search

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
Other
364 stars 81 forks source link

BRAKER3 - source RM must be specified in the extrinsic config file #695

Closed JiyangChang closed 9 months ago

JiyangChang commented 1 year ago

Hi,

Thanks for the great tool! I've tried to switch from BRAKER2 to BRAKER3, however I met some issues I never met with BRAKER2 (with "--softmasking").

ERROR in file /software/shared/apps/x86_64/braker/3.0.3/scripts/braker.pl at line 6708
Failed to execute: /software/shared/apps/x86_64/augustus/3.5.0/bin/augustus --species=Gr4362_draft_braker3 --AUGUSTUS_CONFIG_PATH=/group/annot/usr/augustus/config /scratch/Analysis/Test/Braker3/train.gb.test 1>/scratch/Analysis/Test/Braker3/firsttest.stdout 2>/scratch/Analysis/Test/Braker3/errors/firsttest.stderr!

and the detail message in the stderr file is

When the softmasking option is turned on, the source RM must be specified in the extrinsic config file.

Could not read in file with the configuration of hints: /group/annot/usr/augustus/config/extrinsic/extrinsic.cfg

/software/shared/apps/x86_64/augustus/3.5.0/bin/augustus: ERROR
    When the softmasking option is turned on, the source RM must be specified in the extrinsic config file.

I don't know whether I should use the --extrinsicCfgFiles parameter as I don't use it with BRAKER2, could you kindly give me some suggestions about this issue?

BRs, Jiyang

KatharinaHoff commented 1 year ago

Somewhere in between versions, it changed how AUGUSTUS handles soft masked repeats. In the BRAKER container, we use augustus 3.4.0 from debian. Maybe using that exact version will solve your problem.