HMMER: Unrecognized format error
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jm...@ualberta.ca
Nov 17, 2016, 2:50:21 PM11/17/16
to trinityrnaseq-users
Hi everyone,
Has anyone ever received this error when trying to run HMMER for Trinotate? This error occurred after creating binary files for the Pfam-A.hmm database with hmmpress and trying to run hmmscan:
"Error: Unrecognized format, trying to open hmm file Pfam-A.hmm for reading."
I've already checked that Pfam-A.hmm is readable. I am using the database downloaded from the Trinotate website and my version of HMMER is 3.1b1. Could there be some kind of clash between my version of HMMER and the older database?
I've done some Google searching but haven't been able to find other examples of this error (other than 2 that didn't seem to apply to my situation). I realize this is probably a HMMER-related question, rather than a Trinotate issue, but I haven't been able to find a HMMER help forum. :(
Thanks for your help!
Jasmine
Brian Haas
Nov 18, 2016, 9:49:20 AM11/18/16
to jm...@ualberta.ca, trinityrnaseq-users
Sometimes folks will download the file and call it 'Pfam-A.hmm', but it's actually gzipped. Could that be the case here?
(try copying it to test.gz and running 'gunzip test.gz')
~brian
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Jasmine Mah
Nov 18, 2016, 2:59:52 PM11/18/16
to Brian Haas, trinityrnaseq-users
Hi Brian,
Thanks for replying!
I tried your suggestion, but it still doesn't seem to work.
Someone at my institution had a similar error, and said that it was a known problem that HMMER may not recognize its own database file. She said to try this:
Someone at my institution had a similar error, and said that it was a known problem that HMMER may not recognize its own database file. She said to try this:
hmmconvert --outfmt 3/b Pfam-A.hmm > Pfam-A1.hmm
And then use the Pfam-A1.hmm file. However, it still doesn't work for me.
:(
Thanks for your help. If anyone has any other suggestions, I'm all ears!
Cheers,
Jasmine
On Fri, Nov 18, 2016 at 7:49 AM, Brian Haas <bh...@broadinstitute.org> wrote:
Sometimes folks will download the file and call it 'Pfam-A.hmm', but it's actually gzipped. Could that be the case here?(try copying it to test.gz and running 'gunzip test.gz')~brian
On Thu, Nov 17, 2016 at 2:50 PM, <jm...@ualberta.ca> wrote:
Hi everyone,Has anyone ever received this error when trying to run HMMER for Trinotate? This error occurred after creating binary files for the Pfam-A.hmm database with hmmpress and trying to run hmmscan:"Error: Unrecognized format, trying to open hmm file Pfam-A.hmm for reading."I've already checked that Pfam-A.hmm is readable. I am using the database downloaded from the Trinotate website and my version of HMMER is 3.1b1. Could there be some kind of clash between my version of HMMER and the older database?I've done some Google searching but haven't been able to find other examples of this error (other than 2 that didn't seem to apply to my situation). I realize this is probably a HMMER-related question, rather than a Trinotate issue, but I haven't been able to find a HMMER help forum. :(Thanks for your help!Jasmine
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Brian Haas
Nov 18, 2016, 3:33:33 PM11/18/16
to Jasmine Mah, trinityrnaseq-users
I'd suggest trying to download the pfam file again. If you can get on a different server from the one you're currently using, I'd try that too. (or get a 'free' account on Amazon AWS for exploring and further troubleshooting it).
best,
~brian
jm...@ualberta.ca
Nov 28, 2016, 7:44:35 PM11/28/16
to trinityrnaseq-users, jm...@ualberta.ca
Hi Brian,
Thanks for your help! I tried this on another server and yup - it worked. It seems to have been a permissions issue on the original server. Using 'chmod 777 Pfam-A.hmm' seemed to fix the problem, at least on the head node.
Cheers,
Jas
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Brian Haas
Nov 28, 2016, 8:41:59 PM11/28/16
to Jasmine Mah, trinityrnaseq-users
Great! It's still a weird error to experience based on a permissions issue. This is good to know.
thanks!
~b
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