hmmindex: FATAL: failed to open HMM file Pfam-A.hmm for reading.

Question

[dago]

I need to retrieve some Pfam domains from the PfamA.

I will use hmmfetch for that, and as I read in the hmmer manual first I need to index the PfamA.hmm db.

To do that I need to use hmmindex. It seems to be quite straightforward. I can read in the manual that the usage of hmmindex is:

hmmindex [options] database

Therefore my command is:

hmmindex --av Pfam-A.hmm

But I get the error:

FATAL: failed to open HMM file Pfam-A.hmm for reading.

I tried to re-downolad the PfamA, to use hmmindex before and after hmmpress, but I get always the same error.

I feel really dumb, but I cannot understand what I am missing here.

[h.mon]

Which software (I suppose HMMER) and version? With hmmindex version 2.3.2 I get:

FATAL: No such option "--av".

[sofie.thijs]

Hi, I am still stuck in the same step.

I have HMMER 3.3.1 (Jul 2020); http://hmmer.org/ installed via conda.

And I downloaded the PFAM database here: http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz

But when I do hmmfetch Pfam-A.full PF00115, I get:

Error: File format problem in trying to open HMM file Pfam-A.full.
Format tag is 'A0A1I4YJU4_9ENTR/160-195': unrecognized.
Current H3 format is 'HMMER3/f'. Previous H2/H3 formats also supported.

I have also tried with id PF07714.12, but no luck, the same error.

Can you help me?

[Mensur Dlakic]

The file you downloaded contains sequences. You probably want the file with HMMs.

http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz

After gunziping the file, find the exact accession numbers:

grep PF00115 Pfam-A.hmm

ACC PF00115.21

grep PF07714 Pfam-A.hmm

ACC PF07714.18

Finally:

hmmfetch Pfam-A.hmm PF00115.21 > PF00115.21.hmm
hmmfetch Pfam-A.hmm PF07714.18 > PF07714.18.hmm

Answer 1

[venu]

To retrieve HMM profile of any domain/family from Pfam-A.hmm you don't need hmmindex, I believe. All you need is hmmfetch and accession id of domain/family. Even more if you need MSA of any domain/family convert your accession ids accession number (Example: ADK - PF00406) from here and download from http://pfam.xfam.org/ by looping over each id with wget.

Finally I don't find hmmindex in HMMER 3.1b1 manual. Check here.

[dago]

Thanks for your answer. I tried to use hmmfetch also with not indexing, following the example in the manual:

hmmfetch Pfam-A.hmm PF00045
Error: HMM PF00045 not found in SSI index for file Pfam-A.hmm.h3m

Still does not work.

[venu]

Are you sure the id is correct? Some ids in Pfam-A.hmm contain decimal points like PF00045.12 for example. In such cases this error will come up. First try with this id PF07714.12

[dago]

You re right, this is the problem! Thanks!

Answer 2

[h.mon]

You are probably using HMMER2, but Pfam-A.hmm is built with HMMER3, see here.

[dago]

Hi, thanks for your answer. Actually I am using HMMER 3.1.

# hmmscan :: search sequence(s) against a profile database
# HMMER 3.1b1 (May 2013); http://hmmer.org/
# Copyright (C) 2013 Howard Hughes Medical Institute.

Do you think I should try other versions?

[dago]

I tried also a previous version, but I get always the same problem.