view test-data/jobs_attrs.txt @ 1:c7f4f2ac38f2 draft default tip

" master branch Updating"

[{"command_line": "python '/galaxy/server/lib/galaxy/tools/data_fetch.py' --galaxy-root '/galaxy/server' --datatypes-registry '/galaxy/data/jobs_directory/088/88074/registry.xml' --request-version '1' --request '/galaxy/data/jobs_directory/088/88074/configs/tmp1uj_scc4'", "create_time": "2022-06-23T07:41:06.284983", "encoded_id": "babcc3d885e41dc5", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {}, "job_messages": [], "job_stderr": "", "job_stdout": "environ({'GALAXY_SLOTS': '1', 'PWD': '/galaxy/data/jobs_directory/088/88074/working', 'HOME': '/galaxy/data/jobs_directory/088/88074/home', '_GALAXY_JOB_HOME_DIR': '/galaxy/data/jobs_directory/088/88074/home', 'TMPDIR': '/galaxy/data/tmp', 'PYTHONPATH': '/galaxy/server/lib', 'SHLVL': '2', 'LC_CTYPE': 'C.UTF-8', '_GALAXY_JOB_TMP_DIR': '/galaxy/data/jobs_directory/088/88074/tmp', 'PATH': '/galaxy/server/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PYTHONWARNINGS': 'ignore', 'OLDPWD': '/galaxy/data/jobs_directory/088/88074', '_': '/galaxy/server/.venv/bin/python'})\n", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"output0": ["9e77b3d7d0887128"]}, "params": {"file_count": "1", "files": [{"__index__": 0, "file_data": "/galaxy/data/tmp/c400d309afc6474c8b5d1900ad47051a"}], "paramfile": null, "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"src\": \"path\", \"name\": \"test.rdata\", \"dbkey\": \"?\", \"ext\": \"auto\", \"space_to_tab\": false, \"to_posix_lines\": true, \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/galaxy/data/tmp/c400d309afc6474c8b5d1900ad47051a\", \"object_id\": 232343}]}], \"auto_decompress\": true, \"check_content\": true}", "request_version": "1"}, "state": "ok", "tool_id": "__DATA_FETCH__", "tool_stderr": "", "tool_stdout": "environ({'GALAXY_SLOTS': '1', 'PWD': '/galaxy/data/jobs_directory/088/88074/working', 'HOME': '/galaxy/data/jobs_directory/088/88074/home', '_GALAXY_JOB_HOME_DIR': '/galaxy/data/jobs_directory/088/88074/home', 'TMPDIR': '/galaxy/data/tmp', 'PYTHONPATH': '/galaxy/server/lib', 'SHLVL': '2', 'LC_CTYPE': 'C.UTF-8', '_GALAXY_JOB_TMP_DIR': '/galaxy/data/jobs_directory/088/88074/tmp', 'PATH': '/galaxy/server/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PYTHONWARNINGS': 'ignore', 'OLDPWD': '/galaxy/data/jobs_directory/088/88074', '_': '/galaxy/server/.venv/bin/python'})\n", "tool_version": "0.1.0", "traceback": null, "update_time": "2022-06-23T07:41:14.746997"}, {"command_line": "python '/galaxy/server/lib/galaxy/tools/data_fetch.py' --galaxy-root '/galaxy/server' --datatypes-registry '/galaxy/data/jobs_directory/088/88094/registry.xml' --request-version '1' --request '/galaxy/data/jobs_directory/088/88094/configs/tmpnio5usis'", "create_time": "2022-06-23T14:20:21.490077", "encoded_id": "dce03405192194a9", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {}, "job_messages": [], "job_stderr": "", "job_stdout": "environ({'GALAXY_SLOTS': '1', 'PWD': '/galaxy/data/jobs_directory/088/88094/working', 'HOME': '/galaxy/data/jobs_directory/088/88094/home', '_GALAXY_JOB_HOME_DIR': '/galaxy/data/jobs_directory/088/88094/home', 'TMPDIR': '/galaxy/data/tmp', 'PYTHONPATH': '/galaxy/server/lib', 'SHLVL': '2', 'LC_CTYPE': 'C.UTF-8', '_GALAXY_JOB_TMP_DIR': '/galaxy/data/jobs_directory/088/88094/tmp', 'PATH': '/galaxy/server/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PYTHONWARNINGS': 'ignore', 'OLDPWD': '/galaxy/data/jobs_directory/088/88094', '_': '/galaxy/server/.venv/bin/python'})\n", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"output0": ["9a0ce47bd1734ae7"]}, "params": {"file_count": "1", "files": [{"__index__": 0, "file_data": "/galaxy/data/tmp/e44f6de2f1fd410ab5ab76d3589ed689"}], "paramfile": null, "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"src\": \"path\", \"name\": \"peaklist_fragments.tsv\", \"dbkey\": \"?\", \"ext\": \"auto\", \"space_to_tab\": false, \"to_posix_lines\": true, \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/galaxy/data/tmp/e44f6de2f1fd410ab5ab76d3589ed689\", \"object_id\": 232384}]}], \"auto_decompress\": true, \"check_content\": true}", "request_version": "1"}, "state": "ok", "tool_id": "__DATA_FETCH__", "tool_stderr": "", "tool_stdout": "environ({'GALAXY_SLOTS': '1', 'PWD': '/galaxy/data/jobs_directory/088/88094/working', 'HOME': '/galaxy/data/jobs_directory/088/88094/home', '_GALAXY_JOB_HOME_DIR': '/galaxy/data/jobs_directory/088/88094/home', 'TMPDIR': '/galaxy/data/tmp', 'PYTHONPATH': '/galaxy/server/lib', 'SHLVL': '2', 'LC_CTYPE': 'C.UTF-8', '_GALAXY_JOB_TMP_DIR': '/galaxy/data/jobs_directory/088/88094/tmp', 'PATH': '/galaxy/server/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PYTHONWARNINGS': 'ignore', 'OLDPWD': '/galaxy/data/jobs_directory/088/88094', '_': '/galaxy/server/.venv/bin/python'})\n", "tool_version": "0.1.0", "traceback": null, "update_time": "2022-06-23T14:20:30.838847"}, {"command_line": "python '/galaxy/server/lib/galaxy/datatypes/converters/tabular_csv.py' -o '/galaxy/data/files/000/168/dataset_168768.dat' -i '/galaxy/data/files/000/168/dataset_168730.dat'", "create_time": "2022-06-23T14:31:06.269843", "encoded_id": "5ecaee8292cae53a", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"csv": ["eee378ebc66a66f1"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"tabular": ["2163bfdc66d76d11"]}, "params": {"__input_ext": "input", "__target_datatype__": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "csv": {"values": [{"id": "eee378ebc66a66f1", "src": "hda"}]}, "dbkey": "?"}, "state": "ok", "tool_id": "csv_to_tabular", "tool_stderr": "", "tool_stdout": "", "tool_version": "1.0.0", "traceback": null, "update_time": "2022-06-23T14:31:36.295672"}, {"command_line": "python '/galaxy/server/lib/galaxy/tools/data_fetch.py' --galaxy-root '/galaxy/server' --datatypes-registry '/galaxy/data/jobs_directory/088/88095/registry.xml' --request-version '1' --request '/galaxy/data/jobs_directory/088/88095/configs/tmp48lfm8zy'", "create_time": "2022-06-23T14:20:21.919823", "encoded_id": "dc7f2bdc13c2a0c6", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {}, "job_messages": [], "job_stderr": "", "job_stdout": "environ({'GALAXY_SLOTS': '1', 'PWD': '/galaxy/data/jobs_directory/088/88095/working', 'HOME': '/galaxy/data/jobs_directory/088/88095/home', '_GALAXY_JOB_HOME_DIR': '/galaxy/data/jobs_directory/088/88095/home', 'TMPDIR': '/galaxy/data/tmp', 'PYTHONPATH': '/galaxy/server/lib', 'SHLVL': '2', 'LC_CTYPE': 'C.UTF-8', '_GALAXY_JOB_TMP_DIR': '/galaxy/data/jobs_directory/088/88095/tmp', 'PATH': '/galaxy/server/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PYTHONWARNINGS': 'ignore', 'OLDPWD': '/galaxy/data/jobs_directory/088/88095', '_': '/galaxy/server/.venv/bin/python'})\n", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"output0": ["eee378ebc66a66f1"]}, "params": {"file_count": "1", "files": [{"__index__": 0, "file_data": "/galaxy/data/tmp/7964e374d9fa423cb3438b054c7f91f0"}], "paramfile": null, "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"src\": \"path\", \"name\": \"peaklist_precursors.csv\", \"dbkey\": \"?\", \"ext\": \"auto\", \"space_to_tab\": false, \"to_posix_lines\": true, \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/galaxy/data/tmp/7964e374d9fa423cb3438b054c7f91f0\", \"object_id\": 232385}]}], \"auto_decompress\": true, \"check_content\": true}", "request_version": "1"}, "state": "ok", "tool_id": "__DATA_FETCH__", "tool_stderr": "", "tool_stdout": "environ({'GALAXY_SLOTS': '1', 'PWD': '/galaxy/data/jobs_directory/088/88095/working', 'HOME': '/galaxy/data/jobs_directory/088/88095/home', '_GALAXY_JOB_HOME_DIR': '/galaxy/data/jobs_directory/088/88095/home', 'TMPDIR': '/galaxy/data/tmp', 'PYTHONPATH': '/galaxy/server/lib', 'SHLVL': '2', 'LC_CTYPE': 'C.UTF-8', '_GALAXY_JOB_TMP_DIR': '/galaxy/data/jobs_directory/088/88095/tmp', 'PATH': '/galaxy/server/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PYTHONWARNINGS': 'ignore', 'OLDPWD': '/galaxy/data/jobs_directory/088/88095', '_': '/galaxy/server/.venv/bin/python'})\n", "tool_version": "0.1.0", "traceback": null, "update_time": "2022-06-23T14:20:30.810748"}, {"command_line": "python '/galaxy/server/lib/galaxy/tools/data_fetch.py' --galaxy-root '/galaxy/server' --datatypes-registry '/galaxy/data/jobs_directory/088/88096/registry.xml' --request-version '1' --request '/galaxy/data/jobs_directory/088/88096/configs/tmp21wve2gl'", "create_time": "2022-06-23T14:20:22.336673", "encoded_id": "1b54d7f01620ea51", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {}, "job_messages": [], "job_stderr": "", "job_stdout": "environ({'GALAXY_SLOTS': '1', 'PWD': '/galaxy/data/jobs_directory/088/88096/working', 'HOME': '/galaxy/data/jobs_directory/088/88096/home', '_GALAXY_JOB_HOME_DIR': '/galaxy/data/jobs_directory/088/88096/home', 'TMPDIR': '/galaxy/data/tmp', 'PYTHONPATH': '/galaxy/server/lib', 'SHLVL': '2', 'LC_CTYPE': 'C.UTF-8', '_GALAXY_JOB_TMP_DIR': '/galaxy/data/jobs_directory/088/88096/tmp', 'PATH': '/galaxy/server/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PYTHONWARNINGS': 'ignore', 'OLDPWD': '/galaxy/data/jobs_directory/088/88096', '_': '/galaxy/server/.venv/bin/python'})\n", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"output0": ["7cf499d16bd542b2"]}, "params": {"file_count": "1", "files": [{"__index__": 0, "file_data": "/galaxy/data/tmp/2e503324d9d54059953fac2d6151c762"}], "paramfile": null, "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"src\": \"path\", \"name\": \"compounds_pos.txt\", \"dbkey\": \"?\", \"ext\": \"auto\", \"space_to_tab\": false, \"to_posix_lines\": true, \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/galaxy/data/tmp/2e503324d9d54059953fac2d6151c762\", \"object_id\": 232386}]}], \"auto_decompress\": true, \"check_content\": true}", "request_version": "1"}, "state": "ok", "tool_id": "__DATA_FETCH__", "tool_stderr": "", "tool_stdout": "environ({'GALAXY_SLOTS': '1', 'PWD': '/galaxy/data/jobs_directory/088/88096/working', 'HOME': '/galaxy/data/jobs_directory/088/88096/home', '_GALAXY_JOB_HOME_DIR': '/galaxy/data/jobs_directory/088/88096/home', 'TMPDIR': '/galaxy/data/tmp', 'PYTHONPATH': '/galaxy/server/lib', 'SHLVL': '2', 'LC_CTYPE': 'C.UTF-8', '_GALAXY_JOB_TMP_DIR': '/galaxy/data/jobs_directory/088/88096/tmp', 'PATH': '/galaxy/server/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PYTHONWARNINGS': 'ignore', 'OLDPWD': '/galaxy/data/jobs_directory/088/88096', '_': '/galaxy/server/.venv/bin/python'})\n", "tool_version": "0.1.0", "traceback": null, "update_time": "2022-06-23T14:20:30.164478"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/23314e1192d4/batchcorrection/BC/batch_correction_3Lwrapper.R analyse \"batch_correction\" dataMatrix \"/galaxy/data/files/000/168/dataset_168729.dat\" sampleMetadata \"/galaxy/data/files/000/168/dataset_168768.dat\" variableMetadata \"/galaxy/data/files/000/168/dataset_168729.dat\" method \"linear\" span \"none\" valnull \"none\" ref_factor \"batch\" detail \"no\" dataMatrix_out \"/galaxy/data/files/000/168/dataset_168769.dat\" variableMetadata_out \"/galaxy/data/files/000/168/dataset_168770.dat\" graph_output \"/galaxy/data/files/000/168/dataset_168771.dat\"  rdata_output \"XXXX\"  batch_col_name \"batch\" injection_order_col_name \"injectionOrder\" sample_type_col_name \"sampleType\" sample_type_tags \"blank=blank,pool=pool,sample=sample\"", "create_time": "2022-06-23T14:31:06.422486", "encoded_id": "edbf4dd0b89c2c7c", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["9a0ce47bd1734ae7"], "sampleMetadata": ["2163bfdc66d76d11"], "variableMetadata": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    674\n    674\n    674\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: meth3L -> check.err\nExecution halted\n", "job_stdout": "\nJob starting time:\n Thu 23 Jun 2022 14:31:37 \n\n-------------------------------------------------------------------- \nParameters used:\n\n$analyse\n[1] \"batch_correction\"\n\n$dataMatrix\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$sampleMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168768.dat\"\n\n$variableMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$method\n[1] \"linear\"\n\n$span\n[1] \"none\"\n\n$valnull\n[1] \"none\"\n\n$ref_factor\n[1] \"batch\"\n\n$detail\n[1] \"no\"\n\n$dataMatrix_out\n[1] \"/galaxy/data/files/000/168/dataset_168769.dat\"\n\n$variableMetadata_out\n[1] \"/galaxy/data/files/000/168/dataset_168770.dat\"\n\n$graph_output\n[1] \"/galaxy/data/files/000/168/dataset_168771.dat\"\n\n$rdata_output\n[1] \"XXXX\"\n\n$batch_col_name\n[1] \"batch\"\n\n$injection_order_col_name\n[1] \"injectionOrder\"\n\n$sample_type_col_name\n[1] \"sampleType\"\n\n$sample_type_tags\n[1] \"blank=blank,pool=pool,sample=sample\"\n\n--------------------------------------------------------------------\n\n", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataMatrix_out": ["c5ca7f991d61f101"], "graph_output": ["6af431f3dc1eb3b6"], "variableMetadata_out": ["48b0abe0eb507b5c"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "sampleMetadata": {"values": [{"id": "2163bfdc66d76d11", "src": "hda"}]}, "smcust": {"batch_col_name": "batch", "injection_order_col_name": "injectionOrder", "sampleTypeTagBlank": "blank", "sampleTypeTagPool": "pool", "sampleTypeTagSample": "sample", "sample_type_col_name": "sampleType"}, "span_condition": {"__current_case__": 0, "detail": "no", "method": "linear", "ref_factor": "batch", "valnull": "none"}, "variableMetadata": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/3.0.0", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    674\n    674\n    674\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: meth3L -> check.err\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Thu 23 Jun 2022 14:31:37 \n\n-------------------------------------------------------------------- \nParameters used:\n\n$analyse\n[1] \"batch_correction\"\n\n$dataMatrix\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$sampleMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168768.dat\"\n\n$variableMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$method\n[1] \"linear\"\n\n$span\n[1] \"none\"\n\n$valnull\n[1] \"none\"\n\n$ref_factor\n[1] \"batch\"\n\n$detail\n[1] \"no\"\n\n$dataMatrix_out\n[1] \"/galaxy/data/files/000/168/dataset_168769.dat\"\n\n$variableMetadata_out\n[1] \"/galaxy/data/files/000/168/dataset_168770.dat\"\n\n$graph_output\n[1] \"/galaxy/data/files/000/168/dataset_168771.dat\"\n\n$rdata_output\n[1] \"XXXX\"\n\n$batch_col_name\n[1] \"batch\"\n\n$injection_order_col_name\n[1] \"injectionOrder\"\n\n$sample_type_col_name\n[1] \"sampleType\"\n\n$sample_type_tags\n[1] \"blank=blank,pool=pool,sample=sample\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "3.0.0", "traceback": null, "update_time": "2022-06-23T14:31:45.837046"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/acdf51018708/qualitymetrics/qualitymetrics_wrapper.R dataMatrix_in \"/galaxy/data/files/000/168/dataset_168729.dat\" sampleMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\" variableMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\"  CV \"FALSE\" Compa \"TRUE\" seuil \"1\"  poolAsPool1L \"TRUE\"  sampleMetadata_out \"/galaxy/data/files/000/168/dataset_168779.dat\" variableMetadata_out \"/galaxy/data/files/000/168/dataset_168780.dat\" figure \"/galaxy/data/files/000/168/dataset_168781.dat\" information \"/galaxy/data/files/000/168/dataset_168782.dat\"", "create_time": "2022-06-23T14:48:34.259987", "encoded_id": "73f66eec3f22fc5f", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["9a0ce47bd1734ae7"], "sampleMetadata_in": ["9a0ce47bd1734ae7"], "variableMetadata_in": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    674\n    674\n    674\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: QualityControl -> check.err\nExecution halted\n", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"figure": ["cde3b5fe6f69767f"], "information": ["5d4ae66c2a9bcd5c"], "sampleMetadata_out": ["ca9b35e445ec8625"], "variableMetadata_out": ["025e42e3cdfe620d"]}, "params": {"CV_condition": {"CV": "FALSE", "Compa": "TRUE", "__current_case__": 1, "seuil": "1"}, "__input_ext": "tabular", "advPar": {"__current_case__": 1, "optC": "default", "poolAsPool1L": "TRUE"}, "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "sampleMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "variableMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    674\n    674\n    674\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: QualityControl -> check.err\nExecution halted\n", "tool_stdout": "", "tool_version": "2.2.8", "traceback": null, "update_time": "2022-06-23T14:48:45.202064"}, {"command_line": "python '/galaxy/server/lib/galaxy/tools/data_fetch.py' --galaxy-root '/galaxy/server' --datatypes-registry '/galaxy/data/jobs_directory/088/88292/registry.xml' --request-version '1' --request '/galaxy/data/jobs_directory/088/88292/configs/tmpqb5qsrok'", "create_time": "2022-06-24T13:59:22.519831", "encoded_id": "eecaf5ecc79ffb26", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {}, "job_messages": [], "job_stderr": "", "job_stdout": "environ({'GALAXY_SLOTS': '1', 'PWD': '/galaxy/data/jobs_directory/088/88292/working', 'HOME': '/galaxy/data/jobs_directory/088/88292/home', '_GALAXY_JOB_HOME_DIR': '/galaxy/data/jobs_directory/088/88292/home', 'TMPDIR': '/galaxy/data/tmp', 'PYTHONPATH': '/galaxy/server/lib', 'SHLVL': '2', 'LC_CTYPE': 'C.UTF-8', '_GALAXY_JOB_TMP_DIR': '/galaxy/data/jobs_directory/088/88292/tmp', 'PATH': '/galaxy/server/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PYTHONWARNINGS': 'ignore', 'OLDPWD': '/galaxy/data/jobs_directory/088/88292', '_': '/galaxy/server/.venv/bin/python'})\n", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"output0": ["7a313ff05bbcce6c"]}, "params": {"file_count": "1", "files": [{"__index__": 0, "file_data": "/galaxy/data/tmp/88d2ff5c70f646e182b4b058607d486d"}], "paramfile": null, "request_json": "{\"targets\": [{\"destination\": {\"type\": \"hdas\"}, \"elements\": [{\"src\": \"path\", \"name\": \"image.png\", \"dbkey\": \"?