Question: Mauvealigner Error
0
gravatar for HG
5.8 years ago by
HG1.1k
Germany
HG1.1k wrote:

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!!!

• 3.6k views
ADD COMMENTlink modified 3.1 years ago by Biostar ♦♦ 20 • written 5.8 years ago by HG1.1k

Are there gap characters in your sequences?

ADD REPLYlink written 5.8 years ago by lelle790

Yes, have you checked for a gap at sequence position 61? Do you have a whitespace or a FASTA line return error? This sounds like an error in your first line of data.

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by Josh Herr5.6k

i dont think that there is a gap : i have pasted few header line of reference file as well as contig file .

Ecoli_ref AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTCTCTGACAGCAGC TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC

Ecoli-1_c1 atcgtagtgacgtcaacgcaaggggaaggggaaccgccggaagaagccgtcgcgctgcat aagttcctgttctccaaaaaagcgccaaagctggaaaacaccgcgtttgccgtgtttagc ctcggcgatagctcttatgaatttttctgccagtccgggaaagatttcgacagcaagctg gcggaactgggtggtgaacgcctgctcgaccgtgtcgatgccgatgttgaataccaggct

Now i am following steps like and getting error : ./mauveAligner --output=ec_ec.mauve --output-alignment=ec_vs_ec.alignment Ecoli-1_out.unpadded.fasta Ecoli-1_out.unpadded.fasta.sml sequence..fasta sequence..fasta.sml Sequence loaded successfully. Ecoli-1_out.unpadded.fasta 4982364 base pairs. Exception FileNotOpened thrown from Unknown() in gnFileSource.cpp 67 Called by Unknown() Using weight 15 mers for initial seeds Sorted mer list loaded successfully 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

ADD REPLYlink written 5.8 years ago by HG1.1k

i dont think that there is a gap : i have pasted few header line of reference file as well as contig file .

Ecoli_ref AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTCTCTGACAGCAGC TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC

Ecoli-1_c1 atcgtagtgacgtcaacgcaaggggaaggggaaccgccggaagaagccgtcgcgctgcat aagttcctgttctccaaaaaagcgccaaagctggaaaacaccgcgtttgccgtgtttagc ctcggcgatagctcttatgaatttttctgccagtccgggaaagatttcgacagcaagctg gcggaactgggtggtgaacgcctgctcgaccgtgtcgatgccgatgttgaataccaggct

Now i am following steps like and getting error : ./mauveAligner --output=ec_ec.mauve --output-alignment=ec_vs_ec.alignment Ecoli-1_out.unpadded.fasta Ecoli-1_out.unpadded.fasta.sml sequence..fasta sequence..fasta.sml Sequence loaded successfully. Ecoli-1_out.unpadded.fasta 4982364 base pairs. Exception FileNotOpened thrown from Unknown() in gnFileSource.cpp 67 Called by Unknown() Using weight 15 mers for initial seeds Sorted mer list loaded successfully 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

ADD REPLYlink written 5.8 years ago by HG1.1k
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