I'm trying to run iProphet on some myrimatch (version 2.2.140) results and the call to xinteract crashes at the PeptideProphetParser stage. Using gdb, I've determined that the crash is related to the intermediate xml generated by InteractParser. I've encountered this problem with TPP-4.8.0 and TPP built from the svn repository. I've replicated this problem on CentOS Linux 7, Debian Linux 8.0, and Windows 7.
It appears that interact parser mangles the xml from myrimatch (doesn't matter if it's pepXML directly produced by myrimatch or mzid converted to pepXML via idconvert). Here's a spectrum query line from the myrimatch pepXML: <spectrum_query spectrum="150410_100002687_SCX_1-2.0.0.3" spectrumNativeID="index=0" start_scan="0" end_scan="0" precursor_neutral_mass="2795.09436840277" assumed_charge="3" index="1" retention_time_sec="437.96200000002"> Here's what the tag looks like after InteractParser: <spectrum_query spectrum=" W " spectrumNativeID="index=0" start_scan="32788" end_scan="-1" precursor_neutral_mass="2795.09436840277" assumed_charge="3" index="1" retention_time_sec="437.96200000002" experiment_label="150410_100002687"> Here's my call to xinteract and the output: xinteract -dREVERSED_ -D../../../fasta/150514.fasta -eT -N150410_100002687_myrimatch.pep.xml -E150410_100002687 -OP 150410_100002687_SCX_1-2.myrimatch.pepXML xinteract (TPP v0.0.0D DEVELOPMENT, Build 201505130910-6911M (CentOS-x86_64)) running: "/home/dhyduke/usr/local/stow/tpp-svn/bin/InteractParser '150410_100002687_myrimatch.pep.xml' '150410_100002687_SCX_1-2.myrimatch.pepXML' -D'../../../fasta/150514.fasta' -X'150410_100002687' -L'7' -E'trypsin'" file 1: 150410_100002687_SCX_1-2.myrimatch.pepXML SUCCESS: CORRECTED data file /fastdisk2/hyduke/Data/proteomics/test/mgf/searchgui_150515/150410_100002687_SCX_1-2.mzML in msms_run_summary tag ... SUCCESS: CORRECTED data file /fastdisk2/hyduke/Data/proteomics/test/mgf/searchgui_150515/150410_100002687_SCX_1-2.mzML in msms_run_summary tag ... processed altogether 58174 results INFO: Results written to file: /fastdisk2/hyduke/Data/proteomics/test/mgf/searchgui_150515/150410_100002687_myrimatch.pep.xml command completed in 45 sec Use database specified by -D option: ../../../fasta/150514.fasta. Skip DatabaseParser step. running: "/home/dhyduke/usr/local/stow/tpp-svn/bin/RefreshParser '150410_100002687_myrimatch.pep.xml' '../../../fasta/150514.fasta'" - Building Commentz-Walter keyword tree... - Searching the tree... - Linking duplicate entries... - Printing results... command completed in 18 sec running: "/home/dhyduke/usr/local/stow/tpp-svn/bin/PeptideProphetParser '150410_100002687_myrimatch.pep.xml' DECOY=REVERSED_ NONPARAM" Using Decoy Label "REVERSED_". Using non-parametric distributions (MyriMatch) WARNING!! The discriminant function for Myrimatch is not yet complete. It is presented here to help facilitate trial and discussion. Reliance on this code for publishable scientific results is not recommended. init with MyriMatch trypsin command "/home/dhyduke/usr/local/stow/tpp-svn/bin/PeptideProphetParser '150410_100002687_myrimatch.pep.xml' DECOY=REVERSED_ NONPARAM" exited with non-zero exit code: 139 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
