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. 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
