Question: Error duirng the creation of .sqn file for the submission to NCBI
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gravatar for dago
4.4 years ago by
dago2.6k
Germany
dago2.6k wrote:

I am trying to submit bacterial genomes to NCBI.

I use 'tbl2asn' to create .sqn file using the .fsa and the .tbl files obtained from the annotation I did using PROKKA.

However, I obtained many errors concerning the locus-tag.

Here some errors reported in the discrep file as example:

FATAL: DiscRep_ALL:INCONSISTENT_LOCUS_TAG_PREFIX::4718 features have locus tag prefix AD2.

FATAL: DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, some duplicate)
DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::169 sources have 'AD2' for strain

I looked into the help NCBI provide but I cannot really understand where is the problem and how to fix it.

Any suggestion?

 

 

 

 

.sqn ncbi genome • 1.2k views
ADD COMMENTlink modified 2.4 years ago by BioinfoNovice100 • written 4.4 years ago by dago2.6k

It would be probably easier in that case to convert the gff output file into EMBL flat file with gff3toembl or EMBLmyGFF3 and submit it to the european database ENA, which is part to the INSDC.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Juke-343.3k
0
gravatar for BioinfoNovice
2.4 years ago by
BioinfoNovice100
France
BioinfoNovice100 wrote:

I also have the same kind of problem but different errors messages which are not explained in their web site. Did you find any solution ?

ADD COMMENTlink written 2.4 years ago by BioinfoNovice100
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