[ssml] BLAST fastacmd failed to fetch sequence from database stored on PVFS2 filesystem

Yun He jarod at nlbmol.ibp.ac.cn
Wed Dec 5 09:54:54 EST 2007

Yestoday I found  I always got msg "[blastpgp] WARNING:  [000.000]  Failed to 
initialize search. ISAM Error code is -5" when I run blastpgp against a 
database which is stored on the parallel filesystem PVFS2, but the warning 
did not occur when blast against database shared by NFS. Here is an example:
1) /data/blastdb is a directory holding some database like nr, and this 
directory is shared from the master node of a cluster to several compute 
nodes by NFS filesystem;
2) /pool/blastdb is mount point of PVFS2 (version 2.6.3) filesystem on all 
nodes, the content of this directory is identical to that of /data/blastdb (I 
use rsync to make them identical);
3) I employed a small testset of about 100 sequences to test blastpgp against 
nr database in both of the to directories. All runnings on /pool/blastdb 
complained "[blastpgp] WARNING:  [000.000]  Failed to initialize search. ISAM 
Error code is -5", but those on /data/blastdb did not;
4) It seems that BLAST failed to fetch some sequences from the database on 
PVFS2 filesystem and make the complain; I use fastacmd to fetch some 
a) fetch from database on NFS, this is OK,
$ fastacmd -s "gi|34495614" -d /data/blastdb/nr
>gi|34495614|ref|NP_899829.1| sulfite dehydrogenase - subunitB 
[Chromobacterium violaceum ATCC 12472] >gi|34101469|gb|AAQ57838.1| sulfite 
dehydrogenase - subunitB [Chromobacterium violaceum ATCC 12472]
b) fetch from database on PVFS2, ohhh, 
$ fastacmd -s "gi|34495614" -d /pool/blastdb/nr
[fastacmd] ERROR: Accesion search failed for "gi|34495614" with error code -5

Why this happen?

There is a paper on 2002 (J.D Grant, et al, Bioinformatics 2002, 18(5): 
765-766) said they had developed a distributed BLAST and PSI-BLAST on a 
cluster and the database was really stored on PVFS.

Is PVFS2 suitable for storage?

Yun He   Ph.D.
National Laboratory of Biomacromolecules
Institute of Biophysics, Chinese Academy of Sciences
15 Datun Road, Chaoyang District
Beijing 100101
Tel: +86 010 6488 8487
E-mail: jarod at nlbmol.ibp.ac.cn
  or    jarod at spg.biosci.tsinghua.edu.cn

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