faircloth-lab/picme — Issue #4: 'Namespace' object has no attribute 'epochs'
Author: PrincessG
Created: 2011-10-24 20:01:58+00:00
State: open

I think this error is due to a renaming issue, but I'm having trouble finding where the rename first occurs and in which script.

addr126:picme Princess$ python /Users/Princess/Documents/Research\ Projects/Acanthomorpha/PicMeExperimentation/picme/bin/picme_compute.py PSG_InputFolder dated.tree --output OUTPUT --intervals=32-42,88-98,95-105,164-174 --times=37,93,100,170 --multiprocessing --hyphy ./hyphy2.osx

***************************************************
* *
* picme: PhyDesign - High-Throughput *
* *
* (c) 2011 Brant Faircloth, Jonathan Chang, *
* Mike Alfaro *
* *
* PhyDesign was created by the Townsend Lab *
* (http://phydesign.townsend.yale.edu) *
* *
* To cite Phydesign, please use: *
* *
* - J.P. Townsend, 2007. Profiling *
* phylogenetic informativeness. Systematic *
* Biology, 56(2), 222-231. *
* *
* - Pond, S.L.K., Frost, S.D.W., and S.V. Muse, *
* 2005. Hyphy: hypothesis testing using *
* phylogenies. Bioinformatics, 21(5), 676-9. *
* *
* Many thanks to Francesc Lopez-Giraldez and *
* Jeffrey Townsend for providing us with a copy *
* of their web-application source code. *
* *
***************************************************

Estimating site rates and PI for files:
Traceback (most recent call last):
File "/Users/Princess/Documents/Research Projects/Acanthomorpha/PicMeExperimentation/picme/bin/picme_compute.py", line 162, in
main()
File "/Users/Princess/Documents/Research Projects/Acanthomorpha/PicMeExperimentation/picme/bin/picme_compute.py", line 134, in main
args.times, args.epochs, args.threshold])
AttributeError: 'Namespace' object has no attribute 'epochs'
addr126:picme Princess$