[Bioc-sig-seq] ReadFastq error

[Martin Morgan]

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 at 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 at 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