Closed TangShan99 closed 1 year ago
I could use a bit more information.
(1) Did you build the model(s) yourself, using hmmbuild? If not, where did you get them?
(2) Are the models for nucleotide families, or protein?
(3) Can you please provide the results of the following command (replacing filename.hmm with the name of your file):
head filename.hmm
Hi,
Thank you for your quick reply !
Actually, I didn't use hmmbuild
, I just use my own sequences searching against HMMs database, which I download is Pfam-A.hmm from this web site ( http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz ), and the model could be available for protein. As you suggested,when I run the appointed command there comes the result:
HMMER3/f [3.1b2 | February 2015] NAME 1-cysPrx_C ACC PF10417.12 DESC C-terminal domain of 1-Cys peroxiredoxin LENG 40 ALPH amino RF no MM no CONS yes CS yes
It seems that the old version of HMMER3 associated with Pfam-A.hmm is going wrong, so I was wondering if I would take hmmscan
instead of nhmmscan
to continue running, although more time it would take. Any other solution can help me? Thanks a lot.
Best, Kiarety
That makes sense.
Thanks, I have finally solved it by using hmmscan
. Thank you to tell me so much helpful suggestions.
Hi, I have a confusing but possibly trivial issue,the following prompt appears when I try to run nhmmscan:
Error: No MAXL field in model(s); is this an old model format? nhmmer/hmmscan require HMMER 3.1 models or later.
However, my HMMER version is already the latest (HMMER 3.3.2 ), I wonder why does this issue occur when using nhmmscan? Thanks for your help.
Best, Kiarety