Unicycler and GNU parallel

Question

[emma.a]

Hi,

unfortunately Unicycler forum is inactive and I would like to ask some info.

I'm using a workstation of 56 CPUs with GNU parallel.

When I'm running Unicycler with the "--threads 25" option is going "fast".

When I use GNU parallel, 2 jobs in parallel, is going slower even if I use the "--treads 25" option for all jobs.

I just made a copy of a fastq file (pair-end) to create the samples for the jobs.

Do you have any experience with this and any advice?

Thank you!

Answer 1

[ole.tange]

I have no experience with Unicycler, but what you describe sounds very similar to the problem with multi-threaded tesseract: https://github.com/tesseract-ocr/tesseract/issues/3109

Maybe Unicycler uses the same threading technique?

[emma.a]

Hi, thank you very much for your feedback! I will check what threading technique Unicycler use.

Best