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

[Carson Holt]

Could you check the individual contig GFF3's before merge.  Do any of those
contain array refs?  Also is it exactly 2.31 or the current 2.31.3?

--Carson

From:  Michael Seidl <michael.seidl at wur.nl>
Date:  Tuesday, April 22, 2014 at 8:37 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] thousands of array-refs in merged .gff after
'gff3_merge'

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
> 
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 



-- 
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/ <http://www.php.wur.nl/UK/>
Twitter: @MFSeidl
 
www.disclaimer-uk.wur.nl <http://www.disclaimer-uk.wur.nl/>


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20140422/0af504b6/attachment-0003.html>