Question: WGS upload prep - table2asn
gravatar for ian.will
10 months ago by
ian.will0 wrote:


I've wrapped up an assembly and will soon be uploading a new genome and annotations to NCBI - but am having a little trouble with getting everything packaged nicely for GenBank.

I have a single .fsa and .gff3 with my genome information that I am trying to use with the table2asn_GFF tool, but am getting some errors.

Running my table2asn as so:

./linux64.table2asn_GFF -i myassembly.fsa -t mytemplate.sbt -J -c w -euk -locus-tag-prefix GQ602 -M n -Z -f myannotations.gff -outdir output_dir

I get an error regarding my protein IDs, not sure why:

FEATURE_COUNT: CDS: 7455 present
FEATURE_COUNT: gene: 7455 present
FEATURE_COUNT: mRNA: 7455 present
FATAL: MISSING_PROTEIN_ID: 7455 proteins have invalid IDs.

A bit of my gff:

##gff-version 3
##sequence-region scaffold_01 1 5595695
scaffold_01 FGDB    gene    7249    9339    .   +   .   ID=Ophcf2|00001|gene
scaffold_01 FGDB    mRNA    7249    9339    .   +   .   ID=Ophcf2|00001;Parent=Ophcf2|00001|gene;proteinId=Ophcf2|00001;Name=Ophcf2|00001
scaffold_01 FGDB    exon    7249    7255    .   +   .   ID=Ophcf2|00001|exon1;Parent=Ophcf2|00001
scaffold_01 FGDB    exon    7334    9339    .   +   .   ID=Ophcf2|00001|exon2;Parent=Ophcf2|00001
scaffold_01 FGDB    CDS 7249    7255    .   +   0   ID=Ophcf2|00001|CDS;Parent=Ophcf2|00001
scaffold_01 FGDB    CDS 7334    9339    .   +   2   ID=Ophcf2|00001|CDS;Parent=Ophcf2|00001

Perhaps something to do with my mRNA ID and proteinId being the same?

I do plan to introduce product=* for my CDS's, but later once I can even get this first version to work.

(I've tried to poke around a bit with GAG as well, but am getting some errors I've yet to fully understand, but that's another topic)

A nudge in the right direction would be greatly appreciated, thanks!

ADD COMMENTlink written 10 months ago by ian.will0
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