[EMBOSS] Antwort: Can't get seqmatchall to run, please help me

[david.bauer at bayerhealthcare.com]

Hi Nicolas,

seqmatchall expects as input a "seqset". This means that all sequences 
must be in one file.
If your individual sequences are in fasta format just create one fasta 
file with all sequences.
The coredump just means that something went wrong during program execution 
and the program crashed. You can delete the coredump file.

HTH,
David.

emboss-bounces at lists.open-bio.org schrieb am 01/06/2007 10:28:07:

> hello
> I have this list of files that I want to process with  seqmatchall.
> 
> -rw-r--r--    1 nicolas  user        3394 Jun  1 02:29 rtt109_h_puta.
> -rw-r--r--    1 nicolas  user        2692 Jun  1 02:29 rtt109_h_puta_1.
> -rw-r--r--    1 nicolas  user        3529 Jun  1 02:29 rtt109_h_puta_10.
> -rw-r--r--    1 nicolas  user        3603 Jun  1 02:29 rtt109_h_puta_11.
> -rw-r--r--    1 nicolas  user        3687 Jun  1 02:29 rtt109_h_puta_12.
> -rw-r--r--    1 nicolas  user        2707 Jun  1 02:29 rtt109_h_puta_2.
> -rw-r--r--    1 nicolas  user        2691 Jun  1 02:29 rtt109_h_puta_3.
> -rw-r--r--    1 nicolas  user        2681 Jun  1 02:29 rtt109_h_puta_4.
> -rw-r--r--    1 nicolas  user        2666 Jun  1 02:29 rtt109_h_puta_5.
> -rw-r--r--    1 nicolas  user        2963 Jun  1 02:29 rtt109_h_puta_6.
> -rw-r--r--    1 nicolas  user        2669 Jun  1 02:29 rtt109_h_puta_7.
> -rw-r--r--    1 nicolas  user        2966 Jun  1 02:29 rtt109_h_puta_8.
> -rw-r--r--    1 nicolas  user        3817 Jun  1 02:29 rtt109_h_puta_9.
> 
> I do this
> % seqmatchall
> All-against-all comparison of a set of sequences
> Input sequence set: rtt109_h_puta*
> Segmentation fault (core dumped)
> 
> this is the core
> -rw-r--r--    1 nicolas  user      2490368 Jun  1 03:15 core
> 
> What I am doing wrong? What is the segmentation fault?
> 
> Thanks for any help
> 
> nicolas
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