[AMOS-help] question on AMOScmp

[Ou, Dr H.Y. <hy...@le...>]

Dear Sir or Madam,

Would you please give me a hand to use the comparative assembler =
AMOScmp?

I get the DNA sequences of 177 contigs of a partially sequenced =
bacterial genome as 'target' and its closely related genome as =
'reference', which had been fully sequenced.
The 177 contig sequences are stored in the multi-fasta file 'ok.seq'.
The target genome sequence downloaded from GenBank is saved in the =
ok.1con

To assemble these contigs, I type the following commands on Linux
>./tarchive2amos -o ok ok.seq
>./AMOScmp -D TGT=3Dok.afg -D REF=3Dok.1con okok

But AMOScmp only works for the first three configs. Please see the =
attached log file.

Would you please help me sort out this questions? Many Thanks!=20

I am looking forward for your reply.

Best regards,
Hong-Yu

Hong-Yu Ou, PhD
Department of Infection, Immunity & Inflammation=20
University of Leicester=20
Maurice Shock Building=20
University Road PO Box 138=20
Leicester LE1 9HN=20
United Kingdom
Tel: +44 (0) 116 2522955
Email: hy...@le...