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iqtree / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org
GNU General Public License v2.0
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IQ-TREE CRASHES WITH SIGNAL ABORTED #221

Open wyhhexa opened 1 month ago

wyhhexa commented 1 month ago

Dear Developers, I used IQ-TREE to construct gene trees for individual loci, with a total of 8276 loci. However, only 8229 were successfully constructed. I checked one example of the unsuccessful cases and found that IQ-TREE had crashed (see the attached file). Could you please advise on the possible reasons for this issue? I look forward to your response and appreciate your assistance. Thank you very much. [Uploading error.tar.gz…]()

bqminh commented 1 month ago

The link doesn't work. I can't download any file...

wyhhexa commented 1 month ago

[Uploading error.tar.gz…]()

wyhhexa commented 1 month ago

Dear Dr. Bui Quang Minh,

I apologize for the inconvenience caused by the non-functional link.

I have resent the files via email. Please find the attachment.

Best wishes

bqminh commented 1 month ago

OK i've got the file. From the log:

iqtree2 -s bmge_faa/17223at8782_AA.fna -mset LG,LG4X,Q.bird,Q.mammal -B 1000 -bnni -T 1

and the crash happened when testing model LG4X+I.

The problem is that LG4X is a mixture model with 4 Q matrices, which doesn't work in combination with +I. We'll neeed to look for disallowing this combination (@thomaskf will look at that). But for now, please move LG4X to -madd option:

iqtree2 -s bmge_faa/17223at8782_AA.fna -mset LG,Q.bird,Q.mammal -madd LG4X -B 1000 -bnni -T 1

so that LG4X will stand-alone and is not tested with other rate heterogeneity models.

wyhhexa commented 1 month ago

got it !

Thanks!