Closed drxilu closed 2 years ago
Hi Xi,
This problem is caused by a change in output format in the latest version of Gubbins. I think I've fixed it earlier today in BactDating version 1.1.1, could you please check and confirm?
Best wishes, Xavier
Hi Xavier,
Thanks for your reply and fix on adapting the change from the latest version of Gubbins.
I checked and can confirm that BactDating is now working well with changes.
Appreciate your help.
Best, Xi
Dear Xavier,
When I use
loadGubbins()
to get a phylogeny, and thenunroot()
andinitRoot()
it, then usebactdate()
function withuseRes=T
, to obtain bactdating analysis. Unfortunately, it got stuck at the last step and kept receiving errors likeError in if (log(runif(1)) < l2 - l + dgamma(mu2, shape = 0.001, scale = 1000, : missing value where TRUE/FALSE needed
.After running some debugs and tracing back to the phylogeny after using
loadGubbins()
,t$unrec
values are not always between 0 and 1, which I believe should be a problem.I wonder if you have experienced similar situations or have some suggestions. Appreciate any help!
Best, Xi