Please ignore this post. It was an error in the linked filed that were generated. The linked files were NOT pointing to the mzXML files.
On Thursday, 27 September 2012 20:11:47 UTC-4, Gautam Saxena wrote: > > Just curious if any one has any ideas or might be working on this? I'm > still stuck....couldn't figure it out so far.... > > On Wednesday, 26 September 2012 13:17:00 UTC-4, Gautam Saxena wrote: >> >> Running LIBRA on centos 6.3 (using TPP 4.5.1) against OMSSA output gave >> me the error: >> >> terminate called after throwing an instance of 'std::out_of_range' >>> what(): vector::_M_range_check >> >> >> (And though I don't believe it's rated, there was another odd occurrence: >> LIBRA was expecting to find pep.xml files that ended with mzXML, as in: >> instead of just using the file "cpJ5-egGO-C_A8.pep.xml", it was expecting >> to see the same file suffixed with ".mzXML", as in " cpJ5-egGO-C_A8.pep.xml >> .mzXML". I solved this problem just by creatling soft links, but then I >> got the "terminate called" error described above.). >> >> Any thoughts, workarounds, or complete fixes? >> >> I have provided a tarred/gzipped file here ( >> http://dl.dropbox.com/u/23443825/libra_error/libra_files.tar.gz). It >> contains the >> >> 1. mzXML files, >> 2. the OMSSA pep.xml files (they start off with "cpJ5-egGO-"), >> 3. the linked files that I created (they too start off with >> "cpJ5-egGO-" but they end with .pep.xml.mzXML), >> 4. the PeptideProphet files (they start of with " pep-LasG-v2Zg") >> 5. and the Libra input file. >> >> The libra command used was nothing special --> : >> >>> /usr/ia_working_dir/DASH/DASH_Server/IA_Common/programs/linux_programs/tpp/bin/LibraPeptideParser >>> >>> pep-LasG-v2Zg-12to23.pep.xml -clibra_lajE_input.xml >> >> >> (Also, one more note: the output logs also said: >> >> No index list offset found. Reading this file will be painfully slow. >> >> >> It doesn't seem to say this when I use X!Tandem instead of OMSSA. Why did >> it say this? Any fix? Will this truly be a major bottleneck? Note: The >> pep.xml file from OMSSA was generated simply by asking OMSSA to output its >> results in pep.xml format. When not using LIBRA, this works fine for the >> TPP programs.) >> >> Thanks in advance. >> >> -Gautam >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/EhEiM8L7nlIJ. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
