[maker-devel] missing gene coordinate

[Carson Holt]

Could you send me your maker control files, one of the contigs this occurs on, and the input gff3 file you are using?

Thanks,
Carson





> On Oct 17, 2014, at 2:33 PM, Mack, Brian <Brian.Mack at ARS.USDA.GOV> wrote:
> 
> Hi, 
>  
> I have some strange results after I have added non-overlapping predictions that had InterPro domains using the "pred_gff" option and  “keep_preds=1”. About 19 genes out of 13,000 total now have a missing start coordinate. I copied an example below (maker-168-augustus-gene-0.1). This particular gene was not even a non-overlapping prediction and it had proper coordinates before I added the non-overlapping predictions.
>  
> Brian
>  
> 168        maker    five_prime_UTR 1610      1711      .              +             .              ID=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1:five_prime_utr;Parent=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1
> 168        maker    CDS        1712      1784      .              +             0             ID=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1:cds;Parent=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1
> 168        maker    CDS        1846      1885      .              +             2             ID=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1:cds;Parent=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1
> 168        maker    CDS        2042      2145      .              +             1             ID=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1:cds;Parent=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1
> 168        maker    CDS        2219      2619      .              +             2             ID=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1:cds;Parent=maker-168-pred_gff_JCVI-gene-0.0-mRNA-1
> 168        maker    gene                     6737      .              +             .              ID=maker-168-augustus-gene-0.1;Name=maker-168-augustus-gene-0.1
> 168        maker    mRNA    5531      6737      .              +             .              ID=maker-168-augustus-gene-0.1-mRNA-1;Parent=maker-168-augustus-gene-0.1;Name=maker-168-augustus-gene-0.1-mRNA-1;_AED=0.37;_eAED=0.37;_QI=83|0.6|0.66|1|1|1|6|203|184
> 168        maker    exon      5531      5635      .              +             .              ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3421;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    exon      5692      5802      .              +             .              ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3422;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    exon      5880      5964      .              +             .              ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3423;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    exon      6024      6087      .              +             .              ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3424;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    exon      6193      6314      .              +             .              ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3425;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    exon      6384      6737      .              +             .              ID=maker-168-augustus-gene-0.1-mRNA-1:exon:3426;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    five_prime_UTR 5531      5613      .              +             .              ID=maker-168-augustus-gene-0.1-mRNA-1:five_prime_utr;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    CDS        5614      5635      .              +             0             ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    CDS        5692      5802      .              +             2             ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    CDS        5880      5964      .              +             2             ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    CDS        6024      6087      .              +             1             ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    CDS        6193      6314      .              +             0             ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    CDS        6384      6534      .              +             1             ID=maker-168-augustus-gene-0.1-mRNA-1:cds;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 168        maker    three_prime_UTR             6535      6737      .              +             .              ID=maker-168-augustus-gene-0.1-mRNA-1:three_prime_utr;Parent=maker-168-augustus-gene-0.1-mRNA-1
> 
> 
> 
> 
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