Hello. I feel like I am perhaps missing something obvious. I’m running some custom ncov analyses using the snakemake in the shell version of nextstrain, and while I specified in the configuration file that I want the analysis to use all twelve cores, it’s only using one. iqtree has been running for two days straight, and if I could figure out what’s wrong, I could hopefully get this done quite a bit quicker.
System: Ubuntu 16.04
Processor: Intel® Xeon® CPU E5-2620 v2 @ 2.10GHz × 12
Memory: 62.9 GiB
Both those commands are passing an argument to use 12 threads, but the top command tells me that only one thread is in use, and of the 12 CPUs, one is at 100%, and the rest are at around 5%.