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hahnlab / CAFE5

Version 5 of the CAFE phylogenetics software
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Cafe error #189

Open Ram0619 opened 2 weeks ago

Ram0619 commented 2 weeks ago

Hi, I'm basically a biologist and I am getting into the field of bioinformatics. I'm trying to run CAFE analysis to understand the evolution of a wild legume species against cultivated species and other close relatives. I used orthofinder to determine the orthogroups and species tree. I used the following script,

! cafe

version

date

load -i Orthogroups_input Orthogroups_input.csv .tsv -t 10 -l logfile.txt

tree (sp8:10,((sp5:2.91386,sp3:2.91386):2.04214,((sp1:1.11798,sp2:1.11798):2.26292,(sp4:2.82388,(sp7:1.6567,sp6:1.6567):1.16718):0.557025):1.57509):5.04401)

lambda -s -t (1,((1,1)1,((2,2)2,(2,(2,2)2)1)1)1)

errormodel -model error.txt -p 0.01

report report.txt

I'm getting a warning message as follows, WARNING: Calculated posterior probability for family OG0000000 = 0 Lambda : 0.03280017385259,0.08005850450136 & Score: -inf .WARNING: Calculated posterior probability for family OG0000000 = 0 Lambda : 0.03444018254522,0.08005850450136 & Score: -inf .WARNING: Calculated posterior probability for family OG0000000 = 0 Lambda : 0.03280017385259,0.48035102700815 & Score: -inf. Additionally, I'm attaching the files associated with the analysis Can someone help me out!! Regards, Ram