HMMER error: Unrecognized format with Pfam-A.hmm

Question

[jmah]

Hi everyone,

Has anyone ever received this error when trying to run HMMER for Trinotate? This error occurred after creating binary files for the Pfam-A.hmm database with hmmpress and trying to run hmmscan:

"Error: Unrecognized format, trying to open hmm file Pfam-A.hmm for reading."

I've already checked that Pfam-A.hmm is readable. I am using the database downloaded from the Trinotate website and my version of HMMER is 3.1b1. Could there be some kind of clash between my version of HMMER and the older database? (A very specific database is needed for downstream analysis by Trinotate to work.)

I've done some Google searching but haven't been able to find other examples of this error (other than 2 that didn't seem to apply to my situation). I’ve also tried to follow the recommendations in this thread (define PFAM dir in get_homologues perl script) to no avail.

Thanks for your help! Jasmine

Answer 1

[jmah]

Hello all,

Turns out it was a permissions issue, and chmod 777 Pfam-A.hmm largely fixed everything.

[h.mon]

One doesn't need to execute "Pfam-A.hmm", and if hmmpress has been run already, even write permission isn't necessary. Better would be:

chmod 644 Pfam-A.hmm