PureCN: Error in plot.window(...) : need finite 'ylim' values
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twtoal • 0
@twtoal-15473
Last seen 6 months ago

I'm running PureCN (developer version 1.11.8) on a new project, and a number of errors occur, one of which is:

INFO [2018-06-20 13:46:48] Done.

INFO [2018-06-20 13:46:48] ------------------------------------------------------------

INFO [2018-06-20 13:46:48] Fitting variants for purity 0.39, tumor ploidy 4.09 and contamination 0.01.

Warning message:

In .bcfHeaderAsSimpleList(header) :

  duplicate keys in header will be forced to unique rownames

WARN [2018-06-20 13:46:49] No variants to plot

Error in plot.window(...) : need finite 'ylim' values

Calls: plotAbs ... .plotTypeAF -> plot -> plot.default -> localWindow -> plot.window

In addition: Warning messages:

1: In min(x) : no non-missing arguments to min; returning Inf

2: In max(x) : no non-missing arguments to max; returning -Inf

Execution halted

How can I diagnose this problem?

 

PureCN • 522 views
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Could PureCN be getting some NA values somehow for plotting, and accidentally generating an NA value for ylim?

 

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Can you post the log-file? No variants to plot means that PureCN found no germline SNPs to plot. 

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twtoal • 0
@twtoal-15473
Last seen 6 months ago

I fixed the problem.  There were problems in the VCF files.

 

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