Question about GBFF output reporting all 0 annotations (vs. txt and gff3 file

[patriciatran]

Hello,

I am running bakta v.1.10.2 this way:

$1 = samplename
bakta --db /path/hidden/db \
        $1_assembly.fasta \
        --output bakta_$1 \
        --threads $2

It outputs all the files, but I have a question about the gbff output file.

Could you explain why there is a discrepancy in the reported annotations being 0 in the gbff file vs the .txt and the gff3 file?
I am comparing this with a bakta output from another analysis ran in the past using a previous version:

Current output:
The gbff file looks like this:

LOCUS       contig_1             2902592 bp    DNA     linear   UNK 13-DEC-2024
DEFINITION  contig_1, whole genome shotgun sequence.
ACCESSION   contig_1
VERSION     contig_1
KEYWORDS    .
SOURCE      None
  ORGANISM  .
            .
COMMENT     Annotated with Bakta
            Software: v1.10.2
            Database: v5.1, full
            DOI: 10.1099/mgen.0.000685
            URL: github.com/oschwengers/bakta
            
            ##Genome Annotation Summary:##
            Annotation Date                :: 12/13/2024, 15:06:35
            CDSs                           ::     0
            tRNAs                          ::     0
            tmRNAs                         ::     0
            rRNAs                          ::     0
            ncRNAs                         ::     0
            regulatory ncRNAs              ::     0
            CRISPR Arrays                  ::     0
            oriCs/oriVs                    ::     0
            oriTs                          ::     0
            gaps                           ::     0
            pseudogenes                    ::     0

However, the sample.txt output looks like this:

Sequence(s):
Length: 2902592
Count: 1
GC: 32.8
N50: 2902592
N90: 2902592
N ratio: 0.0
coding density: 85.5

Annotation:
tRNAs: 60
tmRNAs: 1
rRNAs: 16
ncRNAs: 90
ncRNA regions: 25
CRISPR arrays: 0
CDSs: 2704
pseudogenes: 4
hypotheticals: 39
sORFs: 16
gaps: 0
oriCs: 4
oriVs: 0
oriTs: 1

Bakta:
Software: v1.10.2
Database: v5.1, full
DOI: 10.1099/mgen.0.000685
URL: github.com/oschwengers/bakta

Comparing with output from a previous run with another bakta version.
Note: Ignore the actual numbers, this is not ran on the same genome. Just pasting an output here for example purposes.

LOCUS       contig_1             2921883 bp    DNA     linear   UNK 17-OCT-2024
DEFINITION  contig_1, whole genome shotgun sequence.
ACCESSION   contig_1
VERSION     contig_1
KEYWORDS    .
SOURCE      None
  ORGANISM  .
            .
COMMENT     Annotated with Bakta
            Software: v1.6.1
            Database: v4.0
            DOI: 10.1099/mgen.0.000685
            URL: github.com/oschwengers/bakta
            
            ##Genome Annotation Summary:##
            Annotation Date                :: 10/17/2024, 22:36:47
            Annotation Pipeline            :: Bakta
            Annotation Software version    ::  v1.6.1
            Annotation Database version    ::  v4.0
            CDSs                           :: 2,733
            tRNAs                          ::    61
            tmRNAs                         ::     1
            rRNAs                          ::    19
            ncRNAs                         ::    88
            regulatory ncRNAs              ::    25
            CRISPR Arrays                  ::     0
            oriCs/oriVs                    ::     2
            oriTs                          ::     0
            gaps                           ::     0
            pseudogenes                    ::     5

Sequence(s):
Length: 3011165
Count: 3
GC: 32.7
N50: 2921883
N ratio: 0.0
coding density: 85.3

Annotation:
tRNAs: 61
tmRNAs: 1
rRNAs: 19
ncRNAs: 92
ncRNA regions: 25
CRISPR arrays: 0
CDSs: 2825
pseudogenes: 7
hypotheticals: 171
signal peptides: 0
sORFs: 11
gaps: 0
oriCs: 3
oriVs: 0
oriTs: 1

Bakta:
Software: v1.6.1
Database: v4.0
DOI: 10.1099/mgen.0.000685
URL: github.com/oschwengers/bakta

Thank you in advance for your explanation.

Best,
Patricia

[manalcric]

Hello,
I am running bakta 1.10.2 and I have the same problem, but I don't know why. I think that the INSDC export to EMBL and GBFF is not working, since the rest of annotations files are correct.
I have renamed the contigs with really short names but this is not the problem.
Could be related with the Numpy warning?? UserWarning: The value of the smallest subnormal for <class 'numpy.float32'> type is zero

Thanks in advance,
BW,
Manuel

[Dx-wmc]

I have encountered the same problem.

[simone-pignotti]

I am also running into this bug!

EDIT: downgrading to 1.10.1 works

[oschwengers]

Hi, yes, this is obviously a severe bug that I could reproduce. I'm working on it.

[oschwengers]

OK, so this is now fixed by https://github.com/oschwengers/bakta/releases/tag/v1.10.3.

@manalcric In fact, this was just a critical typo and is not related to the numpy warnings.