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 ---------------------------------------------------------------- On Thu, Feb 18, 2010 at 5:47 PM, Martin Morgan <[email protected]> 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 <[email protected]> > 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 > >>> [email protected] > >>> 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
