An unusual error?

I just ran into a problem using HMMER, where it aborts the building of an HMM-profile (using hmmbuild) with this line: “FATAL: illegal state transition B->E in traceback” Is there anyone who has seen this HMMER error before? Anyone who know what it means and/or how to solve it? Please let me know as soon as possible.

hmmbuild - build a hidden Markov model from an alignment
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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Alignment file: alignment1.aln
File format: Clustal
Search algorithm configuration: Multiple domain (hmmls)
Model construction strategy: MAP (gapmax hint: 0.50)
Null model used: (default)
Prior used: (default)
Sequence weighting method: G/S/C tree weights
New HMM file: alignment1.hmm
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Alignment: #1
Number of sequences: 5517
Number of columns: 2305

WARNING: Looks like amino acid sequence, hope that's right
Determining effective sequence number ... done. [1]
Weighting sequences heuristically ... [big alignment! doing PB]... done.
Constructing model architecture ...
FATAL: illegal state transition B->E in traceback

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2 responses to “An unusual error?

  1. It means it didn’t find a consensus at all in your alignment. It went straight from the begin (B) to the end (E) of the model with no consensus columns in between. Your alignment must be full of gaps. You can manually define which columns you intend to be consensus columns, and use hmmbuild –hand;
    or you can use hmmbuild –gapmax to set the allowed gap fraction per column to be something larger than the default of 0.5.

    • Wow, a fast and clear answer directly from
      the source. Some times the blogosphere actually sort of scares me. But a very big thank you for this quick response. I looked at the alignment, and yes, it is full of gaps. I’m not sure whether it is worse than things that I have got hmmbuild to work with earlier, but it looks pretty bad. I will examine the alignment more carefully when I get back to work tomorrow. I will also look at the hand-crafting method and the gap-fraction settings. I tried some different options, but I guess I missed to check the gapmax one… Thanks again for this very clear and useful reply!

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