blastx globally against nr database
hello every body, i have a 200 MB fasta file of nucleotide sequence, i want to blast it against protein database using mpi script. i have used:
/opt/software/intel/impi/4.1.0.024/intel64/bin/mpirun -np 240 \
/opt/software/applications/BIO-Category/SequenceAnalysis/\
MPI/intel/CompXE-2013/IMPI-410024/mpiBLAST-61.6.0/mpiblast -p blastx \
-d nr -i /home/my_id/test.fasta -o test.xml -m 7
but its showing error like
Unable to read mpiBLAST shared storage path from either .ncbirc or the MPIBLAST_SHARED environment variable.
The mpiBLAST configuration in .ncbirc should look like:
[mpiBLAST]
can any body find help it out where is wrong in my command??? what should be the actual command???
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Ram
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Bulbul Ahmed •
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Bulbul Ahmed •
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Isn't the error clear from the message above?
Take a look at this: http://www.mpiblast.org/Docs/Install
Are you doing this task on your local machine - did you install mpiBLAST or did you HPC sysadmin? If it was your sysadmin, you should probably check with them on the location to add to the appropriate PATH variable. Or they may have a module file that does it for you.
i am running in cluster and its already installed in cluster. the path is also correct. i am just confused if i made any mistake in my command...
Just so we're sure, how did you check it's installed in the cluster and loaded in your HPC session?
[my_id@login2 ~]$ mpiblast mpiBLAST requires the following options: -d [database] -i [query file] -p [blast program name]
What @genomax said below. The installation is important, but the loading mechanism is more relevant to your problem here. Clusters usually either set variables such as
$MPIBLAST_SHAREDwhen you load the module, or have a preferences/config file at the appropriate location. Check for the value in the variable as well as the location. You can find where mpiblast binary is located using the commandwhich mpiblastand use that to check if the config file has the appropriate content.What does
echo $MPIBLAST_SHAREDshow? If that value is blank then check the link that @Ram had provided. You need to follow instructions in section #4 and provide correct paths.