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/-/UrI85XAVitoJ. 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.
