The front line support team will be unavailable to answer questions until May 27th 2019 as we are celebrating Memorial Day. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!
I am running GATK on a shared LSF cluster but have unintentionally run afoul of the admins due to resource use. I am running the GATK commands with 'java -Xmx4g -jar $GATK' and am not using -nt or -nct, but CPU usage is exceeding the resources requested which are 1 vCore and 6G memory. I am now running the same commands on our lab server and do indeed see that CPU usage reaches as high as 800% at times. Is there a way to limit the CPU resources claimed by GATK tools, or alternatively a way to anticipate its actual needs so that I can request an appropriate number of CPUs?