\", \"ext\": \"auto\", \"space_to_tab\": false, \"to_posix_lines\": true, \"hashes\": [], \"in_place\": false, \"purge_source\": false, \"path\": \"/galaxy/data/tmp/88d2ff5c70f646e182b4b058607d486d\", \"object_id\": 232870}]}], \"auto_decompress\": true, \"check_content\": true}", "request_version": "1"}, "state": "ok", "tool_id": "__DATA_FETCH__", "tool_stderr": "", "tool_stdout": "environ({'GALAXY_SLOTS': '1', 'PWD': '/galaxy/data/jobs_directory/088/88292/working', 'HOME': '/galaxy/data/jobs_directory/088/88292/home', '_GALAXY_JOB_HOME_DIR': '/galaxy/data/jobs_directory/088/88292/home', 'TMPDIR': '/galaxy/data/tmp', 'PYTHONPATH': '/galaxy/server/lib', 'SHLVL': '2', 'LC_CTYPE': 'C.UTF-8', '_GALAXY_JOB_TMP_DIR': '/galaxy/data/jobs_directory/088/88292/tmp', 'PATH': '/galaxy/server/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin', 'PYTHONWARNINGS': 'ignore', 'OLDPWD': '/galaxy/data/jobs_directory/088/88292', '_': '/galaxy/server/.venv/bin/python'})\n", "tool_version": "0.1.0", "traceback": null, "update_time": "2022-06-24T13:59:30.324598"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/512c2b701d96/camera_annotate//CAMERA_annotateDiffreport.r image '/galaxy/data/files/000/168/dataset_168688.dat'  nSlaves ${GALAXY_SLOTS:-1}  sigma 6 perfwhm 0.6  ppm 5 mzabs 0.015  maxcharge 3 maxiso 4 minfrac 0.5  quick FALSE cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE  polarity negative max_peaks 100 multiplier 3    convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into", "create_time": "2022-06-27T13:49:20.732112", "encoded_id": "e2a7c6eedf3bb175", "exit_code": null, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": "Job output deleted by user before job completed.", "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"image": ["9e77b3d7d0887128"]}, "job_messages": [], "job_stderr": "Terminated\n", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"rdata_quick_false": ["f6ca532f978b6783"], "variableMetadata": ["b3513c3f0773cb5b"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "diffreport": {"options": {"__current_case__": 1, "option": "hide"}}, "export": {"convertRTMinute": "false", "intval": "into", "numDigitsMZ": "4", "numDigitsRT": "0"}, "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "findgeneral": {"mzabs": "0.015", "ppm": "5"}, "findisotopes": {"maxcharge": "3", "maxiso": "4", "minfrac": "0.5"}, "groupfwhm": {"perfwhm": "0.6", "sigma": "6"}, "image": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "quick_block": {"__current_case__": 0, "findadducts": {"max_peaks": "100", "polarity": "negative", "rules_block": {"__current_case__": 0, "multiplier": "3", "rules_select": "FALSE"}}, "groupcorr": {"calcCaS": "false", "calcCiS": "true", "calcIso": "false", "cor_eic_th": "0.75", "graphMethod": "hcs", "pval": "0.05"}, "quick": "FALSE"}}, "state": "deleted", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.6+camera1.48.0-galaxy0", "tool_stderr": "", "tool_stdout": "", "tool_version": "2.2.6+camera1.48.0-galaxy0", "traceback": null, "update_time": "2022-06-27T13:50:30.858886"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/corr_table/29ec7e3afdd4/corr_table/CorrTable/Corr_wrap.r  tab1_in \"/galaxy/data/files/000/168/dataset_168731.dat\" tab2_in \"/galaxy/data/files/000/168/dataset_168731.dat\"  tab1_samples \"row\" tab2_samples \"row\"  corr_method \"pearson\"  test_corr \"no\"  filter \"no\"  reorder_var \"no\"  plot_choice \"auto\" color_heatmap \"no\" tabcorr_out \"/galaxy/data/files/000/169/dataset_169532.dat\" heatmap_out \"/galaxy/data/files/000/169/dataset_169533.dat\"", "create_time": "2022-06-30T14:36:54.969946", "encoded_id": "befb011fe8eee32e", "exit_code": 127, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"tab1_in": ["7cf499d16bd542b2"], "tab2_in": ["7cf499d16bd542b2"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"heatmap_out": ["a6325bfdec96455f"], "tabcorr_out": ["5fb07fb4433ff938"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "corr_method": "pearson", "dbkey": "?", "filter_section": {"filter_cond": {"__current_case__": 1, "filter": "no"}, "testcorr_cond": {"__current_case__": 1, "test_corr": "no"}}, "out_section": {"plot_cond": {"__current_case__": 0, "heatmap_cond": {"__current_case__": 1, "color_heatmap": "no"}, "plot_choice": "auto"}, "reorder_var": "no"}, "tab1_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "tab1_samples": "row", "tab2_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "tab2_samples": "row"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/corr_table/corrtable/1.0.0", "tool_stderr": "/galaxy/data/jobs_directory/088/88454/tool_script.sh: line 43: Rscript: command not found\n", "tool_stdout": "", "tool_version": "1.0.0", "traceback": null, "update_time": "2022-06-30T14:38:15.366451"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/corr_table/29ec7e3afdd4/corr_table/CorrTable/Corr_wrap.r  tab1_in \"/galaxy/data/files/000/168/dataset_168731.dat\" tab2_in \"/galaxy/data/files/000/168/dataset_168731.dat\"  tab1_samples \"row\" tab2_samples \"row\"  corr_method \"pearson\"  test_corr \"no\"  filter \"no\"  reorder_var \"no\"  plot_choice \"auto\" color_heatmap \"no\" tabcorr_out \"/galaxy/data/files/000/169/dataset_169534.dat\" heatmap_out \"/galaxy/data/files/000/169/dataset_169535.dat\"", "create_time": "2022-06-30T14:40:34.142455", "encoded_id": "37480a1109d7a8ae", "exit_code": 127, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"tab1_in": ["7cf499d16bd542b2"], "tab2_in": ["7cf499d16bd542b2"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"heatmap_out": ["b8c15df65a5424cf"], "tabcorr_out": ["b7a7a1e8b4aae9ee"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "corr_method": "pearson", "dbkey": "?", "filter_section": {"filter_cond": {"__current_case__": 1, "filter": "no"}, "testcorr_cond": {"__current_case__": 1, "test_corr": "no"}}, "out_section": {"plot_cond": {"__current_case__": 0, "heatmap_cond": {"__current_case__": 1, "color_heatmap": "no"}, "plot_choice": "auto"}, "reorder_var": "no"}, "tab1_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "tab1_samples": "row", "tab2_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "tab2_samples": "row"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/corr_table/corrtable/1.0.0", "tool_stderr": "/galaxy/data/jobs_directory/088/88455/tool_script.sh: line 43: Rscript: command not found\n", "tool_stdout": "", "tool_version": "1.0.0", "traceback": null, "update_time": "2022-06-30T14:41:54.404244"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/49c36c54e0cf/intensity_checks/Intchecks/wrapper_intensity_check.R  dataMatrix_in \"/galaxy/data/files/000/168/dataset_168731.dat\" sampleMetadata_in \"/galaxy/data/files/000/168/dataset_168731.dat\" variableMetadata_in \"/galaxy/data/files/000/168/dataset_168731.dat\"  method \"no_class\"  chosen_stat \"None\"    variableMetadata_out \"/galaxy/data/files/000/169/dataset_169536.dat\" graphs_out \"/galaxy/data/files/000/169/dataset_169537.dat\"", "create_time": "2022-06-30T14:42:47.727633", "encoded_id": "02f0adf7c5d225ff", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["7cf499d16bd542b2"], "sampleMetadata_in": ["7cf499d16bd542b2"], "variableMetadata_in": ["7cf499d16bd542b2"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"graphs_out": ["cfb84390be448f29"], "variableMetadata_out": ["f1310bf93c1a4ff8"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "dbkey": "?", "method_cond": {"__current_case__": 0, "chosen_stat": null, "method": "no_class"}, "sampleMetadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "variableMetadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.2.8", "tool_stderr": "Error: \n- - - - - - - - -\nYou did not select any computational option. Program can not be executed.\n- - - - - - - - -\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Thu 30 Jun 2022 14:42:50 \n\n-------------------------------------------------------------------- \nIntensity Check parameters:\n\n$dataMatrix_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$sampleMetadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$variableMetadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$method\n[1] \"no_class\"\n\n$chosen_stat\n[1] \"None\"\n\n$variableMetadata_out\n[1] \"/galaxy/data/files/000/169/dataset_169536.dat\"\n\n$graphs_out\n[1] \"/galaxy/data/files/000/169/dataset_169537.dat\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "1.2.8", "traceback": null, "update_time": "2022-06-30T14:42:54.586704"}, {"command_line": "perl /galaxy/server/database/shed_tools/testtoolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/d24ae049de95/hmdb_ms_search/wsdl_hmdb.pl -masses \"/galaxy/data/files/000/168/dataset_168731.dat\" -header_choice \"yes\" -nblineheader \"1\" -colfactor \"1\" -output_tabular \"/galaxy/data/files/000/169/dataset_169538.dat\" -output_html \"/galaxy/data/files/000/169/dataset_169539.dat\" -output_xls \"/galaxy/data/files/000/169/dataset_169540.dat\"  -mode \"neutral\"  -adduct_type \"M\"  -delta \"0.05\" -maxquery \"10\" -advancedFeatures \"0\" -verbose \"1\"", "create_time": "2022-06-30T14:44:08.082109", "encoded_id": "860e49080a429725", "exit_code": 255, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"masses": ["7cf499d16bd542b2"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"HmdbOutWeb": ["7650ce17083ff8aa"], "HmdbOutXlsx": ["025a8803790c5fca"], "variableMetadata": ["0c9ca1e989f7f984"]}, "params": {"__input_ext": "tabular", "advancedFeatures": "0", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "delta": "0.05", "input_type": {"__current_case__": 0, "choice": "YES", "colfactor": "1", "header": {"__current_case__": 0, "header_choice": "yes", "nbHeader": "1"}, "masses": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}}, "maxquery": "10", "mode_type": {"__current_case__": 2, "data_neutral_adducts": ["M"], "mode": "neutral"}, "verbose": "1"}, "state": "ok", "tool_id": "testtoolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/wsdl_hmdb/1.6.1", "tool_stderr": "Error POSTing http://specdb.wishartlab.com/ms/search.csv: Internal Server Error at /galaxy/server/database/shed_tools/testtoolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/d24ae049de95/hmdb_ms_search/lib/hmdb.pm line 321.\n", "tool_stdout": "\tTesting HMDB server connexion (1 time(s) )...\n", "tool_version": "1.6.1", "traceback": null, "update_time": "2022-06-30T14:44:15.115004"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/idchoice/bb19b1d15732/idchoice/IDchoice/IDchoice_wrap.R dataMatrix_in \"/galaxy/data/files/000/168/dataset_168731.dat\" Metadata_in \"/galaxy/data/files/000/168/dataset_168731.dat\"  metatype \"variable\" col_name \"\" makeunique \"no\"  DM_out \"/galaxy/data/files/000/169/dataset_169541.dat\" meta_out \"/galaxy/data/files/000/169/dataset_169542.dat\"", "create_time": "2022-06-30T14:46:49.983057", "encoded_id": "6196d56089936f35", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"Metadata_in": ["7cf499d16bd542b2"], "dataMatrix_in": ["7cf499d16bd542b2"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"DM_out": ["b5c96d611ce0d0b7"], "meta_out": ["51e8e0af03482c6b"]}, "params": {"Metadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "col_name": "", "dataMatrix_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "dbkey": "?", "makeunique": "no", "metatype": "variable"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/idchoice/idchoice/19.12", "tool_stderr": "Error in id.choice(args$dataMatrix_in, args$Metadata_in, args$metatype,  : \n  \n-------\nWarning: no '' column detected in variable metadata!\nPlease check your metadata file (column names are case-sensitive).\n-------\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Thu 30 Jun 2022 14:47:31 \n\n-------------------------------------------------------------------- \nParameters used in \"ID choice\":\n\n$dataMatrix_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$Metadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$metatype\n[1] \"variable\"\n\n$col_name\n[1] \"\"\n\n$makeunique\n[1] \"no\"\n\n$DM_out\n[1] \"/galaxy/data/files/000/169/dataset_169541.dat\"\n\n$meta_out\n[1] \"/galaxy/data/files/000/169/dataset_169542.dat\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "19.12", "traceback": null, "update_time": "2022-06-30T14:47:35.285092"}, {"command_line": "perl /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl   perl /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl -f \"/galaxy/data/files/000/168/dataset_168731.dat\" -m \"/galaxy/data/files/000/168/dataset_168731.dat\" -o 2 -d \"/galaxy/data/files/000/168/dataset_168731.dat\" -v \"/galaxy/data/files/000/168/dataset_168731.dat\"  -rt \"0.1\" -mass \"0.005\"  -r \"intensity\"  -correl \"0.9\" -output_sif \"/galaxy/data/files/000/169/dataset_169543.dat\" -output_tabular \"/galaxy/data/files/000/169/dataset_169544.dat\"", "create_time": "2022-06-30T14:47:53.997938", "encoded_id": "11a26d69899a980e", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["7cf499d16bd542b2"], "file_in": ["7cf499d16bd542b2"], "mass_file|mass_file_in": ["7cf499d16bd542b2"], "variableMetadata_in": ["7cf499d16bd542b2"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"sif_out": ["439a8d05732cb9ce"], "variableMetadata_out": ["f517e0df347ef708"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "correl_threshold": "0.9", "dataMatrix_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "dbkey": "?", "file_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "mass_file": {"__current_case__": 0, "liste": {"__current_case__": 1, "mass_file_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "mass_list": "true"}, "mass_choice": "true", "mass_threshold": "0.005"}, "repres_opt": {"__current_case__": 1, "repres_opt_selector": "intensity"}, "rt_cond": {"__current_case__": 0, "rt_choice": "true", "rt_threshold": "0.1"}, "variableMetadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/acorf/Analytic_correlation_filtration/2019-06-20", "tool_stderr": "Use of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 2.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 2.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 3.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 3.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 4.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 4.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 5.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 5.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 6.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 6.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 7.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 7.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 8.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 8.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 9.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 9.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 10.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 10.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 11.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 11.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 12.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 12.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 13.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 13.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 14.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 14.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 15.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 15.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 16.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 16.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 17.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 17.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 18.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 18.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 19.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 19.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 20.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 20.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 21.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 21.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 22.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 22.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 23.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 23.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 24.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 24.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 25.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 25.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 26.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 26.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 27.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 27.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 28.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 28.\nUse of uninitialized value $bmass in subtraction (-) at 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/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 39.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 39.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 40.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 40.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 41.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 41.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 42.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 42.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 43.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 43.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 44.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 44.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 45.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 45.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 46.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 46.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 47.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 47.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 48.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 48.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 49.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 49.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 50.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 50.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 51.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 51.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 52.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 52.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 53.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 53.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 54.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 54.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 55.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 55.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 56.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 56.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 57.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 57.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 58.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 58.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 59.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 59.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 60.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 60.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 61.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 61.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 62.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 62.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 63.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 63.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 64.\nArgument \"rt\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 64.\n", "tool_stdout": "Cr\u00e9ation of a hash containing all adduits and fragments possible\nCreation of a sif table + correlation filtration done\nAnalytic correlation filtrering follow options done\nJoin groups that have been subdivided done\nAddition of annotation information among groups done\nChoose the representative ion for each group done\nAddition of annotation information relative to the representative ion done\nPrint in result file done\nAll steps done\n", "tool_version": "2019-06-20", "traceback": null, "update_time": "2022-06-30T14:47:59.718649"}, {"command_line": "Rscript '/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/workflow4metabolomics/correlation_analysis/58997c28b268/correlation_analysis/correlation_analysis.r'  sorting 1 variable_metadata '/galaxy/data/files/000/168/dataset_168731.dat' data_matrix '/galaxy/data/files/000/168/dataset_168731.dat' sample_metadata '/galaxy/data/files/000/168/dataset_168731.dat' corrdel 0 param_correlation \"\" param_cytoscape \"\" matrix_corr 0 user_matrix_corr \"\" corr_method \"\"", "create_time": "2022-06-30T14:50:24.345558", "encoded_id": "3fccec56d0ed6d93", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["7cf499d16bd542b2"], "sampleMetadata": ["7cf499d16bd542b2"], "variableMetadata": ["7cf499d16bd542b2"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"sorted_table": ["73bd812cd7c67138"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "cond_input_type": {"__current_case__": 0, "cond_function": {"__current_case__": 0, "select_funtion": "sort_only"}, "dataMatrix": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "sampleMetadata": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "select_input_type": "select_input_from_w4m", "variableMetadata": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}}, "dbkey": "?"