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voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
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-t/--num-cpu-threads doesn't affect the number of threads used #309

Closed iseultj closed 2 years ago

iseultj commented 3 years ago

I'm trying to run megahit v1.2.9 (installed with conda), but am trying to limit the number of cpu threads. When I run

megahit -r ${fastq1} ${fastq2} ${fastq3} --memory 0.4 -t 10 --out-dir megahit

megahit uses all available CPUs (88). I've also tried using the --num-cpu-threads just in case, and the same thing happens.

Is there something really obvious I'm missing, or is this a real issue? Thanks!

sjaenick commented 2 years ago 
  megahit [options] {-1 <pe1> -2 <pe2> | --12 <pe12> | -r <se>} [-o <out_dir>]

Use options before specifying the input files, not afterwards.