Using xdformat on fasta from REPBASE returns erorr.

Question

[asif.zubair]

I am trying to use xdformat to make xdf files from fasta files downloaded from REPBASE - http://www.girinst.org/server/archive/RepBase14.04.

I concatenated all the references:

cat RepBase14.04.fasta/*.ref RepBase14.04.fasta/appendix/*.ref > repbase_all.fasta

and ran the following command using xdformat

./xdformat -n -o db/repbase_all.fasta ~/projects/REPCLASS/1.0.1/repbase/repbase_all.fasta

However, I am getting this error:

XDFORMAT 3.0PE-AB [2009-10-30] [macosx-10.5-x64-I32LPF64 2009-10-30T16:56:42]
Start:  2016-01-30T15:13:46
XDF Output Database:  db/repbase_all.fasta
 Alphabet:  NCBI2na.1
Input: "~/projects/REPCLASS/1.0.1/repbase/repbase_all.fasta"
  In sequence "Mariner-N4_NV" (record no. 11074):
    Invalid letter code encountered:  "l" (0x6c hex)
    Invalid letter code encountered:  "e" (0x65 hex)
XDF database removed

I tried the same steps with the latest version of RepBase but got the same error.

The xdformat program was downloaded from AB-BLAST - http://www.advbiocomp.com/blast.html

Could someone please let me know if they have resolved a similar error? Or is there an alternate version of xdformat which doesn't have this problem?

[Nitin Narwade]

I think this error is not with your xdformat program, your input sequence is having some ambiguous characters as reported in the error, have a look on the sequence entry named "Mariner-N4_NV" in your repbase_all.fasta file.