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/workflow4metabolomics/correlation_analysis/correlation_analysis/1.0.1+galaxy0", "tool_stderr": "Error in `[.data.frame`(new_input, \"pcgroup\") : \n  undefined columns selected\nCalls: do.call ... sorting -> cbind -> cbind -> data.frame -> [ -> [.data.frame\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Thu 30 Jun 2022 14:50:31 \n\n-------------------------------------------------------------------- \nParameters used in 'Metabolites Correlation Analysis':\n\n$sorting\n[1] 1\n\n$variable_metadata\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$data_matrix\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$sample_metadata\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$corrdel\n[1] 0\n\n$param_correlation\n[1] \"\"\n\n$param_cytoscape\n[1] \"\"\n\n$matrix_corr\n[1] 0\n\n$user_matrix_corr\n[1] \"\"\n\n$corr_method\n[1] \"\"\n\n--------------------------------------------------------------------\n\n\nExecuting the sorting function\n", "tool_version": "1.0.1+galaxy0", "traceback": null, "update_time": "2022-06-30T14:50:35.009509"}, {"command_line": "Rscript /galaxy/server/tools/multivariate/multivariate.R  --dataMatrix_in \"/galaxy/data/files/000/168/dataset_168731.dat\" --sampleMetadata_in \"/galaxy/data/files/000/168/dataset_168731.dat\" --variableMetadata_in \"/galaxy/data/files/000/168/dataset_168731.dat\"  --response_component \"1\" --predictive_component_number \"NA\" --orthogonal_component_number \"0\" --test_sample \"FALSE\"  --graphic_type \"summary\" --color_parameter \"None\" --magnify_text \"0.8\" --abcissa_parameter \"1\" --ordinate_parameter \"2\" --ellipsis_component \"NA\" --labels_parameter \"None\"  --algorithm \"default\" --cross_validation_number \"7\" --log10L \"FALSE\" --permutation_number \"20\" --scaling \"standard\"  --sampleMetadata_out \"/galaxy/data/files/000/169/dataset_169562.dat\" --variableMetadata_out \"/galaxy/data/files/000/169/dataset_169563.dat\" --figure \"/galaxy/data/files/000/169/dataset_169564.dat\" --information \"/galaxy/data/files/000/169/dataset_169565.dat\"", "create_time": "2022-07-06T12:30:49.333121", "encoded_id": "0e3b06a9760e7e54", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["7cf499d16bd542b2"], "sampleMetadata_in": ["7cf499d16bd542b2"], "variableMetadata_in": ["7cf499d16bd542b2"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"figure": ["0f507ef71e586927"], "information": ["94ccd7faf1df2475"], "sampleMetadata_out": ["7d202099e4cbca62"], "variableMetadata_out": ["b940ef43d7de9b83"]}, "params": {"__input_ext": "input", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "compute": {"algorithm": "default", "cross_validation_number": "7", "log10L": "FALSE", "permutation_number": "20", "scaling": "standard"}, "dataMatrix_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "dbkey": "?", "graphics": {"abcissa_parameter": "1", "color_parameter": null, "ellipsis_component": "NA", "graphic_type": "summary", "labels_parameter": null, "magnify_text": "0.8", "ordinate_parameter": "2"}, "orthogonal_component_number": "0", "predictive_component_number": "NA", "response_component": "1", "sampleMetadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "save_rdata": "false", "test_sample": "FALSE", "variableMetadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}}, "state": "error", "tool_id": "Multivariate", "tool_stderr": "Error in stopaste(\"Sample names (or number) in the data matrix (first row) and sample\",  : \n  Sample names (or number) in the data matrix (first row) and sample metadata (first column) are not identical; use the 'Check Format' module in the 'Quality Control' section\nExecution halted\n", "tool_stdout": "$help\n[1] FALSE\n\n$dataMatrix_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$sampleMetadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$variableMetadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$sampleMetadata_out\n[1] \"/galaxy/data/files/000/169/dataset_169562.dat\"\n\n$variableMetadata_out\n[1] \"/galaxy/data/files/000/169/dataset_169563.dat\"\n\n$figure\n[1] \"/galaxy/data/files/000/169/dataset_169564.dat\"\n\n$information\n[1] \"/galaxy/data/files/000/169/dataset_169565.dat\"\n\n$test_sample\n[1] FALSE\n\n$abcissa_parameter\n[1] 1\n\n$ordinate_parameter\n[1] 2\n\n$color_parameter\n[1] \"None\"\n\n$ellipsis_component\n[1] \"NA\"\n\n$labels_parameter\n[1] \"None\"\n\n$response_component\n[1] 1\n\n$magnify_text\n[1] 0.8\n\n$predictive_component_number\n[1] \"NA\"\n\n$orthogonal_component_number\n[1] 0\n\n$cross_validation_number\n[1] 7\n\n$log10L\n[1] FALSE\n\n$permutation_number\n[1] 20\n\n$algorithm\n[1] \"default\"\n\n$graphic_type\n[1] \"summary\"\n\n$scaling\n[1] \"standard\"\n\n", "tool_version": "2.4.0", "traceback": null, "update_time": "2022-07-06T12:30:56.059868"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/corr_table/29ec7e3afdd4/corr_table/CorrTable/Corr_wrap.r  tab1_in \"/galaxy/data/files/000/168/dataset_168731.dat\" tab2_in \"/galaxy/data/files/000/168/dataset_168731.dat\"  tab1_samples \"row\" tab2_samples \"row\"  corr_method \"pearson\"  test_corr \"no\"  filter \"no\"  reorder_var \"no\"  plot_choice \"auto\" color_heatmap \"no\" tabcorr_out \"/galaxy/data/files/000/169/dataset_169566.dat\" heatmap_out \"/galaxy/data/files/000/169/dataset_169567.dat\"", "create_time": "2022-07-06T13:35:26.961944", "encoded_id": "3c4d1d4b26ca3ec8", "exit_code": 127, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"tab1_in": ["7cf499d16bd542b2"], "tab2_in": ["7cf499d16bd542b2"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"heatmap_out": ["af09080865e4f957"], "tabcorr_out": ["1aa9c5aa7406981e"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "corr_method": "pearson", "dbkey": "?", "filter_section": {"filter_cond": {"__current_case__": 1, "filter": "no"}, "testcorr_cond": {"__current_case__": 1, "test_corr": "no"}}, "out_section": {"plot_cond": {"__current_case__": 0, "heatmap_cond": {"__current_case__": 1, "color_heatmap": "no"}, "plot_choice": "auto"}, "reorder_var": "no"}, "tab1_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "tab1_samples": "row", "tab2_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "tab2_samples": "row"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/corr_table/corrtable/1.0.0", "tool_stderr": "/galaxy/data/jobs_directory/088/88471/tool_script.sh: line 43: Rscript: command not found\n", "tool_stdout": "", "tool_version": "1.0.0", "traceback": null, "update_time": "2022-07-06T13:37:10.123402"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/512c2b701d96/camera_annotate//CAMERA_annotateDiffreport.r image '/galaxy/data/files/000/168/dataset_168688.dat'  nSlaves ${GALAXY_SLOTS:-1}  sigma 6 perfwhm 0.6  ppm 5 mzabs 0.015  maxcharge 3 maxiso 4 minfrac 0.5  quick FALSE cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE 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This RData should have been created by an old version of XMCS 2.*\nExecution halted\n", "tool_stdout": "\tSESSION INFO\nR version 4.0.5 (2021-03-31) \nMain packages:\nRColorBrewer 1.1.2 \tbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n\tARGUMENTS INFO\nimage\t/galaxy/data/files/000/168/dataset_168688.dat\nmethod\tPeakDensity\nbw\t30\nminFraction\t0.5\nminSamples\t1\nbinSize\t0.25\nmaxFeatures\t50\n\n\n\tARGUMENTS PROCESSING INFO\n\n\n\tINFILE PROCESSING INFO\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:39:51.368178"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/5bd125a3f3b0/xcms_merge//xcms_merge.r  images 'c(\"/galaxy/data/files/000/168/dataset_168688.dat\")'", "create_time": "2022-07-11T08:39:38.832202", "encoded_id": "c6ee0c7e0b3dee47", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"images": ["9e77b3d7d0887128"], "images1": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"sampleMetadataOutput": ["660fc7ff2a3f0694"], "xsetRData": ["a6ffa6feff83767b"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "images": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "sampleMetadata": null}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0", "tool_stderr": "Error in retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) : \n  Cannot access the sample: X20201203_ImjXseeker_70K_blk_01 located: /home/lpavot/Desktop/projects/xseeker/xseekerpreparator/convert/recreate_rdata_from_galaxy/X20201203_ImjXseeker_70K_blk_01.mzML . Please, contact your administrator ... if you have one!\nCalls: mergeXData -> retrieveRawfileInTheWorkingDir\nExecution halted\n", "tool_stdout": "R version 4.0.5 (2021-03-31) \nMain packages:\nbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tRColorBrewer 1.1.2 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n\tXSET MERGING...\n[1] \"Cannot access the sample: X20201203_ImjXseeker_70K_blk_01 located: /home/lpavot/Desktop/projects/xseeker/xseekerpreparator/convert/recreate_rdata_from_galaxy/X20201203_ImjXseeker_70K_blk_01.mzML . Please, contact your administrator ... if you have one!\"\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:39:55.753780"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/b02d1992a43a/xcms_xcmsset//xcms_xcmsSet.r  image '/galaxy/data/files/000/168/dataset_168688.dat'  BPPARAM ${GALAXY_SLOTS:-1}   method MatchedFilter  fwhm 30 binSize 0.1 impute none max 5 snthresh 10 steps 2 mzdiff 0.6 peaklist FALSE      ; return=$?; cat 'log.txt'; sh -c \"exit $return\"", "create_time": "2022-07-11T08:39:42.900215", "encoded_id": "5a7a543694e33064", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"image": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, 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This RData should have been created by an old version of XMCS 2.*\nExecution halted\n", "tool_stdout": "R version 4.0.5 (2021-03-31) \nMain packages:\nbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tRColorBrewer 1.1.2 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:40:01.236321"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/024974037c4e/xcms_plot_chromatogram///xcms_plot_chromatogram.r  images 'c(\"/galaxy/data/files/000/168/dataset_168688.dat\")'", "create_time": "2022-07-11T08:39:48.737637", "encoded_id": "bb7535e772a96d24", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"images": ["9e77b3d7d0887128"], "images1": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"bpisPdf": ["cd6d99f979501c21"], "ticsPdf": ["96b988706e871cd3"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "images": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "sampleMetadata": null}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0", "tool_stderr": "Error in retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) : \n  Cannot access the sample: X20201203_ImjXseeker_70K_blk_01 located: /home/lpavot/Desktop/projects/xseeker/xseekerpreparator/convert/recreate_rdata_from_galaxy/X20201203_ImjXseeker_70K_blk_01.mzML . Please, contact your administrator ... if you have one!\nCalls: mergeXData -> retrieveRawfileInTheWorkingDir\nExecution halted\n", "tool_stdout": "\tSESSION INFO\nR version 4.0.5 (2021-03-31) \nMain packages:\nRColorBrewer 1.1.2 \tbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n\tARGUMENTS INFO\nimages\t/galaxy/data/files/000/168/dataset_168688.dat\n\n\n\tARGUMENTS PROCESSING INFO\n\n\n\tINFILE PROCESSING INFO\n[1] \"Cannot access the sample: X20201203_ImjXseeker_70K_blk_01 located: /home/lpavot/Desktop/projects/xseeker/xseekerpreparator/convert/recreate_rdata_from_galaxy/X20201203_ImjXseeker_70K_blk_01.mzML . Please, contact your administrator ... if you have one!\"\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:40:05.077420"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/26d77e9ceb49/xcms_fillpeaks//xcms_fillpeaks.r  image '/galaxy/data/files/000/168/dataset_168688.dat'  expandMz 0 expandRt 0 ppm 0   convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into naTOzero TRUE       ; return=$?; cat 'log.txt'; sh -c \"exit $return\"", "create_time": "2022-07-11T08:39:53.587990", "encoded_id": "7e48353c1f42ff66", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"image": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataMatrix": ["21da3783e86a28e3"], "variableMetadata": ["fd73fe24f6fc4b2e"], "xsetRData": ["d818ff394d3e3ddd"]}, "params": {"Adv": {"expandMz": "0", "expandRt": "0", "ppm": "0"}, "__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "image": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "peaklist": {"convertRTMinute": "false", "intval": "into", "naTOzero": "true", "numDigitsMZ": "4", "numDigitsRT": "0", "peaklistBool": "True"}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0", "tool_stderr": "Error: \n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*\nExecution halted\n", "tool_stdout": "\tSESSION INFO\nR version 4.0.5 (2021-03-31) \nMain packages:\nbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tRColorBrewer 1.1.2 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 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in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    674\n    674\n    674\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: QualityControl -> check.err\nExecution halted\n", "tool_stdout": "", "tool_version": "2.2.8", "traceback": null, "update_time": "2022-07-11T08:40:32.686966"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/512c2b701d96/camera_annotate//CAMERA_annotateDiffreport.r image '/galaxy/data/files/000/168/dataset_168688.dat'  nSlaves ${GALAXY_SLOTS:-1}  sigma 6 perfwhm 0.6  ppm 5 mzabs 0.015  maxcharge 3 maxiso 4 minfrac 0.5  quick FALSE cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE  polarity negative max_peaks 100 multiplier 3    convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into", "create_time": "2022-07-11T08:41:36.176529", "encoded_id": "ace4c74a7a81ddec", "exit_code": 127, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"image": ["9e77b3d7d0887128"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"rdata_quick_false": ["2ce4466c8ef0a3f7"], "variableMetadata": ["9b1a0b365265c4fc"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "diffreport": {"options": {"__current_case__": 1, "option": "hide"}}, "export": {"convertRTMinute": "false", 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"tool_version": "2.2.6+camera1.48.0-galaxy0", "traceback": null, "update_time": "2022-07-11T08:41:41.271537"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/512c2b701d96/camera_annotate//CAMERA_annotateDiffreport.r image '/galaxy/data/files/000/168/dataset_168688.dat'  nSlaves ${GALAXY_SLOTS:-1}  sigma 6 perfwhm 0.6  ppm 5 mzabs 0.015  maxcharge 3 maxiso 4 minfrac 0.5  quick FALSE cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE  polarity negative max_peaks 100 multiplier 3    convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into", "create_time": "2022-07-11T08:45:31.002527", "encoded_id": "8ce344e7d1228031", "exit_code": 127, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"image": ["9e77b3d7d0887128"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"rdata_quick_false": ["bdb5fc8459d92254"], "variableMetadata": ["db2f69db59e555e2"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "diffreport": {"options": {"__current_case__": 1, "option": "hide"}}, "export": {"convertRTMinute": "false", "intval": "into", "numDigitsMZ": "4", "numDigitsRT": "0"}, "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "findgeneral": {"mzabs": "0.015", "ppm": "5"}, "findisotopes": {"maxcharge": "3", "maxiso": "4", "minfrac": "0.5"}, "groupfwhm": {"perfwhm": "0.6", "sigma": "6"}, "image": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "quick_block": {"__current_case__": 0, "findadducts": {"max_peaks": "100", "polarity": "negative", "rules_block": {"__current_case__": 0, "multiplier": "3", "rules_select": "FALSE"}}, "groupcorr": {"calcCaS": "false", "calcCiS": "true", "calcIso": "false", "cor_eic_th": "0.75", "graphMethod": "hcs", "pval": "0.05"}, "quick": "FALSE"}}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.6+camera1.48.0-galaxy0", "tool_stderr": "/galaxy/data/jobs_directory/089/89436/tool_script.sh: line 128: Rscript: command not found\n", "tool_stdout": "", "tool_version": "2.2.6+camera1.48.0-galaxy0", "traceback": null, "update_time": "2022-07-11T08:45:36.328924"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/512c2b701d96/camera_annotate//CAMERA_annotateDiffreport.r image '/galaxy/data/files/000/168/dataset_168688.dat'  nSlaves ${GALAXY_SLOTS:-1}  sigma 6 perfwhm 0.6  ppm 5 mzabs 0.015  maxcharge 3 maxiso 4 minfrac 0.5  quick FALSE cor_eic_th 0.75 graphMethod hcs pval 0.05 calcCiS TRUE calcIso FALSE calcCaS FALSE  polarity negative max_peaks 100 multiplier 3    convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into", "create_time": "2022-07-11T08:46:43.720001", "encoded_id": "04bcbd95a98c7c86", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"image": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"rdata_quick_false": ["1f3299ca8647ede1"], "variableMetadata": ["e15b0ae531c85e00"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "diffreport": {"options": {"__current_case__": 1, "option": "hide"}}, "export": {"convertRTMinute": "false", "intval": "into", "numDigitsMZ": "4", "numDigitsRT": "0"}, "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "findgeneral": {"mzabs": "0.015", "ppm": "5"}, "findisotopes": {"maxcharge": "3", "maxiso": "4", "minfrac": "0.5"}, "groupfwhm": {"perfwhm": "0.6", "sigma": "6"}, "image": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "quick_block": {"__current_case__": 0, "findadducts": {"max_peaks": "100", "polarity": "negative", "rules_block": {"__current_case__": 0, "multiplier": "3", "rules_select": "FALSE"}}, "groupcorr": {"calcCaS": "false", "calcCiS": "true", "calcIso": "false", "cor_eic_th": "0.75", "graphMethod": "hcs", "pval": "0.05"}, "quick": "FALSE"}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.6+camera1.48.0-galaxy0", "tool_stderr": "Error in retrieveRawfileInTheWorkingDir(singlefile, zipfile) : \n  Cannot access the sample: X20201203_ImjXseeker_70K_blk_01 located: /home/lpavot/Desktop/projects/xseeker/xseekerpreparator/convert/recreate_rdata_from_galaxy/X20201203_ImjXseeker_70K_blk_01.mzML . Please, contact your administrator ... if you have one!