Thanks alot Mr. Chambers, that solved my problem. I already tried zlib compression, but the peakPicking filter did the trick.
Op dinsdag 29 januari 2013 02:32:19 UTC+1 schreef matt.chambers het volgende: > > 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]<javascript:>> > 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] <javascript:>] >> *Sent:* Monday, January 28, 2013 4:12 PM >> *To:* [email protected] <javascript:> >> *Cc:* [email protected] <javascript:> >> *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] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> 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.
