Beagle multithreading
RetGiraffe11235 opened this issue · comments
RetGiraffe commented
Hello, thank you for developing great software.
I tried to run germline genotyping using 16 threads, but it did not work multithreading on Beagle phasing step.
I think it forgets to set "args.nthreads" on Beagle parameter "nthreads" in Monopgen.py.
If you have other aims, I'm sorry for saying things that aren't necessary.
original
cmd3 = java + " -Xmx20g -jar " + beagle
+ " gl=" + out + "/germline/" + jobid + ".gl.vcf.gz"
+ " ref=" + imputation_vcf
+ " chrom=" + record[0]
+ " out=" + out + "/germline/" + jobid
+ ".gp " + "impute=false modelscale=2 nthreads=1 gprobs=true niterations=0"
cmd5 = java + " -Xmx20g -jar " + beagle
+ " gt=" + out + "/germline/" + jobid + ".germline.vcf"
+ " ref=" + imputation_vcf
+ " chrom=" + record[0]
+ " out=" + out + "/germline/" + jobid+ ".phased "
+ "impute=false modelscale=2 nthreads=1 gprobs=true niterations=0"
palliative solution
cmd3 = java + " -Xmx20g -jar " + beagle
+ " gl=" + out + "/germline/" + jobid + ".gl.vcf.gz"
+ " ref=" + imputation_vcf
+ " chrom=" + record[0]
+ " out=" + out + "/germline/" + jobid
+ ".gp " + "impute=false modelscale=2 nthreads=" + str(args.nthreads) + " gprobs=true niterations=0"
cmd5 = java + " -Xmx20g -jar " + beagle
+ " gt=" + out + "/germline/" + jobid + ".germline.vcf"
+ " ref=" + imputation_vcf
+ " chrom=" + record[0]
+ " out=" + out + "/germline/" + jobid+ ".phased "
+ "impute=false modelscale=2 nthreads=" + str(args.nthreads) + " gprobs=true niterations=0"
Best,
Tomoki