[maker-devel] Merge warning = 1

[Carson Holt]

It’s an internal debugging related value used in the beta. It has no meaning for the general user and will eventually disappear.

—Carson


> On Jun 12, 2018, at 9:59 AM, Jennifer Anderson <jennifer.anderson at ebc.uu.se> wrote:
> 
> Hello,
> 
> I am working on the ab initiio annotation of a fungal genome, taking advantage of cDNA and protein evidence from other species. I am looking at my gff file following my first full attempt (hmm files from snap trained 2x, and GenemarkES).
> 
> I have not found information on what it means “merge_warning=1” at the end of the ID line, as in the example below.  Out of 6834 ID lines that include AED scores in this gff file, 5441 contain this warning. I would appreciate it if someone could point me in the right direction.
> 
> 
> 000030F|arrow  maker gene
> 9255 9992
> . -
> . ID=genemark-000030F|arrow-processed-gene-0.43;Name=genemark-000030F|arrow-processed-gene-0.43
> 000030F|arrow
> maker mRNA
> 9255 9992
> . -
> . ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1;Parent=genemark-000030F|arrow-processed-gene-0.43;Name=genemark-000030F|arrow-processed-gene-0.43-mRNA-1;_AED=0.06;_eAED=0.06;_QI=0|0|0|1|1|1|2|0|220;_merge_warning=1
> 000030F|arrow  maker exon
> 9838 9992
> . -
> . ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:2;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1
> 000030F|arrow  maker exon
> 9255 9762
> . -
> . ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:1;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1
> 000030F|arrow  maker CDS
> 9838 9992
> . -
> 0 ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:cds;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1
> 000030F|arrow  maker CDS
> 9255 9762
> . -
> 1 ID=genemark-000030F|arrow-processed-gene-0.43-mRNA-1:cds;Parent=genemark-000030F|arrow-processed-gene-0.43-mRNA-1
> 
> Best,
> 
> Jenni
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> 
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