minillinim/mikezbioscripts — Issue #4: barcodePlotter.py error
Author: fauziharoon
Created: 2012-02-23 06:11:18+00:00
State: open

Hey Mike,

I got a problem with this script. Can you please please help? I would like to do a tetranucleotide binning. Thanks!
This was the error message I got -

uqmharoo@keating:~/Phycisphaera/newbler/assembly2-mi93-ml43$ barcodePlotter.py -b out -c 1:4 -l image
-----------------------------------------------------------------------------------
barcodePlotter.py
Copyright (C) 2009, 2010 Lauren bragg, Michael Imelfort

This program comes with ABSOLUTELY NO WARRANTY;
This is free software, and you are welcome to redistribute it
under certain conditions: See the source for more details.
-----------------------------------------------------------------------------------

***Cluster testing.
you will need to look at the following files:
* heirachical_clusters.pdf
* internal_validation_clusters.pdf
* stability_validation_clusters.pdf

Loading required package: cluster
Loading required package: class

The number of items to be clustered is larger than 'maxitems'
The memory and time required may be excessive, do you wish to continue?
(y to continue, any other character to exit) y
Error in silhouette(cluster, dmatrix = as.matrix(Dist))[, 3] :
incorrect number of dimensions
In addition: Warning message:
In min(interClust, na.rm = TRUE) :
no non-missing arguments to min; returning Inf
Traceback (most recent call last):
File "/srv/whitlam/bio/apps/sw/bioscripts//bin/barcodePlotter.py", line 337, in
clustRTest(opts.numClusts, r)
File "/srv/whitlam/bio/apps/sw/bioscripts//bin/barcodePlotter.py", line 182, in clustRTest
r('intern <- clValid(mymatrix, '+cent_range+', clMethods = c("hierarchical", "kmeans"), validation = "internal");')
File "/srv/whitlam/bio/apps/sw/rpy2/2.2.1/lib/python2.7/site-packages/rpy2/robjects/__init__.py", line 225, in __call__
res = self.eval(p)
File "/srv/whitlam/bio/apps/sw/rpy2/2.2.1/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 82, in __call__
return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
File "/srv/whitlam/bio/apps/sw/rpy2/2.2.1/lib/python2.7/site-packages/rpy2/robjects/functions.py", line 34, in __call__
res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error in silhouette(cluster, dmatrix = as.matrix(Dist))[, 3] :
incorrect number of dimensions