GeneMark ETP crashes if there are no mapped reads in the bamfile

[TomHarrop]

Obviously this is caused by bad input data, but maybe braker3 could check the bamfile and stop with an error message, or run GeneMark-EP instead?

ERROR in file /opt/BRAKER/scripts/braker.pl at line 5465
Failed to execute: /usr/bin/perl /opt/ETP/bin/gmetp.pl

In GeneMark-ETP.stderr:

FASTA index file /path/to/outdir/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.
cat: GT.mat: No such file or directory
cat: AG.mat: No such file or directory
cat: GT.mat: No such file or directory
cat: AG.mat: No such file or directory
cat: GT.mat: No such file or directory
cat: AG.mat: No such file or directory
cat: GC.mat: No such file or directory
cat: GC.mat: No such file or directory
cat: GC.mat: No such file or directory
Illegal division by zero at /opt/ETP/bin/train_super.pl line 184.
error, file/folder not found: /path/to/outdir/GeneMark-ETP/proteins.fa/model/output.mod

Thanks!

[zhouxp9709]

The .bam file generated using STAR produced the same error, but when I used the .bam file generated using Hisat2, the error disappeared and I got the final result from BRAKER3.

[TomHarrop]

Thanks for letting me know @zhouxp9709

I've also had this problem with bamfiles that contain mapped reasds. I think it's only happening with Genemark-ETP, because the bamfile by itself works fine with GeneMark-ET, and GeneMark-EP works (without the bamfile).