Updating anvil-edge README for edge-25-01-03-06-11-1

anvilproject · Jan 3, 2025 · 0e4fe95 · 0e4fe95
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diff --git a/reports/anvil-edge/README.md b/reports/anvil-edge/README.md
diff --git a/reports/anvil-edge/tool-tests/chunks.json b/reports/anvil-edge/tool-tests/chunks.json
@@ -49,11 +49,11 @@
         "date2": "Thu Dec 26 18:33:25 2024"
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-        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-12-27-06-11-1/tools.yml",
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-        "date2": "Fri Dec 20 06:26:59 2024"
+        "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/results.html",
+        "date1": "Fri Jan 03 06:26:56 2025",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/tools.yml",
+        "run2": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-12-27-06-11-1/results.html",
+        "date2": "Fri Dec 27 06:28:36 2024"
     },
     "9": {
         "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-12-27-18-17-1/results.html",

diff --git a/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/chunk.json b/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/chunk.json
@@ -0,0 +1,7 @@
+{
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+        "date1": "Fri Jan 03 06:26:56 2025",
+        "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/tools.yml"
+    }
+}
diff --git a/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/chunk.txt b/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/chunk.txt
@@ -0,0 +1,27 @@
+-t collection_column_join --tool-version 071084070619
+-t collection_column_join --tool-version 58228a4d58fe
+-t deeptools_plot_coverage --tool-version 56bce3c82278
+-t trim_galore --tool-version 084bbd8ba7b8
+-t minimap2 --tool-version f54f5baedfdd
+-t flye --tool-version 3ee0ef312022
+-t poretools_tabular --tool-version 2cb2feb94f0e
+-t hisat2 --tool-version 26371a1df031
+-t hisat2 --tool-version f4af63aaf57a
+-t samtools_merge --tool-version 740ce0a18f0d
+-t samtools_merge --tool-version 36677f429310
+-t bam_to_sam --tool-version 88eedb4abea0
+-t anndata_export --tool-version 707023fa62fe
+-t anndata_export --tool-version 0cb889db0910
+-t alevin --tool-version 04b494623f8e
+-t alevin --tool-version e4c01dcece8b
+-t scanpy_plot --tool-version aa0c474463c2
+-t scanpy_plot --tool-version a8f865950ac4
+-t scanpy_run_pca --tool-version 988edd5fa902
+-t scanpy_run_pca --tool-version ce93e630b55a
+-t table_compute --tool-version 60ff16842fcd
+-t lofreq_viterbi --tool-version aa35ee7f3ab2
+-t bcftools_convert_to_vcf --tool-version fec517907949
+-t bcftools_plugin_fill_an_ac --tool-version 582f8b13873d
+-t vcfaddinfo --tool-version 6ea73d6151ec
+-t vcfleftalign --tool-version 29f9b782727e
+-t ivar_consensus --tool-version 78bbd17d0703
diff --git a/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/0bf151e7ab34816d.json b/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/0bf151e7ab34816d.json
@@ -0,0 +1,58 @@
+{
+    "model_class": "Job",
+    "id": "0bf151e7ab34816d",
+    "history_id": "218df8b1d7cc9fd4",
+    "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2025-01-03T06:41:24.619906",
+    "update_time": "2025-01-03T06:41:29.037661",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-2ksv9",
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+    "job_runner_name": null,
+    "command_line": "ln -f -s '/galaxy/server/database/objects/f/d/4/dataset_fd4cb477-f6ad-41ab-840d-4d79a64be0f4.dat' reference.fa && minimap2 -x sr    --q-occ-frac 0.01  --mask-len 100      -t ${GALAXY_SLOTS:-4} reference.fa '/galaxy/server/database/objects/5/a/6/dataset_5a66b346-efbc-4451-95d2-5903371d1c26.dat' -a | samtools view --no-PG -hT reference.fa | samtools sort -@${GALAXY_SLOTS:-2} -T \"${TMPDIR:-.}\" -O BAM -o '/galaxy/server/database/objects/1/5/1/dataset_1513cb29-3c8f-4755-b47d-251802642d8f.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "__input_ext": "\"input\"",
+        "dbkey": "\"?\"",
+        "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"",
+        "io_options": "{\"K\": \"\", \"L\": false, \"Q\": false, \"Y\": false, \"c\": false, \"cs\": null, \"eqx\": false, \"output_format\": \"BAM\"}",
+        "alignment_options": "{\"A\": \"\", \"B\": \"\", \"E\": \"\", \"E2\": \"\", \"O\": \"\", \"O2\": \"\", \"no_end_flt\": true, \"s\": \"\", \"splicing\": {\"__current_case__\": 0, \"splice_mode\": \"preset\"}, \"z\": \"\", \"z2\": \"\"}",
+        "mapping_options": "{\"F\": \"\", \"N\": \"\", \"X\": false, \"f\": \"\", \"g\": \"\", \"kmer_ocurrence_interval\": {\"__current_case__\": 1, \"interval\": \"\"}, \"m\": \"\", \"mask_len\": \"100\", \"max_chain_iter\": \"\", \"max_chain_skip\": \"\", \"min_occ_floor\": \"\", \"n\": \"\", \"p\": \"\", \"q_occ_frac\": \"0.01\", \"r\": \"\"}",
