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