Bioinformatics Asked on February 6, 2021
I’m trying to run a braker with genome file only to see if it’s working or not before running with all the datasets. But I’m getting this error again and again.
ERROR in file /home/mudith/.conda/envs/braker/bin/braker.pl at line 6293
Failed to execute: perl /work/LAS/dlavrov-lab/dlavrov-lab/mudith/Braker/gmes_linux_64/gmes_petap.pl --verbose --cores=1 --ES --gc_donor 0.001 --sequence=/work/LAS/dlavrov-lab/dlavrov-lab/mudith/Braker/braker_abinitio/braker/genome.fa 1>/work/LAS/dlavrov-lab/dlavrov-lab/mudith/Braker/braker_abinitio/braker/GeneMark-ES.stdout 2>/work/LAS/dlavrov-lab/dlavrov-lab/mudith/Braker/braker_abinitio/braker/errors/GeneMark-ES.stderr
The most common problem is an expired or not present file ~/.gm_key!
I have updated the gm_key as well. But it’s the same. I’m using conda version of braker. This is my script.
#!/bin/bash
# Copy/paste this job script into a text file and submit with the command:
# sbatch thefilename
#SBATCH --time=96:00:00 # walltime limit (HH:MM:SS)
#SBATCH --nodes=1 # number of nodes
#SBATCH --ntasks-per-node=36 # 36 processor core(s) per node
#SBATCH --job-name="braker_abinitio"
#SBATCH [email protected] # email address
#SBATCH --mail-type=BEGIN
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL
#SBATCH --output="output" # job standard output file (%j replaced by job id)
#SBATCH --error="error" # job standard error file (%j replaced by job id)
# LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE
module load miniconda3
source activate braker
cd /work/LAS/dlavrov-lab/dlavrov-lab/mudith/Braker/braker_abinitio
braker.pl --GENEMARK_PATH=/work/LAS/dlavrov-lab/dlavrov-lab/mudith/Braker/gmes_linux_64 --genome=filtered.fasta.masked --esmode
Can someone please help me with this issue? I’m new to this.
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