-o outgroup option causes error

[taua...@gmail.com]

Dear Mihn,

I am trying to iq-tree with the -o option, but I get an error (below). Do you have any ideas of what could be the problem? I believe the taxon I am assigning as outgroup is not present in all partitions, but not sure if this makes a difference in a concatenated analysis.

Let me know if you would like the log file.

Thanks!

Tauana

ERROR: phylotree.cpp:389: void PhyloTree::setRootNode(const char *): Assertion `root' failed.

ERROR: STACK TRACE FOR DEBUGGING:

ERROR: 

ERROR: *** IQ-TREE CRASHES WITH SIGNAL ABORTED

ERROR: *** For bug report please send to developers:

ERROR: ***    Log file: 37taxa.log

ERROR: ***    Alignment files (if possible)

/var/slurmd/spool/slurmd/job29592376/slurm_script: line 35: 52178 Aborted                 ../../scripts/IQ-Tree1.6.beta4/bin/iqtree -nt $cpus -st AA -ninit 10 -bb 1500 -pre $dataset -m MFP+MERGE -rcluster 10 -madd LG4M,LG4X -mrate G,R,E -msub nuclear -s ../matrices/$1/*.nex -sp $3 -o $2

[Bui Quang Minh]

Dear Tauana,

I think somebody else reported similar problem, which means that the taxon does not appear in the (concatenated) alignment. It’s fine if this taxon does not appear in some partitions, as long as it indeed appears in at least one partition.

Nevertheless can you send me the log file to know exactly where iqtree stopped?

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) univie.ac.at

[taua...@gmail.com]

I sent Minh the log file and this was the problem, just in case anyone else gets the same error:

Error: ERROR: phylotree.cppphylotree.cpp::389389: : void PhyloTree::setRootNode(const char *)void PhyloTree::setRootNode(const char *): Assertion `: Assertion `rootroot' failed.' failed.

Minh: I see the problem now: ModelFinder will go through the partitions to find the best-fit model for each partition. And this happens for the partition that does not contain the outgroup. So as a quick solution right now, please do not use -o option. You can anyway reroot the tree later on in any tree viewer. Nevertheless, I log this bug and will fix it for the next release. Thanks for reporting the problem!

Thanks, Minh!