Open MmasterT opened 7 months ago
Hello!
Thank you for reaching out! There is indeed an issue in the way OMArk is looking at taxonomic rank in this case. This is because Hymenoptera (the order) is not explicitly stored in the OMAmer database for species sampling reasons (all Hymenoptera in OMA are also Apocrita, so only the most specific grouping is stored). The way the rank checking is implemented does not handle well this scenario. I agree this is not ideal, I will work on a fix and issue it as soon as possible.
In the meantime, in this particular case you can obtain the same results as if you were using Hymenoptera as a clade of interest by using the taxid of Apocrita rather than the one of your species "-t 7400".
Regarding the HOGs number, it is actually expected than the number of conserved HOGs is lower than the one of the lineage associated HOGs as the former is a subset of the later - only those HOGs found in more than 80% of the species of the clade.
Best wishes, Yannis
Hello I'm trying to understand how omark identyfies what taxonomic rank to use. I'm checking the OMArk result for an annotation of Bombus terrestris (common bee) and specifying the -r order flag it says that it is too narrow or it does not exist, however the one used in the default is Aculeata wich is the infraorder for this particular species, why is this happenning?.
Then the HOGs used to check the consistency are different to the ones used to check the completeness:
16727 HOGs are associated to the query's lineage and will be used for consistency assesment 6496 conserved ancestral HOGs will be used from completeness assesment
I'm including the options used and stderr, and stdout down below: