Entering edit mode
7.7 years ago
zhangjiong960
▴
10
When I use speedseq var on my bam file of a whole genome, it seems going to take forever to finish. I stopped it after 43 hrs, a vcf.gz file was made and the vcf format looks decent. Below is the code I used:
sudo sh -c " speedseq var -t 24 -o $working_dir/WGC083268D.vcf.gz $ref_dir/human_g1k_v37.fasta $working_dir/WGC083268D.bam > $working_dir/var.log" &
I also ran it with "-w $annotations/ceph18.b37.include.2014-01-15.bed
". And this also not finished yet...
At first it ran with 24 threads, however, after few hours only 2 threads were occupied. Could this be the problem? How should I fix it?
Thanks
Every multi-threaded program may not have routines that use all the cores all the time. As long as you are getting a reasonable result file (and cores specified were in use at some point during the run) you should not worry.
Why are you using
sudo
to run this BTW?