+        "indexing_options": "{\"H\": false, \"I\": \"\", \"k\": \"\", \"w\": \"\"}",
+        "fastq_input": "{\"__current_case__\": 0, \"analysis_type_selector\": \"sr\", \"fastq_input1\": {\"values\": [{\"id\": 80, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"single\"}",
+        "reference_source": "{\"__current_case__\": 1, \"ref_file\": {\"values\": [{\"id\": 79, \"src\": \"hda\"}]}, \"reference_source_selector\": \"history\"}"
+    },
+    "inputs": {
+        "fastq_input|fastq_input1": {
+            "id": "5e41ce9a2bd4922d",
+            "src": "hda",
+            "uuid": "5a66b346-efbc-4451-95d2-5903371d1c26"
+        },
+        "reference_source|ref_file": {
+            "id": "413f4dce264bf293",
+            "src": "hda",
+            "uuid": "fd4cb477-f6ad-41ab-840d-4d79a64be0f4"
+        }
+    },
+    "outputs": {
+        "alignment_output": {
+            "id": "d1fd7c7a1669bbb4",
+            "src": "hda",
+            "uuid": "1513cb29-3c8f-4755-b47d-251802642d8f"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "[M::mm_idx_gen::0.004*0.86] collected minimizers\n[M::mm_idx_gen::0.005*1.41] sorted minimizers\n[M::main::0.005*1.40] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.005*1.40] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.005*1.39] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967; total length: 16569\n[M::worker_pipeline::0.008*1.32] mapped 100 sequences\n[M::main] Version: 2.28-r1209\n[M::main] CMD: minimap2 -x sr --q-occ-frac 0.01 --mask-len 100 -t 8 -a reference.fa /galaxy/server/database/objects/5/a/6/dataset_5a66b346-efbc-4451-95d2-5903371d1c26.dat\n[M::main] Real time: 0.010 sec; CPU: 0.012 sec; Peak RSS: 0.004 GB\n",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "[M::mm_idx_gen::0.004*0.86] collected minimizers\n[M::mm_idx_gen::0.005*1.41] sorted minimizers\n[M::main::0.005*1.40] loaded/built the index for 1 target sequence(s)\n[M::mm_mapopt_update::0.005*1.40] mid_occ = 1000\n[M::mm_idx_stat] kmer size: 21; skip: 11; is_hpc: 0; #seq: 1\n[M::mm_idx_stat::0.005*1.39] distinct minimizers: 2777 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.967; total length: 16569\n[M::worker_pipeline::0.008*1.32] mapped 100 sequences\n[M::main] Version: 2.28-r1209\n[M::main] CMD: minimap2 -x sr --q-occ-frac 0.01 --mask-len 100 -t 8 -a reference.fa /galaxy/server/database/objects/5/a/6/dataset_5a66b346-efbc-4451-95d2-5903371d1c26.dat\n[M::main] Real time: 0.010 sec; CPU: 0.012 sec; Peak RSS: 0.004 GB\n",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/1c7d3bc913a9a7cb.json b/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/1c7d3bc913a9a7cb.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "1c7d3bc913a9a7cb",
+    "history_id": "218df8b1d7cc9fd4",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2025-01-03T08:36:10.562195",
+    "update_time": "2025-01-03T08:36:20.626091",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-gf8b4",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/556/registry.xml' '/galaxy/server/database/jobs_directory/000/556/upload_params.json' '725:/galaxy/server/database/objects/d/4/2/dataset_d42af63f-0ed9-443c-8753-89eb551f1193_files:/galaxy/server/database/objects/d/4/2/dataset_d42af63f-0ed9-443c-8753-89eb551f1193.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_xmlf_zqo\"",
+        "files_metadata": "{\"__current_case__\": 325, \"file_type\": \"tabular\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"convert.gs.gt.gen\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_9zmfcxf8\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]",
+        "file_count": "\"auto\"",
+        "file_type": "\"tabular\""
+    },
+    "inputs": {},
+    "outputs": {
+        "output0": {
+            "id": "d685c170d5e0b88d",
+            "src": "hda",
+            "uuid": "d42af63f-0ed9-443c-8753-89eb551f1193"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/1d408020e2de93f4.json b/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/1d408020e2de93f4.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "1d408020e2de93f4",
+    "history_id": "218df8b1d7cc9fd4",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2025-01-03T06:34:06.778643",
+    "update_time": "2025-01-03T06:34:17.573374",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-ngk4z",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/23/registry.xml' '/galaxy/server/database/jobs_directory/000/23/upload_params.json' '32:/galaxy/server/database/objects/b/9/3/dataset_b93b93d6-494b-4ebe-9a01-f548f491566e_files:/galaxy/server/database/objects/b/9/3/dataset_b93b93d6-494b-4ebe-9a01-f548f491566e.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_zohimo56\"",
