Funannotate compare

[Niohuruzh]

Are you using the latest release?
v=1.8.17

Describe the bug
I use gbk files from annotate_result as the input for funanotate compare. But there is something wrong.

[Sep 11 09:06 PM]: OS: Ubuntu 24.04, 48 cores, ~ 132 GB RAM. Python: 3.9.19
[Sep 11 09:06 PM]: Running 1.8.17
[Sep 11 09:06 PM]: Now parsing 1 genomes
[Sep 11 09:06 PM]: working on Talaromyces
Traceback (most recent call last):
File "/home/anaconda3/envs/funannotate/bin/funannotate", line 10, in
sys.exit(main())
File "/home/anaconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/funannotate.py", line 717, in main
mod.main(arguments)
File "/home/anaconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/compare.py", line 297, in main
lib.gb2proteinortho(GBK, protortho, name)
File "/home/anaconda3/envs/funannotate/lib/python3.9/site-packages/funannotate/library.py", line 9976, in gb2proteinortho
fasta.write(">%s %s\n%s\n" % (item, k, v["protein"][i]))
IndexError: list index out of range

What command did you issue?
funannotate compare -i test

Logfiles

[09/11/24 21:06:25]: /home/anaconda3/envs/funannotate/bin/funannotate compare -i test

[09/11/24 21:06:25]: OS: Ubuntu 24.04, 48 cores, ~ 132 GB RAM. Python: 3.9.19
[09/11/24 21:06:25]: Running 1.8.17
[09/11/24 21:06:26]: find_enrichment.py version=NA path=/home/anaconda3/envs/funannotate/bin/find_enrichment.py
[09/11/24 21:06:26]: mafft version=v7.526 (2024/Apr/26) path=/home/anaconda3/envs/funannotate/bin/mafft
[09/11/24 21:06:26]: trimal version=trimAl v1.5.rev0 build[2024-05-27] path=/home/anaconda3/envs/funannotate/bin/trimal
[09/11/24 21:06:26]: proteinortho version=6.3.2 path=/home/anaconda3/envs/funannotate/bin/proteinortho
[09/11/24 21:06:26]: iqtree version=NA path=/home/anaconda3/envs/funannotate/bin/iqtree
[09/11/24 21:06:26]: Input files/folders: ['test']

[09/11/24 21:06:26]: Now parsing 1 genomes
[09/11/24 21:06:28]: working on genome1

OS/Install Information

---

Checking dependencies for 1.8.17

You are running Python v 3.9.19. Now checking python packages...
biopython: 1.79
goatools: 1.4.12
matplotlib: 3.9.2
natsort: 8.4.0
numpy: 1.26.4
pandas: 2.2.2
psutil: 6.0.0
requests: 2.32.3
scikit-learn: 1.5.1
scipy: 1.13.1
seaborn: 0.13.2
All 11 python packages installed

You are running Perl v b'5.032001'. Now checking perl modules...
Carp: 1.50
Clone: 0.46
DBD::SQLite: 1.72
DBD::mysql: 4.050
DBI: 1.643
DB_File: 1.858
Data::Dumper: 2.183
File::Basename: 2.85
File::Which: 1.24
Getopt::Long: 2.58
Hash::Merge: 0.302
JSON: 4.10
LWP::UserAgent: 6.67
Logger::Simple: 2.0
POSIX: 1.94
Parallel::ForkManager: 2.03
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: 5.17
YAML: 1.30
local::lib: 2.000029
threads: 2.25
threads::shared: 1.61
All 27 Perl modules installed

Checking Environmental Variables...
$FUNANNOTATE_DB=/media/funannotate_db
$PASAHOME=/home/anaconda3/envs/funannotate/opt/pasa-2.5.3
$TRINITY_HOME=/home/anaconda3/envs/funannotate/opt/trinity-2.15.2
$EVM_HOME=/home/anaconda3/envs/funannotate/opt/evidencemodeler-2.1.0
$AUGUSTUS_CONFIG_PATH=/home/anaconda3/envs/funannotate/config/
$GENEMARK_PATH=/media/software/gmes_linux_64_4
All 6 environmental variables are set

Checking external dependencies...
PASA: 2.5.3
CodingQuarry: 2.0
Trinity: 2.15.2
augustus: 3.5.0
bamtools: bamtools 2.5.2
bedtools: bedtools v2.31.1
blat: BLAT v39x1
diamond: 2.1.8
emapper.py: 2.1.12
ete3: 3.1.3
exonerate: exonerate 2.4.0
fasta: 36.3.8g
glimmerhmm: 3.0.4
gmap: 2024-08-14
gmes_petap.pl: 4.71_lic
hisat2: 2.2.1
hmmscan: HMMER 3.4 (Aug 2023)
hmmsearch: HMMER 3.4 (Aug 2023)
java: 22.0.1-internal
kallisto: 0.46.1
mafft: v7.526 (2024/Apr/26)
makeblastdb: makeblastdb 2.16.0+
minimap2: 2.28-r1209
pigz: 2.8
proteinortho: 6.3.2
pslCDnaFilter: no way to determine
salmon: salmon 1.10.3
samtools: samtools 1.20
signalp: 5.0b
snap: 2006-07-28
stringtie: 2.2.3
tRNAscan-SE: 2.0.12 (Nov 2022)
tantan: tantan 50
tbl2asn: 25.8
tblastn: tblastn 2.16.0+
trimal: trimAl v1.5.rev0 build[2024-05-27]
trimmomatic: 0.39
All 37 external dependencies are installed