search

dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
GNU General Public License v3.0
72 stars 40 forks source link

STRUCTURE k=1? #400

Closed pabuveery closed 4 years ago

pabuveery commented 4 years ago

Hi! I've been using the STRUCTURE component of iPYRAD analysis through a Jupyter notebook, and I was wondering whether it is possible to run STRUCTURE with k = 1. I've been able to successfully complete analyses at k = 2-5, but when I input the following line:

struct1.run(kpop=1, nreps=10, auto=True)

I get the following error:

Encountered an Error. Message: list.remove(x): x not in list Traceback (most recent call last): File "/gpfs/ysm/project/prum/mdh57/conda_envs/new_ipyrad/lib/python2.7/site-packages/ipyrad/core/Parallel.py", line 313, in wrap_run self.tool._run(ipyclient=self.ipyclient, **self.rkwargs) File "/gpfs/ysm/project/prum/mdh57/conda_envs/new_ipyrad/lib/python2.7/site-packages/ipyrad/analysis/structure.py", line 364, in _run jobs.remove(i) ValueError: list.remove(x): x not in list

Thanks for taking a look!

isaacovercast commented 4 years ago

Hello @pabuveery. I don't know what's going on because it works for me. Can you show me all the output it produces when you call that function? Are you on the most recent version of ipyrad? What version are you on? Can you show more of your notebook code so I can see context? What happens if you just try to run this:

struct1.run(kpop=2, nreps=10, auto=True)

isaacovercast commented 4 years ago

image

pabuveery commented 4 years ago

Thank you so much, I just ran the above code and it worked. Not totally sure what happened but I think I must have been improperly defining the STRUCTURE job. Either way, thank you for your help!