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  • Reinator
    Junior Member
    • Nov 2015
    • 4
    #1

    Mauve exited with error code 11

    Greetings,

    First of all, I would like to congratulate Koadman and all the team for have developed such an amazing tool as Mauve.

    But there are some errors that I am facing and still can't find out a solution. I'm trying to order contigs (althoug I've already got this error while simply aligning sequences) using the command line suggested in the Mauve webpage:

    java -Xmx500m -cp Mauve.jar org.gel.mauve.contigs.ContigOrderer -output results_dir -ref reference.gbk -draft draft.fasta

    When I run the command, I get the following output:

    ref file: org.gel.mauve.contigs.ContigMauveAlignFrame[frame0,0,0,343x383,invalid,hidden,title=Align and Reorder Contigs,normal]
    shown
    OS name is: Linux arch: amd64
    trying path ./progressiveMauve
    Executing:
    progressiveMauve --output=/home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/alignment1 --skip-refinement --weight=200 --output-guide-tree=/home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/alignment1.guide_tree --backbone-output=/home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/alignment1.backbone /home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/Cupriavidus_metallidurans_CH34.fasta /home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/ContigsDeNovoNaoMapeados.fasta
    Storing raw sequence at /tmp/rawseq19925.000
    Sequence loaded successfully.
    /home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/Cupriavidus_metallidurans_CH34.fasta 3928089 base pairs.
    Storing raw sequence at /tmp/rawseq19925.001
    Sequence loaded successfully.
    /home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/ContigsDeNovoNaoMapeados.fasta 1170599 base pairs.
    Using weight 15 mers for initial seeds
    Creating sorted mer list
    Create time was: 1 seconds.
    Creating sorted mer list
    Create time was: 0 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%..done.
    using default bp penalty: 200
    using default bp estimate min score: 446916
    Starting with 11198 multi-matches
    Computing genome content distance matrix...


    Genome conservation distance matrix:
    0 0.895972
    0.895972 0

    Writing guide tree to /home/renatooliveira/ITV/Pasta_Pessoal/Montagens/Genomas_Enrique/CRO-2-B/UniaoMix/Mix2/output_dir/Mix_results_A0_C100/FinalContigs/Ordenacao/OrdenaNaoMapeados/results/alignment1/alignment1.guide_tree
    reading tree...
    initializing alignment tree...
    Constructing seed occurrence lists for repeat detection
    Calculating pairwise breakpoint distances
    Pair 0, 1 has 8168 initial LCBs
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    Exited with error code: 11
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    Caught signal 11
    Cleaning up and exiting!
    Temporary files deleted.


    Is there some solution?

    Thanks in advance.
    Tags: align, error, mauve
  • Reinator
    Junior Member
    • Nov 2015
    • 4
    #2
    I'm startig to think that this error is associated with the order of the fasta files that are used as input.

    For example, if I try to align a fasta file A to a fasta file B (respectively in that order), I get that error 11. But, if I try to align in the inverted order, the aligment occur without error.

    The problem is that when you are trying to order contigs against a reference genome, the order really matters, as I have to input first the reference file, and then the draft file.

    I hope this observation helps in solving this problem.

    Comment

    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #3
      @Reinator: Not answering your question but have you posted this error to Mauve list? Dr. Darling monitors that regularly and you should get an answer there.

      Comment

      • Reinator
        Junior Member
        • Nov 2015
        • 4
        #4
        I searched for that list and couldn't find it.
        Thanks!

        Comment

        • GenoMax
          Senior Member
          • Feb 2008
          • 7142
          #5
          Originally posted by Reinator View Post
          I searched for that list and couldn't find it.
          Thanks!
          You will need to subscribe to mauve-users list before you can post your question (https://lists.sourceforge.net/lists/...fo/mauve-users) there.

          Comment

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