Question: reducing memory consumption of circoletto
0
gravatar for Ric
17 months ago by
Ric190
Australia
Ric190 wrote:

Hi,

  1. I splitted my query genome in 200 parts with pyfasta and I ran each of them separetly with blastall: blastall -p blastn -i ${i} -d ${db} -F F -e 1e-10 -E -1 -v 20000 -b 20000 -a 1 > output/${output}.blast
  2. I merged all blastall results and the output file is 8.8 Tb big: cat BAFB.contigs.*.fasta.clean.blast > BAFB.contigs.all.fasta.clean.blast
  3. Unfortunately, 50gb of RAM was not enough to run circoletto.pl perl /apps/Circoletto/circoletto.pl --blastout BAFB.contigs.all.fasta.clean.blast --cpus 8 --out_dir output

My blastall database is based on a reference genome with 10 chromosomes but my assembly has 16.000 contigs.

How can I reduce memory consumption of circoletto.pl ?

Thank you in advance.

ADD COMMENTlink written 17 months ago by Ric190
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1257 users visited in the last hour