[maker-devel] Error when running maker2zff script

[dhivya arasappan]

Awesome! Thanks Carson.

Dhivya


On Mon, Mar 17, 2014 at 4:14 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Just an update on this.  I've fixed the maker2zff script to handle the
> issues seen.  Looking at this actually brought to light another issue.
> There is inconsistent escape character specification for GFF3 in column 1
> (the source ID), column 8 (the attributes ID and Target_ID), as well as
> the FASTA ID for internal sequence.  We're updating the GFF3 spec to
> clarify this so that everywhere you see the same ID getting treated the
> same way for character escaping.
>
> To be safe though, only use these characters in your contig IDs for the
> assembly when using any tool that reads or outputs GFF3 -->
> a-zA-Z0-9.:^*$@!+_?-|
>
> Any character not in that set has a high chance of breaking some
> downstream tool.  For now just assume the strict interpretation from the
> GFF3 spec for column 1, must be used on all IDs everywhere (see below).
>
> >>Column 1: "seqid"
> >>The ID of the landmark used to establish the coordinate system for the
> >>current feature.
> >>IDs may contain any characters, but must escape any characters not in
> >>the set [a-zA-Z0-9.:^*$@!+_?-|].
> >>In particular, IDs may not contain unescaped whitespace and must not
> >>begin with an unescaped ">".
>
>
> Thanks,
> Carson
>
>
>
> On 3/13/14, 7:35 PM, "dhivya arasappan" <darasappan at gmail.com> wrote:
>
> >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
> >
>
>
>
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