KatharinaHoff
commented
2 months ago It could be a version problem. What compleasm version are you using? Could you switch to using our singularity image?
AAHRU-Ablab @.***> schrieb am Di. 23. Apr. 2024 um 17:00:
BRAKER2 successfully completes when I run the instance without BUSCO lineage (I am using a genome assembly and OrthoDB proteins). I am interested in this additional BUSCO analyses; however, when I run with BUSCO lineage I get an error at the compleasm step. The files are executable and in my path but stalls. Any help would be greatly appreciated. I have recreated the error at "Starting BRAKER on the basis of previously existing BRAKER runs" step with the code:
perl /home/jason/Desktop/software/BRAKER-3.0.8/scripts/braker.pl --threads=78 --GENEMARK_PATH=/home/jason/Desktop/software/gmes_linux_64_4 --DIAMOND_PATH=/home/jason/Desktop/software/diamond_blast --PROTHINT_PATH=/home/jason/Desktop/software/gmes_linux_64_4/ProtHint/bin --TSEBRA_PATH=/home/jason/Desktop/software/TSEBRA/bin --AUGUSTUS_BIN_PATH=/home/jason/Desktop/software/Augustus/bin --AUGUSTUS_SCRIPTS_PATH=/home/jason/Desktop/software/Augustus/scripts --AUGUSTUS_CONFIG_PATH=/home/jason/Desktop/software/Augustus/config --COMPLEASM_PATH=/home/jason/Desktop/software/compleasm_kit --useexisting --skipAllTraining --genome=masked_sequences.fasta --busco_lineage=actinopterygii_odb10 error returned in stdout:
ERROR in file /home/jason/Desktop/software/BRAKER-3.0.8/scripts/braker.pl at line 4551 Failed to execute: /usr/bin/python3 /home/jason/Desktop/software/Augustus/scripts/compleasm_to_hints.py -p /home/jason/Desktop/software/compleasm_kit/compleasm.py -g /home/jason/Desktop/test/braker/braker/genome.fa -d actinopterygii_odb10 -t 78 -o /home/jason/Desktop/test/braker/braker/compleasm_hints.gff 1> /home/jason/Desktop/test/braker/braker/errors/compleasm_to_hints.stderr 2>&1! error returned in the compleasm_to_hints.stderr:
Trying to execute the following command: /home/jason/Desktop/software/compleasm_kit/compleasm.py run -l actinopterygii_odb10 -a /home/jason/Desktop/test/braker/braker/genome.fa -t 78 -o compleasm_genome_out Suceeded in executing command. Error in file /home/jason/Desktop/software/Augustus/scripts/compleasm_to_hints.py at line 49: Return code of subprocess was 1['/home/jason/Desktop/software/compleasm_kit/compleasm.py', 'run', '-l', 'actinopterygii_odb10', '-a', '/home/jason/Desktop/test/braker/braker/genome.fa', '-t', '78', '-o', 'compleasm_genome_out']
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AAHRU-Ablab
BRAKER2 successfully completes when I run the instance without BUSCO lineage (I am using a genome assembly and OrthoDB proteins). I am interested in this additional BUSCO analyses; however, when I run with BUSCO lineage I get an error at the compleasm step. The files are executable and in my path but stalls. Any help would be greatly appreciated. I have recreated the error at "Starting BRAKER on the basis of previously existing BRAKER runs" step with the code:
perl /home/jason/Desktop/software/BRAKER-3.0.8/scripts/braker.pl --threads=78 --GENEMARK_PATH=/home/jason/Desktop/software/gmes_linux_64_4 --DIAMOND_PATH=/home/jason/Desktop/software/diamond_blast --PROTHINT_PATH=/home/jason/Desktop/software/gmes_linux_64_4/ProtHint/bin --TSEBRA_PATH=/home/jason/Desktop/software/TSEBRA/bin --AUGUSTUS_BIN_PATH=/home/jason/Desktop/software/Augustus/bin --AUGUSTUS_SCRIPTS_PATH=/home/jason/Desktop/software/Augustus/scripts --AUGUSTUS_CONFIG_PATH=/home/jason/Desktop/software/Augustus/config --COMPLEASM_PATH=/home/jason/Desktop/software/compleasm_kit --useexisting --skipAllTraining --genome=masked_sequences.fasta --busco_lineage=actinopterygii_odb10error returned in stdout:
ERROR in file /home/jason/Desktop/software/BRAKER-3.0.8/scripts/braker.pl at line 4551 Failed to execute: /usr/bin/python3 /home/jason/Desktop/software/Augustus/scripts/compleasm_to_hints.py -p /home/jason/Desktop/software/compleasm_kit/compleasm.py -g /home/jason/Desktop/test/braker/braker/genome.fa -d actinopterygii_odb10 -t 78 -o /home/jason/Desktop/test/braker/braker/compleasm_hints.gff 1> /home/jason/Desktop/test/braker/braker/errors/compleasm_to_hints.stderr 2>&1!
error returned in the compleasm_to_hints.stderr:
Trying to execute the following command: /home/jason/Desktop/software/compleasm_kit/compleasm.py run -l actinopterygii_odb10 -a /home/jason/Desktop/test/braker/braker/genome.fa -t 78 -o compleasm_genome_out Suceeded in executing command. Error in file /home/jason/Desktop/software/Augustus/scripts/compleasm_to_hints.py at line 49: Return code of subprocess was 1['/home/jason/Desktop/software/compleasm_kit/compleasm.py', 'run', '-l', 'actinopterygii_odb10', '-a', '/home/jason/Desktop/test/braker/braker/genome.fa', '-t', '78', '-o', 'compleasm_genome_out']