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

[Yun He]

Hi,
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 
sequence:
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]
MRAALLALALLAAPAGAASIALPNETAMLPDSGHPGYQAALRRCLVCHSADYIALQPDFDEARWRAVVDKMRLAFKAPIP
AEEAAPIAAYLADAQRRRLLRPHPPQP
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
China
Tel: +86 010 6488 8487
E-mail: jarod at nlbmol.ibp.ac.cn
  or    jarod at spg.biosci.tsinghua.edu.cn