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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