Hello,
I've predicted genes from metagenomic assemblies with FragGeneScan. The next step is to query the predicted peptides against NCBI's nr database. My cluster consists of sixteen Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, which makes up 256 threads altogether. An option would be to use the '-num_threads' flag in blast. However, in my experience, this doesn't parallelize the task entirely.
So what I'm going to do is to run blast with SGE using the below script (after modifying it suitable for blast-2.2.28+). Here's more info.
I have no previous experience with SGE (all I know is that it's setup on the cluster I'm using). So my question is, should I omit the '-num_threads' flag from my query entirely?
I've predicted genes from metagenomic assemblies with FragGeneScan. The next step is to query the predicted peptides against NCBI's nr database. My cluster consists of sixteen Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, which makes up 256 threads altogether. An option would be to use the '-num_threads' flag in blast. However, in my experience, this doesn't parallelize the task entirely.
So what I'm going to do is to run blast with SGE using the below script (after modifying it suitable for blast-2.2.28+). Here's more info.
Code:
#!/bin/bash # #$ -cwd #$ -S /bin/bash #$ -j y export BLASTDB=/share/bio/ncbi/db/ export BLASTMAT=/opt/Bio/ncbi/data/ export PATH=$PATH:/opt/Bio/ncbi/bin blastall -d patnt -p blastn -i $HOME/test.txt -o $HOME/result.txt
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