double free or corruption (out) error for SpeciesRax

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Baqiao Liu

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Apr 9, 2021, 1:51:43 PM4/9/21
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Dear Benoit,

Thanks for developing SpeciesRax! I was using SpeciesRax on some SimPhy datasets, and it crashed on several of the inputs. I isolated it to one of the GFTs and this is what I am reproducing here. Is there any chance that you can take a look at what is happening? I compiled from source from commit f20810f and have attached the input files that I have been using.

Input command:
generax --families isolate.family --species-tree MiniNJ --strategy SKIP --rec-model UndatedDTL --per-family-rates --prune-species-tree --si-estimate-bl --si-quartet-support --prefix output --si-strategy HYBRID


Thanks in advance,
Baqiao
reproduce_files.zip

Benoit Morel

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Apr 9, 2021, 2:45:45 PM4/9/21
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Dear Baqiao,

thanks for your report. I think this happens because you have polytomies in your input gene tree (maybe you used fasttree to generate them), for instance above the gene 91_31_0. SpeciesRax only supports binary trees.
It looks like my parser does not detect it, and then everything crashes. I will add a check in the next release to report a clean error message when this happens. Other users will likely get the same issue.

There is no good solution for dealing with polytomies so far. I suggest to either resolve them randomly or to discard the gene families that are not fully resolved.

Best,
Benoit

Baqiao Liu

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Apr 9, 2021, 2:49:20 PM4/9/21
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Dear Benoit,

Thanks for the quick response! I guess I will randomly resolve the polytomies for now (and indeed they were from FastTree).

Best,
Baqiao

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