Open davidcerny opened 1 month ago
Thanks, David.
I will look at the issue the coming week.
Thanks, Thomas
From: David Černý @.>
Date: Sunday, 14 July 2024 at 3:18 AM
To: iqtree/iqtree2 @.>
Cc: Thomas Wong @.>, Mention @.>
Subject: Re: [iqtree/iqtree2] Crash due to assertion failure in PhyloSuperTreePlen::computeFuncDerv
(Issue #270)
Hmm, so to the best of my understanding, the branch length becomes negative because lambda is negative:
nei1_part->length += lambda*part_info[part].part_rate;
and lambda ultimately comes from BioNJ (it's a distance scaling factor used in a variance reduction formula; see Gascuel 1997). So this problem can be circumvented by not using BioNJ in the starting tree mix (I've tried -t PARS, and it runs fine). Still, though, according to Gascuel lambda should never be outside [0, 1], so this does look like a real problem, though not necessarily one with IQ-TREE. Let me know if you'd like me to close this issue or keep it open, @bqminhhttps://github.com/bqminh @thomaskfhttps://github.com/thomaskf.
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Thank you @thomaskf! Just to clarify, I have deleted my previous comment because it was incorrect. Removing the BioNJ tree from the starting tree mix with -t PARS
is not sufficient to get rid of the issue. Then again, IQ-TREE printed out a .bionj
file for me anyway, so I'm not quite sure what happened there.
So the issue is architecture-specific: I ran into it when I downloaded the precompiled macOS executable for ARM from here, but now that I've compiled IQ-TREE from source for x86_64 (i.e., under emulation), it's no longer occurring.
Bug description
I'm trying to run a partitioned analysis of morphological data (with separate partitions for binary, unordered multistate, and ordered multistate characters, and with proportional branch lengths) as follows:
Some of the runs will be completed just fine, but sooner or later the analysis will crash with the following error message, which seems to be getting triggered by a negative branch length appearing in the tree:
To reproduce
The alignment files, partition file, and log file are all available from this zipped directory.
Expected behavior
No negative branch lengths, and no crash.
Computer info
macOS 14.5 (Sonoma), ARM64 architecture, IQ-TREE v2.3.5 (latest stable release).