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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