Docker Braker3 with example data: ERROR in file /opt/BRAKER/scripts/braker.pl at line 1238

[yzliu01]

Hi, I wonder why I got such an error when just testing the example data. What on earth these are: ERROR in file /opt/BRAKER/scripts/braker.pl at line 1238 Failed to create direcotry /faststorage/project/eDNA/yzliu/DK_proj/data/bee_proj_data/gene_annotation/braker_results_example_data/GeneMark-ES!

Where is the opt folder? Appreciate very much your help with this issue.

My commands

singularity exec braker3.sif braker.pl --genome=$example_data/genome.fa --prot_seq=$example_data/proteins.fa --workingdir=$braker_output_dir --threads 2 --PROTHINT_PATH=/home/yzliu/eDNA/faststorage/yzliu/DK_proj/sofwtare/gmetp_linux_64/bin/gmes/ProtHint/bin --GENEMARK_PATH=/home/yzliu/eDNA/faststorage/yzliu/DK_proj/sofwtare/gmetp_linux_64/bin/gmes

Terminal output err

# Fri Apr 19 10:32:20 2024: Log information is stored in file /faststorage/project/eDNA/yzliu/DK_proj/data/bee_proj_data/gene_annotation/braker_results_example_data/braker.log
ERROR in file /opt/BRAKER/scripts/braker.pl at line 1238
Failed to create direcotry /faststorage/project/eDNA/yzliu/DK_proj/data/bee_proj_data/gene_annotation/braker_results_example_data/GeneMark-ES!

I could not detect the possible causes in the braker.log file below.

