N/As output

[AthinaGav]

I am running OMAmer search on a number of proteomes and I am getting no errors but the output files are full of N/As. For example:

qseqid	hogid	hoglevel	family_p	family_count	family_normcount	subfamily_score	subfamily_count	qseqlen	subfamily_medianseqlen	qseq_overlap
ZOONE00001	N/A	N/A	N/A	N/A	N/A	N/A	N/A	65	N/A	N/A
ZOONE00002	N/A	N/A	N/A	N/A	N/A	N/A	N/A	76	N/A	N/A
ZOONE00003	N/A	N/A	N/A	N/A	N/A	N/A	N/A	65	N/A	N/A
ZOONE00004	N/A	N/A	N/A	N/A	N/A	N/A	N/A	73	N/A	N/A
ZOONE00005	N/A	N/A	N/A	N/A	N/A	N/A	N/A	65	N/A	N/A
ZOONE00006	N/A	N/A	N/A	N/A	N/A	N/A	N/A	87	N/A	N/A
ZOONE00007	N/A	N/A	N/A	N/A	N/A	N/A	N/A	90	N/A	N/A
ZOONE00008	N/A	N/A	N/A	N/A	N/A	N/A	N/A	109	N/A	N/A
ZOONE00009	N/A	N/A	N/A	N/A	N/A	N/A	N/A	98	N/A	N/A
ZOONE00010	N/A	N/A	N/A	N/A	N/A	N/A	N/A	81	N/A	N/A
ZOONE00011	N/A	N/A	N/A	N/A	N/A	N/A	N/A	71	N/A	N/A
ZOONE00012	N/A	N/A	N/A	N/A	N/A	N/A	N/A	119	N/A	N/A
ZOONE00013	N/A	N/A	N/A	N/A	N/A	N/A	N/A	40	N/A	N/A
ZOONE00014	N/A	N/A	N/A	N/A	N/A	N/A	N/A	84	N/A	N/A
ZOONE00015	N/A	N/A	N/A	N/A	N/A	N/A	N/A	72	N/A	N/A
ZOONE00016	N/A	N/A	N/A	N/A	N/A	N/A	N/A	91	N/A	N/A
ZOONE00017	N/A	N/A	N/A	N/A	N/A	N/A	N/A	137	N/A	N/A
ZOONE00018	N/A	N/A	N/A	N/A	N/A	N/A	N/A	86	N/A	N/A
ZOONE00019	N/A	N/A	N/A	N/A	N/A	N/A	N/A	84	N/A	N/A
ZOONE00020	N/A	N/A	N/A	N/A	N/A	N/A	N/A	116	N/A	N/A
ZOONE00021	N/A	N/A	N/A	N/A	N/A	N/A	N/A	150	N/A	N/A
ZOONE00022	N/A	N/A	N/A	N/A	N/A	N/A	N/A	48	N/A	N/A
ZOONE00023	N/A	N/A	N/A	N/A	N/A	N/A	N/A	122	N/A	N/A
ZOONE00024	N/A	N/A	N/A	N/A	N/A	N/A	N/A	123	N/A	N/A
ZOONE00025	N/A	N/A	N/A	N/A	N/A	N/A	N/A	116	N/A	N/A
ZOONE00026	N/A	N/A	N/A	N/A	N/A	N/A	N/A	110	N/A	N/A
ZOONE00027	N/A	N/A	N/A	N/A	N/A	N/A	N/A	102	N/A	N/A
ZOONE00028	N/A	N/A	N/A	N/A	N/A	N/A	N/A	92	N/A	N/A
ZOONE00029	N/A	N/A	N/A	N/A	N/A	N/A	N/A	78	N/A	N/A
ZOONE00030	N/A	N/A	N/A	N/A	N/A	N/A	N/A	101	N/A	N/A
ZOONE00031	N/A	N/A	N/A	N/A	N/A	N/A	N/A	55	N/A	N/A
ZOONE00032	N/A	N/A	N/A	N/A	N/A	N/A	N/A	69	N/A	N/A
ZOONE00033	N/A	N/A	N/A	N/A	N/A	N/A	N/A	120	N/A	N/A
ZOONE00034	N/A	N/A	N/A	N/A	N/A	N/A	N/A	109	N/A	N/A
ZOONE00035	N/A	N/A	N/A	N/A	N/A	N/A	N/A	54	N/A	N/A
ZOONE00036	N/A	N/A	N/A	N/A	N/A	N/A	N/A	77	N/A	N/A
ZOONE00037	N/A	N/A	N/A	N/A	N/A	N/A	N/A	151	N/A	N/A
ZOONE00038	N/A	N/A	N/A	N/A	N/A	N/A	N/A	137	N/A	N/A
ZOONE00039	N/A	N/A	N/A	N/A	N/A	N/A	N/A	73	N/A	N/A
ZOONE00040	N/A	N/A	N/A	N/A	N/A	N/A	N/A	92	N/A	N/A
ZOONE00041	N/A	N/A	N/A	N/A	N/A	N/A	N/A	107	N/A	N/A
ZOONE00042	N/A	N/A	N/A	N/A	N/A	N/A	N/A	126	N/A	N/A

Some info:
I am running OMAmer version in a conda environment.
OMAmer version: 2.1.1
python version: 3.12.11 (same result with v3.8 though)
The output of pip freeze is:

about-time==4.2.1
alive-progress==3.3.0
biopython==1.85
blosc2==3.9.1
certifi==2025.10.5
charset-normalizer==3.4.3
ete3==3.1.3
graphemeu==0.7.2
humanfriendly==10.0
idna==3.10
llvmlite==0.45.1
lxml==6.0.2
msgpack==1.1.2
ndindex==1.10.0
numba==0.62.1
numexpr==2.13.1
numpy==1.26.4
omamer==2.1.1
packaging==25.0
pandas==2.3.3
platformdirs==4.4.0
property-manager==3.0
py-cpuinfo==9.0.0
python-dateutil==2.9.0.post0
pytz==2025.2
requests==2.32.5
Rmath4==4.4.2
scipy==1.16.2
setuptools==78.1.1
six==1.17.0
tables==3.10.2
tqdm==4.67.1
typing_extensions==4.15.0
tzdata==2025.2
urllib3==2.5.0
verboselogs==1.7
wheel==0.45.1