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HadrienG / InSilicoSeq

:rocket: A sequencing simulator
https://insilicoseq.readthedocs.io
MIT License
176 stars 32 forks source link

Huge number of tmp files causing issues on cloud VM #188

Open aquagenomics opened 3 years ago

aquagenomics commented 3 years ago

I'm using InSilicoSeq to produce Illumina MiSeq reads for a draft genome (~4000 contigs) and this results in the generation of thousands of tmp files, which is causing issues on my cloud VM. This is not so much of a problem when using genomes consisting of a small number of contigs, but when using fasta files containing many contigs, it keeps crashing my system. It would be great if during the read generation process the temporary results could be written to a much smaller number of tmp files.

HadrienG commented 3 years ago

Hi!

Thank you for reporting this. I'll keeo this issue in mind and try to improve how temp files are handled in a future release. Meanwhile if it's a big issue reducing the number of cpus iss is using will reduce the number of temp files created.

Best, Hadrien