BRAKER Annotation

Question

[Bioblazer]

perl braker.pl --genome=ATCC26.fa --bam=accepted_hits.bam use --AUGUSTUS_CONFIG_PATH=/home/abc1/Documents/augustus-3.1/config --GENEMARK_PATH=/home/abc1/Documents/gm_et_linux_64/gmes_petap/gmes_petap.pl --BAMTOOLS_PATH=/home/abc1/Desktop/augustus-3.2.2/bamtools/bin

I have used braker for annotation. I got error when I ran above command

NEXT STEP: check files and settings

Error: found neither /../scripts/gff2gbSmallDNA.pl nor /home/abc1/Desktop/BRAKER1/gff2gbSmallDNA.pl!

Please Check the environment variable AUGUSTUS_CONFIG_PATH or install AUGUSTUS again!

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but there is gff2gbSmallDNA.pl in scripts folder.

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Someone if already have come across this type of error Please some give value suggestion.

Answer 1

[Rohit]

Augustus-path needs to be specified prior to running braker, did you specify it through $AUGUSTUS_CONFIG_PATH

This is present in the readme manual.