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mummer4 / mummer

Mummer alignment tool
Artistic License 2.0
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Nucmer can only call ten threads #195

Open mrwangyz opened 1 year ago

mrwangyz commented 1 year ago

I use nucmer to compare the genomes of two corns, but no matter how much I set “-t”， it can only call ten threads. Below is my code, I tried both， nucmer --maxmatch -c 500 -b 500 -l 200 -g 1000 A.fa B.fa --delta=./A-B.delta --threads=60 nucmer -t 60 --maxmatch -c 500 -b 500 -l 200 -g 1000 A.fa B.fa --delta=./A-B.delta

gmarcais commented 1 year ago

How many sequences are in the input fasta files? Parallelism at this point is only "coarse grain", done at the level of sequences.

mrwangyz commented 1 year ago

How many sequences are in the input fasta files? Parallelism at this point is only "coarse grain", done at the level of sequences.

Thank you, I understand, my sequence has only ten chromosomes, so only ten cores are called. So does this mean that I can't complete my comparison faster by using more cores?