These are chat archives for dereneaton/ipyrad

12th
Feb 2018
Lily Roberta Lewis
@LilyRobertLewis_twitter
Feb 12 2018 17:53
Hello! I'm returning to ipyrad analyses after a year long break. Previously I've not had trouble skipping step 1. I've already gotten my data demultiplexed and trimmed, and would like to start at step 3. I keep getting the error message "Error: You must first run step 1 on the assembly...". Any tips on how to skip step 1?
Lily Roberta Lewis
@LilyRobertLewis_twitter
Feb 12 2018 18:07
I see now that I have to run step 1 even if I'm not demultiplexing, but just only specify the path to the demultiplexed data. Sorry for the turning to the discussion board too soon:)
Jay Dimond
@jldimond
Feb 12 2018 20:52
@AnnaMaryMason_twitter re: your Apr 10 2017 post - just curious, what did you find was the best way to get coverage per locus per sample? This is also something I'm interested in.
Dylan
@DylanHCohen_twitter
Feb 12 2018 23:20

Hello all, I am trying to use the BPP jupyter notebook and I am having some problems. I have had it work in the past (December), but now it seems not to generate any output files and finishes almost instantly. I tried these commands, which seemed to work before...
git clone https://github.com/dereneaton/ipyrad.git
conda-build ipyrad/conda.recipe/bpp/
conda install --use-local bpp
I am also getting this new error when trying to run the program : NameErrorTraceback (most recent call last)

<ipython-input-77-f8ca643a34f3> in <module>()
4 ipyclient=ipyclient,
5 randomize_order=True,
----> 6 force=True,
7 )

/rhome/dcohen01/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/bpp.pyc in run(self, ipyclient, nreps, quiet, randomize_order, force)
361
362 ## submit to engines
--> 363 async = lbview.apply(_call_bpp, *(self._kwargs["binary"], ctlfile, alg00))
364 self.asyncs.append(async)
365

NameError: global name 'alg00' is not defined