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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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GeneMark-ETP crashes with an empty evidence.gff file #659

Open BioHlT opened 1 year ago

BioHlT commented 1 year ago

Hello, I am running Braker using singularity. The installation was straightforward forward and all the test runs were completed successfully. When I run my sequence I encountered this error where GeneMark-ETP crashes with an empty evidence.gff file.

Command used: singularity exec /ocean/projects/tra180030p/ytekle/Software/BRAKER/braker3.sif braker.pl --genome=.Mastigamoeba_balamuthi_genome_v5.1_genomic.fasta \ --hints=./prothint_augustus.gff \

GeneMark-ETP.stdout looks as follows:

check before the run

hard_mask is in the 'auto' mode. hard_mask was set to: 1000

creat directories

commit input data

error, output file is empty data/evidence.gff error on call: /opt/ETP/bin/gmes/reformat_gff.pl --out data/evidence.gff --trace info/dna.trace --in /ocean/projects/tra180030p/ytekle/htefera/NCBI_Genome_Annotation/Mastigamoeba_balamuthi/braker/genemark_evidence.gff --quiet

I have seen the same issue posted on #290 from 2020, any suggestions on how to resolve this issue?

Thank you

KatharinaHoff commented 1 year ago

This is a GeneMark-ETP issue. Please contact Alexandre Lomsadze and Mark Borodovsky at Georgia Tech via E-mail.

DustinSokolowski commented 1 year ago

Hello @BioHlT did you end up finding a solution to this issue?

Best, Dustin

lifan18 commented 11 months ago

Hi, I have the same issue. Did any friend solve it?

Best, Fan

Artifice120 commented 5 months ago

Figured out the issue, at least for me

The headers in the hints file only had the first word showing while the input fasta file headers had all the words with spaces in the header.

fixed it with a quick awk print

awk '{ print $1 }' input.fasta > input_headerfix.fasta

to only show the first words in the header of the input fasta file as well.