How to run this ContEst job in multi-thread cluster?

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8.5 years ago

MAPK ★ 2.1k

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

contest hpc-clustering • 1.5k views

ADD COMMENT • link 8.5 years ago by MAPK ★ 2.1k

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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 REPLY • link 8.5 years ago by GenoMax 147k

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