[BioC] an error from ShortRead

wang peter wng.peter at gmail.com
Fri Mar 16 14:37:50 CET 2012

hello all
when i runned the scripts to clean the fastq data, it reported an error.
but if i run it step by step, it has no problem

reads <- readFastq(fastqfile);
seqs <- sread(reads);
qual <- SolexaQuality(quality(quality(reads)))

that is the error place:
myqual_mat <- matrix(charToRaw(as.character(unlist(qual))),
nrow=length(qual), byrow=TRUE)

Error in .Call(.NAME, ..., PACKAGE = PACKAGE) :
  negative length vectors are not allowed
Calls: trimRead ... matrix -> charToRaw -> unlist -> unlist -> .Call2 -> .Call
Execution halted

R version 2.14.1 (2011-12-22)
Platform: x86_64-redhat-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839 at cornell.edu

More information about the Bioconductor mailing list