Problems When Using The Ncbi Tsa Submission, Validation Fails

Question

[lzsph]

Hey guys,

We already submitted our RNA-seq raw data to NCBI SRA dataset. Now we want to submit our de novo assembled transcriptome.

According to the official manual, we prepared the template.sbt file using Sequin (version 12.30) and .fsa file (let's say Demo.fsa) from our FASTA transcriptome data (Demo.fasta).

Our transcriptome data was not annotated, so the head 2 lines in Demo.fsa are

>comp0_c0_seq1 [organism=Medicago sativa]
ATGATGATGATGATGATGATGATG...

I just have only one .fsa file, there are 100,000+ sequences in the Demo.fsa.

Then I wanted to use tbl2asn to generate the .sqn file to feed in TSA submission. I used the code

tbl2asn -t template.sbt -p . -V v

I used -p . because the .fsa file was under current directory.

Then 3 files were generated, named Demo.sqn, Demo.val and errorsummary.val. But the latter two files were empty, means nothing in it.

When I proceeded to the 3rd step in TSA submission portal, I uploaded the Demo.sqn file, and after a while I got an error, error code:

Unfinished at the Sequence step
Error: Could not validate: "no element found at line 1, column 0, byte -1: 53^ 7298384 at /opt/perl-5.8.8/lib/vendor_perl/5.8.8/x86_64-linux/XML/Parser.pm line 187"

I didn't what was going wrong, so I might need your help.

Thank you.

Rigards,

S.H.

p.s. versions

Sequin (12.30) ||| tbl2asn (20.9) ||| MacOS X 10.7.5 Lion

[raveendars]

Hi

I have the same issue with TSA submission,

My Discrepancy Report Results is as follows

Summary
DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)
SHORT_SEQUENCES_200:17 sequences are shorter than 200 bp.
TECHNIQUE_NOT_TSA:249 technique are not set as TSA
MISSING_STRUCTURED_COMMENT:249 sequences do not include structured comments.


Detailed Report

DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same)
DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::249 sources have 'Vicia' for taxname
DiscRep_ALL:SHORT_SEQUENCES_200::17 sequences are shorter than 200 bp.
sativa_seq:NAC-VSspS-4 (length 163)
sativa_seq:NAC-VSspS-9 (length 181)
.
.
sativa_seq:NAC-VSspS-261 (length 171)

DiscRep_ALL:TECHNIQUE_NOT_TSA::249 technique are not set as TSA
sativa_seq:NAC-VSspS-1 (length 274)
.
.
.
sativa_seq:NAC-VSspS-4 (length 163)

DiscRep_ALL:MISSING_STRUCTURED_COMMENT::249 sequences do not include structured comments.
sativa_seq:NAC-VSspS-1 (length 274)
.
.
sativa_seq:NAC-VSspS-4 (length 163)

How to submit seq less than 200 nt

Any idea to solve the issue

Thank you
Sebastin

[federico.gaiti]

Hello,

In regards to this, I am trying to prepare files for a TSA submission. I prepared the .fsa and .sbt files. I was wondering if you know how to prepare the .tbl file that contains the annotation?

So far I've been only getting an empty .val file and no other outputs.

Thanks in advance
Federico

Answer 1

[bioinformatics]

There is a command line option in tbl2asn specifically for TSA submissions (-M t), see the command line suggested on the TSA guide page:

http://www.ncbi.nlm.nih.gov/genbank/tsaguide

tbl2asn -t template.sbt -p.  -Y comment -M t