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
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