Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    Exited with error code: 11
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    scoring error
    Caught signal 11
    Cleaning up and exiting!
    Temporary files deleted.


    Is there some solution?

    Thanks in advance.

  • #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


    • #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


      • #4
        I searched for that list and couldn't find it.
        Thanks!

        Comment


        • #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

          Latest Articles

          Collapse

          • seqadmin
            Strategies for Sequencing Challenging Samples
            by seqadmin


            Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
            03-22-2024, 06:39 AM
          • seqadmin
            Techniques and Challenges in Conservation Genomics
            by seqadmin



            The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

            Avian Conservation
            Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
            03-08-2024, 10:41 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 06:37 PM
          0 responses
          8 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, Yesterday, 06:07 PM
          0 responses
          8 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          49 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          67 views
          0 likes
          Last Post seqadmin  
          Working...
          X