Does anyone have experience with the table2asn tool of NCBI? It is used for submitting annotations of genomes using GFF files.
It can be found at this location: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/table2asn_GFF/
I am having a problem with it.
1) The windows tool I get running, but it gives me an error. The command used is the following: table2asn -M n -J -c w -t template.sbt -a r10k -l paired-ends -i FinalContigs.fsa -f 2700988623.gff -o output_file.sqn -Z output_file.dr -locus-tag-prefix xxxxx
template.sbt is a file generated by NCBI
FinalContigs.fsa is a file containing all the different contigs of the draft genome. The first contig is named Contig001, seconf contig is Contig002, and so on.
2700988623.gffis the file containing the annotation. Column 1 gives the contigs where the CDS and RNA are found in, so Contig001, Contig002, etc.
After running the command (as told by NCBI), I get the following error:
Cannot resolve lcl|Contig002: unknown
Line: 0
So if anyone could assist me with getting the tool running in Windows, that would be very much appreciated as it is the final step of submitting my genome.
Thanks in advance!
Hi, have you seen if the header is the same (.fsa and .gff)? Looks like the error msg is talking about it: your .fsa is Contig002 and the GFF lcl|Contig002.
Usually when I send the genome to Genbank I prefer to use the table2asn with the tbl format.
https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/
You should convert the GFF into TBL before using the table2asn.
You can use this tool: https://genomeannotation.github.io/GAG/
gag.py --fasta organism.fasta --gff organism.gff --out gag_output (tbl)
When you convert the GFF to TBL the probability of error is reduced.
Thank you Juliana for your reply!
In the meanwhile I have tried to use the GAG script, but somehow something goes wrong. The gff table is completely ok, since it gives no errors at NCBI when running their scripts, but when I use it as input for the GAG tool, it somehow does not detect the CDS features.
To give you an idea of how the file looks, I have attached part of it here. Maybe you can see what went wrong?
Hi!
Your file is missing the mRNA and Exon feature.
You can add the mRNA feature
##gff-version 3 ##gff-version 3
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