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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