22k spectra to a 5gb file? Definitely profile mode, uncompressed! Run with peakPicking filter and -z flag. On Jan 28, 2013 6:28 PM, "Eric Deutsch" <[email protected]> wrote:
> Hi SKV, thank you for your note. I don’t really know what the problem > might be based on your description. As you surmise, there can be problems > when files exceed a 2 GB or 4GB limit on some systems, I am forwarding your > message to the spctools-discuss list, because here there are gurus who can > better answer your question. I think they will need to know what type of > computer & operating system you’re running on. Is it Windows or Linux? Is > it 32-bit or 64-bit? Also, can you say which version of the TPP you’re > using. > > > > Is there a wiki page on what’s known to work and not work wrt large files? > > > > With this information, hopefully someone can say how to fix your problem. > You might consider using mzML instead of mzXML, although that may not solve > your problem. > > > > Regards, > > Eric > > > > > > *From:* Adhin, S.K.V. [mailto:[email protected]] > *Sent:* Monday, January 28, 2013 4:12 PM > *To:* [email protected] > *Cc:* [email protected] > *Subject:* TPP / X!Tandem error > > > > Dear Mr. Deutsch > > I am a master student at the Free University Amsterdam, the Netherlands. > Last autumn I visited your talk about the different file formats used for > mass spectrometry data and the Trans-Proteomic Pipeline. Actually nowadays > I am using this tool for my master graduation project. > I succesfully manage to use the TPP for many mass spectrometry files. I > always used MSConvert to convert the .raw files to the mzXML file format. > Unfortunately the new files from qe-jurkat can not be parsed correctly when > I do the database search in the TPP (by using X!Tandem). The error message > that I get is: > * > > * > > *X! TANDEM CYCLONE TPP (2011.12.01.1 - LabKey, Insilicos, ISB) * > > * * > > *Loading spectra (mzParser)............ loaded.* > > *Spectra matching criteria = 22587* > > *Pluggable scoring enabled.* > > *Starting threads .* > > *This application has requested the Runtime to terminate it in an unusual > way.* > > *Please contact the application's support team for more information.* > > I tried to index the mzXML file again, but that did not help. I also read > something about the charge state, so I did put that to zero, still I get > the same error message. The only thing I can think of is that the mzXML I > am working with now are significantly larger (5.5 - 6.0 GB) than the ones I > used before. Could that be a reason that a database search can not be done > on these files? Any kind of help would be very much appreciated. > > Sincerly yours, > > S.K.V. Adhin, BSc > > -- > 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?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- 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?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
