I am attempting to submit a full genome to Genbank. I am using tbl2asn to generate an sqn file for submission from the velvet contigs.fa but I am running into two difficulties.

The command I am using looks like this:

./tbl2asn -i 1383.fsa -t 1383.sbt -j "[organism=Cronobacter sakazakii 1] [strain=1] [host=unknown] [country=UK] [collection_date=1950] [isolation-source=milk powder] [note=multilocus sequence type 4] [gcode=11]" -M n -Z discrep -a r10k

1. The raw velvet output generates no output whatsoever.

2. Believing this might be related to the FASTA headers I used a script to replace this with “>contig0001” etc. (and to filter out scaffolds