Current cmsearch missing required options

[chofski]

Using the latest Infernal package leads to an error from RNIE due to the "--fil-no-qdb" option not being supported. Would suggest updating docs to highlight specific version of Infernal to use or update Perl script to handle these changes.

[ppgardne]

Thanks for the reminder Thomas.
I've been meaning to update the docs for a while. Unfortunately I haven't got around to reparameterising for the latest versions of Infernal.

[NickNCL]

I ran into the same issue and was able to run RNIE with infernal version 1.0 installed

[ppgardne]

Yep, Infernal 1.0 is what was used for optimising the terminator annotations. It would take some work to perform a similar optimisation with the latest Infernal release.