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Re: GNU Parallel Bug Reports GNU parallel with NCBI-BLASTP
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From: |
Ole Tange |
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Subject: |
Re: GNU Parallel Bug Reports GNU parallel with NCBI-BLASTP |
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Date: |
Fri, 15 Jul 2016 20:19:06 +0200 |
On Wed, Jul 13, 2016 at 12:05 AM, Andrew James Alverson <address@hidden> wrote:
> cat Species0.fa | /share/apps/parallel/20160622/bin/parallel --will-cite
> --progress --recstart '>' --pipe
> /share/apps/blast/ncbi-blast-2.3.0+/bin/blastp -outfmt '6 qseqid qlen sseqid
> slen frames pident nident length mismatch gapopen qstart qend sstart send
> evalue bitscore' -evalue 0.001 -num_threads 4 -db BlastDBSpecies0 -out
> Blast0_0.latest_parallel.txt
I think you will see that if you stop writing to the same file in
parallel (Blast0_0.latest_parallel.txt) that your problems will
disappear.
This should work better:
/share/apps/blast/ncbi-blast-2.3.0+/bin/blastp -outfmt '6 qseqid qlen sseqid
slen frames pident nident length mismatch gapopen qstart qend sstart send
evalue bitscore' -evalue 0.001 -num_threads 4 -db BlastDBSpecies0 >
Blast0_0.latest_parallel.txt
/Ole