Inquiry for using gff3toGenePred

[Xin Huang]

Dear Sir or Madam,

My name is Xin Huang, a graduate student at Georgetown University. First I'd like to thank you for your contribution to this tool, which makes conversion between the two file formats possible.

I got stuck on the following error messages (samples):

Can't find annotation record "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:12" Parent attribute
Can't find annotation record "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:11" Parent attribute
Can't find annotation record "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:10" Parent attribute
Can't find annotation record "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1" referenced by "maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:9" Parent attribute
Can't find annotation record "maker-scaffold1193-exonerate_est2genome-gene-2.0-mRNA-2" referenced by "maker-scaffold1193-exonerate_est2genome-gene-2.0-mRNA-1:exon:114" Parent attribute

And my GFF3 file looks something like the following:

scaffold10370 maker gene 32452 54508 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0;Name=AAEL004146

scaffold10370 maker mRNA 32452 54508 44204 - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0;Name=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2;aED=0.00;eAED=0.00;qI=376|1|1|1|0|0|5|316|548

scaffold10370 maker exon 32452 33011 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:exon:15;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker exon 35140 35388 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:12;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker exon 35455 36119 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker exon 36443 36777 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:10;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker exon 53979 54508 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:9;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker five_prime_UTR 54133 54508 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:five_prime_utr;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker CDS 53979 54132 . - 0 ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker CDS 36443 36777 . - 2 ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker CDS 35455 36119 . - 0 ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker CDS 35140 35388 . - 1 ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker CDS 32768 33011 . - 1 ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:cds;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

scaffold10370 maker three_prime_UTR 32452 32767 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2:three_prime_utr;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

If you could provide some guidance on this matter, it would be greatly appreciated!

Best,

Xin

[Jonathan Casper]

Hello Xin,

Thank you for your question about an error message when using the gff3ToGenePred utility. The error message appears to be complaining about the structure of your gff3 file. In the example piece of your gff3 file, you include lines like this:

scaffold10370 maker exon 35455 36119 . - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1:exon:11;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1,maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2

The "Parent" attribute in that line is given two values: maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1 and maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2. Those values are supposed to be IDs that are declared on other lines of the gff3 file. The second parent ID, ending in mRNA-2, is indeed declared on one of the earlier lines that you included:

scaffold10370 maker mRNA 32452 54508 44204 - . ID=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2;Parent=maker-scaffold10370-exonerate_est2genome-gene-0.0;Name=maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-2;aED=0.00;eAED=0.00;qI=376|1|1|1|0|0|5|316|548

Note that our tool does not complain about this identifier being missing. The first value, however, ending in mRNA-1, is not defined in your example. Without seeing the full text of your gff3 file I cannot be sure, but the error messages seem to indicate that there are no lines anywhere in your file that describe the IDs maker-scaffold10370-exonerate_est2genome-gene-0.0-mRNA-1 or maker-scaffold1193-exonerate_est2genome-gene-2.0-mRNA-2. You can try searching for "ID=maker-scaffold1193-exonerate_est2genome-gene-2.0-mRNA-2" in your gff3 file to see if it does actually appear there. If it does not, then I suggest contacting the provider of the gff3 file and asking them for help resolving the missing parent. If it does appear in the file, then there may be a problem with our tool. You are welcome to send me an example file that causes this problem privately, to avoid sharing it with the mailing list, and we can track down the error.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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