GeneMark error on the names in the genome file

[pelotbdr]

Hello,

I have an error message when using BRAKER3 through Singularity that I do not understand. I'm using the standard command lines from the IsoSeq tutorial:

T=48 # adapt to your number of threads
minimap2 -t${T} -ax splice:hq -uf genome.fa isoseq.fa > isoseq.sam     
samtools view -bS --threads ${T} isoseq.sam -o isoseq.bam

singularity exec -B ${PWD}:${PWD} braker3_lr.sif braker.pl --genome=genome.fa --prot_seq=protein_db.fa –-bam=isoseq.bam --threads=${T} 

However I get the following error message :

Failed to execute: /usr/bin/perl /opt/ETP/bin/gmetp.pl --cfg /mnt/d/IsoSeq/braker/GeneMark-ETP/etp_config.yaml --workdir /mnt/d/IsoSeq/braker/GeneMark-ETP --bam /mnt/d/IsoSeq/braker/GeneMark-ETP/etp_data/ --cores 48 --softmask  1>/mnt/d/IsoSeq/braker/errors/GeneMark-ETP.stdout 2>/mnt/d/IsoSeq/braker/errors/GeneMark-ETP.stderr
The most common problem is that GeneMark-ETP didn't receive enough evidence from the input data, in this case, see errors/GeneMark-ETP.stderr!

And at the end of the GeneMark-ETP.stderr:

WARNING: 'NW_026844023.1' does not match any sequence in the fasta file. Maybe the two files do not belong together.
WARNING: 'NW_026844077.1' does not match any sequence in the fasta file. Maybe the two files do not belong together.
WARNING: 'NW_026844017.1' does not match any sequence in the fasta file. Maybe the two files do not belong together.
error
error, file/folder not found: transcripts_merged.fasta.gff

The genome used for the BRAKER script is the same used for the minimap2 alignment so I don't understand how it couldn't match. I saw that this issue was mentioned in https://github.com/Gaius-Augustus/BRAKER/issues/716, the author apparently fixed it by renaming and changing the headers in the genome file but this did not fix anything for me.

Does anyone know how else to fix this issue ?

Thank you