Question: blastx globally against nr database
0
gravatar for Bulbul Ahmed
3.6 years ago by
Bulbul Ahmed20
United States
Bulbul Ahmed20 wrote:

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???

rna-seq blast next-gen mpi • 839 views
ADD COMMENTlink modified 3.6 years ago by RamRS25k • written 3.6 years ago by Bulbul Ahmed20
1

Isn't the error clear from the message above?

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by genomax75k

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.

ADD REPLYlink written 3.6 years ago by RamRS25k

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...

ADD REPLYlink written 3.6 years ago by Bulbul Ahmed20

Just so we're sure, how did you check it's installed in the cluster and loaded in your HPC session?

ADD REPLYlink written 3.6 years ago by RamRS25k

[my_id@login2 ~]$ mpiblast mpiBLAST requires the following options: -d [database] -i [query file] -p [blast program name]

ADD REPLYlink written 3.6 years ago by Bulbul Ahmed20

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_SHARED when 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 command which mpiblast and use that to check if the config file has the appropriate content.

ADD REPLYlink written 3.6 years ago by RamRS25k

What does echo $MPIBLAST_SHARED show? 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.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by genomax75k
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