'ValueError: No usable data points to plot out of 0 probes, 0 segments, 0 variants' in Scatter Plot

Question

[wei.wei]

Hi,

I encountered this error while trying to do a scatter plot of a specified chromosome. Here's my command:

cnvkit.py scatter -s Sample1.cn{s,r} -c chr8

Here's the error I've gotten:

File "/Users/wwei/anaconda2/bin/cnvkit.py", line 13, in <module>
    args.func(args)
  File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/commands.py", line 914, in _cmd_scatter
    **scatter_opts)
  File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/scatter.py", line 49, in do_scatter
    y_min, y_max, title, segment_color)
  File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/scatter.py", line 237, in chromosome_scatter
    y_min=y_min, y_max=y_max, segment_color=segment_color)
  File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/scatter.py", line 381, in cnv_on_chromosome
    set_xlim_from(axis, probes, segments)
  File "/Users/wwei/anaconda2/lib/python2.7/site-packages/cnvlib/scatter.py", line 488, in set_xlim_from
    len(variants) if variants else 0))
ValueError: No usable data points to plot out of 0 probes, 0 segments, 0 variants

What are the probes, segments and variants referring to?

[Kevin Blighe]

Do you not have to run it like this:

cnvkit.py scatter Sample1.cnr -s Sample1.cns -c chr8 -o Sample1-scatter.pdf

Kevin

[wei.wei]

I think both ways of writing mean the same thing? But both gave me the same error. lol

[Kevin Blighe]

Okay, you may want to contact the developer of the program. Sometimes, he (the developer) is on Biostars, but not right now it seems.