[maker-devel] GFF and Dereferencing problem

[Carson Holt]

Could you make sure you are using the most recent version of MAKER?  There was a bug similar to this that was fixed some time ago.  Current version is 2.31.8.  also when rerunning with the most recent version of MAKER, make sure to set the -a flag on the command line to force rerun of logged data.

—Carson


> On Jan 29, 2015, at 11:07 AM, Hamid Ashrafi <ashrafi at ucdavis.edu> wrote:
> 
> Hi,
>  
> After maker finishes its job it generates many files one of them is gff file. I see the following in some of my gff files. It seems it is a dereferencing problem. I am just wondering if affects my annotation.
>  
> Hamid
>  
> uti_cns_0004767 est2genome      match_part      856428  856485  3090    +       .       ID=uti_cns_0004767:hsp:8340:3.2.3.8;Parent=uti_cns_0004767:hit:4230:3.2.3
> uti_cns_0004767 est2genome      match_part      856587  856938  3090    +       .       ID=uti_cns_0004767:hsp:8341:3.2.3.8;Parent=uti_cns_0004767:hit:4230:3.2.3
> uti_cns_0004767 est2genome      match_part      857053  857201  3090    +       .       ID=uti_cns_0004767:hsp:8342:3.2.3.8;Parent=uti_cns_0004767:hit:4230:3.2.3
> uti_cns_0004767 est2genome      match_part      859004  859041  3090    +       .       ID=uti_cns_0004767:hsp:8343:3.2.3.8;Parent=uti_cns_0004767:hit:4230:3.2.3
> uti_cns_0004767 est2genome      expressed_sequence_match        878327  878771  1446    +       .       ID=uti_cns_0004767:hit:4231:3.2.3.8;Name=Sp_Illum_Trans_W
> uti_cns_0004767 est2genome      match_part      878327  878771  1446    +       .       ID=uti_cns_0004767:hsp:8344:3.2.3.8;Parent=uti_cns_0004767:hit:4231:3.2.3
> uti_cns_0004767 est2genome      expressed_sequence_match        884121  886610  2509    +       .       ID=uti_cns_0004767:hit:4232:3.2.3.8;Name=Sp_Illum_Trans_W
> uti_cns_0004767 est2genome      match_part      884121  884195  2509    +       .       ID=uti_cns_0004767:hsp:8345:3.2.3.8;Parent=uti_cns_0004767:hit:4232:3.2.3
> uti_cns_0004767 est2genome      match_part      886180  886610  2509    +       .       ID=uti_cns_0004767:hsp:8346:3.2.3.8;Parent=uti_cns_0004767:hit:4232:3.2.3
> ARRAY(0x1b91f110)
> ARRAY(0x1a686350)
> ARRAY(0x1b06bba0)
> ARRAY(0x1b931e10)
> ARRAY(0x1b13f3a0)
> ARRAY(0x1b6af650)
> ARRAY(0x1b929600)
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