running in parrallel

[Former user]

Hi,

I was trying to run SWAN on a whole genome 50x sample. I run with default setting but the sclip_scan step took more than 10 days and it is still running.

In the paper it is suggested that SWAN can be run in parallel and it should took a day. I was wondering how I can set up that feature to make it use multiple processors.

Thanks

[Charlie Xia]

Thanks for trying it out. Sclip_scan can be parallelized by chromosomes. Did you do that? Thanks.We usually do some test run and divide the region size as acceptable speed.

some of my previous script:

for file in ls *.bam; do for chr in echo {1..22} X; do pf=${file%.bam}; cmd="sclip_scan -c $chr -o $pf.chr$chr $HOME/ws/hg/hg19/human_g1k_v37.fasta $file >$pf.chr$chr.scscan.log 2>&1"; echo $cmd >$pf.chr$chr.scscan.pbs; done; done;

Charlie