Partition finding error

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Steven Mussmann

May 1, 2017, 10:08:33 AM5/1/17

I have been trying to partition some large alignments using IQ-TREE, but keep encountering the following error (a failed assertion):

iqtree: /home/mussmann/local/src/IQ-TREE/phylokernelnew.h:2486: double PhyloTree::computeLikelihoodBranchSIMD(PhyloNeighbor*, PhyloNode*) [with VectorClass = Vec4d; bool SAFE_NUMERIC = true; int nstates = 4; bool FMA = true; bool SITE_MODEL = false]: Assertion `!std::isnan(tree_lh) && !std::isinf(tree_lh) && "Numerical underflow for lh-branch"' failed.

I tried to attach the log file, but it was too large.  It is instead hosted on my google drive:

Thank you in advance for any help you can provide,


Bui Quang Minh

May 2, 2017, 2:31:21 AM5/2/17
to, Steven Mussmann
Hi Steve,

thanks for the report. From one line in the log file:

NOTE: minimal branch length is reduced to 0.000000079048 for long alignment

While this minimal branch length is ok for analysis on your whole alignment, it seems too small for the partitions during the merging phase, which may cause numerical underflow. Therefore, can you pls override this behavior by option -blmin. Eg., -blmin 1e-6 to set min branch length to 10^-6. Let me know how it goes.

Cheers, Minh

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Bui Quang Minh
Center for Integrative Bioinformatics Vienna (CIBIV)
Campus Vienna Biocenter 5, VBC5, Ebene 1
A-1030 Vienna, Austria
Phone: ++43 1 4277 74326
Email: minh.bui (AT)

Steven Mussmann

May 2, 2017, 8:10:47 AM5/2/17
to IQ-TREE,,
Great, thank you.  I will give this a try and report back.


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