Dear Biostar community,
I have problems to run a blastx against nr database. To optimize the process I have read some post which mentioned gnu parallel as a solution to optimize the use of multiple CPUs by ncbi-blast (local mode). Based on different post of this forum I have adapted my code until I stooped to receive error alerts. However, I think the program is not understanding me when I try to modify the predetermined outfmt 6.
There is the chunk of code:
module load gcc module load ncbi-blast module load parallel cat MyTranscriptome.fasta | parallel -q -j 24 --block 100M --recstart '>' --pipe blastx -db /blastdb/nr -num_threads 1 -evalue 1e-5 -outfmt "6 qseqid sseqid stitle pident length mismatch gapopen qstart qend sstart send evalue bitscore" -max_target_seqs 10 -max_hsps 1 > MyTranscriptome_vs_nr.outfmt.6
Before come here to ask you I have serached in to post related with this topic in this (and others) forum but I did not found how to fix the problem.
JUST to clarify (edit), the code ran without problem in a classic way (using -num_threads to my max. numer of cores) so the base code works fine. My problem is the gnu parallel implementation.
Thank you for your time!