I think this post is very relevant to many bioinformaticians who are submitting to Genbank using tbl2asn

I've been following the guidelines here

I've successfully installed tbl2asn on my Mac and have been using through the terminal

The directions say to create 3 files: template.sbt, table.tbl, and fasta.fsa

My fasta format headers look like:

>TCONS_00001810 [organism=Mus musculus] [strain=C57BL/6J] [chromosome=1] olfactory receptor 1415 (Olfr1415) mRNA, complete cds

The corresponding data in the table file looks like:

>Feature TCONS_00001810
1    3422    mRNA
1    186    5'UTR
187    1122    CDS
1123    3422    3'UTR
1    176    exon
177    2079    exon

The template file isn't a text file so I can't provide an example . . .

In terminal, I've opened up tbl2asn and I know it's working because when I do the command:

tbl2asn -

it gives me all of the different commands that I can use.

When I run this command, it works and creates a file in my directory with the template.sbt, table.tbl, and fasta.fsa called errorsummary.val. However, this file is empty (zero bytes). It should create a .sqn file which combines the 3 preliminary files i've described earlier.

tbl2asn -t template.sbt -p . -j "[organism=Mus musculus] [strain=C57BL:6J]" -V vb -a s

The documentation explains -t, -p, -j, -V, and -a

-p specifies the path for the table and sequence files [required]
-t specifies the template file (including the path) [required]
-j allows the addition of source qualifiers that will be the same for each submission
Example: -j "[organism=Saccharomyces cerevisiae] [strain=S288C]"
-V is a verification command when used in conjunction with v (strongly suggested), which will tell the computer to run a validation step to insure that there are no errors in your submission.

This validation step will generate a report (with suffix .val) for each .fsa file and place it in the same directory that houses the data files and tables used in the submission.

If you add a b command (optional) following the v command, the computer will generate a GenBank flat file (.gbf) of your submission and deposit it in the same directory that houses the data files and tables used in the submission. Note that .gbf files are not suitable for submission. They are only to view the file in GenBank flatfile format. The -a command used in conjunction with the s command instructs tbl2asn to read multiple FASTA components in one file as a set of unrelated sequences. This creates a single file of multiple submissions.

Why does the program run, not give any errors, create the errorsummary.val and not create the .sqn file?

How can I get this to work? I feel like I'm very close.

I've already established a working directory which is where all of those files are located.

I've tried to put the directory location after -p, taking out the -j and modifiers, and [optional] commands. Still can't get it to work.

Please help. This should be useful for anyone submitting multiple sequences at a time to Genbank