Some people will get a fatal error when trying to execute hmmsearch with pfam db:

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

**

This issue could be fixed with in 2 step.

1.- Be sure your Pfam-A.hmm and hmmsearch has all permissions.

2.- Check if your hmmsearch and Pfam-A.hmm are in the same version.

• A: In this case, if your hmmsearch version is not the same as your Pfam-A.hmm version, you wont be able to execute the program correctly.

• B: Checking hmmsearch version: In your console ==> $hmmsearch -h

  The second line will show your current V.

  "#hmmsearch :: search profile(s) against a sequence database"

  "#HMMER 3.0rc2 (March 2010); http://hmmer.org/"

• C: Checking Pfam-A.hmm version: In your console ==> $less Pfam-A.hmm

  "# HMMER3/f [3.1b1 | May 2013]"

In this case you need to upgrade your hmmsearch version to 3.1b1 or downgrade your Pfam-A.hmm to 3.0rc2.

Even the difference between V. 3.1b1 and V.3.1b2 may result on a fatal error.

Hope this info will help you.