[{"command_line": "python '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/data/dnb10/galaxy_db/files/3/d/4/dataset_3d4ac293-cadb-4ed7-8ceb-35263b29f021.dat' --output '/data/jwd05e/main/072/395/72395758/outputs/dataset_ab15d3fd-b1db-4584-9c38-71de02b307e6.dat' --input_display_name 'Prodigal Gene Predictor on data 1 : protein translations file' --pattern='__backslash__*$' --replacement=''", "create_time": "2024-08-10T07:40:54.232336", "encoded_id": "9fa5573dd746a59a9ca0eaabf039c5ed", "exit_code": 0, "galaxy_version": "24.1", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"input": ["31e7840b5aedca43c08e5935886a0a6c"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"out_file1": ["31e7840b5aedca43f17b497c109f9250"]}, "params": {"__input_ext": "input", "__workflow_invocation_uuid__": "de6382d056eb11efaaa7001e67d2ec02", "checks": [{"__index__": 0, "pattern": "\\*$", "replacement": ""}], "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "input": {"values": [{"id": "31e7840b5aedca43c08e5935886a0a6c", "src": "hda"}]}}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3", "tool_stderr": "", "tool_stdout": "", "tool_version": "1.0.3", "traceback": null, "update_time": "2024-08-10T07:42:57.503316"}, {"command_line": "prodigal -i '/data/dnb10/galaxy_db/files/a/b/1/dataset_ab15d3fd-b1db-4584-9c38-71de02b307e6.dat' -o '/data/jwd02f/main/072/441/72441670/outputs/dataset_db19b01b-7d38-4609-b671-1e569e928b90.dat' -f 'gbk' -p 'meta' -g '11' -a '/data/jwd02f/main/072/441/72441670/outputs/dataset_660a2840-53c5-408d-86c5-d5a2777a038a.dat' -d '/data/jwd02f/main/072/441/72441670/outputs/dataset_a8776f72-accc-476c-b778-f0412a5296ea.dat' -s '/data/jwd02f/main/072/441/72441670/outputs/dataset_ccddeaba-7c0a-4029-85c3-4e42633443e7.dat'", "create_time": "2024-08-13T09:25:14.970452", "encoded_id": "9fa5573dd746a59a16c44e0bc8a1b749", "exit_code": 0, "galaxy_version": "24.1", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"input_fa": ["31e7840b5aedca43f17b497c109f9250"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"output": ["31e7840b5aedca432119a925ac55d581"], "output_faa": ["31e7840b5aedca4374cfd23e4ed3d5da"], "output_fnn": ["31e7840b5aedca4317743baf0497a123"], "output_start": ["31e7840b5aedca43a6e36fa5272c763e"]}, "params": {"__input_ext": "input", "__workflow_invocation_uuid__": "f11835d0595511ef85ed001e67d2ec02", "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", "closed": "false", "dbkey": "?", "force_nonsd": "false", "input_fa": {"values": [{"id": "31e7840b5aedca43f17b497c109f9250", "src": "hda"}]}, "input_train": null, "masked_seq": "false", "out_format": "gbk", "procedure": "meta", "trans_table": "11"}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/prodigal/prodigal/2.6.3+galaxy0", "tool_stderr": "-------------------------------------\nPRODIGAL v2.6.3 [February, 2016]         \nUniv of Tenn / Oak Ridge National Lab\nDoug Hyatt, Loren Hauser, et al.     \n-------------------------------------\nRequest:  Metagenomic, Phase:  Training\nInitializing training files...done!\n-------------------------------------\nRequest:  Metagenomic, Phase:  Gene Finding\nFinding genes in sequence #1 (123 bp)...done!\nFinding genes in sequence #2 (156 bp)...done!\nFinding genes in sequence #3 (709 bp)...done!\nFinding genes in sequence #4 (397 bp)...done!\nFinding genes in sequence #5 (233 bp)...done!\nFinding genes in sequence #6 (542 bp)...done!\nFinding genes in sequence #7 (203 bp)...done!\nFinding genes in sequence #8 (448 bp)...done!\nFinding genes in sequence #9 (399 bp)...done!\nFinding genes in sequence #10 (47 bp)...done!\nFinding genes in sequence #11 (885 bp)...done!\nFinding genes in sequence #12 (319 bp)...done!\nFinding genes in sequence #13 (400 bp)...done!