\nExecution halted\n", "tool_stdout": "\tSESSION INFO\nR version 4.1.3 (2022-03-10) \nMain packages:\nbatch 1.1.5 \tmulttest 2.48.0 \tCAMERA 1.48.0 \txcms 3.14.0 \tMSnbase 2.18.0 \tProtGenerics 1.24.0 \tS4Vectors 0.30.0 \tmzR 2.26.0 \tRcpp 1.0.9 \tBiocParallel 1.26.0 \tBiobase 2.52.0 \tBiocGenerics 0.38.0 \t\nOther loaded packages:\nbitops 1.0.7 \tmatrixStats 0.62.0 \tdoParallel 1.0.17 \tRColorBrewer 1.1.3 \tGenomeInfoDb 1.28.0 \ttools 4.1.3 \tbackports 1.4.1 \tutf8 1.2.2 \tR6 2.5.1 \taffyio 1.62.0 \trpart 4.1.16 \tHmisc 4.7.0 \tcolorspace 2.0.3 \tnnet 7.3.17 \tgridExtra 2.3 \tcompiler 4.1.3 \tMassSpecWavelet 1.58.0 \tpreprocessCore 1.54.0 \tgraph 1.70.0 \tcli 3.3.0 \thtmlTable 2.4.1 \tDelayedArray 0.18.0 \tscales 1.2.0 \tcheckmate 2.1.0 \tDEoptimR 1.0.11 \trobustbase 0.95.0 \taffy 1.70.0 \tRBGL 1.68.0 \tstringr 1.4.0 \tdigest 0.6.29 \tforeign 0.8.82 \tXVector 0.32.0 \thtmltools 0.5.2 \tbase64enc 0.1.3 \tjpeg 0.1.9 \tpkgconfig 2.0.3 \tMatrixGenerics 1.4.0 \tfastmap 1.1.0 \tlimma 3.48.0 \thtmlwidgets 1.5.4 \trlang 1.0.3 \trstudioapi 0.13 \timpute 1.66.0 \tmzID 1.30.0 \tRCurl 1.98.1.7 \tmagrittr 2.0.3 \tGenomeInfoDbData 1.2.6 \tFormula 1.2.4 \tinterp 1.1.2 \tMALDIquant 1.21 \tMatrix 1.4.1 \tmunsell 0.5.0 \tfansi 1.0.3 \tMsCoreUtils 1.4.0 \tlifecycle 1.0.1 \tvsn 3.60.0 \tstringi 1.7.6 \tMASS 7.3.57 \tSummarizedExperiment 1.22.0 \tzlibbioc 1.38.0 \tplyr 1.8.7 \tgrid 4.1.3 \tcrayon 1.5.1 \tdeldir 1.0.6 \tlattice 0.20.45 \tsplines 4.1.3 \tknitr 1.39 \tpillar 1.7.0 \tigraph 1.3.2 \tGenomicRanges 1.44.0 \tcodetools 0.2.18 \tXML 3.99.0.10 \tglue 1.6.2 \tlatticeExtra 0.6.30 \tdata.table 1.14.2 \tpcaMethods 1.84.0 \tBiocManager 1.30.18 \tvctrs 0.4.1 \tpng 0.1.7 \tforeach 1.5.2 \tgtable 0.3.0 \tRANN 2.6.1 \tclue 0.3.60 \tggplot2 3.3.6 \txfun 0.31 \tncdf4 1.19 \tsurvival 3.3.1 \ttibble 3.1.7 \titerators 1.0.14 \tIRanges 2.26.0 \tcluster 2.1.3 \tellipsis 0.3.2 \t\n\n\n\tARGUMENTS INFO\nimage\t/galaxy/data/files/000/168/dataset_168688.dat\nnSlaves\t1\nsigma\t6\nperfwhm\t0.6\nppm\t5\nmzabs\t0.015\nmaxcharge\t3\nmaxiso\t4\nminfrac\t0.5\nquick\tFALSE\ncor_eic_th\t0.75\ngraphMethod\thcs\npval\t0.05\ncalcCiS\tTRUE\ncalcIso\tFALSE\ncalcCaS\tFALSE\npolarity\tnegative\nmax_peaks\t100\nmultiplier\t3\nconvertRTMinute\tFALSE\nnumDigitsMZ\t4\nnumDigitsRT\t0\nintval\tinto\n\n\n\tINFILE PROCESSING INFO\n\n\n\tARGUMENTS PROCESSING INFO\n[1] \"Cannot access the sample: X20201203_ImjXseeker_70K_blk_01 located: /home/lpavot/Desktop/projects/xseeker/xseekerpreparator/convert/recreate_rdata_from_galaxy/X20201203_ImjXseeker_70K_blk_01.mzML . Please, contact your administrator ... if you have one!\"\n", "tool_version": "2.2.6+camera1.48.0-galaxy0", "traceback": null, "update_time": "2022-07-11T08:47:37.110444"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/aa252eec9229/xcms_retcor//xcms_retcor.r image '/galaxy/data/files/000/168/dataset_168688.dat'  method PeakGroups minFraction 0.9 extraPeaks 1 smooth loess span 0.2 family gaussian      ; return=$?; cat 'log.txt'; sh -c \"exit $return\"", "create_time": "2022-07-11T08:48:01.764176", "encoded_id": "b2724dcae8ff63d5", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"image": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"rawVSadjustedPdf": ["2346b035764945ff"], "xsetRData": ["36eb9fd45bc5adac"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "image": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "methods": {"__current_case__": 0, "extraPeaks": "1", "method": "PeakGroups", "minFraction": "0.9", "smooth_cond": {"PeakGroupsSmoothLoessAdv": {"family": "gaussian", "span": "0.2"}, "__current_case__": 0, "smooth": "loess"}}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/3.12.0+galaxy0", "tool_stderr": "Error: \n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*\nExecution halted\n", "tool_stdout": "\tSESSION INFO\nR version 4.0.5 (2021-03-31) \nMain packages:\nRColorBrewer 1.1.2 \tbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n\tARGUMENTS INFO\nimage\t/galaxy/data/files/000/168/dataset_168688.dat\nmethod\tPeakGroups\nminFraction\t0.9\nextraPeaks\t1\nsmooth\tloess\nspan\t0.2\nfamily\tgaussian\n\n\n\tARGUMENTS PROCESSING INFO\n\n\n\tINFILE PROCESSING INFO\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:48:16.715487"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_summary/018a9771de28/xcms_summary//xcms_summary.r  image '/galaxy/data/files/000/168/dataset_168688.dat' htmlOutput 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"params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "image": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "methods": {"PeakDensityAdv": {"maxFeatures": "50"}, "__current_case__": 0, "binSize": "0.25", "bw": "30.0", "method": "PeakDensity", "minFraction": "0.5", "minSamples": "1"}, "peaklist": {"__current_case__": 1, "peaklistBool": "false"}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0", "tool_stderr": "Error: \n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*\nExecution halted\n", "tool_stdout": "\tSESSION INFO\nR version 4.0.5 (2021-03-31) \nMain packages:\nRColorBrewer 1.1.2 \tbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n\tARGUMENTS INFO\nimage\t/galaxy/data/files/000/168/dataset_168688.dat\nmethod\tPeakDensity\nbw\t30\nminFraction\t0.5\nminSamples\t1\nbinSize\t0.25\nmaxFeatures\t50\n\n\n\tARGUMENTS PROCESSING INFO\n\n\n\tINFILE PROCESSING INFO\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:48:28.924306"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/d45a786cbc40/xcms_group//xcms_group.r image '/galaxy/data/files/000/168/dataset_168688.dat'  method PeakDensity bw 30.0 minFraction 0.5 minSamples 1 binSize 0.25 maxFeatures 50         ; return=$?; cat 'log.txt'; sh -c \"exit $return\"", "create_time": "2022-07-11T08:48:17.266516", "encoded_id": "a6797cd946448e7b", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"image": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"plotChromPeakDensity": ["e0158599f7882364"], "xsetRData": ["43325fb3d8f8d47a"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "image": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "methods": {"PeakDensityAdv": {"maxFeatures": "50"}, "__current_case__": 0, "binSize": "0.25", "bw": "30.0", "method": "PeakDensity", "minFraction": "0.5", "minSamples": "1"}, "peaklist": {"__current_case__": 1, "peaklistBool": "false"}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_group/abims_xcms_group/3.12.0+galaxy0", "tool_stderr": "Error: \n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*\nExecution halted\n", "tool_stdout": "\tSESSION INFO\nR version 4.0.5 (2021-03-31) \nMain packages:\nRColorBrewer 1.1.2 \tbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n\tARGUMENTS INFO\nimage\t/galaxy/data/files/000/168/dataset_168688.dat\nmethod\tPeakDensity\nbw\t30\nminFraction\t0.5\nminSamples\t1\nbinSize\t0.25\nmaxFeatures\t50\n\n\n\tARGUMENTS PROCESSING INFO\n\n\n\tINFILE PROCESSING INFO\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:48:32.972939"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/5bd125a3f3b0/xcms_merge//xcms_merge.r  images 'c(\"/galaxy/data/files/000/168/dataset_168688.dat\")'", "create_time": "2022-07-11T08:48:20.879206", "encoded_id": "dd5dfaff7aba44a7", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"images": ["9e77b3d7d0887128"], "images1": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"sampleMetadataOutput": ["6fcfeac7a64b0a10"], "xsetRData": ["d3d4ca6c84e2eb43"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "images": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "sampleMetadata": null}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_merge/xcms_merge/3.12.0+galaxy0", "tool_stderr": "Error in retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) : \n  Cannot access the sample: X20201203_ImjXseeker_70K_blk_01 located: /home/lpavot/Desktop/projects/xseeker/xseekerpreparator/convert/recreate_rdata_from_galaxy/X20201203_ImjXseeker_70K_blk_01.mzML . Please, contact your administrator ... if you have one!\nCalls: mergeXData -> retrieveRawfileInTheWorkingDir\nExecution halted\n", "tool_stdout": "R version 4.0.5 (2021-03-31) \nMain packages:\nbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tRColorBrewer 1.1.2 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n\tXSET MERGING...\n[1] \"Cannot access the sample: X20201203_ImjXseeker_70K_blk_01 located: /home/lpavot/Desktop/projects/xseeker/xseekerpreparator/convert/recreate_rdata_from_galaxy/X20201203_ImjXseeker_70K_blk_01.mzML . Please, contact your administrator ... if you have one!\"\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:48:38.730743"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_export_samplemetadata/94eb263cfab4/xcms_export_samplemetadata//xcms_export_samplemetadata.r  images 'c(\"/galaxy/data/files/000/168/dataset_168688.dat\")'", "create_time": "2022-07-11T08:48:23.723080", "encoded_id": "082f78f4f8bdfcba", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"images": ["9e77b3d7d0887128"], "images1": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"sampleMetadataOutput": ["1534a4f5ea43db6f"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "images": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_export_samplemetadata/xcms_export_samplemetadata/3.12.0+galaxy0", "tool_stderr": "Error: \n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*\nExecution halted\n", "tool_stdout": "R version 4.0.5 (2021-03-31) \nMain packages:\nbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tRColorBrewer 1.1.2 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:48:39.750641"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/024974037c4e/xcms_plot_chromatogram///xcms_plot_chromatogram.r  images 'c(\"/galaxy/data/files/000/168/dataset_168688.dat\")'", "create_time": "2022-07-11T08:48:27.633357", "encoded_id": "9c5412bfb8d46d63", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"images": ["9e77b3d7d0887128"], "images1": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"bpisPdf": ["3892150f2fe222a4"], "ticsPdf": ["3b2ea3866be8e8e1"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "images": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "sampleMetadata": null}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_plot_chromatogram/xcms_plot_chromatogram/3.12.0+galaxy0", "tool_stderr": "Error in retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) : \n  Cannot access the sample: X20201203_ImjXseeker_70K_blk_01 located: /home/lpavot/Desktop/projects/xseeker/xseekerpreparator/convert/recreate_rdata_from_galaxy/X20201203_ImjXseeker_70K_blk_01.mzML . Please, contact your administrator ... if you have one!\nCalls: mergeXData -> retrieveRawfileInTheWorkingDir\nExecution halted\n", "tool_stdout": "\tSESSION INFO\nR version 4.0.5 (2021-03-31) \nMain packages:\nRColorBrewer 1.1.2 \tbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n\tARGUMENTS INFO\nimages\t/galaxy/data/files/000/168/dataset_168688.dat\n\n\n\tARGUMENTS PROCESSING INFO\n\n\n\tINFILE PROCESSING INFO\n[1] \"Cannot access the sample: X20201203_ImjXseeker_70K_blk_01 located: /home/lpavot/Desktop/projects/xseeker/xseekerpreparator/convert/recreate_rdata_from_galaxy/X20201203_ImjXseeker_70K_blk_01.mzML . Please, contact your administrator ... if you have one!\"\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:48:42.897209"}, {"command_line": "LC_ALL=C Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/26d77e9ceb49/xcms_fillpeaks//xcms_fillpeaks.r  image '/galaxy/data/files/000/168/dataset_168688.dat'  expandMz 0 expandRt 0 ppm 0   convertRTMinute FALSE numDigitsMZ 4 numDigitsRT 0 intval into naTOzero TRUE       ; return=$?; cat 'log.txt'; sh -c \"exit $return\"", "create_time": "2022-07-11T08:48:32.887979", "encoded_id": "ce42c7d545642e44", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"image": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataMatrix": ["03327c57c83dd5fa"], "variableMetadata": ["ed2870de67554863"], "xsetRData": ["a8104466e02ce60a"]}, "params": {"Adv": {"expandMz": "0", "expandRt": "0", "ppm": "0"}, "__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "file_load_section": {"file_load_conditional": {"__current_case__": 0, "file_load_select": "no"}}, "image": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}, "peaklist": {"convertRTMinute": "false", "intval": "into", "naTOzero": "true", "numDigitsMZ": "4", "numDigitsRT": "0", "peaklistBool": "True"}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/xcms_fillpeaks/abims_xcms_fillPeaks/3.12.0+galaxy0", "tool_stderr": "Error: \n\nERROR: The RData doesn't contain any object called 'xdata'. This RData should have been created by an old version of XMCS 2.*\nExecution halted\n", "tool_stdout": "\tSESSION INFO\nR version 4.0.5 (2021-03-31) \nMain packages:\nbatch 1.1.5 \txcms 3.12.0 \tMSnbase 2.16.1 \tProtGenerics 1.22.0 \tS4Vectors 0.28.1 \tmzR 2.24.1 \tRcpp 1.0.9 \tBiocParallel 1.24.1 \tBiobase 2.50.0 \tBiocGenerics 0.36.0 \t\nOther loaded packages:\nSummarizedExperiment 1.20.0 \tlattice 0.20.45 \tcolorspace 2.0.3 \tvctrs 0.4.1 \tvsn 3.58.0 \tutf8 1.2.2 \tXML 3.99.0.10 \trlang 1.0.3 \tpillar 1.7.0 \tglue 1.6.2 \taffy 1.68.0 \tRColorBrewer 1.1.2 \tGenomeInfoDbData 1.2.4 \taffyio 1.60.0 \tmatrixStats 0.62.0 \tforeach 1.5.2 \tlifecycle 1.0.1 \tplyr 1.8.7 \tmzID 1.28.0 \trobustbase 0.95.0 \tzlibbioc 1.36.0 \tMatrixGenerics 1.2.1 \tmunsell 0.5.0 \tpcaMethods 1.82.0 \tgtable 0.3.0 \tcodetools 0.2.18 \tIRanges 2.24.1 \tdoParallel 1.0.17 \tGenomeInfoDb 1.26.4 \tMassSpecWavelet 1.56.0 \tfansi 1.0.3 \tpreprocessCore 1.52.1 \tDEoptimR 1.0.11 \tscales 1.2.0 \tBiocManager 1.30.18 \tDelayedArray 0.16.3 \tlimma 3.46.0 \tXVector 0.30.0 \tMsCoreUtils 1.2.0 \tRANN 2.6.1 \timpute 1.64.0 \tggplot2 3.3.6 \tdigest 0.6.29 \tncdf4 1.19 \tGenomicRanges 1.42.0 \tgrid 4.0.5 \tcli 3.3.0 \ttools 4.0.5 \tbitops 1.0.7 \tmagrittr 2.0.3 \tRCurl 1.98.1.7 \ttibble 3.1.7 \tcrayon 1.5.1 \tpkgconfig 2.0.3 \tMatrix 1.4.1 \tMASS 7.3.57 \tellipsis 0.3.2 \titerators 1.0.14 \tR6 2.5.1 \tMALDIquant 1.21 \tcompiler 4.0.5 \t\n\n\n\tARGUMENTS INFO\nimage\t/galaxy/data/files/000/168/dataset_168688.dat\nexpandMz\t0\nexpandRt\t0\nppm\t0\nconvertRTMinute\tFALSE\nnumDigitsMZ\t4\nnumDigitsRT\t0\nintval\tinto\nnaTOzero\tTRUE\n\n\n\tARGUMENTS PROCESSING INFO\n\n\n\tINFILE PROCESSING INFO\n", "tool_version": "3.12.0+galaxy0", "traceback": null, "update_time": "2022-07-11T08:48:49.734335"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/acdf51018708/qualitymetrics/qualitymetrics_wrapper.R dataMatrix_in \"/galaxy/data/files/000/168/dataset_168731.dat\" sampleMetadata_in \"/galaxy/data/files/000/168/dataset_168731.dat\" variableMetadata_in \"/galaxy/data/files/000/168/dataset_168731.dat\"  CV \"FALSE\" Compa \"TRUE\" seuil \"1\"  poolAsPool1L \"TRUE\"  sampleMetadata_out \"/galaxy/data/files/000/171/dataset_171146.dat\" variableMetadata_out \"/galaxy/data/files/000/171/dataset_171147.dat\" figure \"/galaxy/data/files/000/171/dataset_171148.dat\" information \"/galaxy/data/files/000/171/dataset_171149.dat\"", "create_time": "2022-07-11T08:49:28.924395", "encoded_id": "ee77bb429c7c9f1d", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["7cf499d16bd542b2"], "sampleMetadata_in": ["7cf499d16bd542b2"], "variableMetadata_in": ["7cf499d16bd542b2"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"figure": ["b4994b74e8d48b37"], "information": ["ec66019a424ab8c8"], "sampleMetadata_out": ["1acf05259078d9af"], "variableMetadata_out": ["62cb370746be8776"]}, "params": {"CV_condition": {"CV": "FALSE", "Compa": "TRUE", "__current_case__": 1, "seuil": "1"}, "__input_ext": "tabular", "advPar": {"__current_case__": 1, "optC": "default", "poolAsPool1L": "TRUE"}, "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "dbkey": "?", "sampleMetadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "variableMetadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    The following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    mz\n    rt\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    2-diethylamino-6-methyl pyrimidin-4-ol one\n    5-hydroxy-thiabendazole\n    acetamiprid-N-desmethyl\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: QualityControl -> check.err\nExecution halted\n", "tool_stdout": "", "tool_version": "2.2.8", "traceback": null, "update_time": "2022-07-11T08:49:35.687780"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/49c36c54e0cf/intensity_checks/Intchecks/wrapper_intensity_check.R  dataMatrix_in \"/galaxy/data/files/000/168/dataset_168729.dat\" sampleMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\" variableMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\"  method \"no_class\"  chosen_stat \"None\"    variableMetadata_out \"/galaxy/data/files/000/171/dataset_171150.dat\" graphs_out \"/galaxy/data/files/000/171/dataset_171151.dat\"", "create_time": "2022-07-11T08:49:38.287192", "encoded_id": "212186a890314bf8", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["9a0ce47bd1734ae7"], "sampleMetadata_in": ["9a0ce47bd1734ae7"], "variableMetadata_in": ["9a0ce47bd1734ae7"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"graphs_out": ["8db230ba7dcb6989"], "variableMetadata_out": ["2e64ae6c81ea53d4"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "method_cond": {"__current_case__": 0, "chosen_stat": null, "method": "no_class"}, "sampleMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "variableMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/intensity_checks/intens_check/1.2.8", "tool_stderr": "Error: \n- - - - - - - - -\nYou did not select any computational option. Program can not be executed.\n- - - - - - - - -\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:49:49 \n\n-------------------------------------------------------------------- \nIntensity Check parameters:\n\n$dataMatrix_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$sampleMetadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$variableMetadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$method\n[1] \"no_class\"\n\n$chosen_stat\n[1] \"None\"\n\n$variableMetadata_out\n[1] \"/galaxy/data/files/000/171/dataset_171150.dat\"\n\n$graphs_out\n[1] \"/galaxy/data/files/000/171/dataset_171151.dat\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "1.2.8", "traceback": null, "update_time": "2022-07-11T08:49:53.973761"}, {"command_line": "perl /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl   perl /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl -f \"/galaxy/data/files/000/168/dataset_168729.dat\" -m \"/galaxy/data/files/000/168/dataset_168729.dat\" -o 2 -d \"/galaxy/data/files/000/168/dataset_168729.dat\" -v \"/galaxy/data/files/000/168/dataset_168729.dat\"  -rt \"0.1\" -mass \"0.005\"  -r \"intensity\"  -correl \"0.9\" -output_sif \"/galaxy/data/files/000/171/dataset_171152.dat\" -output_tabular \"/galaxy/data/files/000/171/dataset_171153.dat\"", "create_time": "2022-07-11T08:49:47.034504", "encoded_id": "ab8e2e26fd4e70b4", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["9a0ce47bd1734ae7"], "file_in": ["9a0ce47bd1734ae7"], "mass_file|mass_file_in": ["9a0ce47bd1734ae7"], "variableMetadata_in": ["9a0ce47bd1734ae7"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"sif_out": ["92626a4def3a6ddc"], "variableMetadata_out": ["4c8d2eafb9372cfc"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "correl_threshold": "0.9", "dataMatrix_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "file_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "mass_file": {"__current_case__": 0, "liste": {"__current_case__": 1, "mass_file_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "mass_list": "true"}, "mass_choice": "true", "mass_threshold": "0.005"}, "repres_opt": {"__current_case__": 1, "repres_opt_selector": "intensity"}, "rt_cond": {"__current_case__": 0, "rt_choice": "true", "rt_threshold": "0.1"}, "variableMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/acorf/Analytic_correlation_filtration/2019-06-20", "tool_stderr": "Use of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 2.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 3.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 4.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 5.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 6.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 7.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 8.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 9.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 10.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 11.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 12.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 13.