The flag --threads seems not to be working

[WeiYang-BAI]

Holle,

The --threads option does not seem to be functioning (version is 4.1.6). Here are my settings:

minimac4 \
    chr1.msav \
    chr1.array.vcf.gz \
    --sample-ids-file samples.ID \
    --output chr1.impu.vcf.gz \
    --sites chr1.impu.sites_only.vcf.gz \
    --empirical-output chr1.impu.empirical_dosages.vcf.gz \
    --format GT,DS,GP \
    --map genetic_map_hg38_withX_3cols.tsv.gz \
    --output-format vcf.gz \
    --threads 6

Anyone can help? Many thanks in advance!

Best regards, Weiyang

[WeiYang-BAI]

I found the reason. The program runs HMM with parallel processing and uses one CPU to merge files.