Colab

Question

[bala]

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.

[GenoMax]

--use-GPU is deprecated!

Guess the version of megahit you installed either no longer supports this option or you are not calling the right command line parameter.

Using colab for genome assembly sounds like a far fetched use case.

[bala]

Thank you

Answer 1

[Mensur Dlakic]

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.

• https://github.com/voutcn/megahit/issues/152
• https://github.com/voutcn/megahit/issues/138