Colab
Hi everyone I am trying to run Megahit genome assembler in google colab, I have chosen the option GPU and successfully installed megahit.
!./megahit -1 /content/drive/MyDrive/Megahit/AST2_R1_M75_Paired_end.fastq.gz -2 /content/drive/MyDrive/Megahit/AST2_R2_M75_Paired_end.fastq.gz --use-gpu -o AST2_kmin21
But I got an error --use-GPU is deprecated!
How to activate or use GPU.
Thank you for your comment and time.
1 answer
The option --use-GPU is deprecated because it doesn't provide a significant speedup compared to running a program on many threads. That's what the authors concluded after their own testing.
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Mensur Dlakic
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Guess the version of
megahityou installed either no longer supports this option or you are not calling the right command line parameter.Using
colabfor genome assembly sounds like a far fetched use case.Thank you