Hi

I have noticed that samtools consensus command always uses 1 thread despite more (-@ 8) threads have been specified in the command. As shown in the processing time stats below, multiple thread specification does not have any substantial impact.

time samtools consensus -X r10.4_sup -o ~/analyses/samtools_test_cons.fa ~/analyses/BIOINFO_plasmid_test/results/minimap2/TEST_1_1/TEST_1_1_mapped.bam

real    3m12.478s
user    3m11.181s
sys     0m1.286s

time samtools consensus -@ 8 -X r10.4_sup -o ~/analyses/samtools_test_cons.fa ~/analyses/BIOINFO_plasmid_test/results/minimap2/TEST_1_1/TEST_1_1_mapped.bam

real    3m18.814s
user    3m19.436s
sys     0m1.992s

Results are for a smaller subset of data (~25k ONT reads), but I have observed this for large datasets too. samtools consensus threading is creating a bottleneck in data processing. Is this behaviour anticipated? Any suggestions on how to tackle this would be appreciated.

Thanks
Sej