hey jimmy, somehow you are always right :-) the parameter order fixed the problem.
many thanks jimmy and also to you greg, andreas On Fri, Oct 2, 2009 at 9:16 PM, Jimmy Eng <[email protected]> wrote: > > Can you confirm that you're passing the right arguments in the right order? > > Out2XML <path_to_directory_with_outs> <#_top_hits_to_report> <options> > > e.g. Out2XML /some/path/myoutsdir 1 -pI -P/path/to/sequest.params > > On Fri, Oct 2, 2009 at 12:12 PM, Andreas Quandt > <[email protected]> wrote: > > 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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