"No hits satisfy inclusion thresholds; no alignment saved" for example files.

[MikekyT]

Unable to pass make_msa.RNA nhmmer step as nothing passes and therefore no sequence data is given to subsequent steps. Currently says "No sequences found in file RNA.wquery.unfilt.afa" in the stderr log file.

I am fairly confident that all databases utilized in this step are available and correctly downloaded -is there potentially another reason this may not be passing with the example files? Everything was initialized/downloaded as mentioned in the most recent README, and in order.

[huangtinglin]

I also have the same problem. Have you solved it?

[j-degroot]

In an older version, the last line rm nhmmer.a2m in make_rna_msa.sh was commented. It works but I'm not sure if it is important to delete the file.