a7dfd2b2-410d-4873-9807-4ac9304c45be.dat'",
+    "traceback": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_tqypnle8\"",
+        "files_metadata": "{\"__current_case__\": 677, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"medaka_test.bam\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_s7ttc1t7\", \"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": "abce0cf98c871e18",
+            "src": "hda",
+            "uuid": "a7dfd2b2-410d-4873-9807-4ac9304c45be"
+        }
+    },
+    "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-24-09-03-00-32-1/errors/2ab23876e8d29207.json b/reports/anvil-production/tool-tests/prod-24-09-03-00-32-1/errors/2ab23876e8d29207.json
@@ -0,0 +1,84 @@
+{
+    "model_class": "Job",
+    "id": "2ab23876e8d29207",
+    "state": "error",
+    "exit_code": 1,
+    "update_time": "2024-09-03T00:53:34.843041",
+    "create_time": "2024-09-03T00:53:25.259366",
+    "galaxy_version": "23.1",
+    "command_version": "",
+    "copied_from_job_id": null,
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5",
+    "history_id": "5cea9815ef649afa",
+    "external_id": "gxy-4qh7z",
+    "command_line": "gx-fastq-manipulation '/galaxy/server/database/objects/2/8/b/dataset_28b48c91-2079-4cd3-b92f-ed3ba840f4a5.dat' '/galaxy/server/database/jobs_directory/000/22/configs/tmpfh35axln' '/galaxy/server/database/objects/4/a/6/dataset_4a657d2f-56ff-47f0-bf7c-b1f60e794708.dat' '/galaxy/server/database/objects/4/a/6/dataset_4a657d2f-56ff-47f0-bf7c-b1f60e794708_files' 'sanger'",
+    "traceback": null,
+    "params": {
+        "__input_ext": "\"fastqsanger\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "manipulate_blocks": "[{\"__index__\": 0, \"manipulation_type\": {\"__current_case__\": 1, \"manipulation\": {\"__current_case__\": 4, \"manipulation_selector\": \"dna_to_rna\"}, \"manipulation_type_selector\": \"sequence\"}}]",
+        "match_blocks": "[{\"__index__\": 0, \"match_type\": {\"__current_case__\": 0, \"match\": {\"__current_case__\": 0, \"match_by\": \".*\", \"match_selector\": \"regex\"}, \"match_type_selector\": \"identifier\"}}]"
+    },
+    "inputs": {
+        "input_file": {
+            "id": "ee8b432010ad06b7",
+            "src": "hda",
+            "uuid": "28b48c91-2079-4cd3-b92f-ed3ba840f4a5"
+        }
+    },
+    "outputs": {
+        "output_file": {
+            "id": "2ab23876e8d29207",
+            "src": "hda",
+            "uuid": "4a657d2f-56ff-47f0-bf7c-b1f60e794708"
+        }
+    },
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "Traceback (most recent call last):\n  File \"/usr/local/bin/gx-fastq-manipulation\", line 6, in <module>\n    from galaxy_utils.sequence.scripts.fastq_manipulation import main\n  File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_manipulation.py\", line 5, in <module>\n    import imp\nModuleNotFoundError: No module named 'imp'\n",
+    "job_stdout": "",
+    "job_stderr": "",
+    "stderr": "Traceback (most recent call last):\n  File \"/usr/local/bin/gx-fastq-manipulation\", line 6, in <module>\n    from galaxy_utils.sequence.scripts.fastq_manipulation import main\n  File \"/usr/local/lib/python3.12/site-packages/galaxy_utils/sequence/scripts/fastq_manipulation.py\", line 5, in <module>\n    import imp\nModuleNotFoundError: No module named 'imp'\n",
+    "stdout": "",
+    "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": "2024-09-03 00:53:26",
+            "plugin": "core",
+            "name": "end_epoch",
+            "raw_value": "1725324806.0000000"
+        },
+        {
+            "title": "Job Start Time",
+            "value": "2024-09-03 00:53:26",
+            "plugin": "core",
+            "name": "start_epoch",
+            "raw_value": "1725324806.0000000"
+        },
+        {
+            "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"
+        }
+    ]
+}