Dear All, I used MIRA for genome assembly and i got contigfile "
Ecoli-1_out.unpadded.fasta". Now i want to do alignment with this contig
with another Ecoli genome " refseq.fasta". In command line i am typinglike
this and getting error message.
Attempt 1: ./mauveAligner --output=ec_ec.mauve
--output-alignment=ec_vs_ec.alignment Ecoli-1_out.unpadded.fasta
refseq.fasta Sequence loaded successfully. Ecoli-1_out.unpadded.fasta
4982364 base pairs. Using weight 15 mers for initial seeds Creating sorted
mer list Create time was: 2 seconds.
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..10%..
11%..12%..13%..14%..15%..16%..17%..18%..19%..20%..
21%..22%..23%..24%..25%..26%..27%..28%..29%..30%..
31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..Starting with 0 MUMs
Eliminating overlaps yields 0 MUMs
Attempt2: ./mauveAligner --output=jb50vsSpmito.mauve
--output-alignment=jb50vsSpmito.alignment Ecoli-1_out.unpadded.fasta
jb50contigs.fa.sslist refseq.fasta Sp.may2011.extras_mito.fasta.sslist
Sequence loaded successfully. Ecoli-1_out.unpadded.fasta 4982364 base
pairs. Sequence loaded successfully. refseq.fasta 2435000 base pairs. Using
weight 15 mers for initial seeds Creating sorted mer list Create time was:
2 seconds. Creating sorted mer list ERROR! gap character encountered at
genome sequence position 61 Input sequences must be unaligned and ungapped!
Kindly help me out. Responses are highly appreciated!!!
Regards
Hiren ghosh
--
*Hiren Ghosh, Doctoral Research Scholar *
*Biomedizinisches Forschungszentrum Seltersberg
Institut für Medizinische Mikrobiologie
Justus-Liebig-Universität
Schubertstr. 81
35392 Gießen , Germany
*
*Mobile No: 017672157634
*
*Email:[email protected]*
.
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