I think if you look in the mgf files you'll notice there's no retention time info, so Mascot2XML seeks out the corresponding mzXML files (that's the raw data I mentioned) and pulls it from there instead. This can increase the amount of disk IO, which can slow things down.
Other possibilities are things like you have some files (the database?) accessed on a network share, etc. Brian On Mon, Sep 28, 2009 at 8:14 AM, Andreas Quandt <[email protected]>wrote: > hi brian, > > i did not use RAW files but mgf files. hence, i am not very sure what you > mean... > > the converter execution looked like this: > > /usr/local/apps/tpp/bin/Mascot2XML > /IMSB/results/workflow/188/mascot_createAscFile/125380469701.dat > -D/IMSB/data/databases/swissprot_57.7/sp_9606.fasta -E trypsin -Ip > > > cheers, > andreas > > > On Mon, Sep 28, 2009 at 5:01 PM, Brian Pratt <[email protected]>wrote: > >> It also depends to some degree on what kind of data it's coverting. For >> example, in some cases it has to root through the raw mass spec data files >> to recover retention time info that didn't get passed through Mascot. It's >> hard to generalize. >> >> Brian >> >> On Mon, Sep 28, 2009 at 7:55 AM, Matthew Chambers < >> [email protected]> wrote: >> >>> >>> HI Andreas, >>> >>> It sounds like it used up all the system memory and started thrashing >>> the disk (constantly paging things in and out to the swap file) which >>> slows down any operation tremendously. Quite possibly the parser wasn't >>> designed for files that big (maybe it's storing something internally >>> that's taking up too much space?). >>> >>> -Matt >>> >>> >>> Andreas Quandt wrote: >>> > dear list, >>> > >>> > i tried to convert a mscot dat file of > 7gb and it took several days. >>> > hence, i would like to ask if any of you knows how to speed this up? >>> > >>> > 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] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
