Zachary Konkel comments

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                                            Zachary Konkel

orthofiller's hmmer commands raise a makehmmerdb bug that may lead to memory reallocation errors

This Git is not being maintained, so I've implemented a general orthofiller update [here](https://gitlab.com/xonq/OrthoFiller)

$genome not recognized in reference tdv file

This error suggests that OrthoFiller is recognizing your paths, however, there are some coordinates in your `gtf` that are referencing areas in your genome that do not exist. How did...

$genome not recognized in reference tdv file

@14zac2 yeah, so OrthoFiller requires your `gtf` to be perfectly formatted beforehand. that program may be doing it's job, but it may leave discrepancies orthofiller cannot handle. I have found...

$genome not recognized in reference tdv file

> Thanks, @xonq ! I fixed my gtf with gffread (which seems to do a pretty good job at standardizing gtf files by making them as simple as possible). I...

Version of Orthofinder?

You are correct about this error. I have an updated version of OrthoFiller at https://gitlab.com/xonq/OrthoFiller that addresses these dependency issues and others.

Sequences not multiple of 3: poor stderr information

Specifically, this is BioPython. Not sure if much can be done without altering the BioPython code

[Rabies] Initialize Lyssavirus rabies all-clades community dataset

Thank you. Rabies is indeed very diverse - I contemplated creating independent datasets for each clade, but the genotyping of this "all-clades" dataset has been sufficient for our SME partners....

[Rabies] Initialize Lyssavirus rabies all-clades community dataset

hey @rneher, just wanted to reply and inform you that I cannot return to this to address your concerns until a later date. not sure when, but hopefully within the...