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miriammiyagi / QuIBL

Quantifying Introgression via Branch Lengths
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How to set numsteps with 20,000 trees #15

Open Morriyaty opened 3 years ago

Morriyaty commented 3 years ago

Hi !

I have a 20,000 trees in my tree file. I set numsteps for 300, but I got the error : ValueError: math domain error How can I fixed it ? Thanks.

Bests, Yinjia

miriammiyagi commented 3 years ago

Hi Yinjia,

Do you have any more details on the error message? Does the treefile have trees with 0-length branches?

Thanks! Mia

Morriyaty commented 3 years ago

Hi Mia,

Thanks for your reply. I will shou you my tree file and log file. And this is my inputfile.txt: [Input] treefile: new.tree numdistributions: 2 likelihoodthresh: 0.01 numsteps: 50 gradascentscalar: 0.5 multiproc: True totaloutgroup: 4 maxcores:15 [Output] OutputPath: ./wyj.csv The tree file contain part of 20,000 trees

Thanks! Yinjia wyj.log new.txt

matthewglasenapp commented 3 years ago

Were you able to resolve this error? I am also getting "ValueError: math domain error" with 7,645 input trees. I'm running the program on an Intel 24 core node with 128 GB memory capacity. I've tried running with 50 and 100 steps. I don't believe I have any trees with 0-length branches. error_report.txt InputFile.txt trees.txt

Morriyaty commented 3 years ago

Hi mathhe,

Which method did you use to get the trees? When I used fasttree, I got the same error. But when I used iqtree, it run well. I didn't know if I solved this error by iqtree was correct. You may try it and let me know.

Bests, Yinjia @matthewglasenapp

matthewglasenapp commented 3 years ago

Hi Yinjia, Thanks for the reply. I used iqtree version 2.1.4 to infer the gene trees. Not sure what's going wrong.