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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
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ERROR in file bin/braker.pl at line 7852 #687

Closed mloberme closed 11 months ago

mloberme commented 1 year ago

Hey, I was running Braker3 and got an error at the Augustus gene calling step.

ERROR in file /DATARAID/mlobermeier/data/.snakemake/conda/37f04191d5c028db1d074ffa2a16db0c/bin/braker.pl at line 7852 Failed to execute: /DATARAID/mlobermeier/data/.snakemake/conda/37f04191d5c028db1d074ffa2a16db0c/bin//augustus --species=Verticilliumstrains --AUGUSTUS_CONFIG_PATH=/DATARAID/mlobermeier/data/.snakemake/conda/37f04191d5c028db1d074ffa2a16db0c/config/ --extrinsicCfgFile=/DATARAID/mlobermeier/data/.snakemake/conda/37f04191d5c028db1d074ffa2a16db0c/bin/cfg/etp.cfg --alternatives-from-evidence=true --hintsfile=/DATA_RAID/mlobermeier/data/Pacbio/Verticillium_dahliae_85S_PacBio/braker/hintsfile.gff --UTR=off --exonnames=on --codingseq=on --allow_hinted_splicesites=gcag,atac --softmasking=1 /DATA_RAID/mlobermeier/data/Pacbio/Verticillium_dahliae_85S_PacBio/braker/genome.fa 1>/DATA_RAID/mlobermeier/data/Pacbio/Verticillium_dahliae_85S_PacBio/braker/augustus.hints.gff 2>/DATA_RAID/mlobermeier/data/Pacbio/Verticillium_dahliae_85S_PacBio/braker/errors/augustus.hints.stderr!

The Augustus hints.gff contains this:

reading in the file /DATA_RAID/mlobermeier/data/Pacbio/Verticillium_dahliae_85S_PacBio/braker/hintsfile.gff ...

Have extrinsic information about 53 sequences (in the specified range).

Initializing the parameters using config directory /DATARAID/mlobermeier/data/.snakemake/conda/37f04191d5c028db1d074ffa2a16db0c/config/ ...

Verticilliumstrains version. Using default transition matrix.

I successfully run Braker3 on other genomes, assembled with the same pipeline, but am stuck with this.

Would love some help.

LarsGab commented 1 year ago

Hi,

what version of BRAKER3 are you running? What is the content of errors/augustus.hints.stderr?

Best, Lars

mloberme commented 1 year ago

I am running Braker3 3.0.3. /DATARAID/mlobermeier/data/.snakemake/conda/37f04191d5c028db1d074ffa2a16db0c/bin//augustus: ERROR ExonModel: Couldn't open file /DATARAID/mlobermeier/data/.snakemake/conda/37f04191d5c028db1d074ffa2a16db0c/config/species/Verticilliumstrains/Verticilliumstrains_exon_probs.pbl

KatharinaHoff commented 1 year ago

It looks like BRAKER for some reason cannot access the species parameters folder. This can either be a permanent problem (you should be able to see it from the file permission flags), or it was a temporary problem (e.g. if a shared file system had an i/o overload at a certain point in time).

wuyh0328 commented 3 months ago

I also encountered the same problem. Have you solved it？