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Nesvilab / TMT-Integrator

A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.
http://tmt-integrator.nesvilab.org
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java.lang.NullPointerException #34

Open carajj opened 6 months ago

carajj commented 6 months ago

Hi, when i run the TMT-Integrator to integrate results of TMT-11, i can not get result report and the error as follow: *java -jar -Xmx16g /home/F/zjj/CPTAC_PAAD/MS/TMTIntegrator_v4.0.1.jar tmt-i_param_v4.0.1.yml /home/F/zjj/CPTAC/MS/psm/_psm.tsv TMT-Integrator v4.0 Warning: No gene report is generated because all gene symbols in /home/F/zjj/CPTAC_PAAD/MS/psm/01CPTAC_PDA_W_JHU_20191125_LUMOS_f01_psm.tsv are missing. The protein ID will be used as gene in other reports. UpdateColumns--- 0.61553 min. Error at: /home/F/zjj/CPTAC/MS/psm/01CPTAC_PDA_W_JHU_20191125_LUMOS_f02_psm.tsv java.lang.NullPointerException**

tmt-i_param_v4.0.1.yml was changed: path: /home/F/zjj/CPTAC/MS/TMTIntegrator_v4.0.1.jar
memory: 30
protein_database: /home/F/zjj/CPTAC/MS/2024-01-04-decoys-01output_fastq.fasta.fas
output: /home/F/zjj/CPTAC/MS/psm
channel_num: 11
ref_tag: 126

the dir of psm: image

the annotation of TMT-11 like this: annotation.txt example the each psm.tsv like this: 1.txt

this is the script of MSFragger:

    philosopher workspace --init

    MSFragger-3.8/MSFragger-3.8.jar ${params} ${s}.mzML
    philosopher peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev_ --database ${fa} --nonparam ${s}.pepXML

    philosopher proteinprophet interact-${s}.pep.xml
    philosopher database --annotate ${fa} --prefix rev_
    philosopher filter --sequential --razor --picked --tag rev_ --pepxml interact-${s}.pep.xml --protxml interact.prot.xml
    philosopher freequant --dir ${out}/${s}
    philosopher labelquant --brand tmt --plex 11 --dir ${out}/${s}
    philosopher report
    philosopher workspace --clean --nocheck
haowBio commented 2 months ago

I meet the same error, have you solved it ?