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hmm calibrate failure (Read 3530 times)
Mar 14th, 2014 at 9:49pm

Ruhshan_Ahmed   Offline
YaBB Newbies

Posts: 1
I'm trying to use hmmcalibrate of hmm2, it requires a .hmm file.
But, while i add a file and click calibrate it says file format is not supported and shows following error(in screenshot):
the file i tried is here too:

gbb.hmm (68 KB | )
err.png (26 KB | )
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Reply #1 - May 29th, 2014 at 10:33am

German   Offline
Full Member

Posts: 118
Hello, Ahmed. The problem is that you try to run the hmm2 tool with the hmm3 input data. If you open your file (gbb.hmm) with a text editor you will see that the first line is "HMMER3/b [3.0 | March 2010]". Unfortunately, hmm files of different versions have the same file extension ".hmm".

The current version of UGENE Workflow Designer (WD) supports only the hmm2 tool. We have already integrated hmm3 into WD but is will be available in the 1.14 version of UGENE that will be released in a month.

So, there are two temporary solutions for you:
1) Use hmm3 in the usual way. See the documentation here: http://ugene.unipro.ru/documentation/manual/plugins/hmm3.html
2) If using of WD is necessary (if there are a lot of files you need to process) then you need to build (or download somewhere) the hmm2 profile and use it in your workflow. Here is the documentation about building hmm2 profiles: http://ugene.unipro.ru/documentation/manual/plugins/hmm2.html#building-hmm-model...
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