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Nucmer can only call ten threads #195

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mrwangyz opened this issue Apr 13, 2023 · 2 comments
Open

Nucmer can only call ten threads #195

mrwangyz opened this issue Apr 13, 2023 · 2 comments

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

@mrwangyz
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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?

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