[maker-devel] Error when running maker2zff script

[Carson Holt]

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
>