\nFinding genes in sequence #14 (114 bp)...done!\nFinding genes in sequence #15 (236 bp)...done!\nFinding genes in sequence #16 (556 bp)...done!\n", "tool_stdout": "", "tool_version": "2.6.3+galaxy0", "traceback": null, "update_time": "2024-08-13T09:26:19.283306"}, {"command_line": "python '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/503bcd6ebe4b/regex_find_replace/regex.py' --input '/data/dnb10/galaxy_db/files/6/6/0/dataset_660a2840-53c5-408d-86c5-d5a2777a038a.dat' --output '/data/jwd02f/main/072/441/72441672/outputs/dataset_e2b65e28-1d69-499d-942b-c37b4c78a37c.dat' --input_display_name 'Prodigal Gene Predictor on data 15 : protein translations file' --pattern='__backslash__*$' --replacement=''", "create_time": "2024-08-13T09:25:15.153043", "encoded_id": "9fa5573dd746a59a20cb235df7b9ba32", "exit_code": 0, "galaxy_version": "24.1", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"input": ["31e7840b5aedca4374cfd23e4ed3d5da"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"out_file1": ["31e7840b5aedca433cc63e1516943862"]}, "params": {"__input_ext": "input", "__workflow_invocation_uuid__": "f11835d0595511ef85ed001e67d2ec02", "checks": [{"__index__": 0, "pattern": "\\*$", "replacement": ""}], "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "input": {"values": [{"id": "31e7840b5aedca4374cfd23e4ed3d5da", "src": "hda"}]}}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.3", "tool_stderr": "", "tool_stdout": "", "tool_version": "1.0.3", "traceback": null, "update_time": "2024-08-13T09:27:31.850817"}, {"command_line": "sanntis --ip-file '/data/dnb10/galaxy_db/files/4/5/f/dataset_45fd5f1d-d9ad-4d88-90c9-f39ca3d90547.dat' --outfile 'output_sanntis.gff' '/data/dnb10/galaxy_db/files/1/f/2/dataset_1f21b738-cfc6-46f9-ab5a-551552a39dee.dat'", "create_time": "2024-08-13T09:25:15.305922", "encoded_id": "9fa5573dd746a59a49a4a47fe1e54585", "exit_code": 0, "galaxy_version": "24.1", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"selection|input_genbank": ["31e7840b5aedca43d3dc3d19fd74d6a0"], "selection|input_interpro": ["31e7840b5aedca43d660e51bac8b61ae"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"output_sanntis": ["31e7840b5aedca4390780e07c9f86a59"]}, "params": {"__input_ext": "input", "__workflow_invocation_uuid__": "f11835d0595511ef85ed001e67d2ec02", "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "selection": {"__current_case__": 0, "input_genbank": {"values": [{"id": "31e7840b5aedca43d3dc3d19fd74d6a0", "src": "hda"}]}, "input_interpro": {"values": [{"id": "31e7840b5aedca43d660e51bac8b61ae", "src": "hda"}]}, "which_sanntis": "sanntis"}}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1", "tool_stderr": "", "tool_stdout": "LOG_FILE: /data/jwd05e/main/072/441/72441674/working/dataset_1f21b738-cfc6-46f9-ab5a-551552a39dee.dat.sanntis/sanntis.log\nSanntiS succesful\n", "tool_version": "0.9.3.5+galaxy1", "traceback": null, "update_time": "2024-08-13T09:43:15.625623"}, {"command_line": "sanntis_build_gb  -n '/data/dnb10/galaxy_db/files/a/b/1/dataset_ab15d3fd-b1db-4584-9c38-71de02b307e6.dat' -a '/data/dnb10/galaxy_db/files/6/6/0/dataset_660a2840-53c5-408d-86c5-d5a2777a038a.dat' -o 'output_sanntis_gb.gb'", "create_time": "2024-08-13T09:25:15.070637", "encoded_id": "9fa5573dd746a59a76cb7d5cdbb8b23d", "exit_code": 0, "galaxy_version": "24.1", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"selection|input_nuc": ["31e7840b5aedca43f17b497c109f9250"], "selection|input_prot": ["31e7840b5aedca4374cfd23e4ed3d5da"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"output_sanntis_gb": ["31e7840b5aedca43d3dc3d19fd74d6a0"]}, "params": {"__input_ext": "input", "__workflow_invocation_uuid__": "f11835d0595511ef85ed001e67d2ec02", "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "selection": {"__current_case__": 