hi brian, this might be an explanation. i use network shares in the process but they should not be a bottleneck. i will investigate a little bit and see if i am wrong.
many thanks :-) andreas On Mon, Sep 28, 2009 at 5:19 PM, Brian Pratt <[email protected]>wrote: > 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 -~----------~----~----~----~------~----~------~--~---
