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Kraken can't find Jellyfish/does not find the correct version

Hi,

I'm new to Kraken and I'm trying to do a standard Database. I've been trying to use Kraken with my server using a .sbatch file. My .sbatch file is as follows:

#!/bin/bash 
module load jellyfish/1.1.11
module load kraken/1.1 

kraken-build --standard --threads 24 --db SampleKraken

But, running it just ends up as a failure job and it shows the following text in the .out file:

The following have been reloaded with a version change:
  1) jellyfish/1.1.11 => jellyfish/2.2.6

Found jellyfish v2.2.6
Kraken requires jellyfish version 1

I don't know why is it switching if I am loading the correct Jellyfish version.

Any idea on how to solve this?

Thanks for any answer you could give me.

genome software error next-gen sequencing
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updated by Devon Ryan Devon Ryan • written by camilacv • camilacv

1 answer

Whoever wrote the environment module on your system for kraken wrote it just that it would change any loaded version of jellyfish to 2.2.6, which is incompatible with kraken according to the documentation. What you can probably do is load kraken and then try module load jellyfish/1.1.11, perhaps lmod (what you're using) will allow that. Regardless, contact your system administrator to have this fixed.

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written by Devon Ryan Devon Ryan

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