These are chat archives for dereneaton/ipyrad

18th
Jul 2018
Siadjeu
@Siadjeu
Jul 18 2018 10:18

Hi @isaacovercast I used the cookbook-PCA-pedicularis.ipynb to my ipyrad GBS data but I got a error message when I run this script line:
pca = ipa.pca(vcffile)
print(pca.samples_vcforder). AttributeErrorTraceback (most recent call last)

<ipython-input-14-60222635656a> in <module>()
----> 1 pca = ipa.pca(vcffile)
2 print(pca.samples_vcforder)

AttributeError: 'module' object has no attribute 'pca'

Could you give to me the reason of this error message please, thanks!
Isaac Overcast
@isaacovercast
Jul 18 2018 11:26
You need to install the newest version of ipyrad conda install -c ipyrad ipyrad -f
@tommydevitt Which part of the structure cookbook are you running that isn't doing what you think it should be? Are you running ipcluster? How do you know it's not just running in the background? Can you see processes running in top?
Siadjeu
@Siadjeu
Jul 18 2018 11:30
OK, Thanks @isaacovercast !
tommydevitt
@tommydevitt
Jul 18 2018 15:45

@isaacovercast This is the cell where I'm not sure anything is happening:
## init an analysis object
s = ipa.structure( name="quick", workdir="/work/02745/tdevitt/lonestar/Eurycea/JA17735/structure-analysis/", data="/work/02745/tdevitt/lonestar/Eurycea/JA17735/sosorum-min110_outfiles/sosorum-min110.ustr", )

## set main params (use much larger values in a real analysis)
s.mainparams.burnin = 1000
s.mainparams.numreps = 5000

## submit N replicates of each test to run on parallel client
for kpop in kvalues: s.run(kpop=kpop, nreps=4, ipyclient=ipyclient)

## wait for parallel jobs to finish
ipyclient.wait()

I am running ipcluster. I don't know that it's not running in the background, but the only processes I see running are the notebook itself and the terminal. In the folder where output should be written, all I see is a file called quick-K-2.indfile.