Hi Daniel, This looks like an bug. InteractParser attempts to generate spectrum names based on the info in spectrumNativeID, it is clearly getting it wrong on your input example. If you can share one of the problem input files I can fix it.
Thanks, -David On Fri, May 15, 2015 at 2:57 PM, Daniel Hyduke <[email protected] > wrote: > 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. > -- 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.
