error, file not found: option --f1 complete.gtf

[methylome]

BRAKER3 worked for several genomes, but did not for a genome. As shown below, the error occurred as described in the title.

singularity exec -B /ddn:/ddn /app/centos8/braker/braker-20230308/braker3.sif braker.pl --useexisting --threads=24 --alternatives-from-evidence=true --AUGUSTUS_ab_initio --gff3 --species=Cyanoptyche_gloeocystis --workingdir=. --genome=/ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/repeat/assembly.repeatsoftmasked.fa --bam=/ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/tophat/accepted_hits.bam --prot_seq=/ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/proteins.faa --softmasking

braker.log
#**********************************************************************************
#                               BRAKER CONFIGURATION                               
#**********************************************************************************
# BRAKER CALL: /opt/BRAKER/scripts/braker.pl --useexisting --threads=24 --alternatives-from-evidence=true --AUGUSTUS_ab_initio --gff3 --species=Cyanoptyche_gloeocystis --workingdir=. --genome=/ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/repeat/assembly.repeatsoftmasked.fa --bam=/ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/tophat/accepted_hits.bam --prot_seq=/ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/proteins.faa --softmasking
# Fri Mar 24 11:20:39 2023: braker.pl version 3.0.2
...
#**********************************************************************************
#                              RUNNING GENEMARK-EX                                 
#**********************************************************************************
# Fri Mar 24 11:20:52 2023: Preparing genemark_evidence file hints from manual hints...
# Fri Mar 24 11:20:52 2023: Running GeneMark-ETP
# Fri Mar 24 11:20:52 2023: changing into GeneMark-ETP directory /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/GeneMark-ETP
cd /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/GeneMark-ETP
# Fri Mar 24 11:20:52 2023: sorting RNA-Seq BAM files
samtools sort /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/tophat/accepted_hits.bam -o /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/GeneMark-ETP/etp_data/accepted_hits.bam 1> /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/errors/samtools.sort.accepted_hits.stdout 2> /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/errors/samtools.sort.accepted_hits.stderr
# Fri Mar 24 11:21:34 2023: Running gmetp.pl
/usr/bin/perl /opt/ETP/bin/gmetp.pl --cfg /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/GeneMark-ETP/etp_config.yaml --workdir /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/GeneMark-ETP --bam /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/GeneMark-ETP/etp_data/ --cores 24 --softmask  1>/ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/errors/GeneMark-ETP.stdout 2>/ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/errors/GeneMark-ETP.stderr

GeneMark-ETP.stderr
FASTA index file /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/GeneMark-ETP/data/genome.softmasked.fasta.fai created.
error, file not found: option --f1 complete.gtf
error on open file complete.id: No such file or directory
mv: cannot stat 'complete_uniq.gtf': No such file or directory
error on open file /ddn/datacenter/genomes/Cyanoptyche_gloeocystis/annotation/dgp/braker/GeneMark-ETP/rnaseq/hints/proteins.fa/complete.gtf: No such file or directory
error on create_regions.pl at /opt/ETP/bin/gmetp.pl line 2162.

[KatharinaHoff]

@MarioStanke could be fixed either in ETP, or caught in BRAKER @LarsGab

[methylome]

V 3.0.6 ran into the same error.