These are chat archives for dereneaton/ipyrad

8th
Nov 2017
Akanksha Pandey
@aakanksha12
Nov 08 2017 15:02
@isaacovercast : Thanks for your reply. I re ran the analysis with -d tag and it crashes at step 3 with the following error message

INFO:ipyrad.core.assembly:interrupted engine 5 w/ SIGINT to 25499
INFO:ipyrad.core.assembly: shutting down engines
INFO:ipyrad.core.assembly: finished shutdown

Encountered an unexpected error (see ./ipyrad_log.txt)
Error message is below -------------------------------
IndexError(list index out of range)
INFO:ipyrad:debugging turned off

The ipyrad_log.txt doesn't show any error messages at the end.
Isaac Overcast
@isaacovercast
Nov 08 2017 16:29
@aakanksha12 It still would be helpful to see the contents of the ipyrad_log.txt. The error will be inside the file somewhere. Can you email it to me? I'll pm my email address.
toczydlowski
@toczydlowski
Nov 08 2017 17:04
@dereneaton @isaacovercast Quick question - is there a way to force ipyrad to use only maj rule (and not statistical)? I tried setting mindepth_majrule to 10 and mindepth_statistical to 0 or leaving it blank but both threw errors. Thanks! - Rachel
Isaac Overcast
@isaacovercast
Nov 08 2017 19:12
@toczydlowski Oh, yeah, actually this is easy, but a little counterintuitive. If you set mindept_statistical > maxdepth (parameter 13) then it will always fall back to mindepth_majrule.
Deren Eaton
@dereneaton
Nov 08 2017 20:50
Hi @tangerzhang, that is the expected behavior. Those are not errors, they are the two objects which are returned by the plotting function. You can suppress them by adding a ; at the end of the function call. It has no effect on the result. Either way it returns two objects which represent the Canvas and Axes objects of the plot. If you are using a Jupyter notebook then the plot will also be embedded in the output of the cell. If you are running your code in something else, like ipython, then you will need to save the Canvas object. Which can be done in several ways, see the toyplot docs for details: http://toyplot.readthedocs.io/en/stable/rendering.html#rendering
toczydlowski
@toczydlowski
Nov 08 2017 21:47
@isaacovercast Oh. OK thanks! Definitely counterintuitive. You might add that officially to the assembly params "manual". (I'm just using this for testing, not final assembly, but I'm guessing others might want to do the same.)
Deren Eaton
@dereneaton
Nov 08 2017 22:55
@Wind-ant this looks like a problem with the installation. Try reinstalling both with conda install.