mmseqs don't use enough CPU

[shihai-gong]

HI，I am using mmseqs easy-linclust --threads 40 in docker, but I’ve noticed that steps like kmermatcher and rescorediagonal are not utilizing all 40 CPUs. In fact, during the rescorediagonal step, the CPU usage is only about 20% for most of the time. during the kmermatcher step, the CPU usage is only about 300%, Do you have any good solutions?

• mmseqs version：17-b804f
• input proteion size: 138G

[milot-mirdita]

Do the speed issue happen without Docker too? Usually this happens if MMseqs2 is blocked by slow disk reads.

[shihai-gong]

The issue occurs with both Docker and binary files