I´m processing a fastq file of reads that have already paired. Trying to get the GC content i get this error ???

> fq <- readFastq(file)
> fq
class: ShortReadQ
length: 50545 reads; width: 79..503 cycles
> gc <- gcContent(fq)
Warning messages:
1: In if (nbins > .Machine$integer.max) stop("attempt to make a table with >= 2^31 elements") :
  the condition has length > 1 and only the first element will be used
2: In if (is.na(nbins)) stop("invalid value of 'nbins'") :
  the condition has length > 1 and only the first element will be used

Looking at the fastqfile

> qual <- as(quality(fq), "matrix")
> qual
    [,501] [,502] [,503]
    [1,]     NA     NA     NA
    [2,]     NA     NA     NA
   

I´ve noticed that the qual object contains NA values at the end of the sequence. Any idea ??

I have merged pairs using bbmerge first but don´t see any problem in the fastq file. I have tried other programs and fastq file look ok.

Sorry,

Got it from the manual.

gcContent <- function(x)
{
  abc <- alphabetFrequency(sread(x), baseOnly=TRUE)
  gcPerRead <- rowSums(abc[,c("G", "C")])
  wd <- unique(width(sread(x)))
  tabulate(1 + gcPerRead, 1 + wd)
}

  tabulate(1 + gcPerRead, 1 + wd) seems to returning the previous error

great,

thanks so much,

david