Option -T is ignored: multi-threading with OpenMP is NOT enabled!

Saskia-Oosterbroek / decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads

MIT License

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Option -T is ignored: multi-threading with OpenMP is NOT enabled! #28

Closed MMAThijssen closed 2 years ago

MMAThijssen commented 2 years ago

Hi,

When I run Decona with -T 4, the error message 'Option -T is ignored: multi-threading with OpenMP is NOT enabled!' is given. I suspect this to be something with cd-hit-est. I tried explicitly exporting OMP_NUM_THREADS=4, but the issue remained. Do you know how this can be solved?

Saskia-Oosterbroek commented 2 years ago

Hello,

Yes, it has to do with the installation of CD-hit, in the standard version you get through Bioconda it does not seem to be included. If you install via the instructions on their Github it should work: https://github.com/weizhongli/cdhit/wiki/2.-Installation

MMAThijssen commented 2 years ago

Thank you for your response! The use of the CD hit version from their GitHub gave me some other errors. Therefore I decided to use the bioconda version as this is not the most time consuming step.