failure to calculate GC on chrUn_gl000220

[anatolydryga]

Error in loadFUN(x, seqname, ranges) :
trying to load regions beyond the boundaries of non-circular sequence "chrUn_gl000220"
18 stop("trying to load regions beyond the boundaries ", "of non-circular sequence "",
seqname, """)
17 loadFUN(x, seqname, ranges)
16 loadFUN(x, seqname, ranges)
15 loadSubseqsFromStrandedSequence(x@single_sequences, seqname,
ranges(gr), strand(gr), is_circular)
14 FUN(1:81[[52L]], ...)
13 lapply(seq_len(length(grl)), function(i) {
gr <- grl[[i]]
if (length(gr) == 0L)
return(DNAStringSet()) ...
12 lapply(seq_len(length(grl)), function(i) {
gr <- grl[[i]]
if (length(gr) == 0L)
return(DNAStringSet()) ...
11 .extractFromBSgenomeSingleSequences(x, sseq_args$names, sseq_args$start,
sseq_args$end, sseq_args$width, sseq_args$strand)
10 .local(x, ...)
9 getSeq(reference_genome_sequence, rangesToCalc, as.character = F)
8 getSeq(reference_genome_sequence, rangesToCalc, as.character = F) at GCcontent.R#21
7 getGCpercentage(site, "GC", window_size, reference)
6 system.time(getGCpercentage(site, "GC", window_size, reference)) at timing_GCcontent.R#14
5 FUN(X[[5L]], ...)
4 lapply(X = X, FUN = FUN, ...)
3 sapply(sites, function(site) {
window_size <- c(large = 100)
GC_time <- system.time(getGCpercentage(site, "GC", window_size,
reference))["user.self"] ...
2 sapply(sites, function(site) {
window_size <- c(large = 100)
GC_time <- system.time(getGCpercentage(site, "GC", window_size,
reference))["user.self"] ... at timing_GCcontent.R#12
1 time_GC()