hello jimmy and greg, i was not aware that each directory has to be processed individually but i agreed this can be wrapped up in a script ;-)
but i tried the command greg suggested and still get the segmentation fault :-( cheers, andreas On Fri, Oct 2, 2009 at 8:49 PM, Jimmy Eng <[email protected]> wrote: > > Andreas, I'm not sure if I'm missing something but each file/directory > you process will be an individual Out2XML call. Out2XML doesn't > support the notion of multiple inputs although you can easily wrap it > with a simple script if you want to do batch pepXML conversions. > > On Fri, Oct 2, 2009 at 11:31 AM, Andreas Quandt > <[email protected]> wrote: > > hey greg, > > > > many thanks for your answer! > > apparently this would explain a lot ,-) > > but what do i have to do when i process multiple files and have therefore > > multiple directories? > > do i have to specify all the directories or do i have to specify only the > > location of the 'original' directory? > > > > cheers, > > andreas > > > > On Fri, Oct 2, 2009 at 2:55 PM, Greg Bowersock <[email protected]> > wrote: > >> > >> It looks like you aren't giving Out2XML a directory to work on. Try > >> something like: > >> tpp/bin/Out2XML -pI > >> > -P/IMSB/results/workflow/324/sorcerer/output/10300/original/sequest.params > >> /IMSB/results/workflow/324/sorcerer/output/10300/original/O08-10093_c > >> > >> You shouldn't need the -E option, since Out2XML will use the enzyme from > >> the sequest.params file. > >> > >> Greg > >> > >> On Fri, Oct 2, 2009 at 5:32 AM, Andreas Quandt < > [email protected]> > >> wrote: > >>> > >>> dear list, > >>> > >>> sorry the previous email was not send with its complete content: > >>> > >>> > >>>> i was trying to use Out2XML to convert some sequest .out files. > >>>> unfortunately i am always getting a segmentation fault as output. i > >>>> tried several paramter sets and also peak lists but no success. > >>>> > >>>> here the command i executed: > >>>> > >>>> tpp/bin/Out2XML -pI -P > >>>> /IMSB/results/workflow/324/sorcerer/output/10300/original/ -Etrypsin > >>>> > >>>> and the error message: > >>>> Segmentation fault > >>>> > >>>> > >>> > >>> here the structure of the directory i was processing: > >>> > >>> ll /IMSB/results/workflow/324/sorcerer/output/10300/original/ > >>> total 12820 > >>> drwxrwxrwx 24 501 501 4096 2009-10-01 14:39 . > >>> drwxrwxrwx 3 501 501 4096 2009-10-01 13:48 .. > >>> drwxrwxrwx 2 501 501 933888 2009-10-01 15:07 O08-10093_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:45 O08-10093_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10093_c.mzXML > >>> drwxrwxrwx 2 501 501 909312 2009-10-01 15:10 O08-10094_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:46 O08-10094_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10094_c.mzXML > >>> drwxrwxrwx 2 501 501 831488 2009-10-01 15:07 O08-10095_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:46 O08-10095_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10095_c.mzXML > >>> drwxrwxrwx 2 501 501 798720 2009-10-01 15:08 O08-10096_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:46 O08-10096_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10096_c.mzXML > >>> drwxrwxrwx 2 501 501 675840 2009-10-01 15:08 O08-10097_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:47 O08-10097_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10097_c.mzXML > >>> drwxrwxrwx 2 501 501 151552 2009-10-01 15:07 O08-10098_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:46 O08-10098_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10098_c.mzXML > >>> drwxrwxrwx 2 501 501 561152 2009-10-01 15:06 O08-10099_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:46 O08-10099_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10099_c.mzXML > >>> drwxrwxrwx 2 501 501 851968 2009-10-01 15:11 O08-10100_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:45 O08-10100_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10100_c.mzXML > >>> drwxrwxrwx 2 501 501 798720 2009-10-01 15:10 O08-10102_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:46 O08-10102_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10102_c.mzXML > >>> drwxrwxrwx 2 501 501 761856 2009-10-01 15:10 O08-10103_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:47 O08-10103_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10103_c.mzXML > >>> drwxrwxrwx 2 501 501 749568 2009-10-01 15:06 O08-10104_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:46 O08-10104_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10104_c.mzXML > >>> drwxrwxrwx 2 501 501 593920 2009-10-01 15:10 O08-10105_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:45 O08-10105_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10105_c.mzXML > >>> drwxrwxrwx 2 501 501 532480 2009-10-01 15:10 O08-10106_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:47 O08-10106_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10106_c.mzXML > >>> drwxrwxrwx 2 501 501 614400 2009-10-01 15:06 O08-10107_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:45 O08-10107_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10107_c.mzXML > >>> drwxrwxrwx 2 501 501 655360 2009-10-01 15:08 O08-10108_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:47 O08-10108_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10108_c.mzXML > >>> drwxrwxrwx 2 501 501 327680 2009-10-01 15:07 O08-10109_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:47 O08-10109_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10109_c.mzXML > >>> drwxrwxrwx 2 501 501 135168 2009-10-01 15:11 O08-10111_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:46 O08-10111_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10111_c.mzXML > >>> drwxrwxrwx 2 501 501 217088 2009-10-01 15:10 O08-10112_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:47 O08-10112_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10112_c.mzXML > >>> drwxrwxrwx 2 501 501 286720 2009-10-01 15:07 O08-10113_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:47 O08-10113_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10113_c.mzXML > >>> drwxrwxrwx 2 501 501 499712 2009-10-01 15:08 O08-10114_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:45 O08-10114_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10114_c.mzXML > >>> drwxrwxrwx 2 501 501 552960 2009-10-01 15:07 O08-10115_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:47 O08-10115_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10115_c.mzXML > >>> drwxrwxrwx 2 501 501 585728 2009-10-01 15:08 O08-10116_c > >>> lrwxrwxrwx 1 501 501 39 2009-10-01 13:46 O08-10116_c.mzXML -> > >>> /IMSB/scratch/andreas/O08-10116_c.mzXML > >>> -rwxrwxrwx 1 501 501 2523 2009-10-01 14:39 sequest.params > >>> > >>> does anyone of you point me in the right direction because i do not > know > >>> what i am doing wrong... > >>> > >>> many thanks in advance, > >>> andreas > >>> > > > > > > > > > > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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