[maker-devel] Error with maker_functional_gff

[Carson Holt]

I’ve seen this exact same error before (https://groups.google.com/forum/#!searchin/maker-devel/$2Fmaker_functional_gff$20line$2058/maker-devel/cBuQMKTJj2M/aXGnARZ7JhsJ).

It is caused by the ID from the blast report and input protein fasta. maker_functional_gff is not a generic script that can work on any input, it only works on blast results against Uniprot/Swiss-prot.  The script is expecting a very specific header format in both the report and the protein fasta and if it doesn’t see it, then it is missing certain pieces of needed information.

Thanks,
Carson

> On Dec 16, 2015, at 12:27 PM, Daniel Ence <dence at genetics.utah.edu> wrote:
> 
> Hi Ole, can you send a line for a gene feature that does work? 
> 
> 
> Daniel Ence
> Graduate Student
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> 
>> On Dec 14, 2015, at 12:21 PM, Ole Kristian Tørresen <ole.toerresen at gmail.com <mailto:ole.toerresen at gmail.com>> wrote:
>> 
>> Hi,
>> I'm trying to update my annotation with some functional annotations with maker_functional_gff, but get this annoying error:
>> Can't use string ("") as a HASH ref while "strict refs" in use at /cluster/software/VERSIONS/maker-2.31.8/bin/maker_functional_gff line 58, <$IN> line 108947.
>> Line 108947 in the input gff is this:
>> 
>> LG08    maker   gene    13786695        13806565        .       -       .       ID=GAMO_00029233;Name=GAMO_00029233;Alias=maker-LG08-snap-gene-46.343;
>> It seems like the regexp in line 55 in the maker_functional_gff script doesn't pick up the ID, but I can't see any difference between that line and other similar lines. 
>> 
>> Any help to trace down this is really appreciated. Do you need any other information?
>> 
>> Thank you.
>> 
>> Sincerely,
>> 
>> Ole Kristian Tørresen
>> 
>> 
>> 
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