[maker-devel] missing gene coordinate

[Mack, Brian]

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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