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Saskia-Oosterbroek / decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
MIT License
41 stars 12 forks source link

Medaka accepts no thead limit #4

Closed joran520 closed 2 years ago

joran520 commented 3 years ago

Dear Ms. Oosterbroek

I have used you script with the -T option set to 20. As it reaches the medaka consensus step it uses over 60 threads on our server causing lags and craches. Is it possible to set the thread limiter in all steps?

With kind regards Joran Vanhollebeke

Saskia-Oosterbroek commented 3 years ago

Dear Joran,

Thank you for pointing out this issue, this is quite a big problem! I have had some more notifications about unexpected behaviour of the multi-threading option, but rather that it didn't work, too many threads is new for me. I will look into it in the next week or so and hope to release an update soon, in version 0.1.3 this problem should be solved.

Kind regards, Saskia