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. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