BRAKER.log

#**********************************************************************************
#                               BRAKER CONFIGURATION                               
#**********************************************************************************
# BRAKER CALL: /opt/BRAKER/scripts/braker.pl --genome=/home/yzliu/eDNA/faststorage/yzliu/DK_proj/population_genomics/gene_annotation/example_data/genome.fa --prot_seq=/home/yzliu/eDNA/faststorage/yzliu/DK_proj/population_genomics/gene_annotation/example_data/proteins.fa --workingdir=/home/yzliu/eDNA/faststorage/yzliu/DK_proj/data/bee_proj_data/gene_annotation/braker_results_example_data --threads 2 --PROTHINT_PATH=/home/yzliu/eDNA/faststorage/yzliu/DK_proj/sofwtare/gmetp_linux_64/bin/gmes/ProtHint/bin --GENEMARK_PATH=/home/yzliu/eDNA/faststorage/yzliu/DK_proj/sofwtare/gmetp_linux_64/bin/gmes
# Fri Apr 19 10:32:20 2024: braker.pl version 3.0.8
# Fri Apr 19 10:32:20 2024: Only Protein input detected, BRAKER will be executed in EP mode (BRAKER2).
# Fri Apr 19 10:32:20 2024: Configuring of BRAKER for using external tools...
# Fri Apr 19 10:32:20 2024: Trying to set $AUGUSTUS_CONFIG_PATH...
# Fri Apr 19 10:32:20 2024: Found environment variable $AUGUSTUS_CONFIG_PATH.
# Fri Apr 19 10:32:20 2024: Checking /opt/Augustus/config/ as potential path for $AUGUSTUS_CONFIG_PATH.
# Fri Apr 19 10:32:20 2024: Success! Setting $AUGUSTUS_CONFIG_PATH to /opt/Augustus/config/!
# Fri Apr 19 10:32:20 2024: Trying to set $AUGUSTUS_BIN_PATH...
# Fri Apr 19 10:32:20 2024: Found environment variable $AUGUSTUS_BIN_PATH.
# Fri Apr 19 10:32:20 2024: Checking /opt/Augustus/bin/ as potential path for $AUGUSTUS_BIN_PATH.
# Fri Apr 19 10:32:20 2024: Success! Setting $AUGUSTUS_BIN_PATH to /opt/Augustus/bin/!
# Fri Apr 19 10:32:20 2024: Trying to set $AUGUSTUS_SCRIPTS_PATH...
# Fri Apr 19 10:32:20 2024: Found environment variable $AUGUSTUS_SCRIPTS_PATH.
# Fri Apr 19 10:32:20 2024: Checking /opt/Augustus/scripts/ as potential path for $AUGUSTUS_SCRIPTS_PATH.
# Fri Apr 19 10:32:20 2024: Success! Setting $AUGUSTUS_SCRIPTS_PATH to /opt/Augustus/scripts/!
# Fri Apr 19 10:32:20 2024: Trying to set $PYTHON3_PATH...
# Fri Apr 19 10:32:20 2024: Did not find environment variable $PYTHON3_PATH.
# Fri Apr 19 10:32:20 2024: Trying to guess PYTHON3_PATH from location of python3 executable that is available in your $PATH
# Fri Apr 19 10:32:20 2024: Checking /opt/conda/bin as potential path for $PYTHON3_PATH.
# Fri Apr 19 10:32:20 2024: Success! Setting $PYTHON3_PATH to /opt/conda/bin!
# Fri Apr 19 10:32:20 2024: Trying to set $GENEMARK_PATH...
# Fri Apr 19 10:32:20 2024: Found command line argument $GENEMARK_PATH.
# Fri Apr 19 10:32:20 2024: Checking /home/yzliu/eDNA/faststorage/yzliu/DK_proj/sofwtare/gmetp_linux_64/bin/gmes as potential path for $GENEMARK_PATH.
# Fri Apr 19 10:32:20 2024: Success! Setting $GENEMARK_PATH to /home/yzliu/eDNA/faststorage/yzliu/DK_proj/sofwtare/gmetp_linux_64/bin/gmes!
# Fri Apr 19 10:32:20 2024: Trying to set $DIAMOND_PATH...
# Fri Apr 19 10:32:20 2024: Did not find environment variable $DIAMOND_PATH.
# Fri Apr 19 10:32:20 2024: Trying to guess DIAMOND_PATH from location of diamond executable that is available in your $PATH
# Fri Apr 19 10:32:20 2024: Checking /opt/ETP/tools as potential path for $DIAMOND_PATH.
# Fri Apr 19 10:32:20 2024: Success! Setting $DIAMOND_PATH to /opt/ETP/tools!
# Fri Apr 19 10:32:20 2024: Trying to set $PROTHINT_PATH...
# Fri Apr 19 10:32:20 2024: Found command line argument $PROTHINT_PATH.
# Fri Apr 19 10:32:20 2024: Checking /home/yzliu/eDNA/faststorage/yzliu/DK_proj/sofwtare/gmetp_linux_64/bin/gmes/ProtHint/bin as potential path for $PROTHINT_PATH.
# Fri Apr 19 10:32:20 2024: Success! Setting $PROTHINT_PATH to /home/yzliu/eDNA/faststorage/yzliu/DK_proj/sofwtare/gmetp_linux_64/bin/gmes/ProtHint/bin!
# Fri Apr 19 10:32:20 2024: Trying to set $TSEBRA_PATH...
# Fri Apr 19 10:32:20 2024: Did not find environment variable $TSEBRA_PATH.
# Fri Apr 19 10:32:20 2024: Trying to guess TSEBRA_PATH from location of tsebra.py executable that is available in your $PATH
# Fri Apr 19 10:32:20 2024: Checking /opt/TSEBRA/bin as potential path for $TSEBRA_PATH.
# Fri Apr 19 10:32:20 2024: Success! Setting $TSEBRA_PATH to /opt/TSEBRA/bin!
# Fri Apr 19 10:32:20 2024: Trying to set $CDBTOOLS_PATH...
# Fri Apr 19 10:32:20 2024: Did not find environment variable $CDBTOOLS_PATH.
# Fri Apr 19 10:32:20 2024: Trying to guess CDBTOOLS_PATH from location of cdbfasta executable that is available in your $PATH
# Fri Apr 19 10:32:20 2024: Checking /opt/cdbfasta as potential path for $CDBTOOLS_PATH.
# Fri Apr 19 10:32:20 2024: Success! Setting $CDBTOOLS_PATH to /opt/cdbfasta!
# Fri Apr 19 10:32:20 2024: BRAKER will execute GeneMark-EP for training GeneMark and generating a training gene set for AUGUSTUS, using protein information as sole extrinsic evidence source.
#*********
# IMPORTANT INFORMATION: no species for identifying the AUGUSTUS  parameter set that will arise from this BRAKER run was set. BRAKER will create an AUGUSTUS parameter set with name Sp_1. This parameter set can be used for future BRAKER/AUGUSTUS prediction runs for the same species. It is usually not necessary to retrain AUGUSTUS with novel extrinsic data if a high quality parameter set already exists.
#*********
#**********************************************************************************
#                               CREATING DIRECTORY STRUCTURE                       
#**********************************************************************************
# Fri Apr 19 10:32:20 2024: creating file that contains citations for this BRAKER run at /faststorage/project/eDNA/yzliu/DK_proj/data/bee_proj_data/gene_annotation/braker_results_example_data/what-to-cite.txt...

[KatharinaHoff]

The /opt folder sits in the container, but the /opt folder is not your problem. The problem are lacking writing permissions or a bandwidth/harddrive accessibility issue at /faststorage/project/eDNA/yzliu/DK_proj/data/bee_proj_data/gene_annotation/braker_results_example_data/GeneMark-ES

[yzliu01]

Thanks. I checked the property of this folder, which shows it can be written. How can it be addressed actually?

ll
total 8
-rw-rw-r-- 1 yzliu eDNA 5768 Apr 19 10:32 braker.log
drwxrwsr-x 2 yzliu eDNA    4 Apr 19 10:25 errors
-rw-rw-r-- 1 yzliu eDNA   93 Apr 19 10:25 gc_content.out
drwxrwsr-x 2 yzliu eDNA    0 Apr 19 10:25 GeneMark-EP
drwxrwsr-x 2 yzliu eDNA    0 Apr 19 10:25 GeneMark-ES
drwxrwsr-x 2 yzliu eDNA    0 Apr 19 10:25 species
-rw-rw-r-- 1 yzliu eDNA  741 Apr 19 10:32 what-to-cite.txt