[maker-devel] Error when running maker2zff script

[Carson Holt]

I’m glad you were able to fix it.  I’ll check to see why it was failing as
well.

Thanks,
Carson


From:  dhivya arasappan <darasappan at gmail.com>
Date:  Friday, March 14, 2014 at 10:16 AM
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: Error when running maker2zff script

Kindly ignore my previous question. I was able to manipulate the scaffold
names in the gff file to get maker2zff to work.

Thanks
dhivya

On Mar 14, 2014, at 10:55 AM, dhivya arasappan <darasappan at gmail.com> wrote:

> My message got flagged by the maker list again, so I’m forwarding this
> separately to you.  Is there a better way to send biggish files?
> 
> 
> Thank you
> Dhivya
> 
> 
> 
> Begin forwarded message:
> 
>> From: dhivya arasappan <darasappan at gmail.com>
>> Subject: Error when running maker2zff script
>> Date: March 13, 2014 at 8:35:27 PM CDT
>> To: Carson Holt <carsonhh at gmail.com>, maker-devel at yandell-lab.org
>> 
>> Hi Carson,
>> 
>> I used gff3_merge to create my gff file from maker output. I've attached it
>> here. But when I run maker2zff on it, I get the following error:
>> 
>> Can't use an undefined value as an ARRAY reference at
>> /opt/apps/maker/2.30/bin/maker2zff line 177, <GFF> line 7294251.
>> 
>> It produces an incomplete output file and it looks like it may be running
>> into problems when it encounters scaffold3%2F0.  I'm wondering if its having
>> problems with my scaffold names. There seem to be some inconsistencies
>> because it's referred to as  scaffold3%F0 and scaffold3/0 in the gff file.
>> It goes through other scaffolds like SCAFFOLD3_873, SCAFFOLD3_95 etc just
>> fine.   I did try replacing the scaffold names in the gff file, but still get
>> the same error.   Any ideas?
>> 
>> Substitution command I used, for your reference:  sed 's/3\%2F/3_/g' gfffile|
>> sed 's/\//\_/'  > mod.gfffile
>> 
>> Thanks
>> Dhivya
>> 
> <head.gff.gz>
> 



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