Hi, I have 15 files from an experiment and all of them ran smoothly on TPP except for one file. i am trying to get iTRAQ quantities and this one file keeps failing. it doesnt even recognize which instrument the data came from. i re-run sequest on bioworks it didnt help. here is the command line thank you for your help in advance gogce run_in c:/Inetpub/wwwroot/ISB/data/McGill-Cortex; xinteract - N0826009McGillRat_Group4_40ACN_PP.pep.xml -p0.05 -l7 -O - Lcondition.xml-1 c:/Inetpub/wwwroot/ISB/data/McGill-Cortex/ 0826009McGillRat_Group4_40ACN.pep.xml
C:\Inetpub\tpp-bin\xinteract.exe (TPP v4.2 JETSTREAM rev 1, Build 200904071723 (MinGW)) running: "C:/Inetpub/tpp-bin/InteractParser "0826009McGillRat_Group4_40ACN_PP.pep.xml" "c:/Inetpub/wwwroot/ISB/ data/McGill-Cortex/0826009McGillRat_Group4_40ACN.pep.xml" -L"7"" file 1: c:/Inetpub/wwwroot/ISB/data/McGill-Cortex/ 0826009McGillRat_Group4_40ACN.pep.xml processed altogether 2831 results results written to file c:/Inetpub/wwwroot/ISB/data/McGill-Cortex/ 0826009McGillRat_Group4_40ACN_PP.pep.xml direct your browser to http://localhost/ISB/data/McGill-Cortex/0826009McGillRat_Group4_40ACN_PP.pep.shtml command completed in 2 sec running: "C:/Inetpub/tpp-bin/PeptideProphetParser "0826009McGillRat_Group4_40ACN_PP.pep.xml" MINPROB=0.05" (SEQUEST) init with SEQUEST trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN PeptideProphet (TPP v4.2 JETSTREAM rev 1, Build 200904071723 (MinGW)) akel...@isb read in 0 1+, 1769 2+, 529 3+, 154 4+, 79 5+, 26 6+, and 0 7+ spectra. Initialising statistical models ... Iterations: .........10.........20.........30.........40... WARNING: Mixture model quality test failed for charge (1+). WARNING: Mixture model quality test failed for charge (4+). WARNING: Mixture model quality test failed for charge (5+). model complete after 44 iterations command completed in 2 sec running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i 0826009McGillRat_Group4_40ACN_PP.pep.xml" Analyzing 0826009McGillRat_Group4_40ACN_PP.pep.xml ... Parsing search results "c:/Inetpub/wwwroot/ISB/data/McGill-Cortex/ 0826009McGillRat_Group4_40ACN (SEQUEST)"... => Total of 978 hits. command completed in 1 sec running: "C:/Inetpub/tpp-bin/LibraPeptideParser "0826009McGillRat_Group4_40ACN_PP.pep.xml" -ccondition.xml" could not open input file c:/Inetpub/wwwroot/ISB/data/McGill-Cortex/ 0826009McGillRat_Group4_40ACN.mzXML command "C:/Inetpub/tpp-bin/LibraPeptideParser "0826009McGillRat_Group4_40ACN_PP.pep.xml" -ccondition.xml" failed: Operation not permitted command "C:/Inetpub/tpp-bin/LibraPeptideParser "0826009McGillRat_Group4_40ACN_PP.pep.xml" -ccondition.xml" exited with non-zero exit code: 1 QUIT - the job is incomplete command "C:\Inetpub\tpp-bin\xinteract.exe - N0826009McGillRat_Group4_40ACN_PP.pep.xml -p0.05 -l7 -O - Lcondition.xml-1 c:/Inetpub/wwwroot/ISB/data/McGill-Cortex/ 0826009McGillRat_Group4_40ACN.pep.xml" failed: Operation not permitted Command FAILED
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