1, "input_nuc": {"values": [{"id": "31e7840b5aedca43f17b497c109f9250", "src": "hda"}]}, "input_prot": {"values": [{"id": "31e7840b5aedca4374cfd23e4ed3d5da", "src": "hda"}]}, "which_sanntis": "genbank"}}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/ecology/sanntis_marine/sanntis_marine/0.9.3.5+galaxy1", "tool_stderr": "", "tool_stdout": "Done!.. outfile :output_sanntis_gb.gb\n", "tool_version": "0.9.3.5+galaxy1", "traceback": null, "update_time": "2024-08-13T09:28:18.601604"}, {"command_line": "mkdir -p $HOME/.interproscan-5 && sed 's|^\\(data.directory=\\).*$|\\1/data/db/data_managers/interproscan/5.59-91.0/data|' $(dirname $(readlink -f $(command -v interproscan.sh)))/interproscan.properties > $HOME/.interproscan-5/interproscan.properties && export _JAVA_OPTIONS=-Duser.home=$HOME &&  interproscan.sh  -dp --input '/data/dnb10/galaxy_db/files/e/2/b/dataset_e2b65e28-1d69-499d-942b-c37b4c78a37c.dat' --seqtype p -f TSV  --applications TIGRFAM,FunFam,SFLD,SUPERFAMILY,PANTHER,Gene3D,Hamap,PrositeProfiles,Coils,SMART,CDD,PRINTS,PIRSR,PrositePatterns,AntiFam,Pfam,MobiDBLite,PIRSF --tempdir ${TEMP:-$_GALAXY_JOB_TMP_DIR}  --pathways --goterms   --cpu ${GALAXY_SLOTS:-4}  --output-file-base 'output'", "create_time": "2024-08-13T09:25:15.227987", "encoded_id": "9fa5573dd746a59a07c86e0b49ac51cf", "exit_code": 0, "galaxy_version": "24.1", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"input": ["31e7840b5aedca433cc63e1516943862"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"outfile_tsv": ["31e7840b5aedca43d660e51bac8b61ae"]}, "params": {"__input_ext": "input", "__workflow_invocation_uuid__": "f11835d0595511ef85ed001e67d2ec02", "applications": ["TIGRFAM", "FunFam", "SFLD", "SUPERFAMILY", "PANTHER", "Gene3D", "Hamap", "PrositeProfiles", "Coils", "SMART", "CDD", "PRINTS", "PIRSR", "PrositePatterns", "AntiFam", "Pfam", "MobiDBLite", "PIRSF"], "chromInfo": "/opt/galaxy/tool-data/shared/ucsc/chrom/?.len", "database": "5.59-91.0", "dbkey": "?", "goterms": "true", "input": {"values": [{"id": "31e7840b5aedca433cc63e1516943862", "src": "hda"}]}, "iprlookup": "false", "licensed": {"__current_case__": 0, "use": "false"}, "oformat": "TSV", "pathways": "true", "seqtype": "p"}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/interproscan/interproscan/5.59-91.0+galaxy3", "tool_stderr": "Picked up _JAVA_OPTIONS: -Duser.home=/data/jwd05e/main/072/441/72441673/home\n", "tool_stdout": "13/08/2024 11:21:45:145 Welcome to InterProScan-5.59-91.0\n13/08/2024 11:21:45:147 Running InterProScan v5 in STANDALONE mode... on Linux\n13/08/2024 11:22:39:803 RunID: vgcnbwc-worker-c28m475-0014.novalocal_20240813_112238385_2g2q\n13/08/2024 11:22:57:905 Loading file /data/dnb10/galaxy_db/files/e/2/b/dataset_e2b65e28-1d69-499d-942b-c37b4c78a37c.dat\n13/08/2024 11:22:57:910 Running the following analyses:\n[AntiFam-7.0,CDD-3.18,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2021_04,MobiDBLite-2.0,PANTHER-17.0,Pfam-35.0,PIRSF-3.10,PIRSR-2021_05,PRINTS-42.0,ProSitePatterns-2022_01,ProSiteProfiles-2022_01,SFLD-4,SMART-7.1,SUPERFAMILY-1.75,TIGRFAM-15.0]\nPre-calculated match lookup service DISABLED.  Please wait for match calculations to complete...\n13/08/2024 11:23:15:640 25% completed\n13/08/2024 11:23:56:576 51% completed\n13/08/2024 11:24:52:155 77% completed\n13/08/2024 11:25:05:957 90% completed\n13/08/2024 11:25:23:567 100% done:  InterProScan analyses completed \n\n2024-08-13 11:25:24,081 [main] [uk.ac.ebi.interpro.scan.jms.main.Run:1801] WARN - deleteWorkingDirectoryOnCompletion : false\n", "tool_version": "5.59-91.0+galaxy3", "traceback": null, "update_time": "2024-08-13T09:33:15.983927"}]