Question: How to run this ContEst job in multi-thread cluster?
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gravatar for MAPK
3.8 years ago by
MAPK1.5k
United States
MAPK1.5k wrote:

I have this command for ContEst program to identify contaminated samples. I want to run this job in multi-thread cluster. How can I make java tool use all the resource allocated in qsub -I -l select=1:ncpus=10:mem=100g,walltime=100:00:00. The problem I have is when I submit the interactive job, it only uses one cpu and less than 2gb memory instead of all the allocated memory.

command to run ContEst:

 java -jar ContEst.jar -T Contamination -B:genotypes,vcf /mypath/myvcf.vcf -BTI genotypes -B:pop,vcf /mypath/hapmap_3.3.hg19.vcf -I /mypath/bam_156samples.list -R /mypath/hg19.fasta -pc 0.1 -o test_contaminated.txt
hpc-clustering contest • 948 views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by MAPK1.5k

Interactive jobs may be limited to 1CPU/2GB by your cluster administrators. Check on that possibility.
Why are you running the job interactively if your command line already has all the options?

ADD REPLYlink written 3.8 years ago by genomax78k
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