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Villen-Lab / isobaricquant

MIT License
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Problem parsing hits file #4

Closed wsnoble closed 1 year ago

wsnoble commented 1 year ago

I tried to create my own hits file, but apparently the syntax is not correct. Here is the command line and error message:

java -jar /Users/wnoble/software/IsobaricQuant_MACOS.jar -c config.yml -mzf mzml/Pf_MedVII-Biotin_MixES-WCE_STREP-1_rKCTi_L2_103.mzML -h Pf_MedVII-Biotin_MixES-WCE_STREP-1_rKCTi_L2_103/hits.txt -o Pf_MedVII-Biotin_MixES-WCE_STREP-1_rKCTi_L2_103
Reading configuration file...
Quantifying...
Writing output in Pf_MedVII-Biotin_MixES-WCE_STREP-1_rKCTi_L2_103
Apr 05, 2023 8:52:24 AM villeninputs.input.peptidesequence.PeptideFileFactory create
SEVERE: null
java.lang.Exception: Invalid file format for Pf_MedVII-Biotin_MixES-WCE_STREP-1_rKCTi_L2_103/hits.txt
    at villeninputs.input.peptidesequence.PeptideFileFactory.create(PeptideFileFactory.java:30)
    at edu.uw.villenlab.isobaricquant.Quantification.quantify(Quantification.java:1016)
    at edu.uw.villenlab.isobaricquant.IsobaricQuant.main(IsobaricQuant.java:98)

Exception in thread "main" java.lang.NullPointerException: Cannot invoke "villeninputs.input.peptidesequence.PeptideFile.getPeptides()" because "this.peptideFile" is null
    at edu.uw.villenlab.isobaricquant.Quantification.quantify(Quantification.java:1017)
    at edu.uw.villenlab.isobaricquant.IsobaricQuant.main(IsobaricQuant.java:98)

I am attaching the files, renamed to end with txt so github will allow them to be added.

config.yml.txt hits.txt

The mzML file is too big to attach, but I can send it to you.