Maker_functional_gff error "Can't use string ("") as a HASH ref"

Question

[luca]

Hi all, I am using the “maker_functional_gff” script to update my gff3 by adding functional annotation from blast results against uniprot, however I do get the following error when running the code:

Can't use string ("") as a HASH ref while "strict refs" in use at /opt/maker/bin/maker_functional_gff line 55, <$IN> line 277933.

I checked the line and it appears like the other lines in the gff3 file so I was wondering if you guys know what is causing the error? The “offending” line and the following one are:

tig00632243    maker  gene    2926    22617  .           -           . ID=Gacu_00045928;Name=Gacu_00045928;Alias=maker-tig00632243-snap-gene-0.9;Dbxref=MobiDBLite:mobidb-lite,PANTHER:PTHR15288,PANTHER:PTHR15288:SF5; 

tig00632243    maker  mRNA  2926    22617  .           -           .   ID=Gacu_00045928-RA;Parent=Gacu_00045928;Name=Gacu_00045928-RA;Alias=maker-tig00632243-snap-gene-0.9-mRNA-1;_AED=0.08;_QI=0|0|0|0.75|0.81|0.83|12|0|714;_eAED=0.34;Dbxref=MobiDBLite:mobidb-lite,PANTHER:PTHR15288,PANTHER:PTHR15288:SF5;

Thanks Luca

Answer 1

[Juke34]

I have seen the problem long time ago, I had added some print to spot the problem and realised the code has some weakness. I don't remember what was the problem but I think it was not related to the gff but rather to some info missing in the header of the fasta sequence used for the blast.
Anyway I use my own script and never had issue anymore... it is called agat_sp_manage_functional_annotation.pl and it is part of AGAT.

[luca]

Hi Juke! Thanks for your reply and your suggestion. I will definitely try AGAT (I had a quick look and it seems a very comprehensive suite of scripts for working with gff3 files). Thanks again man! :D