Nesvilab/FragPipe

java.lang.NullPointerException

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haowBio commented

Hellow,

I encountered an issue while running the TMT-Integrator. When attempting to integrate the results from multiple psm.tsv files into TMT-11, I'm unable to generate the result report and receive the following error message: java.lang.NullPointerException at java.base/java.util.TreeMap.getEntry(TreeMap.java:345) at java.base/java.util.TreeMap.get(TreeMap.java:277) at integrate.LoadPsms(integrate.java:155) at integrate.run(integrate.java:31) at TMTIntegrator.main(TMTIntegrator.java:109) Error at: /data/haowu/proteome/Pancreas/Result/test/result/02CPTAC_PDA_Proteome_JHU_20191022/psm.tsv java.lang.NullPointerException Process 'TmtIntegrator' finished, exit code: 1 Process returned non-zero exit code, stopping Interestingly, the process runs successfully when working with a single psm.tsv file. Any suggestions on how to resolve this?
log_2024-04-24_17-15-54.txt

fcyu commented

You are using old versions of the tools. The bug might have been fixed in the new version. Could you upgrade FragPipe, MSFragger, IonQuant, and Philosopher, and try again?

Thanks,

Fengchao