Orthofiller failing `Error: hmmerfm is not a recognized sequence database file format`

Question

[xonq]

I have tried different hmmer binaries, but orthofiller keeps failing with:

Error: hmmerfm is not a recognized sequence database file format

I suspect there is some sort of integration problem with nhmmer and orthofiller, but I'm curious if anyone has run into this problem using orthofiller or some other program. Trying to run orthofiller using two organisms. I wrote a script to convert gff to gtf and from colleagues' experiences we suspected there is some gtf error, but now I'm not so sure.

[h.mon]

What were the versions of the nhmmer binaries you tested? It seems the hmmerfm database format is new from HMMER3 version 3.1b2, and possibly not implemented in older versions.

[xonq]

I tried two different installations of hmmer 3.2.1

[h.mon]

I wrote a script to convert gff to gtf

Why did you write one, instead of using the one recommended / supplied by OrthoFiller?

[xonq]

It doesn't work for some of the gffs I'm working with, so for uniformity I wrote one that does. This had to be done for a previous analysis as well and it worked, however, the sources of some of the gffs in that analysis are different than this one.

Answer 1

[xonq]

The solution here is that future versions of nhmmer implicitly recognize the hmmerfm database format, only hmmer 3.1b2 had the explicit call. Simply remove the --tformat flag for future versions.