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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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I occured a question when i try to convert .mzid to tsv #139

Open fengwei-li opened 2 years ago

fengwei-li commented 2 years ago

Describe the question or problem I occured a question when i try to convert .mzid to tsv

Details java -Xmx35000M -cp MSGFPlus.jar edu.ucsd.msjava.ui.MzIDToTsv -i /mnt/c/Users/Dr-Li/Desktop/20171024_HF_ZHW_total_liver05_F43.mzid -o /mnt/c/Users/Dr-Li/Desktop/test.tsv MzIDToTsv v9108 (18 April 2022) Java 17.0.3 (Private Build) Linux (amd64, version 5.10.16.3-microsoft-standard-WSL2) Converting 20171024_HF_ZHW_total_liver05_F43.mzid into test.tsv Exception in thread "main" java.lang.NullPointerException: Cannot invoke "uk.ac.ebi.jmzidml.model.mzidml.Tolerance.getCvParam()" because "parentTolerance" is null at edu.ucsd.msjava.mzid.MzIDParser.unmarshallAnalysisProtocolCollection(MzIDParser.java:294) at edu.ucsd.msjava.mzid.MzIDParser.writeToTSVFile(MzIDParser.java:58) at edu.ucsd.msjava.mzid.MzIDParser.writeToTSVFile(MzIDParser.java:50) at edu.ucsd.msjava.ui.MzIDToTsv.convert(MzIDToTsv.java:126) at edu.ucsd.msjava.ui.MzIDToTsv.main(MzIDToTsv.java:84)

Useful extras java --version openjdk 17.0.3 2022-04-19 OpenJDK Runtime Environment (build 17.0.3+7-Ubuntu-0ubuntu0.20.04.1) OpenJDK 64-Bit Server VM (build 17.0.3+7-Ubuntu-0ubuntu0.20.04.1, mixed mode, sharing)