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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The most common problem is an expired or not present file ~/.gm_key! #839
Previously, I executed the script without any problems. But now is error.
And here is the error that i got
Sat Jun 15 11:38:19 2024: Log information is stored in file /home/gen/01.Analysis/2.ONT/N579-YeastWGS/Analysis/gene_prediction/braker/braker.log
*****
WARNING: Detected whitespace in fasta header of file /home/gen/01.Analysis/2.ONT/N579-YeastWGS/Analysis/reference/protein_brakerdb.fasta. This may later on cause problems! The pipeline will create a new file without spaces or "|" characters and a genome_header.map file to look up the old and new headers. This message will be suppressed from now on!
*****
ERROR in file /home/gen/Apps/BRAKER/BRAKER/scripts/braker.pl at line 6595
Failed to execute: perl /home/gen/Apps/BRAKER/BRAKER/dependencies/GeneMark_ES/gmes_petap.pl --verbose --cores=1 --ES --gc_donor 0.001 --sequence=/home/gen/01.Analysis/2.ONT/NGS-579-YeastWGS/Analysis/gene_prediction/braker/genome.fa --soft_mask auto 1>/home/gen/01.Analysis/2.ONT/NGS-579-YeastWGS/Analysis/gene_prediction/braker/GeneMark-ES.stdout 2>/home/gen/01.Analysis/2.ONT/N579-YeastWGS/Analysis/gene_prediction/braker/errors/GeneMark-ES.stderr
The most common problem is an expired or not present file ~/.gm_key!
I already replace the gm_key to the newest one that i downloaded from http://topaz.gatech.edu/GeneMark/license_download.cgi. However still not working, producing same error in the next run with same script in above.
Hay people, could anyone help me please? I got an error to execute my Fungal assembled sequence in Braker.
This is my script to execute Braker
/home/gen/Apps/BRAKER/BRAKER/scripts/braker.pl --genome=final_sequence/final_sequence.fasta --prot_seq=reference/protein_brakerdb.fasta --softmasking --workingdir=gene_prediction/braker
Previously, I executed the script without any problems. But now is error. And here is the error that i got
Sat Jun 15 11:38:19 2024: Log information is stored in file /home/gen/01.Analysis/2.ONT/N579-YeastWGS/Analysis/gene_prediction/braker/braker.log
*****
WARNING: Detected whitespace in fasta header of file /home/gen/01.Analysis/2.ONT/N579-YeastWGS/Analysis/reference/protein_brakerdb.fasta. This may later on cause problems! The pipeline will create a new file without spaces or "|" characters and a genome_header.map file to look up the old and new headers. This message will be suppressed from now on!
*****
ERROR in file /home/gen/Apps/BRAKER/BRAKER/scripts/braker.pl at line 6595 Failed to execute: perl /home/gen/Apps/BRAKER/BRAKER/dependencies/GeneMark_ES/gmes_petap.pl --verbose --cores=1 --ES --gc_donor 0.001 --sequence=/home/gen/01.Analysis/2.ONT/NGS-579-YeastWGS/Analysis/gene_prediction/braker/genome.fa --soft_mask auto 1>/home/gen/01.Analysis/2.ONT/NGS-579-YeastWGS/Analysis/gene_prediction/braker/GeneMark-ES.stdout 2>/home/gen/01.Analysis/2.ONT/N579-YeastWGS/Analysis/gene_prediction/braker/errors/GeneMark-ES.stderr The most common problem is an expired or not present file ~/.gm_key!
I already replace the gm_key to the newest one that i downloaded from http://topaz.gatech.edu/GeneMark/license_download.cgi. However still not working, producing same error in the next run with same script in above.
Thanks a lots! Cherrs,