Question: WGS upload prep - table2asn
0
gravatar for ian.will
10 months ago by
ian.will0
ian.will0 wrote:

Hi,

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
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1880 users visited in the last hour