Error - trying to load regions beyond the boundaries of non-circular sequence "chr3"

[umasaxena]

I am trying to analyse mutational data (aligned to GRCh38) and the code is here -

MutSpot(run.to=4.2, snv.mutations=baseline_maf, genome.build="Ch38", 
              cores = 2, cutoff.nucleotide.new = 1, drop=TRUE, top.nucleotide = 3,
              genomic.features=genomic_feature, dilution.analysis = TRUE,
              top.features = 15, working.dir=workdir)

I keep getting this error, the input data was modified as the tutorial suggested but the number of sample is about 100-
What am I doing wrong ?

[1] "Predict hotspot mutations for snv/indel"
[1] ">> Reading compact MAF ..."
[1] "Sample 20% sites"
[1] "Downsample SNV mutations as number of SNV mutations exceeded 48560.512"
[1] "Sample 40% sites"
[1] "Downsample SNV mutations as number of SNV mutations exceeded 97121.024"
[1] "Sample 60% sites"
[1] "Downsample SNV mutations as number of SNV mutations exceeded 145681.536"
[1] "Sample 80% sites"
[1] "Downsample SNV mutations as number of SNV mutations exceeded 194242.048"
[1] "Nucleotide selection for 20% sites"
[1] "SNV mutations available..."
Error in loadFUN(x, seqname, ranges) : 
  trying to load regions beyond the boundaries of
  non-circular sequence "chr3"
In addition: Warning message:
In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 137 out-of-bound ranges located on
  sequences chr17, chr18, chr20, chr3, chr5, and chrX. Note
  that ranges located on a sequence whose length is unknown
  (NA) or on a circular sequence are not considered
  out-of-bound (use seqlengths() and isCircular() to get the
  lengths and circularity flags of the underlying
  sequences). You can use trim() to trim these ranges. See
  ?`trim,GenomicRanges-method` for more information.

[AmandaMilou]

Hello,

Do you still get the same error if you turn dilution.analysis = FALSE? Also, could you check if all SNVs in the input are within the range of the BSgenome.Hsapiens.UCSC.hg38 annotation package? You may get this error if the SNVs are close to the chromosome ends (within 5bp), because we need to extract flanking sequences to compute the nucleotide context.