These are chat archives for dereneaton/ipyrad

21st
Nov 2018
solomonchak
@solomonchak
Nov 21 2018 17:46
@isaacovercast @gscabanne When the kernel restarts, I lost the 'variable' new. How do I save it and load it back the next time? Or somehow save the entire environment like Rstudio?
gscabanne
@gscabanne
Nov 21 2018 17:49
@solomonchak , you have mentioned that the analysis stopped in the middle of step3. Since step progression is serial, I understand that step 1 and 2 are completed and its results saved. Does not work starting from -s3?
Isaac Overcast
@isaacovercast
Nov 21 2018 18:54
@solomonchak If the kernel crashes you can reload your json file and restart from whatever step you want, like this:
new = ipyrad.load_json("synalpheus.json")
new.run("3")
gscabanne
@gscabanne
Nov 21 2018 18:58
And @isaacovercast ...what would be the difference with ....ipyrad -p synalpheus -s3 ....?
Isaac Overcast
@isaacovercast
Nov 21 2018 20:15
@gscabanne This amounts to the exact same thing.
Assuming the params file is called 'syanlpheus' and not 'params-synalpheus.txt', the -p param takes the file name, not the assembly name.
solomonchak
@solomonchak
Nov 21 2018 21:01
Thanks a lot! @isaacovercast @gscabanne