iqtree3 crash: phylotree.cpp:489: virtual void PhyloTree::setRootNode

[hildebra]

Hey,
iqtree3 crashed with the following error:
"
ERROR: phylotree.cpp:489: virtual void PhyloTree::setRootNode(const char*, bool): Assertion `root' failed.
ERROR:
ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED
ERROR: *** For bug report please send to developers:
ERROR: *** Log file: /ei/projects/8/88e80936-2a5d-4f4a-afab-6f74b374c765/data/geneCats/famDrama7/Bin_SB/intra2_20Feb_D5//MGS.121//phylo//IQtree_allsites.log
ERROR: *** Alignment files (if possible)
"

IQtree_allsites.log

I attached the log. This is a highly similar MSA of closely related bacteria I used as input (filesize: 156MB), let me know if you would like to also see this. Could it be too many sites were automatically removed?
best,
Falk

[thomaskf]

Hi Falk, Thanks for reporting the issue. Can you download the latest codes from the Master branch, compile the codes and try? There was a similar issue which was resolved in the latest codes. If the issue still exists, can you share the alignment and the partition files so that we can look into the issue in details? Thank you! From: Falk Hildebrand ***@***.***> Date: Sunday, 22 February 2026 at 2:42 am To: iqtree/iqtree3 ***@***.***> Cc: Subscribed ***@***.***> Subject: [iqtree/iqtree3] iqtree3 crash: phylotree.cpp:489: virtual void PhyloTree::setRootNode (Issue #135) [https://avatars.githubusercontent.com/u/19647604?s=20&v=4]hildebra created an issue (iqtree/iqtree3#135)<#135> Hey, iqtree3 crashed with the following error: " ERROR: phylotree.cpp:489: virtual void PhyloTree::setRootNode(const char*, bool): Assertion `root' failed. ERROR: ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED ERROR: *** For bug report please send to developers: ERROR: *** Log file: /ei/projects/8/88e80936-2a5d-4f4a-afab-6f74b374c765/data/geneCats/famDrama7/Bin_SB/intra2_20Feb_D5//MGS.121//phylo//IQtree_allsites.log ERROR: *** Alignment files (if possible) " IQtree_allsites.log<https://github.com/user-attachments/files/25459119/IQtree_allsites.log> I attached the log. This is a highly similar MSA of closely related bacteria I used as input (filesize: 156MB), let me know if you would like to also see this. Could it be too many sites were automatically removed? best, Falk — Reply to this email directly, view it on GitHub<#135>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AENQCRXJH7EUTNRSGSEVSWD4NB4EXAVCNFSM6AAAAACV3L7TZ6VHI2DSMVQWIX3LMV43ASLTON2WKOZTHE3TEMRTGU4DOMA>. You are receiving this because you are subscribed to this thread.