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