FASTA program discussion list

[Georgios Magklaras <>]

On 31/10/13 15:25, 

 wrote:
> Hi,
> I am running into a problem with segmentation fault while using fasta through
> another program (PASA, http://pasa.sourceforge.net).
>
> Here is the command and the error message:
> fasta /tmp/50438.seq1 /tmp/50438.seq2 > /tmp/50438.grasta_result
> Segmentation fault
>
> The server I'm running on:
> Linux rna 3.0.0 #1 SMP Thu Aug 4 15:10:31 CEST 2011 x86_64 Intel(R) Xeon(R) 
> CPU
> X7550 @ 2.00GHz GenuineIntel GNU/Linux
>
> Fasta version: version 36.3.6 Sep, 2013(preload9)
>
> Below is what the three files look like.
>
> 1. /tmp/50438.seq1:
> > seq1
> MNGPVDYIQEHTLKDVGAFMFTSESVGEGHPDKICDQISDAVLDAHLSQDPDAKVACETV
> CKTGMVLLCGEITSRAVVDYQKIVRDTIKYIGYDDSEKGFDYKTCNVLVALEQQSPDIAQ
> GVHLDRQEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGVLPWLRPD
> SKTQVTVKYIQKNGAVIPVRVHTIVISVQHDETISLSDMQDALKEQVIKAVVPEKYLDEK
> TVYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAAR
> WVAKSLVHAKLCHRVLVQVHLIWVFMKQIKLHISKHIVRDW*
>
> 2. /tmp/50438.seq2:
> > seq2
> MVLLCGEITSRAVVDYQKIVRDTIKYIGYDDSEKGFDYKTCNVLVALEQQSPDIAQGVHL
> DRQEEDIGAGDQGLMFGYATDETEECMPLTIVLAHKLNAKLAELRRNGVLPWLRPDSKTQ
> VTVKYIQKNGAVIPVRVHTIVISVQHDETISLSDMQDALKEQVIKAVVPEKYLDEKTVYH
> LQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGGGAFSGKDYTKVDRSAAYAARWVAK
> SLVHAKLCHRVLVQVHLIWVFMKQIKLHISKHIVRDW*
>
>
> 3. /tmp/50438.grasta_result:
> # fasta /tmp/50438.seq1 /tmp/50438.seq2
> FASTA searches a protein or DNA sequence data bank
>   version 36.3.6 Sep, 2013(preload9)
> Please cite:
>   W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
>
> Query: /tmp/50438.seq1
>    1>>>seq1 - 342 aa
> Library: /tmp/50438.seq2
>      44997 residues in    1 sequences
>
> Statistics: Altschul/Gish params: n0: 342 Lambda: 0.158 K: 0.019 H: 0.100
>   statistics sampled from 0 (1) to 0 sequences
> Algorithm: FASTA (3.8 Nov 2011) [optimized]
> Parameters: BL50 matrix (15:-5), open/ext: -10/-2
>   ktup: 2, E-join: 1 (0.5), E-opt: 0.2 (0.5), width:  16
>   Scan time:  0.040
>
> The best scores are:                                      opt bits E(2)
> seq2                                               (44997) 1854 429.0 2.2e-122
> seq2                                               (44997)    0 6.9       2
>
>
> Could someone explain why I get a segmentation fault? And how to get around it
> so I can continue the PASA run?
>
> Best regards,
> Helena
>
> Helena Storvall
> PhD student
> Sandberg lab
> Karolinska Institutet
> Stockholm, Sweden
> email: 

Hei,

There could be a number of different reasons why the PASA pipeline 
segfaults and one needs more info.

1)On the working directory is there a pasa_killer.input file after the 
crash?

2)If yes, then could you do a: pasa pasa_killer.input and post here the 
output?


GM


Best regards,

--
--
George Magklaras PhD
RHCE no: 110-320-413
 
Head of IT/Senior Systems Engineer
Biotechnology Center of Oslo and
the Norwegian Center for Molecular Medicine/
Vitenskapelig Databehandling (VD) -
Research Computing Services - USIT

EMBnet TMPC Chair

http://folk.uio.no/georgios
http://www.uio.no/english/services/it/research/hpc/abel/

Tel: +47 22840535