EC_number, eggnog and COG terms not in annotate_results/annotations.txt

[slsy9965]

Are you using the latest release?
If you are not using the latest release of funannotate, please upgrade, if bug persists then report here.
yes, installed via conda

Describe the bug
A clear and concise description of what the bug is.
I ran funnannotate annotate with --eggnog flag, providing my own eggnog annotation (gff) file produced from running eggnogg independently from funannotate. When checking annotate_misc/annotation.eggnog.txt, it seems to be parsed fine. but the resulting annotate_results/annotations.txt file shows empty EC number, Eggnog and COG columns.

Was wondering what could've went wrong that the information weren't included in the final annotation output?

What command did you issue?
Copy/paste the command used.
for Eggnog:
emapper.py -m diamond --cpu 24 --itype genome .../funannotate/predict_results/Pseudogymonascus.scaffolds.fasta --output AKSP4_eggnog --output_dir .../eggnog

for funannotate annotate:
funannotate annotate -i .../AKSP4_predicted -o .../AKSP4_annotated --iprscan .../Pseudogymonascus.proteins.fa.xml --antismash .../AKSP4_antismash.gbk --eggnog .../AKSP4_eggnog.emapper.annotations

Logfiles
Please provide relavent log files of the error.

output generated by emapper.py
AKSP4_eggnog.emapper.annotations.txt

for annotate_misc/annotation.egg.txt
annotations.eggnog.txt

for annotate_results/Pseudogymnoascus.annotations.txt (a snippet of it)
Pseudogymnoascus.annotations.snippet.txt
(shows empty EC numbers Eggnog and COG boxes)

logfile for funning funannotate annotate
AKSP4funannotate_log.txt

OS/Install Information

• output of funannotate check --show-versions

Checking dependencies for 1.8.15
-------------------------------------------------------
You are running Python v 3.8.15. Now checking python packages...
biopython: 1.81
goatools: 1.2.3
matplotlib: 3.4.3
natsort: 8.4.0
numpy: 1.24.4
pandas: 1.5.3
psutil: 5.9.5
requests: 2.31.0
scikit-learn: 1.3.1
scipy: 1.10.1
seaborn: 0.13.0
All 11 python packages installed


You are running Perl v b'5.032001'. Now checking perl modules...
Carp: 1.38
Clone: 0.46
DBD::SQLite: 1.72
DBD::mysql: 4.046
DBI: 1.643
DB_File: 1.858
Data::Dumper: 2.183
File::Basename: 2.85
File::Which: 1.24
Getopt::Long: 2.54
Hash::Merge: 0.302
JSON: 4.10
LWP::UserAgent: 6.67
Logger::Simple: 2.0
POSIX: 1.94
Parallel::ForkManager: 2.02
Pod::Usage: 1.69
Scalar::Util::Numeric: 0.40
Storable: 3.15
Text::Soundex: 3.05
Thread::Queue: 3.14
Tie::File: 1.06
URI::Escape: 5.12
YAML: 1.30
local::lib: 2.000029
threads: 2.25
threads::shared: 1.61
All 27 Perl modules installed


Checking Environmental Variables...
$PASAHOME=/home/user/slsy9965/funannotate/opt/pasa-2.5.3
$TRINITY_HOME=/home/user/slsy9965/funannotate/opt/trinity-2.8.5
$EVM_HOME=/home/user/slsy9965/funannotate/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/home/user/slsy9965/funannotate/config/
       ERROR: FUNANNOTATE_DB not set. export FUNANNOTATE_DB=/path/to/dir
       ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir
-------------------------------------------------------
Checking external dependencies...
PASA: 2.5.3
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: 3.5.0
bamtools: bamtools 2.5.1
bedtools: bedtools v2.31.0
blat: BLAT v37x1
diamond: 2.1.8
ete3: 3.1.3
exonerate: exonerate 2.4.0
fasta: 36.3.8g
glimmerhmm: 3.0.4
gmap: 2023-07-20
hisat2: 2.2.1
hmmscan: HMMER 3.3.2 (Nov 2020)
hmmsearch: HMMER 3.3.2 (Nov 2020)
java: 17.0.3-internal
kallisto: 0.46.1
mafft: v7.520 (2023/Mar/22)
makeblastdb: makeblastdb 2.14.1+
minimap2: 2.26-r1175
pigz: 2.6
proteinortho: 6.3.0
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.18
snap: 2006-07-28
stringtie: 2.2.1
tRNAscan-SE: 2.0.12 (Nov 2022)
tantan: tantan 40
tbl2asn: 25.8
tblastn: tblastn 2.14.1+
trimal: trimAl v1.4.rev15 build[2013-12-17]
trimmomatic: 0.39
       ERROR: emapper.py not installed
       ERROR: gmes_petap.pl not installed
       ERROR: signalp not installed

[IanDMedeiros]

@slsy9965 It looks like your eggnog annotations are using a different format for gene identifiers (e.g., AKSP4_contig_1_104). I'm guessing that is why they are getting parsed to annotations.eggnog but not included in the file with all annotations.