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 14.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 15.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 16.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 17.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 18.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 19.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 20.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 21.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 22.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 23.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 24.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 25.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 26.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 27.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 28.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 29.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 30.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 31.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 32.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 33.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 34.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 35.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 36.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 37.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 38.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 39.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 40.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at 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105, <F5> line 45.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 46.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 47.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 48.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 49.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at 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105, <F5> line 54.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 55.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 56.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 57.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 58.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at 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105, <F5> line 63.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 64.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 65.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 66.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 67.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 68.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 69.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 70.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 71.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 72.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 73.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 74.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 75.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 76.\nUse of uninitialized value $hheader_line{\"rt\"} in array element at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/lib/IonFiltration.pm line 105, <F5> line 77.\nUse of uninitialized value $hheader_line{\"rt\"} in \n..\nline 113, <F1> line 1045.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1045.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1046.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1046.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1047.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1047.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1048.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1048.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1049.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1049.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1050.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1050.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1051.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1051.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1052.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1052.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1053.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1053.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1054.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1054.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1055.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1055.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1056.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1056.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1057.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1057.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1058.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1058.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1059.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1059.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1060.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1060.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1061.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1061.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1062.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1062.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1063.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1063.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1064.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1064.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1065.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1065.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1066.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1066.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1067.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1067.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1068.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1068.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1069.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1069.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1070.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1070.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1071.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1071.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1072.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1072.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1073.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1073.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1074.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1074.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1075.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1075.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1076.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1076.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1077.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1077.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1078.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1078.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1079.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1079.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1080.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1080.\nUse of uninitialized value $bmass in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 113, <F1> line 1081.\nArgument \"precursorScanNum\" isn't numeric in subtraction (-) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/acorf/15430e89c97d/acorf/ACF/Analytic_correlation_filtration.pl line 148, <F1> line 1081.\n", "tool_stdout": "The mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 322 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 326 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 328 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 330 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 332 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 334 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 336 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4260 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4264 !\nThe mass difference already exists : 4268 !\nThe mass difference alrea\n..\nady exists : 5834 !\nThe mass difference already exists : 5834 !\nThe mass difference already exists : 5834 !\nThe mass difference already exists : 5834 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3587 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3590 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3593 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3596 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3602 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3938 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3944 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3950 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3956 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 3968 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6148 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6154 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6160 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6166 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6172 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nThe mass difference already exists : 6178 !\nCr\u00e9ation of a hash containing all adduits and fragments possible\nCreation of a sif table + correlation filtration done\nAnalytic correlation filtrering follow options done\nJoin groups that have been subdivided done\nAddition of annotation information among groups done\nChoose the representative ion for each group done\nAddition of annotation information relative to the representative ion done\nPrint in result file done\nAll steps done\n", "tool_version": "2019-06-20", "traceback": null, "update_time": "2022-07-11T08:49:58.551131"}, {"command_line": "Rscript '/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/workflow4metabolomics/correlation_analysis/58997c28b268/correlation_analysis/correlation_analysis.r'  sorting 1 variable_metadata '/galaxy/data/files/000/168/dataset_168731.dat' data_matrix '/galaxy/data/files/000/168/dataset_168731.dat' sample_metadata '/galaxy/data/files/000/168/dataset_168731.dat' corrdel 0 param_correlation \"\" param_cytoscape \"\" matrix_corr 0 user_matrix_corr \"\" corr_method \"\"", "create_time": "2022-07-11T08:50:10.948083", "encoded_id": "0b0fc8d1b535b635", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["7cf499d16bd542b2"], "sampleMetadata": ["7cf499d16bd542b2"], "variableMetadata": ["7cf499d16bd542b2"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"sorted_table": ["a7dc208e4eb7b2f7"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "cond_input_type": {"__current_case__": 0, "cond_function": {"__current_case__": 0, "select_funtion": "sort_only"}, "dataMatrix": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "sampleMetadata": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "select_input_type": "select_input_from_w4m", "variableMetadata": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}}, "dbkey": "?"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/workflow4metabolomics/correlation_analysis/correlation_analysis/1.0.1+galaxy0", "tool_stderr": "Error in `[.data.frame`(new_input, \"pcgroup\") : \n  undefined columns selected\nCalls: do.call ... sorting -> cbind -> cbind -> data.frame -> [ -> [.data.frame\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:50:22 \n\n-------------------------------------------------------------------- \nParameters used in 'Metabolites Correlation Analysis':\n\n$sorting\n[1] 1\n\n$variable_metadata\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$data_matrix\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$sample_metadata\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$corrdel\n[1] 0\n\n$param_correlation\n[1] \"\"\n\n$param_cytoscape\n[1] \"\"\n\n$matrix_corr\n[1] 0\n\n$user_matrix_corr\n[1] \"\"\n\n$corr_method\n[1] \"\"\n\n--------------------------------------------------------------------\n\n\nExecuting the sorting function\n", "tool_version": "1.0.1+galaxy0", "traceback": null, "update_time": "2022-07-11T08:50:27.096987"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/ethevenot/transformation/0ccfc3e15710/transformation/transformation_wrapper.R dataMatrix_in \"/galaxy/data/files/000/168/dataset_168729.dat\" method \"log2\"  dataMatrix_out \"/galaxy/data/files/000/171/dataset_171155.dat\" information \"/galaxy/data/files/000/171/dataset_171156.dat\"", "create_time": "2022-07-11T08:50:17.005606", "encoded_id": "a76ddfe9cc0832fc", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataMatrix_out": ["87ebb5861861a6c6"], "information": ["e82d31b63bfcce14"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "method": "log2"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/transformation/Transformation/2.2.0", "tool_stderr": "Error in read.table(argVc[[\"dataMatrix_in\"]], check.names = FALSE, header = TRUE,  : \n  duplicate 'row.names' are not allowed\nCalls: t -> as.matrix -> read.table\nExecution halted\n", "tool_stdout": "", "tool_version": "2.2.0", "traceback": null, "update_time": "2022-07-11T08:50:39.454200"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/normalization/221cbd549c40/normalization/NmrNormalization_wrapper.R  dataMatrix /galaxy/data/files/000/168/dataset_168729.dat  scalingMethod None  graphType None  logOut /galaxy/data/files/000/171/dataset_171157.dat dataMatrixOut /galaxy/data/files/000/171/dataset_171158.dat graphOut XXXX", "create_time": "2022-07-11T08:50:20.930379", "encoded_id": "6fdf81221074c427", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataMatrixOut": ["648f2f60b1d3703b"], "logOut": ["06a085d607e91aa1"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "graphType": "None", "scalingMethod": {"__current_case__": 0, "method": "None"}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/marie-tremblay-metatoul/normalization/normalization/1.0.7", "tool_stderr": "Error in read.table(argLs[[\"dataMatrix\"]], check.names = FALSE, header = TRUE,  : \n  duplicate 'row.names' are not allowed\nExecution halted\n", "tool_stdout": "", "tool_version": "1.0.7", "traceback": null, "update_time": "2022-07-11T08:50:38.987078"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/23314e1192d4/batchcorrection/BC/batch_correction_3Lwrapper.R analyse \"determine_bc\" sampleMetadata \"/galaxy/data/files/000/168/dataset_168729.dat\" dataMatrix \"/galaxy/data/files/000/168/dataset_168729.dat\" ref_factor \"batch\" span \"none\" out_graph_pdf \"/galaxy/data/files/000/171/dataset_171159.dat\" out_preNormSummary \"/galaxy/data/files/000/171/dataset_171160.dat\"  batch_col_name \"batch\" injection_order_col_name \"injectionOrder\" sample_type_col_name \"sampleType\" sample_type_tags \"blank=blank,pool=pool,sample=sample\"", "create_time": "2022-07-11T08:50:25.663044", "encoded_id": "4fefeddf7f518267", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["9a0ce47bd1734ae7"], "sampleMetadata": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"out_graph_pdf": ["705c8448e3da51ac"], "out_preNormSummary": ["223f8486bbcbff21"]}, "params": {"__input_ext": "tabular", "advance": {"__current_case__": 1, "option": "hide"}, "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "ref_factor": "batch", "sampleMetadata": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "smcust": {"batch_col_name": "batch", "injection_order_col_name": "injectionOrder", "sampleTypeTagBlank": "blank", "sampleTypeTagPool": "pool", "sampleTypeTagSample": "sample", "sample_type_col_name": "sampleType"}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Determine_BC/3.0.0", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    674\n    674\n    674\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: meth3L -> check.err\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:50:37 \n\n-------------------------------------------------------------------- \nParameters used:\n\n$analyse\n[1] \"determine_bc\"\n\n$sampleMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$dataMatrix\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$ref_factor\n[1] \"batch\"\n\n$span\n[1] \"none\"\n\n$out_graph_pdf\n[1] \"/galaxy/data/files/000/171/dataset_171159.dat\"\n\n$out_preNormSummary\n[1] \"/galaxy/data/files/000/171/dataset_171160.dat\"\n\n$batch_col_name\n[1] \"batch\"\n\n$injection_order_col_name\n[1] \"injectionOrder\"\n\n$sample_type_col_name\n[1] \"sampleType\"\n\n$sample_type_tags\n[1] \"blank=blank,pool=pool,sample=sample\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "3.0.0", "traceback": null, "update_time": "2022-07-11T08:50:47.176008"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/23314e1192d4/batchcorrection/BC/batch_correction_3Lwrapper.R analyse \"batch_correction\" dataMatrix \"/galaxy/data/files/000/168/dataset_168729.dat\" sampleMetadata \"/galaxy/data/files/000/168/dataset_168729.dat\" variableMetadata \"/galaxy/data/files/000/168/dataset_168729.dat\" method \"linear\" span \"none\" valnull \"none\" ref_factor \"batch\" detail \"no\" dataMatrix_out \"/galaxy/data/files/000/171/dataset_171161.dat\" variableMetadata_out \"/galaxy/data/files/000/171/dataset_171162.dat\" graph_output \"/galaxy/data/files/000/171/dataset_171163.dat\"  rdata_output \"XXXX\"  batch_col_name \"batch\" injection_order_col_name \"injectionOrder\" sample_type_col_name \"sampleType\" sample_type_tags \"blank=blank,pool=pool,sample=sample\"", "create_time": "2022-07-11T08:50:32.133479", "encoded_id": "ab33fc55ef4e6ef3", "exit_code": 127, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["9a0ce47bd1734ae7"], "sampleMetadata": ["9a0ce47bd1734ae7"], "variableMetadata": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 127 ()", "error_level": 3, "exit_code": 127, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataMatrix_out": ["9aa8d81dc8bcf907"], "graph_output": ["ec9fccd9398c4918"], "variableMetadata_out": ["f3da5e47224170ed"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "sampleMetadata": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "smcust": {"batch_col_name": "batch", "injection_order_col_name": "injectionOrder", "sampleTypeTagBlank": "blank", "sampleTypeTagPool": "pool", "sampleTypeTagSample": "sample", "sample_type_col_name": "sampleType"}, "span_condition": {"__current_case__": 0, "detail": "no", "method": "linear", "ref_factor": "batch", "valnull": "none"}, "variableMetadata": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/3.0.0", "tool_stderr": "/galaxy/data/jobs_directory/089/89454/tool_script.sh: line 77: Rscript: command not found\n", "tool_stdout": "", "tool_version": "3.0.0", "traceback": null, "update_time": "2022-07-11T08:50:37.846452"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/23314e1192d4/batchcorrection/BC/batch_correction_3Lwrapper.R analyse \"batch_correction\" dataMatrix \"/galaxy/data/files/000/168/dataset_168729.dat\" sampleMetadata \"/galaxy/data/files/000/168/dataset_168729.dat\" variableMetadata \"/galaxy/data/files/000/168/dataset_168729.dat\" method \"linear\" span \"none\" valnull \"none\" ref_factor \"batch\" detail \"no\" dataMatrix_out \"/galaxy/data/files/000/171/dataset_171164.dat\" variableMetadata_out \"/galaxy/data/files/000/171/dataset_171165.dat\" graph_output \"/galaxy/data/files/000/171/dataset_171166.dat\"  rdata_output \"XXXX\"  batch_col_name \"batch\" injection_order_col_name \"injectionOrder\" sample_type_col_name \"sampleType\" sample_type_tags \"blank=blank,pool=pool,sample=sample\"", "create_time": "2022-07-11T08:52:12.304732", "encoded_id": "56c0d8e6c86a1764", "exit_code": 127, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["9a0ce47bd1734ae7"], "sampleMetadata": ["9a0ce47bd1734ae7"], "variableMetadata": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 127 ()", "error_level": 3, "exit_code": 127, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataMatrix_out": ["d6d2a48066758eba"], "graph_output": ["3bddab42140681a3"], "variableMetadata_out": ["291fd64ff7d8ccd4"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "sampleMetadata": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "smcust": {"batch_col_name": "batch", "injection_order_col_name": "injectionOrder", "sampleTypeTagBlank": "blank", "sampleTypeTagPool": "pool", "sampleTypeTagSample": "sample", "sample_type_col_name": "sampleType"}, "span_condition": {"__current_case__": 0, "detail": "no", "method": "linear", "ref_factor": "batch", "valnull": "none"}, "variableMetadata": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/3.0.0", "tool_stderr": "/galaxy/data/jobs_directory/089/89455/tool_script.sh: line 77: Rscript: command not found\n", "tool_stdout": "", "tool_version": "3.0.0", "traceback": null, "update_time": "2022-07-11T08:52:17.936045"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/23314e1192d4/batchcorrection/BC/batch_correction_3Lwrapper.R analyse \"batch_correction\" dataMatrix \"/galaxy/data/files/000/168/dataset_168729.dat\" sampleMetadata \"/galaxy/data/files/000/168/dataset_168729.dat\" variableMetadata \"/galaxy/data/files/000/168/dataset_168729.dat\" method \"linear\" span \"none\" valnull \"none\" ref_factor \"batch\" detail \"no\" dataMatrix_out \"/galaxy/data/files/000/171/dataset_171167.dat\" variableMetadata_out \"/galaxy/data/files/000/171/dataset_171168.dat\" graph_output \"/galaxy/data/files/000/171/dataset_171169.dat\"  rdata_output \"XXXX\"  batch_col_name \"batch\" injection_order_col_name \"injectionOrder\" sample_type_col_name \"sampleType\" sample_type_tags \"blank=blank,pool=pool,sample=sample\"", "create_time": "2022-07-11T08:52:40.679133", "encoded_id": "3f9d30066f6a43a5", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["9a0ce47bd1734ae7"], "sampleMetadata": ["9a0ce47bd1734ae7"], "variableMetadata": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataMatrix_out": ["717c674a3dc82438"], "graph_output": ["e41cbff630693073"], "variableMetadata_out": ["82b59b7aa276ad0d"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "sampleMetadata": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "smcust": {"batch_col_name": "batch", "injection_order_col_name": "injectionOrder", "sampleTypeTagBlank": "blank", "sampleTypeTagPool": "pool", "sampleTypeTagSample": "sample", "sample_type_col_name": "sampleType"}, "span_condition": {"__current_case__": 0, "detail": "no", "method": "linear", "ref_factor": "batch", "valnull": "none"}, "variableMetadata": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/3.0.0", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    674\n    674\n    674\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: meth3L -> check.err\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:52:52 \n\n-------------------------------------------------------------------- \nParameters used:\n\n$analyse\n[1] \"batch_correction\"\n\n$dataMatrix\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$sampleMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$variableMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$method\n[1] \"linear\"\n\n$span\n[1] \"none\"\n\n$valnull\n[1] \"none\"\n\n$ref_factor\n[1] \"batch\"\n\n$detail\n[1] \"no\"\n\n$dataMatrix_out\n[1] \"/galaxy/data/files/000/171/dataset_171167.dat\"\n\n$variableMetadata_out\n[1] \"/galaxy/data/files/000/171/dataset_171168.dat\"\n\n$graph_output\n[1] \"/galaxy/data/files/000/171/dataset_171169.dat\"\n\n$rdata_output\n[1] \"XXXX\"\n\n$batch_col_name\n[1] \"batch\"\n\n$injection_order_col_name\n[1] \"injectionOrder\"\n\n$sample_type_col_name\n[1] \"sampleType\"\n\n$sample_type_tags\n[1] \"blank=blank,pool=pool,sample=sample\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "3.0.0", "traceback": null, "update_time": "2022-07-11T08:53:00.928692"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/23314e1192d4/batchcorrection/BC/batch_correction_3Lwrapper.R analyse \"determine_bc\" sampleMetadata \"/galaxy/data/files/000/168/dataset_168731.dat\" dataMatrix \"/galaxy/data/files/000/168/dataset_168731.dat\" ref_factor \"batch\" span \"none\" out_graph_pdf \"/galaxy/data/files/000/171/dataset_171170.dat\" out_preNormSummary \"/galaxy/data/files/000/171/dataset_171171.dat\"  batch_col_name \"batch\" injection_order_col_name \"injectionOrder\" sample_type_col_name \"sampleType\" sample_type_tags \"blank=blank,pool=pool,sample=sample\"", "create_time": "2022-07-11T08:53:11.477121", "encoded_id": "ca492c7005ee175e", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["7cf499d16bd542b2"], "sampleMetadata": ["7cf499d16bd542b2"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"out_graph_pdf": ["70c41105a71d6c96"], "out_preNormSummary": ["01b10cdd9064a60a"]}, "params": {"__input_ext": "tabular", "advance": {"__current_case__": 1, "option": "hide"}, "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "dbkey": "?", "ref_factor": "batch", "sampleMetadata": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "smcust": {"batch_col_name": "batch", "injection_order_col_name": "injectionOrder", "sampleTypeTagBlank": "blank", "sampleTypeTagPool": "pool", "sampleTypeTagSample": "sample", "sample_type_col_name": "sampleType"}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Determine_BC/3.0.0", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    The following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    mz\n    rt\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    2-diethylamino-6-methyl pyrimidin-4-ol one\n    5-hydroxy-thiabendazole\n    acetamiprid-N-desmethyl\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: meth3L -> check.err\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:53:12 \n\n-------------------------------------------------------------------- \nParameters used:\n\n$analyse\n[1] \"determine_bc\"\n\n$sampleMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$dataMatrix\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$ref_factor\n[1] \"batch\"\n\n$span\n[1] \"none\"\n\n$out_graph_pdf\n[1] \"/galaxy/data/files/000/171/dataset_171170.dat\"\n\n$out_preNormSummary\n[1] \"/galaxy/data/files/000/171/dataset_171171.dat\"\n\n$batch_col_name\n[1] \"batch\"\n\n$injection_order_col_name\n[1] \"injectionOrder\"\n\n$sample_type_col_name\n[1] \"sampleType\"\n\n$sample_type_tags\n[1] \"blank=blank,pool=pool,sample=sample\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "3.0.0", "traceback": null, "update_time": "2022-07-11T08:53:16.973567"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/23314e1192d4/batchcorrection/BC/batch_correction_3Lwrapper.R analyse \"batch_correction\" dataMatrix \"/galaxy/data/files/000/168/dataset_168731.dat\" sampleMetadata \"/galaxy/data/files/000/168/dataset_168731.dat\" variableMetadata \"/galaxy/data/files/000/168/dataset_168731.dat\" method \"linear\" span \"none\" valnull \"none\" ref_factor \"batch\" detail \"no\" dataMatrix_out \"/galaxy/data/files/000/171/dataset_171172.dat\" variableMetadata_out \"/galaxy/data/files/000/171/dataset_171173.dat\" graph_output \"/galaxy/data/files/000/171/dataset_171174.dat\"  rdata_output \"XXXX\"  batch_col_name \"batch\" injection_order_col_name \"injectionOrder\" sample_type_col_name \"sampleType\" sample_type_tags \"blank=blank,pool=pool,sample=sample\"", "create_time": "2022-07-11T08:54:20.507678", "encoded_id": "f514e5f531b51ecd", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["7cf499d16bd542b2"], "sampleMetadata": ["7cf499d16bd542b2"], "variableMetadata": ["7cf499d16bd542b2"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataMatrix_out": ["5035859f64c2f04f"], "graph_output": ["de47ad8552edec91"], "variableMetadata_out": ["c44fb0b01495f2a0"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "dbkey": "?", "sampleMetadata": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "smcust": {"batch_col_name": "batch", "injection_order_col_name": "injectionOrder", "sampleTypeTagBlank": "blank", "sampleTypeTagPool": "pool", "sampleTypeTagSample": "sample", "sample_type_col_name": "sampleType"}, "span_condition": {"__current_case__": 0, "detail": "no", "method": "linear", "ref_factor": "batch", "valnull": "none"}, "variableMetadata": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Batch_correction/3.0.0", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    The following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    mz\n    rt\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    2-diethylamino-6-methyl pyrimidin-4-ol one\n    5-hydroxy-thiabendazole\n    acetamiprid-N-desmethyl\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: meth3L -> check.err\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:54:21 \n\n-------------------------------------------------------------------- \nParameters used:\n\n$analyse\n[1] \"batch_correction\"\n\n$dataMatrix\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$sampleMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$variableMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$method\n[1] \"linear\"\n\n$span\n[1] \"none\"\n\n$valnull\n[1] \"none\"\n\n$ref_factor\n[1] \"batch\"\n\n$detail\n[1] \"no\"\n\n$dataMatrix_out\n[1] \"/galaxy/data/files/000/171/dataset_171172.dat\"\n\n$variableMetadata_out\n[1] \"/galaxy/data/files/000/171/dataset_171173.dat\"\n\n$graph_output\n[1] \"/galaxy/data/files/000/171/dataset_171174.dat\"\n\n$rdata_output\n[1] \"XXXX\"\n\n$batch_col_name\n[1] \"batch\"\n\n$injection_order_col_name\n[1] \"injectionOrder\"\n\n$sample_type_col_name\n[1] \"sampleType\"\n\n$sample_type_tags\n[1] \"blank=blank,pool=pool,sample=sample\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "3.0.0", "traceback": null, "update_time": "2022-07-11T08:54:26.051507"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/23314e1192d4/batchcorrection/BC/batch_correction_3Lwrapper.R analyse \"determine_bc\" sampleMetadata \"/galaxy/data/files/000/168/dataset_168729.dat\" dataMatrix \"/galaxy/data/files/000/168/dataset_168729.dat\" ref_factor \"batch\" span \"none\" out_graph_pdf \"/galaxy/data/files/000/171/dataset_171175.dat\" out_preNormSummary \"/galaxy/data/files/000/171/dataset_171176.dat\"  batch_col_name \"batch\" injection_order_col_name \"injectionOrder\" sample_type_col_name \"sampleType\" sample_type_tags \"blank=blank,pool=pool,sample=sample\"", "create_time": "2022-07-11T08:54:26.136121", "encoded_id": "4b386b475561332d", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix": ["9a0ce47bd1734ae7"], "sampleMetadata": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"out_graph_pdf": ["feb6b28c817c88e1"], "out_preNormSummary": ["4c3421ed8791b2ee"]}, "params": {"__input_ext": "tabular", "advance": {"__current_case__": 1, "option": "hide"}, "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "ref_factor": "batch", "sampleMetadata": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "smcust": {"batch_col_name": "batch", "injection_order_col_name": "injectionOrder", "sampleTypeTagBlank": "blank", "sampleTypeTagPool": "pool", "sampleTypeTagSample": "sample", "sample_type_col_name": "sampleType"}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/batchcorrection/Determine_BC/3.0.0", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    674\n    674\n    674\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: meth3L -> check.err\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:54:27 \n\n-------------------------------------------------------------------- \nParameters used:\n\n$analyse\n[1] \"determine_bc\"\n\n$sampleMetadata\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$dataMatrix\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$ref_factor\n[1] \"batch\"\n\n$span\n[1] \"none\"\n\n$out_graph_pdf\n[1] \"/galaxy/data/files/000/171/dataset_171175.dat\"\n\n$out_preNormSummary\n[1] \"/galaxy/data/files/000/171/dataset_171176.dat\"\n\n$batch_col_name\n[1] \"batch\"\n\n$injection_order_col_name\n[1] \"injectionOrder\"\n\n$sample_type_col_name\n[1] \"sampleType\"\n\n$sample_type_tags\n[1] \"blank=blank,pool=pool,sample=sample\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "3.0.0", "traceback": null, "update_time": "2022-07-11T08:54:35.428642"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/corr_table/29ec7e3afdd4/corr_table/CorrTable/Corr_wrap.r  tab1_in \"/galaxy/data/files/000/168/dataset_168731.dat\" tab2_in \"/galaxy/data/files/000/168/dataset_168731.dat\"  tab1_samples \"row\" tab2_samples \"row\"  corr_method \"pearson\"  test_corr \"no\"  filter \"no\"  reorder_var \"no\"  plot_choice \"auto\" color_heatmap \"no\" tabcorr_out \"/galaxy/data/files/000/171/dataset_171177.dat\" heatmap_out \"/galaxy/data/files/000/171/dataset_171178.dat\"", "create_time": "2022-07-11T08:54:55.601461", "encoded_id": "8e6116b8d2af6164", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"tab1_in": ["7cf499d16bd542b2"], "tab2_in": ["7cf499d16bd542b2"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"heatmap_out": ["13b522f310900ee9"], "tabcorr_out": ["d18e96b689cbc930"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "corr_method": "pearson", "dbkey": "?", "filter_section": {"filter_cond": {"__current_case__": 1, "filter": "no"}, "testcorr_cond": {"__current_case__": 1, "test_corr": "no"}}, "out_section": {"plot_cond": {"__current_case__": 0, "heatmap_cond": {"__current_case__": 1, "color_heatmap": "no"}, "plot_choice": "auto"}, "reorder_var": "no"}, "tab1_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "tab1_samples": "row", "tab2_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "tab2_samples": "row"}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/corr_table/corrtable/1.0.0", "tool_stderr": "", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:54:57 \n\n-------------------------------------------------------------------- \nParameters used in \"Between-table Correlation\":\n\n$tab1_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$tab2_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$tab1_samples\n[1] \"row\"\n\n$tab2_samples\n[1] \"row\"\n\n$corr_method\n[1] \"pearson\"\n\n$test_corr\n[1] \"no\"\n\n$filter\n[1] \"no\"\n\n$reorder_var\n[1] \"no\"\n\n$plot_choice\n[1] \"auto\"\n\n$color_heatmap\n[1] \"no\"\n\n$tabcorr_out\n[1] \"/galaxy/data/files/000/171/dataset_171177.dat\"\n\n$heatmap_out\n[1] \"/galaxy/data/files/000/171/dataset_171178.dat\"\n\n--------------------------------------------------------------------\n\n\n- - - - - - - - -\n \nYou chose the same table for the two dataset inputs. \nTo allow filtering options, we will turn the diagonal to 0 in the correlation matrix during the filtering process.\n \n- - - - - - - - -\n\n\n-------------------------------------------------------------------- \nInformation about R (version, Operating System, attached or loaded packages):\n\nR version 3.5.1 (2018-07-02)\nPlatform: x86_64-conda_cos6-linux-gnu (64-bit)\nRunning under: Ubuntu 22.04 LTS\n\nMatrix products: default\nBLAS/LAPACK: /galaxy/server/database/dependencies/_conda/envs/mulled-v1-4613fcf00add6493ff827811a0604164f098e89a7dfa25ad5882ce915c8d5c89/lib/R/lib/libRlapack.so\n\nlocale:\n [1] LC_CTYPE=C.UTF-8    LC_NUMERIC=C        LC_TIME=C          \n [4] LC_COLLATE=C        LC_MONETARY=C       LC_MESSAGES=C      \n [7] LC_PAPER=C          LC_NAME=C           LC_ADDRESS=C       \n[10] LC_TELEPHONE=C      LC_MEASUREMENT=C    LC_IDENTIFICATION=C\n\nattached base packages:\n[1] stats     graphics  grDevices utils     datasets  methods   base     \n\nother attached packages:\n[1] reshape2_1.4.3 ggplot2_3.0.0  batch_1.1-4   \n\nloaded via a namespace (and not attached):\n [1] Rcpp_1.0.4.6     digest_0.6.25    withr_2.2.0      crayon_1.3.4    \n [5] grid_3.5.1       R6_2.4.1         plyr_1.8.6       lifecycle_0.2.0 \n [9] gtable_0.3.0     magrittr_1.5     scales_1.1.0     pillar_1.4.3    \n[13] stringi_1.4.6    rlang_0.4.5      farver_2.0.3     lazyeval_0.2.2  \n[17] vctrs_0.2.4      ellipsis_0.3.0   labeling_0.3     tools_3.5.1     \n[21] stringr_1.4.0    munsell_0.5.0    compiler_3.5.1   pkgconfig_2.0.3 \n[25] colorspace_1.4-1 tibble_3.0.1    \n--------------------------------------------------------------------\n \nJob ending time:\n Mon 11 Jul 2022 08:55:00", "tool_version": "1.0.0", "traceback": null, "update_time": "2022-07-11T08:55:04.048044"}, {"command_line": "Rscript /galaxy/server/tools/multivariate/multivariate.R  --dataMatrix_in \"/galaxy/data/files/000/168/dataset_168729.dat\" --sampleMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\" --variableMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\"  --response_component \"1\" --predictive_component_number \"NA\" --orthogonal_component_number \"0\" --test_sample \"FALSE\"  --graphic_type \"summary\" --color_parameter \"None\" --magnify_text \"0.8\" --abcissa_parameter \"1\" --ordinate_parameter \"2\" --ellipsis_component \"NA\" --labels_parameter \"None\"  --algorithm \"default\" --cross_validation_number \"7\" --log10L \"FALSE\" --permutation_number \"20\" --scaling \"standard\"  --sampleMetadata_out \"/galaxy/data/files/000/171/dataset_171179.dat\" --variableMetadata_out \"/galaxy/data/files/000/171/dataset_171180.dat\" --figure \"/galaxy/data/files/000/171/dataset_171181.dat\" --information \"/galaxy/data/files/000/171/dataset_171182.dat\"", "create_time": "2022-07-11T08:55:02.906475", "encoded_id": "229f5c7cde6eed4a", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["9a0ce47bd1734ae7"], "sampleMetadata_in": ["9a0ce47bd1734ae7"], "variableMetadata_in": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"figure": ["e643ab2ce5e3f927"], "information": ["6cb86ed7e8dbb4f7"], "sampleMetadata_out": ["3d934f0f525fc6d5"], "variableMetadata_out": ["32457860c3cc7dd4"]}, "params": {"__input_ext": "input", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "compute": {"algorithm": "default", "cross_validation_number": "7", "log10L": "FALSE", "permutation_number": "20", "scaling": "standard"}, "dataMatrix_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "graphics": {"abcissa_parameter": "1", "color_parameter": null, "ellipsis_component": "NA", "graphic_type": "summary", "labels_parameter": null, "magnify_text": "0.8", "ordinate_parameter": "2"}, "orthogonal_component_number": "0", "predictive_component_number": "NA", "response_component": "1", "sampleMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "save_rdata": "false", "test_sample": "FALSE", "variableMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "Multivariate", "tool_stderr": "Error in read.table(parameters$dataMatrix_in, check.names = FALSE, header = TRUE,  : \n  duplicate 'row.names' are not allowed\nCalls: t -> as.matrix -> read.table\nExecution halted\n", "tool_stdout": "$help\n[1] FALSE\n\n$dataMatrix_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$sampleMetadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$variableMetadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$sampleMetadata_out\n[1] \"/galaxy/data/files/000/171/dataset_171179.dat\"\n\n$variableMetadata_out\n[1] \"/galaxy/data/files/000/171/dataset_171180.dat\"\n\n$figure\n[1] \"/galaxy/data/files/000/171/dataset_171181.dat\"\n\n$information\n[1] \"/galaxy/data/files/000/171/dataset_171182.dat\"\n\n$test_sample\n[1] FALSE\n\n$abcissa_parameter\n[1] 1\n\n$ordinate_parameter\n[1] 