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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?
Could PureCN be getting some NA values somehow for plotting, and accidentally generating an NA value for ylim?
Can you post the log-file? No variants to plot means that PureCN found no germline SNPs to plot.