Fixing "Error: Unrecognized format, trying to open hmm file Pfam-A.hmm for reading."
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Entering edit mode
3.9 years ago

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.

genome hmmer pfam • 4.2k views
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Entering edit mode
8 months ago

Indeed, I also encountered the same problem。

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find interproscan-5.48-83.0 -name 'hmmsearch' 2>/dev/null

interproscan-5.48-83.0/bin/hmmer/hmmer3/3.3/hmmsearch

interproscan-5.48-83.0/bin/hmmer/hmmer3/3.1b1/hmmsearch

interproscan-5.48-83.0/bin/hmmer/hmmer2/2.3.2/hmmsearch

2

head interproscan-5.48-83.0/data/pfam/33.1/pfam_a.hmm

HMMER3/f [3.1b2 | February 2015]

NAME 1-cysPrx_C

ACC PF10417.10

DESC C-terminal domain of 1-Cys peroxiredoxin

version 3.1b2 and version 3.1b1 conflict

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conda install hmmer=3.1b2

ln -s /opt/anaconda3/envs/snakemake/bin/hmmsearch /opt/interproscan-5.48-83.0/bin/hmmer/hmmer3/3.1b1/hmmsearch

ln -s /opt/anaconda3/envs/snakemake/bin/hmmpress /opt/interproscan-5.48-83.0/bin/hmmer/hmmer3/3.1b1/hmmpress

ln -s /opt/anaconda3/envs/snakemake/bin/hmmscan /opt/interproscan-5.48-83.0/bin/hmmer/hmmer3/3.1b1/hmmscan

It started working

Hope this info will help you.

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