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tseemann / ekidna

Assembly based core genome SNP alignments for bacteria
GNU General Public License v3.0
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faster infile processing #18

Open chrisgulvik opened 5 years ago

chrisgulvik commented 5 years ago

I specified 32 CPUs with -j 32 but it looks like any2fasta calls were done sequentially. Would you consider parallelizing that step or making an option to skip it?

For 1445 FNA files without lowercase or ambiguous sites, it took 30 min to save new FA files.

tseemann commented 5 years ago

ekidna is alpha status, doens't even generate names yet. But yes, the plan was to use a dependency system like make so it does it in parallel.

tseemann commented 5 years ago

Related to https://github.com/tseemann/ekidna/issues/3