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What should the -s option be for creating the perfect index? #1

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iamh2o opened this issue Apr 30, 2023 · 1 comment

iamh2o commented Apr 30, 2023

When I run

bwa-mem2.scale.avx512bw perfect-index –l 148 human_1kg_v37.fasta

I get the following error, and do not know what the value of -s should be.

ERROR: the seed length must be given.
Usage: bwa-mem2 perfect-index [-l seed_length] [-s slack] <prefix>
       -s (float) ==> the hash table will have (slack) * (length of reference sequence) entries
Total time taken: 0.0014

Thank you-

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iamh2o commented Apr 30, 2023

Weird, I ran the command a second time and this error went away...... no -s was specified?

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