Does the file pass general XML validation? That is, did you possibly damage it structurally?
It's hard to discuss these things without looking at the actual file, can you upload to the group's files area? Brian On Tue, Mar 23, 2010 at 1:20 PM, Andreas Quandt <[email protected]>wrote: > hey luis, > > nice to hear from you and many thanks for your fast answer! > unfortunately this does not do the trick :-( > > i renumbered the scans starting from 1 (for ms1 and ms2 in ascending > order), > ran indexmzXML on the file (successfully) and > tried 'MzXML2Search -mgf' afterwards. > and then MzXML2Search fails with an segmentation fault: > > $ /usr/local/apps/tpp/bin/MzXML2Search -mgf modified.mzXML > > output mode selected: Mascot Generic Format > MzXML2Search - Mascot Generic Format > > Reading modified.mzXML > Getting the index offset > Reading the index > scan: 34 000%Segmentation fault > > Do you have any further ideas? > > cheers, > andreas > > > > > > > On Tue, Mar 23, 2010 at 5:49 PM, Luis Mendoza <[email protected] > > wrote: > >> Hi Andreas, >> You may need to re-number the indices so that the scans start at 1 >> have no gaps between subsequent ones, as well as adjust the total scan >> count in the header of the file. Then apply the re-indexing. >> >> Hope this helps, >> --Luis >> >> >> >> On Tue, Mar 23, 2010 at 9:46 AM, Andreas Quandt >> <[email protected]> wrote: >> > dear list, >> > >> > i modified some of my mzXML files by removing ms2 spectra which did not >> > fulfill certain criteria. >> > afterwards i tried to analyze them via xtandem but got error messages >> like >> > "might be a corrupted file". >> > to overcome this problem i used indexmzXML which corrected the index by >> > generating a new mzXML file. >> > unfortunately this did not solve the problem as neither xtandem nor >> > mzxml2search where accepting the modified mzXML files as correct input. >> > >> > hence, i was wondering if there is either a better way to remove my ms2 >> > scans from the file or if i am using indexmzXML not in a proper way? >> > >> > cheers, >> > andreas >> > >> > -- >> > You received this message because you are subscribed to the Google >> Groups >> > "spctools-discuss" group. >> > To post to this group, send email to [email protected]. >> > To unsubscribe from this group, send email to >> > [email protected]<spctools-discuss%[email protected]> >> . >> > For more options, visit this group at >> > http://groups.google.com/group/spctools-discuss?hl=en. >> > >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]<spctools-discuss%[email protected]> >> . >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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.
