Question: Unable to perform tbl2asn for submission of transcriptome to Genbank
0
gravatar for arsilan324
2.0 years ago by
arsilan32470
arsilan32470 wrote:

Hi all,

I am need to submit transcriptome annotation of Juncus plant to NCBI, for which I have to create asn.1 file. This file can be generated using tbl2asn. When I try doing so, I see the following error.

ubt80:table2scan arslan$ tbl2asn -t template.sbt -i je.fasta -V v
[tbl2asn 25.6] File contains unexpected extra data
[tbl2asn 25.6] Validating je

Top few lines of feature table and fasta seq. are can be seen in the links given. I generated feature table it using GAG - genome annotation generator after validating the annotated gff3 file using genometools.

https://www.dropbox.com/s/kcb4hmdge9duvki/fasta.txt?dl=0 https://www.dropbox.com/s/mtu3rwbooa6vf5e/ft.txt?dl=0

I believe that there is no problem with tbl2asn installation. Since its running all fine. I would be very grateful for the help!

Best,

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by arsilan32470

I'm receiving error "[linux64.tbl2asn] File contains unexpected extra data" as well. This error message is not documented on NCBI. In the source code of tbl2asn (https://www.ncbi.nlm.nih.gov/IEB/ToolBox/C_DOC/lxr/source/demo/tbl2asn.c) I can see that this error appears when "FileHasMoreData" is true, but I'm not sure what does it imply: static Boolean FileHasMoreData (FILE *fp) { Pointer dataptr; Uint2 datatype; Boolean rval = FALSE;

   if (fp == NULL) {
3375     return FALSE;
   }
   dataptr = ReadAsnFastaOrFlatFile (fp, &datatype, NULL, TRUE, FALSE, TRUE, FALSE);
   if (dataptr != NULL) {
     rval = TRUE;
     ObjMgrFree (datatype, dataptr);
   }
   return rval;
 }

I hope to see some comments on this old question.

ADD REPLYlink written 5 months ago by al-ash130
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