I'm using the PureCN package to calculate GC-normalized coverage, but I'm receiving the following error below (bottom of page).
After execution is halted, a compressed bed-type text file is produced that has intervals for each of the chromosomes:
chr1:925918-926037 2150 25 1 0.880952380952381 chr1:930126-930365 4548 36 1 0.898016997167139 chr1:931005-931124 3449 41 1 0.871875
Can someone help me troubleshoot what the problem is and how to fix the error?
INFO [2020-07-12 13:30:25] Loading PureCN 1.18.0... INFO [2020-07-12 13:30:26] Processing WARN [2020-07-12 13:30:35] Found 398 overlapping intervals, starting at line 2422. WARN [2020-07-12 14:52:25] tumor.coverage.file and interval.file do not align. WARN [2020-07-12 14:52:25] Intervals in coverage and interval.file have conflicting on/off-target annotation. Error in simpleLoess(y, x, w, span, degree = degree, parametric = parametric, : invalid 'x' Calls: .gcNormalize ... correctCoverageBias -> .correctCoverageBiasLoess -> loess -> simpleLoess Execution halted