shm and se operation changes #114
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Was running out the door before. We've been doing processing at 5gb chunks, and requesting 120GB to ensure we have sufficient shared memory, until barnacle supports shared memory as a resource. We have been using 16 cores but our efficiency great, so recommend reducing to 10 or 12 |
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...I think this covers the differences.
The changed demux method is here (
/home/mcdonadt/2023.08.09-pangenome-human-depletion/human-depletion-se-pe/demux-inline-all.py). The splitter is (/home/mcdonadt/2023.08.09-pangenome-human-depletion/human-depletion-se-pe/splitter/target/release/splitter) with the source in the corresponding parent directory. This code depends as well onfastq_pairwhich is installable from bioconda