Greetings
I have what I think is a simple problem, but I can't figure it out to save
my life. I have a script:
#
# This is written to have the .ncbirc file contain
#
# [mpiBLAST]
# Shared=/scratch/uahmam
# NCBI=/opt/asn/bio/unzipped/genomes
#
setenv data_root H_sapiens/CHR_01
setenv blast_root /opt/asn/apps/mpiBlast_1.4.0/bin
setenv MPI_REQUEST_MAX 128000
setenv MPI_TYPE_MAX 128000
echo "blast_root is "$blast_root
echo "data_root is "$data_root
rm -f -r /scratch/uahmam/H_sapiens
mkdir /scratch/uahmam/H_sapiens
mkdir /scratch/uahmam/H_sapiens/CHR_01
cp /opt/asn/bio/unzipped/genomes/$data_root/hs_ref_chr1.gbk.*
/scratch/uahmam/$data_root/.
cp human_v4.fa /scratch/uahmam/$data_root/.
cd /scratch/uahmam/$data_root/
time /usr/bin/mpirun -np 5 $blast_root/mpiblast -p blastn -d
$data_root/hs_ref_chr1.gbk -i human_v4.fa -W 7 -F F > blast.output
which yields this output:
============================================================
===== Summary of your script job =====
============================================================
The script file is: run_blast_Hsol_v_ch1
The time limit is 40:00:00 HH:MM:SS
The target directory is: /home/uahmam
The memory limit is: 500mb
The file size limit is: 1gb
The number of CPUs is: 6
The job will start running after: 200601101735.07
Look for: runblastHsolvc in queue: batch
blast_root is /opt/asn/apps/mpiBlast_1.4.0/bin
data_root is H_sapiens/CHR_01
[blastall] WARNING: oligo_id|RefSeq|GB_accession: Could not find index
files for database
/scratch/uahmam/H_sapiens/CHR_01/H_sapiens/CHR_01/hs_ref_chr1.gbk.001
[blastall] WARNING: oligo_id|RefSeq|GB_accession: Could not find index
files for database /scratch/uahmam/H_sapiens/CHR_01/hs_ref_chr1.gbkAOq1u1
[blastall] WARNING: oligo_id|RefSeq|GB_accession: Could not find index
files for database
/scratch/uahmam/H_sapiens/CHR_01/H_sapiens/CHR_01/hs_ref_chr1.gbk.001
[blastall] WARNING: oligo_id|RefSeq|GB_accession: Could not find index
files for database /scratch/uahmam/H_sapiens/CHR_01/hs_ref_chr1.gbkAOq1u1
[blastall] FATAL ERROR: oligo_id|RefSeq|GB_accession: Database
/scratch/uahmam/H_sapiens/CHR_01/hs_ref_chr1.gbkAOq1u1 was not found or
does not exist
3 1477.8 Bailing out with signal -1
MPI: On host altix3.asc.edu, Program
/opt/asn/apps/mpiBlast_1.4.0/bin/mpiblast, Rank 3, Process 18098 called
MPI_Abort(<communicator>, 0)
MPI: --------stack traceback-------
sh: line 1: idb: command not found
MPI: -----stack traceback ends-----
MPI: MPI_COMM_WORLD rank 3 has terminated without calling MPI_Finalize()
MPI: aborting job
0.002u 0.014s 24:38.39 0.0% 0+0k 0+0io 124pf+0w
I thought I had the paths set up correctly according to my understanding
of the documentation, but something ain't right.
Can anybody offer any ideas where to look?
Thanks
Mike
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