Question: HMMER: Failed to open target sequence database for reading
0
gravatar for Cayro
21 months ago by
Cayro0
Brazil/ Natal/ Universidade Federal do Rio Grande do Norte
Cayro0 wrote:

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 • 1.8k views
ADD COMMENTlink modified 21 months ago by cryptogenomicon150 • written 21 months ago by Cayro0
1

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.

ADD REPLYlink modified 21 months ago • written 21 months ago by Carlos Caicedo130
1

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

ADD REPLYlink written 21 months ago by cryptogenomicon150

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?

ADD REPLYlink written 21 months ago by Cayro0

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.

ADD REPLYlink written 21 months ago by Cayro0
1

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.)

ADD REPLYlink written 21 months ago by cryptogenomicon150

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

ADD REPLYlink modified 21 months ago • written 21 months ago by Cayro0

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

ADD REPLYlink written 14 months ago by hudak70
1
gravatar for cryptogenomicon
21 months ago by
United States
cryptogenomicon150 wrote:

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).

ADD COMMENTlink written 21 months ago by cryptogenomicon150
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