Stopping BEAST run early

[Suzanne Williams]

Dear Beast Users,

I've just started to use BEAST and I set up a run that was way too long, so
I cut it short, by pressing command . Although I can open the log file in
Tracer, I cannot open the tree file. I get an error message: Number of taxa
doesn't match NTAXA field. I tried editing the file and adding end; but it
didn't help.

The only other thing I can think of is that I deleted four taxa using the
delete command in BEAUTI, but the number of taxa in the tree file appears to
be correct, so I'm not sure its a real error.

Does anyone have any ideas?

Suzanne

[Andrew Rambaut]

Suzanne,

It should be possible to fix this using a text editor. Could you send me
the start of the tree file (i.e., all the header information and up to
and including the first actual tree - I would say send me the whole
file,
but it is probably too large). It seems likely that it is something to
do with the deleting taxa in BEAUTi (rather than terminating the run
early).

In general, if you stop a BEAST run early you have to check the
following:

1) Both the log file and the trees file to check that the last line
was complete
(the program may have been stopped in the middle of writing a line).

2) Both the log file and the trees file have the same number of
states - if
not, delete lines from one or the other so that they finish on the
same state.

3) Add a single line to the end of the trees file:
End;

Andrew

___________________________________________________________________
Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624

[joe parker]

btw would it be easy to alter the beast output buffer to make sure you
can always retrieve the information even in a forced exit? happens
fairly frequently in my experience...

> EMAIL - a.ramb...@ed.ac.uk TEL - +44 131 6508624