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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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Error reading newick tree #96

Closed cmorganl closed 4 years ago

cmorganl commented 4 years ago

Hello,

I'm attempting to run raxml-ng -- evaluate for a phylogeny I'd like to use with EPA-NG. RAxML-NG is detecting a formatting issue, but I'm not sure if it actually exists.

The error I'm getting is:

raxml-ng: /home/connor/bin/raxml-ng/libs/pll-modules/libs/libpll/src/parse_utree.y:500: utree_wraptree: Assertion `inner_index == tip_count + inner_count' failed.
Aborted (core dumped)

Here is the log file NirK.raxml.log and the tree NirK.FastTree.nwk.txt.

The tree was built using FastTree 2.1.10. This error occurs in both the latest release and the version on the master branch. I'm running Ubuntu 18.04. Let me know if you need any more information.

Thank you!

amkozlov commented 4 years ago

Hi Connor,

thanks for reporting!

Your tree contains multifurcations (aka polythomies), while raxml-ng requires a strictly bifurcating tree. I will add a respective check and print a clear error message.

cmorganl commented 4 years ago

Oh, excellent - an easy patch! Thanks for figuring that out so quickly, Alexey!

amkozlov commented 4 years ago

check added in the coarse branch -> closing