Hi Martin,
Is there a debug mode so  I can display the line causing the problem ?
Thanks.



Kind regards / Met vriendelijke groet,
Mohamed-Ramzi Temanni,
Prinsenstraat 1,
2316 HH Leiden
The Netherlands
+31616394074
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On Thu, Feb 18, 2010 at 5:47 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 02/18/2010 07:42 AM, Ramzi TEMANNI wrote:
> > Dear Martin,
> > Thanks for your reply,
> > The file are scraf file generated by the GA2, the files are converted
> from
> > scaf using the fq_all2std.pl script.
> > what is surprising is that the message i get dosen't appear
> sistematically,
> > other file from the same flowcell works fine. on 20 diffrent fastq file i
> > get it on 3 files.
> > thanks again for your help.
>
> If there's an error in readFastq then it would be great to have a
> reproducible example, e.g., the single record that causes problems.
>
> Martin
>
> > Regards,
> > Ramzi
> > ----------------------------------------------------------------
> >
> >
> > On Thu, Feb 18, 2010 at 4:33 PM, Martin Morgan <mtmorgan@fhcrc.org>
> wrote:
> >
> >> On 02/18/2010 06:58 AM, Ramzi TEMANNI wrote:
> >>> Hi,
> >>> I'm encountering the following error when trying to load fastq file:
> >>>
> >>> Error in .local(dirPath, pattern, ...) :
> >>>   _DNAencode(): key 73 not in lookup table
> >>
> >> Your fastq file is not conforming to readFastq's expectations, probably
> >> reading say a quality string or identifier and thinking it should be
> >> reading a DNA sequence. Maybe there's a missing carriage return or other
> >> problem? Also, readFastq handles files as specified in ?readFastq and in
> >> particular expects a fastq record to consist of exactly four lines. If
> >> fastq files in a different format are being produced, then I'll take the
> >> opportunity to update ShortRead.
> >>
> >> Martin
> >>
> >>>
> >>> Key 73 in ascii table is "I" (capital i)
> >>>
> >>> Anyone had encountered such error before ?
> >>>
> >>> Thanks in advance for your help
> >>>
> >>> Regards,
> >>> Ramzi
> >>>
> >>>> sessionInfo()
> >>> R version 2.10.1 (2009-12-14)
> >>> x86_64-pc-linux-gnu
> >>>
> >>> locale:
> >>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >>>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >>>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> >>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >>>
> >>> attached base packages:
> >>> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>>
> >>> other attached packages:
> >>> [1] biomaRt_2.2.0      ShortRead_1.4.0    lattice_0.18-3
> >>> BSgenome_1.14.2
> >>> [5] Biostrings_2.14.12 IRanges_1.4.11
> >>>
> >>> loaded via a namespace (and not attached):
> >>> [1] Biobase_2.6.1 grid_2.10.1   hwriter_1.1   RCurl_1.3-1   XML_2.6-0
> >>>
> >>>       [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-sig-sequencing mailing list
> >>> Bioc-sig-sequencing@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >>
> >>
> >> --
> >> Martin Morgan
> >> Computational Biology / Fred Hutchinson Cancer Research Center
> >> 1100 Fairview Ave. N.
> >> PO Box 19024 Seattle, WA 98109
> >>
> >> Location: Arnold Building M1 B861
> >> Phone: (206) 667-2793
> >>
> >
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>

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