Problem with hmmpress for Superfamily_1.75 hmmlib
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2.3 years ago
karenkvn ▴ 40

Hello,

Please could someone help me with this frustrating issue? I am using HMMER3.3. I am trying to run hmmscan with Superfamily HMM models, following the steps here:

I downloaded the HMM library hmmlib_1.75. When I try to compress and index this file using hmmpress, I get the following error: "SSI index construction failed: secondary keys not unique: '100879' occurs more than once."

A previous post from 5.4 years ago, having a different issue with hmmpress, suggests that there could be a mismatch between the version of the models and the version of HMMER, but I am pretty sure that HMMER and Superfamily are "on the same page"?

A related issue with anvio indicates that HMMER3.2 > requires more stringency than previous versions.

Is there a workaround for this, or another application to index and compress the hmmlib file? I would find it rather difficult to switch to HMMER3.1 just for this, and it seems rather odd to me that this problem exists at all.

Thanks very much for any input!

Karen

HMMER_3.3 SUPERFAMILY hmmpress hmmscan • 1.1k views
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2.3 years ago
Mensur Dlakic ★ 18k

It is almost certainly a mismatch between program versions, as SUPERFAMILY version 1.75 goes way back. Typing head hmmlib_1.75 will tell you what version of HMMer was used.

If you have the original alignments available, the models can be created from scratch using your current hmmbuild version. Alternatively, you can try to convert the database before pressing, as pointed out here.

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You are correct - hmmpress works just fine with HMMER3.1b2. Thank you.