These are chat archives for dereneaton/ipyrad

19th
Nov 2018
Joel A. Mercado-Diaz
@jamercadodiaz
Nov 19 2018 04:56
Hi @isaacovercast . Thanks for the prompt response. I will check on all these questions tomorrow with the person managing the server. That link you share seems super useful!
@gscabanne ..nothing happened after reinstalling h5py. I just got the same error again.
solomonchak
@solomonchak
Nov 19 2018 17:25

This should be a common question, but I couldn't find an answer.

I started an assembly and were at the middle of step 3 when the HPC node restarted. After reconnecting the notebook, how do I reload and resume the analysis from step 3? All the folders associated with the previous run are still there.

new = ipyrad.Assembly("synalpheus")
new.set_params(......)
new.run("123")

Thanks for your help!

gscabanne
@gscabanne
Nov 19 2018 19:41
@solomonchak , why not just restarting from step 3?
Isaac Overcast
@isaacovercast
Nov 19 2018 20:29
@solomonchak Yes, you will need to restart step 3 from the beginning, as there are not intelligent checkpoints within this step (yet).
leclearnm
@leclearnm
Nov 19 2018 23:12
Hi @isaacovercast. I was reading up through some previous comments about whether or not the output from ipyrad includes phased loci suitable for input into fineRADstructure. The ipyrad docs page doesn't currently describe the alleles.loci format, though the introductory tutorial indicates this information is in the hdf5 file. What is the current status?