Problem with PeptideProphet

[Tanmay Singh]

Dear all

I keep trying to run PeptideProphet on two * pep.xml files but keep getting this error. What could the issue be and how can I solve it?

Error

C:/TPP/bin/xinteract (TPP v6.3.2 Arcus, Build 202305092202-8951 (Windows_NT-x86_64)) using MAXTHREADS=1 for PeptideProphet... running: "C:/TPP/bin/InteractParser "interact.pep.xml" "OR20080317_S_SILAC-LH_1-1_01.pep.xml" "OR20080320_S_SILAC-LH_1-1_11.pep.xml" -L"7"" file 1: OR20080317_S_SILAC-LH_1-1_01.pep.xml file 2: OR20080320_S_SILAC-LH_1-1_11.pep.xml processed altogether 17620 results command "C:/TPP/bin/InteractParser "interact.pep.xml" "OR20080317_S_SILAC-LH_1-1_01.pep.xml" "OR20080320_S_SILAC-LH_1-1_11.pep.xml" -L"7"" failed: Unknown error command "C:/TPP/bin/InteractParser "interact.pep.xml" "OR20080317_S_SILAC-LH_1-1_01.pep.xml" "OR20080320_S_SILAC-LH_1-1_11.pep.xml" -L"7"" exited with non-zero exit code: -1073741819 QUIT - the job is incomplete

Any help would be appreciated

Many thanks

Tanmay 

[Luis Mendoza]

Hello Tanmay,

How did you generate the input pepXML files?  Which search engine did you use?  Are you able to open both of those files and verify that they have results?

Can you process results from another search engine (e.g. Comet or X!Tandem) of the same mzML data?

Cheers,

--Luis

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