[Primeusers] problem running primeGSR

[James Cotton]

We've having difficulty getting PrimeGSR to run - it looks like the  
input files are read in sucessfully, but before it reports any results  
from the MCMC, we get a message
'Probability: Division with zero attempted!'

We don't get any output file.

My initial thought was that this was something to do with the  
likelihood of some position being effectively zero, but we get this  
whatever starting parameter values we try, and on input files with  
different (ultrametric) branch lengths.

Following suggestions on this forum, I've tried setting -c to a big number (up to 500), and I've tried scaling the tree so the root is at 1.0,  so I'm not sure what else to  try. A command  line is:


../primeGSR -o testjac -Sm JC69 -i 100000 -t 100 -Bp 0.001 0.001 -c 150 -Ed Gamma -Hi lyz-species-bl.tre.jac.len1 lyz_code_100323.fa.jac lyz-gene-species-map.gs.jac



Anything you can do to help would be much appreciated.
Yours,
James Cotton