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Old 11-25-2010, 05:03 PM   #1
ZhigangLi
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Location: Beijing, China

Join Date: Nov 2010
Posts: 11
Question Failure of transforming Velvet .afg file into GDE .contig file

I did a hybrid assembly using Velvet. There were three typs of data, Solexa, 454 and sanger data. Then I wantted to scaffold the contigs using Bambus. I have to transform velvet_asm.afg file into GDE .contig file .

First tansform .afg to AMOS bank file
'bank-transact -m velvet_asm.afg -b velvet_amos.bank -c'

Second transform AMOS bank file into .contig file
'bank2contig velvet_amos.bank >velvet.contitg'

The first step was ok. The second step fail.
Error returned:
'ERROR: -- Fatal AMOS Exception --
WHAT: Invalid sequence subrange
LINE: 90
FILE: Sequence_AMOS.cc

'

Who can tell me the reason and how to resolve it? Thank You!
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