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frubino / mgkit

MGKit: Metagenomics Framework
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multithreading #3

Closed thierryjanssens closed 2 years ago

thierryjanssens commented 2 years ago

Dear Francesco,

I was looking around for an argument to set the number of threads utilized, but I could not find any. Is there a way to parallelize the analyses somehow?

Regards,

Thierry

frubino commented 2 years ago

Hi Thierry,

no, I avoided multithreading in general. If you are working with huge GFF or FASTA files, I tend to instead split the GFF files with the script get-gff-info split, which makes sure that all annotations of a sequence are in the same file.

When split then I have multiple submissions in the queuing system or a loop in the shell with background jobs. That usually is enough for my workflows. Hope that helps.

Francesco