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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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Very low number of genes predicted #792

Closed camille-cornet closed 2 months ago

camille-cornet commented 3 months ago

Dear Katharina,

I am running BRAKER2 on high quality genomes assemblies of closely related species, using the Arthropoda orthoDB 11. For all species except one, everything runs and I get the output as expected. For one species, the pipeline runs but I get approximately 5x less genes predicted. The genes I get are spread on all chromosomes.

The only difference I can notice in the log and errors files is this: In braker.log, at the Running Genemark-EX section:

# WARNING:
# The hints file(s) for GeneMark-EX contain less than 150 introns with multiplicity >= 4! (In total, 16466 unique introns are contained. 47 have a multiplicity >= 4.)
# Possibly, you are trying to run braker.pl on data that does not provide sufficient multiplicity information. This will e.g. happen if you try to use introns generated from assembled RNA-Seq transcripts; or if you try to run braker.pl in epmode with mappings from proteins without sufficient hits per locus. Or if you use the example data set.
# A low number of intron hints with sufficient multiplicity may result in a crash of GeneMark-EX (it should not crash with the example data set).

Also, in GeneMark-EP.stderr:

Use of uninitialized value $ph1 in addition (+) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 102.
Use of uninitialized value $ph2 in addition (+) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 102.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 106.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 107.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 108.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 109.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 109.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 110.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 110.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 111.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 112.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 112.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 113.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 113.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 116.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 117.
Use of uninitialized value $ph1 in addition (+) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 102.
Use of uninitialized value $ph2 in addition (+) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 102.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 106.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 107.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 108.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 109.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 109.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 110.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 110.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 111.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 112.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 112.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 113.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 113.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 116.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 117.
Use of uninitialized value $ph1 in addition (+) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 102.
Use of uninitialized value $ph2 in addition (+) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 102.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 106.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 107.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 108.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 109.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 109.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 110.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 110.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 111.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 112.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 112.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 113.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 113.
Use of uninitialized value $ph1 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 116.
Use of uninitialized value $ph2 in division (/) at /lustre/scratch122/tol/teams/blaxter/users/cc51/software/GeneMark-ETP/bin/gmes/parse_ET.pl line 117.

However, I do not get the "Illegal division by zero" that some other issues are reporting. Also, I have tried with and without compleasm and am getting the same output.

Let me know if you need any other information.

Thanks in advance for your help, and thank you for a great tool!

Camille

KatharinaHoff commented 3 months ago

I am afraid I cannot really help you with that. It is an GeneMark issue. Maybe Alex will at some point in time respond.

camille-cornet commented 2 months ago

Still not sure what has caused this problem with only one of my species, but trying again with a new repeat library before soft-masking and a new install of BRAKER has eventually solved it. Thanks!