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


  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 perl /apps/Circoletto/ --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 ?

Thank you in advance.

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