2\n\n$color_parameter\n[1] \"None\"\n\n$ellipsis_component\n[1] \"NA\"\n\n$labels_parameter\n[1] \"None\"\n\n$response_component\n[1] 1\n\n$magnify_text\n[1] 0.8\n\n$predictive_component_number\n[1] \"NA\"\n\n$orthogonal_component_number\n[1] 0\n\n$cross_validation_number\n[1] 7\n\n$log10L\n[1] FALSE\n\n$permutation_number\n[1] 20\n\n$algorithm\n[1] \"default\"\n\n$graphic_type\n[1] \"summary\"\n\n$scaling\n[1] \"standard\"\n\n", "tool_version": "2.4.0", "traceback": null, "update_time": "2022-07-11T08:55:20.792963"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/ethevenot/biosigner/fa80bd02055f/biosigner/biosigner_wrapper.R  dataMatrix_in \"/galaxy/data/files/000/168/dataset_168729.dat\" sampleMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\" variableMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\"  respC \"\"   variableMetadata_out \"/galaxy/data/files/000/171/dataset_171183.dat\" figure_tier \"/galaxy/data/files/000/171/dataset_171184.dat\" figure_boxplot \"/galaxy/data/files/000/171/dataset_171185.dat\" information \"/galaxy/data/files/000/171/dataset_171186.dat\"", "create_time": "2022-07-11T08:55:08.804048", "encoded_id": "1a3fc71f7e426427", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["9a0ce47bd1734ae7"], "sampleMetadata_in": ["9a0ce47bd1734ae7"], "variableMetadata_in": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"figure_boxplot": ["ca2002853acbb064"], "figure_tier": ["5fbfc6ca7afbdb07"], "information": ["b1c4587dfe17688f"], "variableMetadata_out": ["dfe1c8c3a14ed3fb"]}, "params": {"__input_ext": "tabular", "advCpt": {"__current_case__": 0, "opcC": "default"}, "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "respC": "", "sampleMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "variableMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/biosigner/biosigner/2.2.7", "tool_stderr": "Error in h(simpleError(msg, call)) : \n  error in evaluating the argument 'x' in selecting a method for function 't': duplicate 'row.names' are not allowed\nCalls: t -> as.matrix -> read.table\nExecution halted\n", "tool_stdout": "", "tool_version": "2.2.7", "traceback": null, "update_time": "2022-07-11T08:55:29.542243"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/3017385625f6/univariate/univariate_wrapper.R  dataMatrix_in \"/galaxy/data/files/000/168/dataset_168731.dat\" sampleMetadata_in \"/galaxy/data/files/000/168/dataset_168731.dat\" variableMetadata_in \"/galaxy/data/files/000/168/dataset_168731.dat\"  facC \"\" tesC \"ttest\" adjC \"fdr\" thrN \"0.05\"  variableMetadata_out \"/galaxy/data/files/000/171/dataset_171187.dat\" figure \"/galaxy/data/files/000/171/dataset_171188.dat\" information \"/galaxy/data/files/000/171/dataset_171189.dat\"", "create_time": "2022-07-11T08:55:35.386766", "encoded_id": "01f1a014f517267b", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["7cf499d16bd542b2"], "sampleMetadata_in": ["7cf499d16bd542b2"], "variableMetadata_in": ["7cf499d16bd542b2"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"figure": ["f1ee1179b7d81811"], "information": ["49fffafcc87c982f"], "variableMetadata_out": ["a4b5eda1a6930d5a"]}, "params": {"__input_ext": "tabular", "adjC": "fdr", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "dbkey": "?", "facC": "", "sampleMetadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "tesC": "ttest", "thrN": "0.05", "variableMetadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/univariate/Univariate/2.2.4", "tool_stderr": "Error: Column names of the dataMatrix are not identical to the row names of the sampleMetadata; check your data with the 'Check Format' module in the 'Quality Control' section\nExecution halted\n", "tool_stdout": "", "tool_version": "2.2.4", "traceback": null, "update_time": "2022-07-11T08:55:51.341644"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/lecorguille/anova/102049093b7d/anova/abims_anova.r file '/galaxy/data/files/000/168/dataset_168729.dat' sampleinfo '/galaxy/data/files/000/168/dataset_168729.dat' varinfo '/galaxy/data/files/000/168/dataset_168729.dat' mode 'row' condition \"c('' )\" interaction F method none threshold 0.01 selection_method intersection sep 'tabulation' dec '.' outputdatapvalue '/galaxy/data/files/000/171/dataset_171190.dat' outputdatasignif '/galaxy/data/files/000/171/dataset_171191.dat'", "create_time": "2022-07-11T08:55:44.270729", "encoded_id": "7dd64083fb4cb0a0", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"input": ["9a0ce47bd1734ae7"], "sampleinfo": ["9a0ce47bd1734ae7"], "varinfo": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataSignif": ["fd6c123d85d5c88c"], "varMetaPValue": ["fdf275d80f342804"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "condition_1": "", "conditions": [], "dbkey": "?", "dec": ".", "input": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "interaction": "false", "method": "none", "mode": "row", "sampleinfo": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "selection_method": "intersection", "sep": "tabulation", "threshold": "0.01", "varinfo": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/lecorguille/anova/abims_anova/1.2.1", "tool_stderr": "Error in read.table(file, header = TRUE, row.names = 1, sep = sep, quote = \"\\\"\",  : \n  duplicate 'row.names' are not allowed\nCalls: do.call -> <Anonymous> -> read.table\nExecution halted\n", "tool_stdout": "ANOVA\n\nArguments\n [1] \"file\"                                         \n [2] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n [3] \"sampleinfo\"                                   \n [4] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n [5] \"varinfo\"                                      \n [6] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n [7] \"mode\"                                         \n [8] \"row\"                                          \n [9] \"condition\"                                    \n[10] \"c('' )\"                                       \n[11] \"interaction\"                                  \n[12] \"F\"                                            \n[13] \"method\"                                       \n[14] \"none\"                                         \n[15] \"threshold\"                                    \n[16] \"0.01\"                                         \n[17] \"selection_method\"                             \n[18] \"intersection\"                                 \n[19] \"sep\"                                          \n[20] \"tabulation\"                                   \n[21] \"dec\"                                          \n[22] \".\"                                            \n[23] \"outputdatapvalue\"                             \n[24] \"/galaxy/data/files/000/171/dataset_171190.dat\"\n[25] \"outputdatasignif\"                             \n[26] \"/galaxy/data/files/000/171/dataset_171191.dat\"\n", "tool_version": "1.2.1", "traceback": null, "update_time": "2022-07-11T08:56:00.841399"}, {"command_line": "perl /galaxy/server/tools/hmdb/1.7.2/wsdl_hmdb.pl -masses \"/galaxy/data/files/000/168/dataset_168731.dat\" -header_choice \"yes\" -nblineheader \"1\" -colfactor \"1\" -output_tabular \"/galaxy/data/files/000/171/dataset_171192.dat\" -output_html \"/galaxy/data/files/000/171/dataset_171193.dat\" -output_xlsx \"/galaxy/data/files/000/171/dataset_171194.dat\"  -mode \"neutral\"  -adduct_type \"M\"  -delta \"0.05\" -maxquery \"10\" -advancedFeatures \"0\" -verbose \"1\"", "create_time": "2022-07-11T08:56:27.561908", "encoded_id": "6aba90e30136eba8", "exit_code": 255, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"masses": ["7cf499d16bd542b2"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"HmdbOutWeb": ["d5307cd15c435fcb"], "HmdbOutXlsx": ["1a4b8ebf08df6a10"], "variableMetadata": ["b76811ec1656e435"]}, "params": {"__input_ext": "tabular", "advancedFeatures": "0", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "delta": "0.05", "input_type": {"__current_case__": 0, "choice": "YES", "colfactor": "1", "header": {"__current_case__": 0, "header_choice": "yes", "nbHeader": "1"}, "masses": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}}, "maxquery": "10", "mode_type": {"__current_case__": 2, "data_neutral_adducts": ["M"], "mode": "neutral"}, "verbose": "1"}, "state": "ok", "tool_id": "wsdl_hmdb", "tool_stderr": "Error GETing https://hmdb.ca/spectra/ms/generate_csv.csv?results%5Baction%5D=search&results%5Badduct_type%5D%5B%5D=M&results%5Bccs_predictors%5D=&results%5Bccs_tolerance%5D=&results%5Bcommit%5D=Search&results%5Bcontroller%5D=specdb%2Fms&results%5Bms_search_ion_mode%5D=neutral&results%5Bquery_masses%5D=2-diethylamino-6-methyl%20pyrimidin-4-ol%20one%0D%0A5-hydroxy-thiabendazole%0D%0Aacetamiprid-N-desmethyl%0D%0AAcetochlor%0D%0AAvermectin%20B1a%20(Abamectin)%0D%0A&results%5Btolerance%5D=0.05&results%5Btolerance_units%5D=Da&results%5Butf8%5D=%E2%9C%93: Internal Server Error at /galaxy/server/tools/hmdb/1.7.2/lib/hmdb.pm line 649.\n", "tool_stdout": "\tTesting HMDB server connexion (1 time(s) )...\nStatus: 200\tThe HMDB server returns that your request (connexion test) was fulfilled\n\tAll searches should be sent successfully to HMDB...(Set verbose to \"High\" for more information!)\n", "tool_version": "1.7.2", "traceback": null, "update_time": "2022-07-11T08:56:36.878584"}, {"command_line": "perl /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bank_inhouse/52798007c6b2/bank_inhouse/bank_inhouse.pl  -input \"/galaxy/data/files/000/171/dataset_171194.dat\" -nbheader \"1\"  -colmass \"1\" -colrt \"1\" -rt_delta \"0.1\"  -mz_delta \"Da\" -mass_delta \"0.005\"  -bank_in \"/galaxy/data/files/000/171/dataset_171194.dat\" -bank_name \"compounds_p.HMDB_XLS.txt\" -mzdb \"1\" -rtdb \"1\"  -outputTab \"/galaxy/data/files/000/171/dataset_171195.dat\" -outputXls \"/galaxy/data/files/000/171/dataset_171196.dat\"", "create_time": "2022-07-11T08:56:32.104917", "encoded_id": "3ddc4daa5b471511", "exit_code": 255, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"bank_in": ["1a4b8ebf08df6a10"], "variableMetadata_in": ["1a4b8ebf08df6a10"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"bankInhouseResXls_filein": ["01ac0a8751d9c247"], "variableMetadata_out": ["b688fce8e466a80a"]}, "params": {"__input_ext": "tabular", "bank_type": {"__current_case__": 0, "bank_in": {"values": [{"id": "1a4b8ebf08df6a10", "src": "hda"}]}, "bank_rt": {"__current_case__": 0, "bank_rt_choice": "true", "rtdb": "1"}, "mzdb": "1", "perso_bank": "true"}, "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "input_type": {"__current_case__": 0, "choice": "YES", "colmass": "1", "header": {"__current_case__": 0, "header_choice": "true", "nbheader": "1"}, "use_file_rt": {"__current_case__": 0, "colrt": "1", "rt_file_choice": "true", "rt_file_delta": "0.1"}, "variableMetadata_in": {"values": [{"id": "1a4b8ebf08df6a10", "src": "hda"}]}}, "mz_delta_type": {"__current_case__": 0, "mass_delta": "0.005", "mz_delta": "Da"}, "outfiles": "NO"}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/fgiacomoni/bank_inhouse/bank_inhouse/1.2.1", "tool_stderr": "Can't work : missing paramaters (list of ids, masses, delta, ionization, characterization or inhouse_bank)\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bank_inhouse/52798007c6b2/bank_inhouse/bank_inhouse.pl line 325.\n", "tool_stdout": "The bank_inhouse program is launched as:\n./bank_inhouse.pl --input /galaxy/data/files/000/171/dataset_171194.dat --rest no --nbheader 1 --colrt 1 --rt_delta 0.1 --colmass 1 --mz_delta Da --mass_delta 0.005 --bank_in /galaxy/data/files/000/171/dataset_171194.dat --bank_name compounds_p.HMDB_XLS.txt --mzdb 1 --rtdb 1 --outputXls /galaxy/data/files/000/171/dataset_171196.dat --outputTab /galaxy/data/files/000/171/dataset_171195.dat \n", "tool_version": "1.2.1", "traceback": null, "update_time": "2022-07-11T08:56:42.700888"}, {"command_line": "perl /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4bloodexposome/94eeed7f737f/bih4bloodexposome/bih4bloodexposome.pl -input /galaxy/data/files/000/168/dataset_168729.dat -mzCol 1  -header \"1\"  -ppmError 5.0 -mode POSITIVE -outputTab /galaxy/data/files/000/171/dataset_171198.dat -outputFull /galaxy/data/files/000/171/dataset_171197.dat -verbose 1", "create_time": "2022-07-11T08:56:36.473292", "encoded_id": "f22e2057729e45c8", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"variableMetadata_in": ["9a0ce47bd1734ae7"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"outFull": ["1818c0744f54583c"], "outputTab": ["59261f87693eaee6"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "colmass": "1", "dbkey": "?", "has_header": {"__current_case__": 0, "header": "1", "header_choice": "true"}, "mode": "POSITIVE", "ppm_error": "5.0", "variableMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "verbose": "1"}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4bloodexposome/bih4bloodexposome/0.1.2", "tool_stderr": "[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak\n..\nndef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n[WARN] the method _getPeak_ANNOTATION_TYPE can't _getPeak a undef or void string value\n", "tool_stdout": "loading /galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/auto/share/dist/Metabolomics-Fragment-Annotation/BloodExposome_v1_0.txt...\n", "tool_version": "0.1.2", "traceback": null, "update_time": "2022-07-11T10:20:15.991906"}, {"command_line": "perl /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl -input /galaxy/data/files/000/168/dataset_168731.dat -mzCol 1  -header \"1\"  -ppmError 5.0 -mode POSITIVE -outputTab /galaxy/data/files/000/171/dataset_171200.dat -outputFull /galaxy/data/files/000/171/dataset_171199.dat -verbose 1", "create_time": "2022-07-11T08:56:40.948284", "encoded_id": "4857bd18ba8474b3", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"variableMetadata_in": ["7cf499d16bd542b2"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"outFull": ["14a0f2f70dbd63a9"], "outputTab": ["0c7d0b5cfc5fcdb8"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "colmass": "1", "dbkey": "?", "has_header": {"__current_case__": 0, "header": "1", "header_choice": "true"}, "mode": "POSITIVE", "ppm_error": "5.0", "variableMetadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "verbose": "1"}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/bih4maconda/0.1.4", "tool_stderr": "[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtION_FORM return unknown if getting a undef value\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtION_FORM return unknown if getting a undef value\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtION_FORM return unknown if getting a undef value\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtION_FORM return unknown if getting a undef value\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtION_FORM return unknown if getting a undef value\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtION_FORM return unknown if getting a undef value\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtION_FORM return unknown if getting a undef value\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtION_FORM return unknown if getting a undef value\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtION_FORM return unknown if getting a undef value\n[WARN] the method _getContaminantExtEXACT_ADDUCT_MASS return undef when no value is available\n[WARN] the method _getContaminantExtION_FORM return unknown if getting a undef value\nArgument \"2-diethylamino-6-methyl pyrimidin-4-ol one\" isn't numeric in numeric\n\tgt (>) at /galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n    (W numeric) The indicated string was fed as an argument to an operator\n    that expected a numeric value instead.  If you're fortunate the message\n    will identify which operator was so unfortunate.\n    \n    Note that for the Inf and NaN (infinity and not-a-number) the\n    definition of \"numeric\" is somewhat unusual: the strings themselves\n    (like \"Inf\") are considered numeric, and anything following them is\n    considered non-numeric.\n    \nArgument \"5-hydroxy-thiabendazole\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\nArgument \"acetamiprid-N-desmethyl\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Acetochlor\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Avermectin B1a (Abamectin)\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Benzophenone-3 (Oxybenzone)\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Butocarboxim\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Carbendazim\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Cefoperazone\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Chlorfenvinphos\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Chlormequat\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Desisopropylatrazine\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Dichlorvos\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Dimethyldithiophosphate\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Emamectin B1a\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Fluopyram\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Hydroxy-tebuconazole\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Isoproturon\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Ivermectin B1a \" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Malathion dicarboxilic acid\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Methamidophos\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Metolachlor\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"N,N-diethyl-m-toluamide ou DEET\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Nigericin\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Omethoate\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Prochloraz\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"p-Toluenesulfonamide\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Rifaximin\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Spinosad A (Spinosyn A)\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"TCMTB\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Trichlorfon (Dylox)\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\nArgument \"Tylosin\" isn't numeric in numeric gt (>) at\n\t/galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/Metabolomics/Banks.pm line 566 (#1)\n[ERROR] the method _setPeakMESURED_MONOISOTOPIC_MASS can't set any undef or non numerical value\n at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/bih4maconda/2744d20c830a/bih4maconda/bih4maconda.pl line 186.\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n[WARN] the method _getPeakMESURED_MONOISOTOPIC_MASS can't _getPeak a undef or non numerical value\n", "tool_stdout": "loading /galaxy/server/database/dependencies/_conda/envs/__perl-metabolomics-fragment-annotation@0.6.3/lib/perl5/site_perl/auto/share/dist/Metabolomics-Fragment-Annotation/MaConDa__v1_0__extensive.xml...\nMode selected is POSITIVE...and detected query mode is ION...