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FerRacimo / PolyGraph

A method to detect polygenic adaptation in an admixture graph
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Error in running MCMC part #1

Open worny1017 opened 1 year ago

worny1017 commented 1 year ago

Hi! I'm trying to implement PolyGraph, but I got the issue from running the MCMC part. Right now, I use the dog GWAS dataset, and I got the admix graph using admixtool2, then converted it to the 'admixtruegraph' format. I got the q_file output format, but the trace_output did not come out properly and stopped because of the 'if (replace == TRUE) {: missing value where TRUE/FALSE needed' error. I assumed the error came out because the alpha parameter did not load.. but did not know which part was the problem. Can you help me?

this is the error log ''' The following objects are masked from ‘package:admixturegraph’:

f2, f3, f4

[1] "Loading data..." [1] "Computing F matrix..." [1] "Computing Q_b statistics..." [1] "Computing sign-randomized P-values, using 1000 pseudo-replicates..." [1] "Running MCMC..." if (replace == TRUE) {: missing value where TRUE/FALSE needed' '''

worny1017 commented 1 year ago

--update I just got the print some steps, and I got some "log_prob_new_graph: -InF", and I think the calculating innerfreqs part is fine