Question: Kraken can't find Jellyfish/does not find the correct version
0
gravatar for camilacv
18 months ago by
camilacv0
camilacv0 wrote:

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.

ADD COMMENTlink modified 18 months ago by Devon Ryan93k • written 18 months ago by camilacv0
1
gravatar for Devon Ryan
18 months ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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.

ADD COMMENTlink written 18 months ago by Devon Ryan93k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2389 users visited in the last hour