Thanks, David! I've posted the myrimatch-generated pepXML file here: https://drive.google.com/file/d/0B3GLxknZ3gYRTFlPdUdyUVNVTXc/view?usp=sharing
On Friday, May 15, 2015 at 4:25:13 PM UTC-7, David Shteynberg wrote: > > 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 <daniel...@stemcentrx.com > <javascript:>> 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 spctools-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