+        "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"bwa-mem-fastq1.fq\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_iji1_89x\", \"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": "e85e466162ff4c28",
+            "src": "hda",
+            "uuid": "b93b93d6-494b-4ebe-9a01-f548f491566e"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/307e380ccf17659b.json b/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/307e380ccf17659b.json
diff --git a/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/37113b82c174ef04.json b/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/37113b82c174ef04.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "37113b82c174ef04",
+    "history_id": "218df8b1d7cc9fd4",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2025-01-03T08:19:29.027240",
+    "update_time": "2025-01-03T08:19:39.103926",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-r2cj7",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/492/registry.xml' '/galaxy/server/database/jobs_directory/000/492/upload_params.json' '661:/galaxy/server/database/objects/8/3/4/dataset_8346dcf0-d8e9-48ec-8032-863a6bb5e649_files:/galaxy/server/database/objects/8/3/4/dataset_8346dcf0-d8e9-48ec-8032-863a6bb5e649.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_8ltz1_cq\"",
+        "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"small.tsv\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_kltmku54\", \"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": "3a7b78d5009274f9",
+            "src": "hda",
+            "uuid": "8346dcf0-d8e9-48ec-8032-863a6bb5e649"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/4855bbcaea4c176c.json b/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/4855bbcaea4c176c.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "4855bbcaea4c176c",
+    "history_id": "218df8b1d7cc9fd4",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2025-01-03T06:42:03.600791",
+    "update_time": "2025-01-03T06:42:13.112530",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-kfpf6",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/69/registry.xml' '/galaxy/server/database/jobs_directory/000/69/upload_params.json' '86:/galaxy/server/database/objects/1/c/a/dataset_1caf140e-0988-4336-b3de-38bf73e387ab_files:/galaxy/server/database/objects/1/c/a/dataset_1caf140e-0988-4336-b3de-38bf73e387ab.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_4t_kvh1j\"",
+        "files_metadata": "{\"__current_case__\": 81, \"file_type\": \"fastqsanger\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"pacbio_hifi_reads.fasta.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_fe_ehxxv\", \"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": "98a66939cf0677be",
+            "src": "hda",
+            "uuid": "1caf140e-0988-4336-b3de-38bf73e387ab"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}
diff --git a/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/4902a9d4b5ff3caf.json b/reports/anvil-edge/tool-tests/edge-25-01-03-06-11-1/errors/4902a9d4b5ff3caf.json
@@ -0,0 +1,45 @@
+{
+    "model_class": "Job",
+    "id": "4902a9d4b5ff3caf",
+    "history_id": "218df8b1d7cc9fd4",
+    "tool_id": "upload1",
+    "state": "error",
+    "exit_code": null,
+    "create_time": "2025-01-03T07:05:39.840477",
+    "update_time": "2025-01-03T07:05:51.236431",
+    "galaxy_version": "24.1",
+    "external_id": "gxy-7wgfq",
+    "handler": null,
+    "job_runner_name": null,
+    "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/206/registry.xml' '/galaxy/server/database/jobs_directory/000/206/upload_params.json' '242:/galaxy/server/database/objects/7/1/3/dataset_7131880f-cd1b-41fd-b264-4beb496c04da_files:/galaxy/server/database/objects/7/1/3/dataset_7131880f-cd1b-41fd-b264-4beb496c04da.dat'",
+    "user_email": "tests@fake.org",
+    "command_version": null,
+    "params": {
+        "paramfile": "\"/galaxy/server/database/tmp/upload_params_4p2fv8fx\"",
+        "files_metadata": "{\"__current_case__\": 75, \"file_type\": \"fasta\"}",
+        "dbkey": "\"?\"",
+        "force_composite": "\"false\"",
+        "files": "[{\"NAME\": \"phiX.fa\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_0nz9zpxy\", \"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": "1e6aaeeda391132d",
+            "src": "hda",
+            "uuid": "7131880f-cd1b-41fd-b264-4beb496c04da"
+        }
+    },
+    "copied_from_job_id": null,
+    "output_collections": {},
+    "tool_stdout": "",
+    "tool_stderr": "",
+    "job_stdout": null,
+    "job_stderr": null,
+    "stdout": "",
+    "stderr": "",
+    "job_messages": null,
+    "dependencies": [],
+    "job_metrics": []
+}