exit code 1 #1
Description
My MS/MS runs are giving this error (below) yet I can run them on my lap top with MS-GF+ (MSGFPlus_v20190122) and they run without errors plus they parse to TSV files just fine.
MS-GF+ support said it was a bug with MzTabUtils. Can you help with this Pls.
These are Agilent QTof LC-MS/MS runs that have been converted to mzML format using msconvert (default parameters:proteowizered:pwiz-setup-3.0.19014.f9d5b8a3b-x86_64). The mzML files are still on the server.
---------- createConvertConfig command: [java -Xmx512M -cp /data/ccms-proteomics/tools/MzTabUtils/2016.0517/MzTabUtils.jar edu.ucsd.mztab.TSVToMzTabParamGenerator -tsv 'tsvResult/TEST_NUMBER_3_9c18a21f2401465d87e5d4d72ae3df78.tsv' -params 'parameters/params.xml' -output 'convertParameters/TEST_NUMBER_3_9c18a21f2401465d87e5d4d72ae3df78.properties' -header_line 'true' -filename '#SpecFile' -modified_sequence 'Peptide' -mod_pattern '#' -fixed_mods_reported 'true' -match_mass_precision '3' -scan 'ScanNum' -index 'SpecID' -accession 'Protein' -charge 'Charge'] ---------- Reading input TSV file [TEST_NUMBER_3_9c18a21f2401465d87e5d4d72ae3df78.tsv]... Exception in thread "main" java.lang.RuntimeException: There was an error parsing the input tab-delimited result file, line 2: Could not determine the spectrum ID type of the input TSV file, since the values of neither the scan column [-1] nor the index column [scanId=277467] in the first data row were valid for their type. at edu.ucsd.mztab.TSVToMzTabParamGenerator.(TSVToMzTabParamGenerator.java:321) at edu.ucsd.mztab.TSVToMzTabParamGenerator.extractArguments(TSVToMzTabParamGenerator.java:981) at edu.ucsd.mztab.TSVToMzTabParamGenerator.main(TSVToMzTabParamGenerator.java:901) Caused by: java.lang.IllegalArgumentException: Could not determine the spectrum ID type of the input TSV file, since the values of neither the scan column [-1] nor the index column [scanId=277467] in the first data row were valid for their type. at edu.ucsd.mztab.TSVToMzTabParamGenerator.determineSpectrumIDType(TSVToMzTabParamGenerator.java:650) at edu.ucsd.mztab.TSVToMzTabParamGenerator.(TSVToMzTabParamGenerator.java:293) ... 2 more createConvertConfig command failed with exit code [1]. Tool execution terminates abnormally with exit code [1]