*beast log files returns infinity for posterior and likelihood and a constant prior at aprox 22 million generations
Opened this issue · 2 comments
GoogleCodeExporter commented
What steps will reproduce the problem?
1. 20 species (is this too many?) 3 mit genes and 2 nuc genes unliked
models all with gtr estimate freq and gamma+i none are partitioned by
codon. Only one individuals per species. Trees are all unlinked because
BEauti v1.5.2.app will not create a working beast file if i link the mit
genes together. Relaxed clock:uncorrelated lognormal all estimate box
checked but one, this gene rate = 1 with sequences error model off. all
trees are randomly generated using speciestree:yule process pop size
continuous and root constant. All other priors and operators left default.
MCMC changed to 100 million.
What is the expected output? What do you see instead?
No infinity values.
*beast log files returns infinity for posterior and likelihood and a
constant prior at aprox 22 million generations
What version of the product are you using? On what operating system?
Beuti v1.5.2 and beast 1.5.2
Beuti v1.5.2 mac
beast run on a Linux cluster consisting of 320 nodes (Dell PowerEdge M610).
Each node is equipped with two quad-core Intel Nehalem processors (2.8 GHz)
and 24 GB of memory.
Please provide any additional information below.
this has occurred 6 times on multiple xml files with same settings as
described above.
Original issue reported on code.google.com by jessebre...@gmail.com on 12 Nov 2009 at 3:52
GoogleCodeExporter commented
This looks like an issue with the model/data being analysed rather than BEAST.
My guess would be over-
parameterization or improper priors resulting in some parameters going to a
limit. It may be a bug in the XML
generated by BEAUti. More information is required to solve this - the XML file
for example and the final line of
the log file to see which components have become -Inf. Look for other
parameters approaching extreme values
in the lead up to this.
Original comment by ramb...@gmail.com on 16 Nov 2009 at 9:54
- Added labels: Type-Other
- Removed labels: Type-Defect
GoogleCodeExporter commented
Original comment by ramb...@gmail.com on 25 Nov 2009 at 11:42
- Added labels: BEAST, v1.5.2