Issue sometimes with augustus-runner and leishmania tarentolae

[michoug]

Hi,
I had success running the run pipeline on 20+ mags but on a few of them the augustus-runner.sh fails

#!/bin/bash
cd /scratch/gmichoud/ENSEMBLE/EukAssemblyTiaraConcoct/out/wdir/concoct_144/AbinitioAugustus.Augustus || return

/home/gmichoud/miniconda3/envs/EukMS_run/bin/augustus --codingseq=on --stopCodonExcludedFromCDS=false --species=leishmania_tarentolaeout/wdir/GCA_000277815.3_ASM27781v3_genomic/ --outfile=/scratch/gmichoud/ENSEMBLE/EukAssemblyTiaraConcoct/out/wdir/concoct_144/AbinitioAugustus.Augustus/concoct_144.0.fasta.1.gff --gff3=off /scratch/gmichoud/ENSEMBLE/EukAssemblyTiaraConcoct/out/wdir/concoct_144/AbinitioAugustus.Augustus/concoct_144.0.fasta &
/home/gmichoud/miniconda3/envs/EukMS_run/bin/augustus --codingseq=on --stopCodonExcludedFromCDS=false --species=leishmania_tarentolaeout/wdir/GCA_000277815.3_ASM27781v3_genomic/ --outfile=/scratch/gmichoud/ENSEMBLE/EukAssemblyTiaraConcoct/out/wdir/concoct_144/AbinitioAugustus.Augustus/concoct_144.1.fasta.1.gff --gff3=off /scratch/gmichoud/ENSEMBLE/EukAssemblyTiaraConcoct/out/wdir/concoct_144/AbinitioAugustus.Augustus/concoct_144.1.fasta &
/home/gmichoud/miniconda3/envs/EukMS_run/bin/augustus --codingseq=on --stopCodonExcludedFromCDS=false --species=leishmania_tarentolaeout/wdir/GCA_000277815.3_ASM27781v3_genomic/ --outfile=/scratch/gmichoud/ENSEMBLE/EukAssemblyTiaraConcoct/out/wdir/concoct_144/AbinitioAugustus.Augustus/concoct_144.2.fasta.1.gff --gff3=off /scratch/gmichoud/ENSEMBLE/EukAssemblyTiaraConcoct/out/wdir/concoct_144/AbinitioAugustus.Augustus/concoct_144.2.fasta &

The message is :

FileNotFoundError: [Errno 2] No such file or directory: '/scratch/gmichoud/ENSEMBLE/EukAssemblyTiaraConcoct/out/wdir/concoct_144/AbinitioAugustus.Augustus/concoct_144.0.fasta.1.gff'

The folder contains

augustus-runner.sh
concoct_144.10.fasta
concoct_144.12.fasta
concoct_144.14.fasta
concoct_144.2.fasta
concoct_144.4.fasta
concoct_144.6.fasta
concoct_144.8.fasta
concoct_144.0.fasta
concoct_144.11.fasta
concoct_144.13.fasta
concoct_144.1.fasta
concoct_144.3.fasta
concoct_144.5.fasta
concoct_144.7.fasta
concoct_144.9.fasta
slurm-runner.sh
task.log
task.err

the task.log file starts with

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --tasks=1
#SBATCH --cpus-per-task=14
#SBATCH --mem=8GB
#SBATCH --time=24:00:00
#SBATCH --job-name=EukMS
#SBATCH --partition=parallel

/scratch/gmichoud/ENSEMBLE/EukAssemblyTiaraConcoct/out/wdir/concoct_144/AbinitioAugustus.Augustus/augustus-runner.sh

------BEGIN SLURM LOG OUTPUT SECTION------
Could not find the config file Could not find the config file /home/gmichoud/miniconda3/envs/EukMS_run/config/species/leishmania_tarentolaeout/wdir/GCA_000277815.3_ASM27781v3_genomic//leishmania_tarentolaeout/wdir/GCA_000277815.3_ASM27781v3_genomic/_parameters.cfg/home/gmichoud/miniconda3/envs/EukMS_run/config/species/leishmania_tarentolaeout/wdir/GCA_000277815.3_ASM27781v3_genomic//leishmania_tarentolaeout/wdir/GCA_000277815.3_ASM27781v3_genomic/_parameters.cfg..

 Looking for  Looking for _parameters.cfg_parameters.cfg in the configuration directory instead ... in the configuration directory instead ... not not found. found.

and repeats the same error.

I noted that it arrived 3 times and there was always the issue with the species leishmania tarentolaeout,

It's probably an issue with the file taxon_ids.py in src/dependencies/augustus/taxon_ids.py at line 106

Best
Greg

[cjneely10]

Hi Greg,

Thank you for letting me know the issue. I went ahead and pushed a fix to the code.

For your installation, running git pull from within your local installation of EukMetaSanity should accomplish all that is needed for the fix.

Thanks again,

• Chris