Error - GeneMark-ETP/proteins.fa/model/output.mod file is missing

[rlibouba]

Hello,

I get an error when I want to run a braker3 analysis on a masked genome using an RNAseq alignment and protein sequences. This is what I have in the GeneMark-ETP.stderr file:

FASTA index file /home/jovyan/braker/GeneMark-ETP/data/genome.softmasked.fasta.fai created.
Use of uninitialized value $ph1 in addition (+) at /opt/ETP/bin/gmes/parse_set.pl line 205.
Use of uninitialized value $ph0 in addition (+) at /opt/ETP/bin/gmes/parse_set.pl line 205.
Use of uninitialized value $ph2 in addition (+) at /opt/ETP/bin/gmes/parse_set.pl line 205.
Use of uninitialized value $ph0 in division (/) at /opt/ETP/bin/gmes/parse_set.pl line 208.
Illegal division by zero at /opt/ETP/bin/gmes/parse_set.pl line 208.
Illegal division by zero at /opt/ETP/bin/train_super.pl line 184.
error, file/folder not found: /home/jovyan/braker/GeneMark-ETP/proteins.fa/model/output.mod

I restarted braker3 by putting only the RNAseq alignment file with the masked genome. I got a result. I did the same thing again but with the protein sequences and I got a result. But when I put both files (RNAseq and protein sequences), it doesn't work.

It seems that the GeneMark-ETP/proteins.fa/model/output.mod file is missing.

Do you have any idea why adding just one file (RNAseq or proteins) gives me an output? But when I add both, the analysis fails?

I used the latest version of braker3 for my analyses.

Thank you! Have a nice day!
Romane

[rlibouba]

I forgot to give more information.
I used the last singularity image.

For the dataset, I used:

• https://zenodo.org/records/14289529/files/genome_masked.fasta?download=1
• https://zenodo.org/records/14289529/files/rnaseq.bam?download=1
• https://zenodo.org/records/14289529/files/SwissProt.fasta?download=1

And for the command line: braker.pl --genome genome_masked.fasta --BAM rnaseq.bam --prot_seq SwissProt.fasta