[maker-devel] thousands of array-refs in merged .gff after 'gff3_merge'

[Michael Seidl]

Hi Carson,

I am using maker 2.31.

Thanks
Michael



On Tue, Apr 22, 2014 at 4:31 PM, Carson Holt <carsonhh at gmail.com> wrote:

> I've never seen this.  What version of MAKER are you using?
>
> --Carson
>
> From: Michael Seidl <michael.seidl at wur.nl<mailto:michael.seidl at wur.nl>>
> Date: Tuesday, April 22, 2014 at 8:27 AM
> To: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
> Subject: [maker-devel] thousands of array-refs in merged .gff after
> 'gff3_merge'
>
> Hi,
>
> I have a question on the post-processing of my maker output. I finished a
> maker run on a draft genome (231 scaffolds) without an error. To get a
> merged gff3 I run ~/local_progs/maker/bin/gff3_merge -d
> master_datastore_index.log. However, I realized that I contains next to
> gff3 conform output, thousands of lines of array refs, e.g.
> ARRAY(0x188a8578)). The total number of produced scaffolds is correct,
> however I have my doubts if I successfully retrieved all
> annotations...Could you maybe point me to a possible solution...
>
> Thanks in advance
> Michael
>
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>


-- 
*Michael F Seidl, PhD*
Research Fellow (Postdoc)
Laboratory of Phytopathology
Wageningen University
 P.O. Box 8025, 6700 EE Wageningen
Wageningen Campus, building 107 (Radix)
Droevendaalsesteeg 1, 6708 PB Wageningen

Tel.: +31-317-481288
Fax: +31-317-483412

Email: michael.seidl at wur.nl
Website: http://www.php.wur.nl/UK/
Twitter: @MFSeidl

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