We are trying to run sampe on sai files generated from fastq files obtained with hiseq2000. There is about 100 million pair ended 104 bases reads.
we have estimated insert size at about 200 to 500 depending on libraries.
we are running the following command line
bwa sampe -P -a 300 (or -a 600). We also tried -o values of 1, 100 or 100000.
but bwa runs really slowly. so far it has has run for 4 days and generated files about 1Gb. bwa is install on HPC system that should have the CPU and RAM it needs.
Any idea about what is causing the slow behavior?
we have estimated insert size at about 200 to 500 depending on libraries.
we are running the following command line
bwa sampe -P -a 300 (or -a 600). We also tried -o values of 1, 100 or 100000.
but bwa runs really slowly. so far it has has run for 4 days and generated files about 1Gb. bwa is install on HPC system that should have the CPU and RAM it needs.
Any idea about what is causing the slow behavior?
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