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BLAST: Difference between revisions
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Use faSplit instead
m (Update to lastest BLAST+) |
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==== Preprocessing ==== <!--T:16--> | ==== Preprocessing ==== <!--T:16--> | ||
In order to accelerate the search, the <tt>seq.fa</tt> file must be split into smaller chunks. These should be at least <tt>1MB</tt> or greater, but '''not smaller''' as it may hurt the parallel filesystem. | In order to accelerate the search, the <tt>seq.fa</tt> file must be split into smaller chunks. These should be at least <tt>1MB</tt> or greater, but '''not smaller''' as it may hurt the parallel filesystem. | ||
<!--T:18--> | <!--T:18--> | ||
Using the <tt> | Using the <tt>faSplit</tt> utility: | ||
{{Command| | {{Command|module load kentutils/20180716}} | ||
will create 10 files named <tt> | {{Command|faSplit sequence seqs.fa 10 seq}} | ||
will create 10 files named <tt>seqN.fa</tt> where <tt>N</tt> is in the range of <tt>[0..9]</tt> for 10 queries (sequences). | |||
==== Job submission ==== <!--T:19--> | ==== Job submission ==== <!--T:19--> | ||
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See also [[GNU Parallel#Handling_large_files|Handling large files]] in the GNU Parallel page. | See also [[GNU Parallel#Handling_large_files|Handling large files]] in the GNU Parallel page. | ||
==== Running with multiple cores on one node==== | |||
<!--T:34--> | <!--T:34--> | ||
{{File | {{File | ||
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Note: The file must not be compressed. | Note: The file must not be compressed. | ||
==== Job submission ==== <!--T:31--> | ===== Job submission ===== <!--T:31--> | ||
With the above submission script, we can submit our search and it will run after the database has been created. | With the above submission script, we can submit our search and it will run after the database has been created. | ||
{{Command|sbatch --dependency{{=}}afterok:$(sbatch makeblastdb.sh) blastn_gnu.sh}} | {{Command|sbatch --dependency{{=}}afterok:$(sbatch makeblastdb.sh) blastn_gnu.sh}} | ||
==== Running with multiple cores on one node==== | |||
=== Additional tips === <!--T:32--> | === Additional tips === <!--T:32--> | ||