These are chat archives for dereneaton/ipyrad

7th
Nov 2018
Alex Linan
@alx552
Nov 07 2018 15:47 UTC

hi @dereneaton and @isaacovercast I tried to run tetrad on a computing cluster using a jupyter notebook and got this error. Do you know what could be going wrong? I am using ipyrad 0.7.28

data.run()

host compute node: [36 cores] on compute-012
inferring 636035400 induced quartet trees
[ ] 0% initial tree | 0:01:01 |
Exception found: error in 'inference'
EngineError(Engine 'd6bfc6d1-78d4e551142dc22ec8d8f37a' died while running task u'77ae3adf-e2b4307a7474ff992dc36ca0')

warning: error during shutdown:
error in 'inference'
EngineError(Engine 'd6bfc6d1-78d4e551142dc22ec8d8f37a' died while running task u'77ae3adf-e2b4307a7474ff992dc36ca0')

Isaac Overcast
@isaacovercast
Nov 07 2018 18:31 UTC
@ywckusuma Yes this should be fine. If it's SE you can run it as datatype 'rad', unless you used forward and reverse primers for the same locus in which case you should run it as 'gbs'. It's okay to leave the cutsites as the default value in this case.
@alx552 This is normally a resource allocation issue (not enough RAM).
@sarahjjacobs What happens when you type 'python' at the command line and then do 'import toytree'?
Deren Eaton
@dereneaton
Nov 07 2018 18:45 UTC
@alx552 , you will need to downgrade toytree to an earlier version by running conda install toytree=0.1.6 -c eaton-lab. The latest update has not been made compatible with tetrad yet. Working on fixing that now actually.
well, first check: toytree.__version__
Sarah J Jacobs
@sarahjjacobs
Nov 07 2018 20:15 UTC
@isaacovercast it appears to import toytree just fine ... i.e., it returns the python prompt with no warnings or anything
Sarah J Jacobs
@sarahjjacobs
Nov 07 2018 20:39 UTC
@isaacovercast hey isaac! per @dereneaton conversation with @alx552 just a little bit ago, I downgraded my toytree version and now I can import ipyrad.analysis with no problems!
Isaac Overcast
@isaacovercast
Nov 07 2018 21:33 UTC
Wicked.
Thanks for letting me know.
Yayan Kusuma
@ywckusuma
Nov 07 2018 22:11 UTC
@dereneaton noted. thanks a lot!