\n", "tool_version": "0.1.4", "traceback": null, "update_time": "2022-07-11T08:56:46.675756"}, {"command_line": "perl /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/hr2/86296c048e46/hr2/hr2_manager.pl -input \"/galaxy/data/files/000/168/dataset_168729.dat\" -nblineheader \"1\" -colId \"1\" -colmass \"1\"  -tolerance \"1.0\" -mode \"neutral\" -charge \"0\"  -regleOr \"NO\" -atomes \"C,N,O,H,P\" -atomessup \"None\" -output1 \"/galaxy/data/files/000/171/dataset_171201.dat\" -outputView \"/galaxy/data/files/000/171/dataset_171202.dat\" -verbose \"1\"", "create_time": "2022-07-11T08:56:48.665611", "encoded_id": "80dda503b690b98a", "exit_code": null, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"input": ["9a0ce47bd1734ae7"]}, "job_messages": null, "job_stderr": null, "job_stdout": null, "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"hr2ResView": ["e86562c804ca5387"], "variableMetadata": ["b379da601dbce29e"]}, "params": {"__input_ext": "tabular", "atomes_basic": ["C", "N", "O", "H", "P"], "atomes_sup": null, "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "input_type": {"__current_case__": 0, "choice": "YES", "colId": "1", "colmass": "1", "header": {"__current_case__": 0, "header_choice": "true", "nbHeader": "1"}, "input": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "mode_condition": {"__current_case__": 0, "mode": "neutral"}, "regleOr": "NO", "tol": "1.0", "verbose": "1"}, "state": "running", "tool_id": "toolshed.g2.bx.psu.edu/repos/fgiacomoni/hr2/hr2/1.1.1.7", "tool_stderr": null, "tool_stdout": null, "tool_version": "1.1.1.7", "traceback": null, "update_time": "2022-07-11T08:56:52.287870"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/yguitton/metams_rungc/c75532b75ba1/metams_rungc/metams.r  xset  /galaxy/data/files/000/168/dataset_168688.dat  settings \"default\" rtrange \"NULL\" ri \"NULL\" rishift \"none\" db \"NULL\" nSlaves ${GALAXY_SLOTS:-1} unkn \"c(1:5)\"", "create_time": "2022-07-11T08:57:41.882745", "encoded_id": "06a03c2a173074c3", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"xset": ["9e77b3d7d0887128"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"bpcsRawPdf": ["1def263a62efb79c"], "dataMatrix": ["31aa8fb1a3335842"], "log": ["922879d02aaf3c7e"], "peakspectra": ["8707131ca4c58182"], "peaktable": ["dba13cc23f388e58"], "rungcRData": ["46ababf9e7399751"], "sampleMetadata": ["9834d2cdb16d41df"], "ticsRawPdf": ["0dc74b9057f68cac"], "unknownPdf": ["9a6404cc34e43342"], "variableMetadata": ["7cedebd3668b57ec"], "zip": ["af7bdcee22f3c8ce"]}, "params": {"__input_ext": "rdata", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dbkey": "?", "inputs": {"__current_case__": 1, "input": "xset", "xset": {"values": [{"id": "9e77b3d7d0887128", "src": "hda"}]}}, "options_rifilter": {"__current_case__": 1, "option": "false"}, "settings": {"__current_case__": 0, "options_db": {"__current_case__": 1, "option": "hide"}, "options_ri": {"__current_case__": 1, "option": "hide"}, "options_rtrange": {"__current_case__": 1, "option": "hide"}, "setting": "gcdefault"}, "unkn": "1:5"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/yguitton/metams_rungc/metams_runGC/2.1.1", "tool_stderr": "Loading required package: CAMERA\nLoading required package: Biobase\nLoading required package: BiocGenerics\nLoading required package: parallel\n\nAttaching package: \u2018BiocGenerics\u2019\n\nThe following objects are masked from \u2018package:parallel\u2019:\n\n    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n    clusterExport, clusterMap, parApply, parCapply, parLapply,\n    parLapplyLB, parRapply, parSapply, parSapplyLB\n\nThe following objects are masked from \u2018package:stats\u2019:\n\n    IQR, mad, sd, var, xtabs\n\nThe following objects are masked from \u2018package:base\u2019:\n\n    Filter, Find, Map, Position, Reduce, anyDuplicated, append,\n    as.data.frame, basename, cbind, colMeans, colSums, colnames,\n    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,\n    intersect, is.unsorted, lapply, lengths, mapply, match, mget,\n    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,\n    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,\n    union, unique, unsplit, which, which.max, which.min\n\nWelcome to Bioconductor\n\n    Vignettes contain introductory material; view with\n    'browseVignettes()'. To cite Bioconductor, see\n    'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n\nLoading required package: xcms\nLoading required package: mzR\nLoading required package: Rcpp\nLoading required package: ProtGenerics\nError: package or namespace load failed for \u2018xcms\u2019:\n package \u2018xcms\u2019 was installed by an R version with different internals; it needs to be reinstalled for use with this R version\nError: package \u2018xcms\u2019 could not be loaded\nExecution halted\n", "tool_stdout": "", "tool_version": "2.1.1", "traceback": null, "update_time": "2022-07-11T08:58:42.804354"}, {"command_line": "perl /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search/golm_ws_lib_search.pl -inputFile \"/galaxy/data/files/000/168/dataset_168729.dat\" -output_tabular \"/galaxy/data/files/000/171/dataset_171214.dat\" -output_html \"/galaxy/data/files/000/171/dataset_171215.dat\" -output_xls \"/galaxy/data/files/000/171/dataset_171216.dat\" -ri \"1898\" -riWindow \"5\" -gcColumn \"VAR5\" -mzRes \"0\" -maxHits \"100\" -maxIons \"0\" -JaccardDistanceThreshold \"0.9\" -s12GowerLegendreDistanceThreshold \"0.9\" -DotproductDistanceThreshold \"0.5\" -HammingDistanceThreshold \"500.0\" -EuclideanDistanceThreshold \"0.5\" -relative \"true\"", "create_time": "2022-07-11T08:57:48.384527", "encoded_id": "e068fd2f3e729f2c", "exit_code": 2, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"masses": ["9a0ce47bd1734ae7"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"GolmOutTab": ["681d5df1cc46e913"], "GolmOutWeb": ["fa68e87a50af12b3"], "GolmOutXlsx": ["5c30ceded02186bf"]}, "params": {"DotproductDistanceThreshold": "0.5", "EuclideanDistanceThreshold": "0.5", "HammingDistanceThreshold": "500.0", "JaccardDistanceThreshold": "0.9", "__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "columnType": "VAR5", "dbkey": "?", "input_type": {"__current_case__": 0, "choice": "YES", "masses": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "intensity_type": "true", "maxHits": "100", "maxIons": "0", "mzRes": "0", "ri": "1898", "riWindow": "5", "s12GowerLegendreDistanceThreshold": "0.9"}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/golm_ws_lib_search/2016-12-05", "tool_stderr": "Can't locate List/MoreUtils.pm in @INC (you may need to install the List::MoreUtils module) (@INC contains: /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search /galaxy/server/database/dependencies/_conda/envs/mulled-v1-3589140a91dde328cd83c624d0f4655640709027dbf7aa2f34009a8f8d36b51d/lib/site_perl/5.26.2/x86_64-linux-thread-multi /galaxy/server/database/dependencies/_conda/envs/mulled-v1-3589140a91dde328cd83c624d0f4655640709027dbf7aa2f34009a8f8d36b51d/lib/site_perl/5.26.2 /galaxy/server/database/dependencies/_conda/envs/mulled-v1-3589140a91dde328cd83c624d0f4655640709027dbf7aa2f34009a8f8d36b51d/lib/5.26.2/x86_64-linux-thread-multi /galaxy/server/database/dependencies/_conda/envs/mulled-v1-3589140a91dde328cd83c624d0f4655640709027dbf7aa2f34009a8f8d36b51d/lib/5.26.2 .) at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search/lib/msp.pm line 9.\nBEGIN failed--compilation aborted at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search/lib/msp.pm line 9.\nCompilation failed in require at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search/golm_ws_lib_search.pl line 23.\nBEGIN failed--compilation aborted at /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/golm_ws_lib_search/11779b6402bc/golm_ws_lib_search/golm_ws_lib_search.pl line 23.\n", "tool_stdout": "", "tool_version": "2016-12-05", "traceback": null, "update_time": "2022-07-11T08:57:58.745497"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/tablemerge/902ab790fb7b/tablemerge/TableMerge/tablemerge_wrap.R dataMatrix_in \"/galaxy/data/files/000/168/dataset_168729.dat\" Metadata_in \"/galaxy/data/files/000/168/dataset_168731.dat\"  metatype \"sample\"  combined_out \"/galaxy/data/files/000/171/dataset_171217.dat\"", "create_time": "2022-07-11T08:58:06.869565", "encoded_id": "e0e638e3cdd09043", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"Metadata_in": ["7cf499d16bd542b2"], "dataMatrix_in": ["9a0ce47bd1734ae7"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"combined_out": ["712f6c3369c5c166"]}, "params": {"Metadata_in": {"values": [{"id": "7cf499d16bd542b2", "src": "hda"}]}, "__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "metatype": "sample"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/tablemerge/tablemerge/1.0.1", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    2-diethylamino-6-methyl pyrimidin-4-ol one\n    5-hydroxy-thiabendazole\n    acetamiprid-N-desmethyl\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: tab.merge -> check.err\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:58:08 \n\n-------------------------------------------------------------------- \nParameters used in \"Table Merge\":\n\n$dataMatrix_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$Metadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168731.dat\"\n\n$metatype\n[1] \"sample\"\n\n$combined_out\n[1] \"/galaxy/data/files/000/171/dataset_171217.dat\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "1.0.1", "traceback": null, "update_time": "2022-07-11T08:58:14.244221"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/idchoice/bb19b1d15732/idchoice/IDchoice/IDchoice_wrap.R dataMatrix_in \"/galaxy/data/files/000/168/dataset_168729.dat\" Metadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\"  metatype \"variable\" col_name \"\" makeunique \"no\"  DM_out \"/galaxy/data/files/000/171/dataset_171218.dat\" meta_out \"/galaxy/data/files/000/171/dataset_171219.dat\"", "create_time": "2022-07-11T08:58:12.669586", "encoded_id": "ee83b2398bd91895", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"Metadata_in": ["9a0ce47bd1734ae7"], "dataMatrix_in": ["9a0ce47bd1734ae7"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"DM_out": ["fce4c671b05d96c0"], "meta_out": ["68f40da658754d64"]}, "params": {"Metadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "col_name": "", "dataMatrix_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "makeunique": "no", "metatype": "variable"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/idchoice/idchoice/19.12", "tool_stderr": "Error in id.choice(args$dataMatrix_in, args$Metadata_in, args$metatype,  : \n  \n-------\nWarning: no '' column detected in variable metadata!\nPlease check your metadata file (column names are case-sensitive).\n-------\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:58:15 \n\n-------------------------------------------------------------------- \nParameters used in \"ID choice\":\n\n$dataMatrix_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$Metadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$metatype\n[1] \"variable\"\n\n$col_name\n[1] \"\"\n\n$makeunique\n[1] \"no\"\n\n$DM_out\n[1] \"/galaxy/data/files/000/171/dataset_171218.dat\"\n\n$meta_out\n[1] \"/galaxy/data/files/000/171/dataset_171219.dat\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "19.12", "traceback": null, "update_time": "2022-07-11T08:58:20.418525"}, {"command_line": "Rscript '/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/cfd7c4aa5c26/generic_filter/GalFilter/filter_wrap.R' dataMatrix_in \"/galaxy/data/files/000/168/dataset_168729.dat\" sampleMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\" variableMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\"  Numeric \"FALSE\"  Factors \"FALSE\"  dataMatrix_out \"/galaxy/data/files/000/171/dataset_171220.dat\" sampleMetadata_out \"/galaxy/data/files/000/171/dataset_171221.dat\" variableMetadata_out \"/galaxy/data/files/000/171/dataset_171222.dat\"", "create_time": "2022-07-11T08:58:20.586503", "encoded_id": "e2df485a3816ce19", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["9a0ce47bd1734ae7"], "sampleMetadata_in": ["9a0ce47bd1734ae7"], "variableMetadata_in": ["9a0ce47bd1734ae7"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"dataMatrix_out": ["05dbaecc47f3d900"], "sampleMetadata_out": ["1ffec668af5b38c6"], "variableMetadata_out": ["a5247333ab4996eb"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "numeric_condition": {"Factors": "FALSE", "__current_case__": 1}, "qualitative_condition": {"Factors": "FALSE", "__current_case__": 1}, "sampleMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "variableMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/melpetera/generic_filter/generic_filter/2020.01", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    674\n    674\n    674\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: filters -> check.err\nExecution halted\n", "tool_stdout": "\nJob starting time:\n Mon 11 Jul 2022 08:58:22 \n\n-------------------------------------------------------------------- \nParameters used in \"Generic Filter\":\n\n$dataMatrix_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$sampleMetadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$variableMetadata_in\n[1] \"/galaxy/data/files/000/168/dataset_168729.dat\"\n\n$Numeric\n[1] \"FALSE\"\n\n$Factors\n[1] \"FALSE\"\n\n$dataMatrix_out\n[1] \"/galaxy/data/files/000/171/dataset_171220.dat\"\n\n$sampleMetadata_out\n[1] \"/galaxy/data/files/000/171/dataset_171221.dat\"\n\n$variableMetadata_out\n[1] \"/galaxy/data/files/000/171/dataset_171222.dat\"\n\n--------------------------------------------------------------------\n\n", "tool_version": "2020.01", "traceback": null, "update_time": "2022-07-11T08:58:29.625740"}, {"command_line": "python /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/626658afe4cb/column_maker/column_maker.py /galaxy/data/files/000/168/dataset_168729.dat /galaxy/data/files/000/171/dataset_171223.dat \"c3-c2\" no 14 \"int,int,int,int,int,float,float,float,float,int,int,int,int,int\"", "create_time": "2022-07-11T08:58:27.151261", "encoded_id": "6b7610073ba9bd55", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"input": ["9a0ce47bd1734ae7"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"out_file1": ["79c7ce84f3ac839b"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "cond": "c3-c2", "dbkey": "?", "input": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "round": "no"}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.1.0", "tool_stderr": "  File \"/galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/626658afe4cb/column_maker/column_maker.py\", line 107\n    exec code\n    ^^^^^^^^^\nSyntaxError: Missing parentheses in call to 'exec'. Did you mean exec(...)?\n", "tool_stdout": "", "tool_version": "1.1.0", "traceback": null, "update_time": "2022-07-11T08:58:32.792136"}, {"command_line": "perl /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/cut_columns/cec635fab700/cut_columns/cutWrapper.pl \"/galaxy/data/files/000/168/dataset_168729.dat\" \"c1,c2\" \"T\" \"/galaxy/data/files/000/171/dataset_171224.dat\"", "create_time": "2022-07-11T08:58:35.891597", "encoded_id": "f48d5840e497fe72", "exit_code": 0, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"input": ["9a0ce47bd1734ae7"]}, "job_messages": [], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"out_file1": ["2971c5537d299db4"]}, "params": {"__input_ext": "tabular", "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "columnList": "c1,c2", "dbkey": "?", "delimiter": "T", "input": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "ok", "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cut_columns/Cut1/1.0.2", "tool_stderr": "", "tool_stdout": "", "tool_version": "1.0.2", "traceback": null, "update_time": "2022-07-11T08:58:41.645419"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/acdf51018708/qualitymetrics/qualitymetrics_wrapper.R dataMatrix_in \"/galaxy/data/files/000/171/dataset_171216.dat\" sampleMetadata_in \"/galaxy/data/files/000/171/dataset_171216.dat\" variableMetadata_in \"/galaxy/data/files/000/171/dataset_171216.dat\"  CV \"FALSE\" Compa \"TRUE\" seuil \"1\"  poolAsPool1L \"TRUE\"  sampleMetadata_out \"/galaxy/data/files/000/171/dataset_171225.dat\" variableMetadata_out \"/galaxy/data/files/000/171/dataset_171226.dat\" figure \"/galaxy/data/files/000/171/dataset_171227.dat\" information \"/galaxy/data/files/000/171/dataset_171228.dat\"", "create_time": "2022-07-11T09:50:19.915887", "encoded_id": "82fedebbca744c31", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["5c30ceded02186bf"], "sampleMetadata_in": ["5c30ceded02186bf"], "variableMetadata_in": ["5c30ceded02186bf"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"figure": ["d7cce06221fced1d"], "information": ["39801b7a8e3aff00"], "sampleMetadata_out": ["f511e1fd77a53e45"], "variableMetadata_out": ["f7f4898518887897"]}, "params": {"CV_condition": {"CV": "FALSE", "Compa": "TRUE", "__current_case__": 1, "seuil": "1"}, "__input_ext": "tabular", "advPar": {"__current_case__": 1, "optC": "default", "poolAsPool1L": "TRUE"}, "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "5c30ceded02186bf", "src": "hda"}]}, "dbkey": "?", "sampleMetadata_in": {"values": [{"id": "5c30ceded02186bf", "src": "hda"}]}, "variableMetadata_in": {"values": [{"id": "5c30ceded02186bf", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8", "tool_stderr": "Error in read.table(ion.file.in, sep = \"\\t\", header = TRUE, check.names = FALSE,  : \n  no lines available in input\nCalls: QualityControl -> read.table\nExecution halted\n", "tool_stdout": "", "tool_version": "2.2.8", "traceback": null, "update_time": "2022-07-11T09:50:27.146665"}, {"command_line": "Rscript /galaxy/server/database/shed_tools/toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/acdf51018708/qualitymetrics/qualitymetrics_wrapper.R dataMatrix_in \"/galaxy/data/files/000/168/dataset_168729.dat\" sampleMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\" variableMetadata_in \"/galaxy/data/files/000/168/dataset_168729.dat\"  CV \"FALSE\" Compa \"TRUE\" seuil \"1\"  poolAsPool1L \"TRUE\"  sampleMetadata_out \"/galaxy/data/files/000/171/dataset_171229.dat\" variableMetadata_out \"/galaxy/data/files/000/171/dataset_171230.dat\" figure \"/galaxy/data/files/000/171/dataset_171231.dat\" information \"/galaxy/data/files/000/171/dataset_171232.dat\"", "create_time": "2022-07-11T09:50:50.765058", "encoded_id": "85b7df1e846649ed", "exit_code": 1, "galaxy_version": "22.01", "implicit_output_dataset_collection_mapping": {}, "info": null, "input_dataset_collection_element_mapping": {}, "input_dataset_collection_mapping": {}, "input_dataset_mapping": {"dataMatrix_in": ["9a0ce47bd1734ae7"], "sampleMetadata_in": ["9a0ce47bd1734ae7"], "variableMetadata_in": ["9a0ce47bd1734ae7"]}, "job_messages": [{"code_desc": "", "desc": "Fatal error: Exit code 1 ()", "error_level": 3, "exit_code": 1, "type": "exit_code"}], "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_dataset_collection_mapping": {}, "output_dataset_mapping": {"figure": ["5925749ba92fe34e"], "information": ["e448c300372b4cc9"], "sampleMetadata_out": ["63ccf149b0a55b01"], "variableMetadata_out": ["b9d67c701c9febf7"]}, "params": {"CV_condition": {"CV": "FALSE", "Compa": "TRUE", "__current_case__": 1, "seuil": "1"}, "__input_ext": "tabular", "advPar": {"__current_case__": 1, "optC": "default", "poolAsPool1L": "TRUE"}, "chromInfo": "/galaxy/server/tool-data/shared/ucsc/chrom/?.len", "dataMatrix_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "dbkey": "?", "sampleMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}, "variableMetadata_in": {"values": [{"id": "9a0ce47bd1734ae7", "src": "hda"}]}}, "state": "error", "tool_id": "toolshed.g2.bx.psu.edu/repos/ethevenot/qualitymetrics/quality_metrics/2.2.8", "tool_stderr": "Error in check.err(table.check) : \n- - - - - - - - -\n\nData matrix and sample metadata do not match regarding sample identifiers.\n    For example, the following identifiers found in the data matrix\n    do not appear in the sample metadata file:\n    pid\n    precursorScanNum\n    acquisitionNum\n\n    For example, the following identifiers found in the sample metadata file\n    do not appear in the data matrix:\n    674\n    674\n    674\n\nPlease check your data.\n\n- - - - - - - - -\nCalls: QualityControl -> check.err\nExecution halted\n", "tool_stdout": "", "tool_version": "2.2.8", "traceback": null, "update_time": "2022-07-11T09:51:01.169119"}]