[Bioc-sig-seq] ShortRead qa() no longer working
mtmorgan at fhcrc.org
Wed Aug 25 19:20:10 CEST 2010
Hi Dario --
On 8/25/2010 12:00 AM, Dario Strbenac wrote:
> I've updated my ShortRead and IRanges packages recently and the qa function doesn't
I'm guessing that you mean you updated from ShortRead 1.6.0. to 1.6.2.
There don't look like there are code changes that would cause problems
> work for me anymore. It spends a couple of minutes processing, then fails with an error :
> chr "C:/Users/dario/Documents/Garvan/rawData/seq/Ramaciotti/25-03-2010/s_1_1"
>  "12627LN-FFPET_MBD2IP_1.Rdata" "12627LN-FFPET_MBD2IP_1.wig.gz" "12627LN-FFPET_MBD2IP_1_GR.Rdata" "mapping.log" "s_1_sequence.fastq.gz" "s_1_sequence.uniq.map.gz"
>> QAfastq<- qa(path, "fastq.gz", "fastq")
> Error in stop(msg, " ", errors, domain = NA) :
> no function to return from, jumping to top level
> Error in slot(object, ".srlist") :
> cannot get a slot (".srlist") from an object of type "NULL"
> In addition: Warning message:
> elements: 1
> UnspecifiedError: qa(readFastq(dirPath, pattern, ...), pattern, verbose = verbose)
> error in evaluating the argument 'dirPath' in selecting a method for function 'qa'
fl = list.files(path, "fastq.gz", full=TRUE)
return something sensible (just the path to s_1_seqeunce.fastq.gz)?
.Call(ShortRead:::.read_solexa_fastq, fl, TRUE)
return a list containing the sequences, ids, and qualities? If not, then
there are problems parsing the fastq file. The parser expects the reads
/ qualities to occupy a single line each, and the qualities to be
encoded. Is that the case for these reads? Also, how many and what
length are the reads supposed to be?
> R version 2.11.0 (2010-04-22)
>  LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 LC_NUMERIC=C LC_TIME=English_Australia.1252
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  ShortRead_1.6.2 Rsamtools_1.0.0 lattice_0.18-5 Biostrings_2.16.0 GenomicRanges_1.0.7 IRanges_1.6.15
> loaded via a namespace (and not attached):
>  Biobase_2.8.0 grid_2.11.0 hwriter_1.2 tools_2.11.0
> Could this be a bug in the function ?
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
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