CREST is not running.

Question

[sbogen]

Hello All,

I recently posted with concerns about a run of CREST (clipping reveals structure) seeming to take a long time to run. I checked the CPU usage on the job and noticed that it was using none.

Why is nothing happening? Has anybody else had this problem?

My pipeline script is below:

module load perl
module load samtools/0.1.19
module load Blat
module load crest

#set up BLAT server
path/to/Blat/linux.x86_64/gfServer start compute-1-13.local 6667 /pub/sbogen/ce10.2bit
sleep 60

#add necessary directory to @INC
export PERL5LIB = path/to/crest/1.0

path/to//crest/1.0/extractSClip.pl -i /path/to/D4M-2-1.concat.map.sorted.bam --ref_genome /path/to/ref.fa

/path/to/crest/1.0.CREST.pl -f D4M-2-1.concat.map.sorted.bam.cover -d /pub/sbogen/D4M-2-1.concat.map.sorted.bam --ref_genome /path/to/ref.fa -t /path/to/ce10.2bit --blatserver compute-1-13.local --blatport 6667 >& crest_out.log

#cleanup server
/path/to/Blat/linux.x86_64/gfServer stop compute-1.13.local 6667

[Devon Ryan]

Try to add in some echo statements so you can tell when it stops running. Then you'll know which step is the problem and can try to see if you can reproduce the problem locally.