[Bioclusters] mpirun:

P Sravan Kumar. PAsst sravan at www.cdfd.org.in
Sun May 22 07:28:34 EDT 2005

Dear Sir, Thanks for your kind assitance. I have initiated the mpiblast
successfully yesterday. While running I have faced some error message.
It is as follows:
1. Process:
NCBI: /apps/Software/NCBI-2.2.10-5.x86_64.rpm
mpiblast: /apps/Software/mpiblast-1.3.0-2LAM.x86_64.rpm
        Data=/apps/Databases/ncbi/data ( In this directory all the BLOSUM
and other ncbi data is there)
        BLASTDB=/apps/Databases/blastdb ( Its aimed to database created by
mpiformatdb at /apps/Databases/blastdb)
        BLASTMAT=/apps/Databases/ncbi/data ( It also to ncbidata).
        Shared=/apps/Databases/blastdb ( full permission)
        Local=/tmp/mpiblast(full permission)
in /home/sravan:
        mpiformatdb -N 250 -i /apps/Databases/silkbase/scaffolds(368MB) -p
F : has created a dataabase in /apps/Database/blastdb
        Then it has given: it has created a database with scaffolds(368MB)
- 250 fragments each with 2MB.

        /usr/local/lam/bin/mpirun -np 3 /usr/local/bin/mpiblast -p blastn
-i <input> -d <db> -o mpiblast.out

Error Message:
The sequence file has 1000 sequences of different sizes and as whole has
490kb. When I started the script , it ran properly upto 90 or 100 se
quences. Then also it continued. But during the process it has giving the
message serially:
[Blastall] ERROR: ncbiapi [000.000]  ObjMgrNextAvailEntityID failed with
idx 2048.

Kindly assist me in resolving this problem.

Thank you very much.
P.Sravana Kumar.
Laboratory of Molecular Genetics.
Center for DNA Fingerprinting and Diagnostics.
ECIL road, Nacharam.
Hyderabad 500 076.
Ph: 91-40-27151344-1102.
Ph: 91-40-27151344-1209.
e-mail: sravan at cdfd.org.in,sravan_mar at yahoo.com

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