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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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best_by_compleasm.py unable to find compleasm.py #818

Open SAMtoBAM opened 5 months ago

SAMtoBAM commented 5 months ago

Hi there

I am trying to add the busco/compleasm step to my pipeline as adding rnaseq data appears to be making my output too conservative I am using a conda environment with braker v3.0.8 and giving the path to all the other prerequisites.

For tests without rnaseq data I am running

braker.pl --fungus --gff3 \
--genome=1.curation/4.softmasked/${genome} \
--workingdir=2.braker3/${genome2}_nornaseq_compleasm \
--threads=32 \
--busco_lineage=eurotiales_odb10 \
--COMPLEASM_PATH=/home/saodonnell/compleasm_kit/ \
--prot_seq=/home/saodonnell/eurotiales_odb10/refseq_db.faa \
--AUGUSTUS_CONFIG_PATH=/home/saodonnell/Augustus/config/ \
--AUGUSTUS_SCRIPTS_PATH=/home/saodonnell/Augustus/bin/ \
--GENEMARK_PATH=/home/saodonnell/ETP/bin/ \
--PROTHINT_PATH=/home/saodonnell/gmes_linux_64_4/ProtHint/bin/ \
--SRATOOLS_PATH=/home/saodonnell/sratoolkit.3.1.0-ubuntu64/bin/

The last step in the braker.log file is

# Wed May  1 14:10:48 2024: selecting best gene set by BUSCO completeness via compleasm.
# Wed May  1 14:10:48 2024: /home/saodonnell/miniconda3/envs/braker3/bin/python3 /home/saodonnell/miniconda3/envs/braker3/bin/best_by_compleasm.py -m /mnt/cephfs/scratch/saodonnell/projects/flavus/annotation/2.braker3/GCA002214955_nornaseq_compleasm/bbc -d /mnt/cephfs/scratch/saodonnell/projects/flavus/annotation/2.braker3/GCA002214955_nornaseq_compleasm -g /mnt/cephfs/scratch/saodonnell/projects/flavus/annotation/2.braker3/GCA002214955_nornaseq_compleasm/genome.fa -t 32 -p eurotiales_odb10 -y /home/saodonnell/miniconda3/envs/braker3/bin/tsebra.py -f /home/saodonnell/miniconda3/envs/braker3/bin/getAnnoFastaFromJoingenes.py 1> /mnt/cephfs/scratch/saodonnell/projects/flavus/annotation/2.braker3/GCA002214955_nornaseq_compleasm/best_by_compleasm.log 2> /mnt/cephfs/scratch/saodonnell/projects/flavus/annotation/2.braker3/GCA002214955_nornaseq_compleasm/errors/best_by_compleasm.err

In my error log I got these messages

ERROR in file /home/saodonnell/miniconda3/envs/braker3/bin/braker.pl at line 9962
Failed to execute: /home/saodonnell/miniconda3/envs/braker3/bin/python3 /home/saodonnell/miniconda3/envs/braker3/bin/best_by_compleasm.py -m /mnt/cephfs/scratch/saodonnell/projects/flavus/annotation/2.braker3/GCA002214955_nornaseq_compleasm/bbc -d /mnt/cephfs/scratch/saodonnell/projects/flavus/annotation/2.braker3/GCA002214955_nornaseq_compleasm -g /mnt/cephfs/scratch/saodonnell/projects/flavus/annotation/2.braker3/GCA002214955_nornaseq_compleasm/genome.fa -t 32 -p eurotiales_odb10 -y /home/saodonnell/miniconda3/envs/braker3/bin/tsebra.py -f /home/saodonnell/miniconda3/envs/braker3/bin/getAnnoFastaFromJoingenes.py 1> /mnt/cephfs/scratch/saodonnell/projects/flavus/annotation/2.braker3/GCA002214955_nornaseq_compleasm/best_by_compleasm.log 2> /mnt/cephfs/scratch/saodonnell/projects/flavus/annotation/2.braker3/GCA002214955_nornaseq_compleasm/errors/best_by_compleasm.err

I checked the best_by_compleasm.log and it just had the below ERROR: compleasm.py binary not found in PATH

compleasm.py is definitely in the path given, as it was used in a previous step so I am unsure of where braker is now looking for this script and how to correct for it My guess is that this last step begins using the tsebra path for the best_by_compleasm.py script which is in my conda environment and because of this it looks for compleasm.py in the same place. I downloaded compleasm from the github because braker was unable to find compleasm.py in my conda environment (although compleasm is installed, it looks for the python script which is hidden in pkgs). Hope that makes sense

Thanks for your help

KatharinaHoff commented 4 months ago

Could you use the singularity container?