[Biojava-l] A Exception Has Occurred During Parsing.

[Richard Holland]

Hello. Could you also post the relevant parts of your code that you are running when this exception happens?

cheers,
Richard

On 11 Dec 2009, at 00:46, Ilhami Visne wrote:

> Hi,
> 
> I'm following the suggestion "Please submit the details that follow to
> biojava-l at biojava.org or post a bug report to http://bugzilla.open-bio.org/"
> .
> 
> The sequence of concerns is at
> http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=39645757&rettype=gb&seq_start=1353&seq_stop=2128&strand=1
> 
> Format_object=org.biojavax.bio.seq.io.GenbankFormat
> Accession=null
> Id=null
> Comments=Bad section
> Parse_block=
> Stack trace follows ....
> 
> 
>        at
> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:603)
>        at
> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:278)
>        at
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110)
>        ... 8 more
> Caused by: java.lang.NullPointerException
>        at
> org.biojavax.bio.seq.io.GenbankFormat.readSection(GenbankFormat.java:593)
>        ... 10 more
> org.biojava.bio.BioException: IO failure whilst reading from Genbank
> 
> Any quick fix,patch?
> 
> thanks.
> Ilhami Visne
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--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/