The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
What is status of multithreading in GATK 3.4?
I am running GATK 3.4.0-g7e26428 on a 64-bit 8-core 16-thread Linux system, using a test case of 5 million paired short reads on chr15 of the human genome to extrapolate the full-genome timing for HaplotypeCaller. For the 5 million pairs, without the -nct option I get ~ 26 minutes; with -nct 8 it's ~ 20 minutes. My Java version is OpenJDK 64-Bit Server VM 1.7.0_79-b14. I would expect more like a x8 speedup; why am I not seeing that?
HaplotypeCaller does not appear to accept the -nt option. Is there any way (besides farming out the individual chromosomes) to run multiple data threads?
Thanks in advance for any helpful advice.