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HMMER: Failed to open target sequence database for reading

Good Afternoon

I'm trying to run a protein search through HMMER (phmmer) against PFam database in command line. However the process is interrupted and the following message appears: Failed to open target database sequence HMMER/database/Pfam-A.fasta for reading. I would like to know what's happening.

hmmer phmmer database
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updated by cryptogenomicon cryptogenomicon • written by Cayro • Cayro

Hi cayro

Did you prepare your database with hmmpress?

hmmpress creates four binary files. The database cannot be read because it needs to have those four auxiliary binary files generated by hmmpress.

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written by Carlos Caicedo Carlos Caicedo

hmmpress is for HMM files that you're going to search with hmmscan; not for FASTA files that'll be searched with phmmer.

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written by cryptogenomicon cryptogenomicon

How could I run this database? Because I tried with the uniprot database in fasta format and it worked. Would I have to change the format of my bank?

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written by Cayro • Cayro

I tried this approach, however the following message appears:

Error: File format problem in trying to open HMM file database/Pfam/Pfam-A.fasta. Format tag is '>S6ENI5_9CLOT/170-197': unrecognized. Current H3 format is 'HMMER3/f'. Previous H2/H3 formats also supported.

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written by Cayro • Cayro

Pfam-A.fasta is a FASTA sequence file. It is not a profile HMM database. (Have you looked at it? If not, look at it.)

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written by cryptogenomicon cryptogenomicon

It's a fasta sequence. I can't understand why it does not work. Should I change the format of my database?

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written by Cayro • Cayro

Hi, Did you ever find a solution to this problem? I am getting the same exact error message.

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written by hudak7 • hudak7

1 answer

It means that your file HMMER/database/Pfam-A.fasta can't be opened for reading. It either doesn't exist, or you don't have read permission for it.

Also, if you are trying to search a protein sequence against Pfam, you generally want to be using hmmscan or hmmsearch, not phmmer. phmmer is for searching sequence(s) against a sequence database (like UniProt or NCBI NR).

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written by cryptogenomicon cryptogenomicon

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