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Gaius-Augustus / TSEBRA

TSEBRA: Transcript Selector for BRAKER
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braker2 - proteins #12

Closed minhasbushra closed 2 years ago

minhasbushra commented 2 years ago

When using the command mentioned

"braker.pl --genome=genome.fasta.masked --prot_seq=proteins.fa \ --softmasking --species=species_name --epmode --prg=ph \ --workingdir=braker2_out"

i am getting this error

ERROR: in file /projects/***/local/opt/braker-2.1.6/scripts/braker.pl at line 3740

--prg option is not compatible with --epmode/--etpmode. In these modes, BRAKER uses ProtHint to map and align proteins.

is --prg not supposed to go with --epmode?

LarsGab commented 2 years ago

Hi,

thanks for pointing this out. The --prg option was changed some time ago so that ProtHint is the default mode and the option tag is only specified if another program is used instead. The correct command is: "braker.pl --genome=genome.fasta.masked --prot_seq=proteins.fa --softmasking --species=species_name --epmode --workingdir=braker2_out"

Best, Lars

LarsGab commented 2 years ago

I close this issue since all questions have been answered or it has been inactive for a long time.