Busco runs directly on cluster but not sbatch
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4.3 years ago

Hi,

I can run busco directly on terminal. It gives me output.

export BUSCO_CONFIG_FILE=./config.ini
busco -m geno -i /home/Whole_genome_analysis/bacteria/FLYE/assembly.fasta -o Assembly-busco --auto-lineage-prok

But when i run in terminal.

!/bin/bash -l

SBATCH -J busco

SBATCH -o myjob.%A_%a.output

SBATCH -e myjob.%A_%a.error

SBATCH -p med

SBATCH -t 09:99:99

SBATCH -N 1

SBATCH -n 12

SBATCH --mem 16000

module load python3/3.7.4

export BUSCO_CONFIG_FILE=./config.ini
busco -m geno -i /home/Whole_genome_analysis/bacteria/FLYE/assembly.fasta -o Assembly-busco --auto-lineage-prok

(same with python3 busco -m geno -i /home/Whole_genome_analysis/bacteria/FLYE/assembly.fasta -o Assembly-busco --auto-lineage-prok)

I get following error.

import Bio ModuleNotFoundError: No module named 'Bio'

Any help would be really appreciated.

Thanks

error running busco • 1.7k views
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Need to install biopython.

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Hi cschu181,

module load python3/3.7.4 module load biopython/1.68

I loaded the module. Now the error is: No module named 'busco' There was a problem installing BUSCO or importing one of its dependencies. See the user guide and the GitLab issue board (https://gitlab.com/ezlab/busco/issues) if you need further assistance.

However, this only happens with sbatch, if i run directly in terminal there is no error.

Thanks

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I think this might be an issue for your cluster admin.

An alternative would be to install busco via conda (for busco 4 you need to set the conda-forge channel, I think).

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module load python3/3.7.4 module load biopython/1.68

Chances are that you installed BUSCO as a user rather than root, so you need to tell SLURM where that is. Most likely you need to export your $PYTHONPATH or the location of your local python programs.

Generally speaking, this is a question for your administrator because we will probably keep guessing until kingdom come without knowing the configuration of your cluster.

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