--initvalues

[Anita Wray]

Hello All, 

I am attempting to run bootstrapped iterations of my best model in order to get 95% CIs and I'm running into issues (see here). I wanted to try adding the --initvalues command to see if that could fix my issue, but I don't think I fully understand the command and would greatly appreciate any assistance. I am trying to run fastsimcoal using the following command:

PREFIX='CQB_boot'
fastsimcoal2 -t ${PREFIX}.tpl -e ${PREFIX}.est -m -0 -C 10 -n 100000 –initvalues bidirectional_admixture.pv -L 40 -s0 -M -q -c 20 -B 20

My understanding of --initvalues was that it should start at the values provided in the .pv file (attached). When I look at the first row of the .brentlhoods file, I noticed that they are drastically different values (see attached). Is this not what --initvalues does? If not, should my values be close to the --initvalues parameters? 

Best, 

Anita

[Sarah Wells]

Late reply but for anyone experiencing the same problem. I had the same issue, it was due to --initValues needing a capital "V". The fastsimcoal2 manual unfortunately gives examples where both are used, but --initvalues will not use starting values as the flag is not recognised. Only --initValues is recognised. Once changed, the program started using my specified starting parameter values as designed.

Hope that helps someone!

Sarah