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I am getting an error in AllelicCNV only in few samples: java.lang.IllegalArgumentException: Initial point in slice sampler is not within specified range. at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:609) at o…
(Quote) The problem was that I was running too many samples in parallel and spark apparently ran out of ports. It works now after reducing the number of running jobs.
Thank you @shlee. It worked after removing the chr characters and sorting the chromosomes :)
@shlee It is the same problem seen by @shilin and answered by @slee I tried the latest version (alpha1.2.3) without success and my reference genome is hg19.
how can I disable spark in AllelicCNV?
PlotSegmentedCopyRatio plots have only the axes and chromosomes without points, any idea why?