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  • Mitobim-Any one used?- iteration problem

    I am trying to use MITObim for mitchondrial genome assembly project. I have tried tutorial provided in MITObim:https://github.com/chrishah/MITObim

    I have installed Mira 3.4.1.1 and MITObim 1.6. Mapping assembly with MIRA 3.4.1.1 was sucessful, however wrapper script MITObim 1.6 stops at iteration 1, it should iterate upto 8 according the the tutorial, it says error "mirabait seems to have failed". What will be the reason

    mapping assembly with MIRA 3.4.1.1:
    mira --project=initial-mapping-testpool-to-Salpinus-mt --job=mapping,genome,accurate,solexa -MI:somrnl=0 -AS:nop=1 -SB:bft=fasta:bbq=30:bsn=Salpinus-mt-genome SOLEXA_SETTINGS -CO:msr=no -SB:dsn=testpool

    for MITObim 1.6:
    MITObim.pl -start 1 -end 10 -strain testpool -ref Salpinus_mt_genome -readpool initial-mapping-testpool-to-Salpinus-mt_in.solexa.fastq -maf initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf &> log

    below is the log file:

    MITObim - mitochondrial baiting and iterative mapping
    version 1.6
    author: Christoph Hahn, (c) 2012-2013


    Full command run: ../MITObim_1.6.pl -start 1 -end 10 -strain testpool -ref Salpinus_mt_genome -readpool initial-mapping-testpool-to-Salpinus-mt_in.solexa.fastq -maf initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf

    All paramters seem to make sense:
    startiteration: 1
    enditeration: 10
    strainname: testpool
    refname: Salpinus_mt_genome
    readpool: /PATH/MITObim-master/testdata1/initial-mapping-testpool-to-Salpinus-mt_in.solexa.fastq
    maf: /PATH/Downloads/MITObim-master/testdata1/initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf
    quick: 0
    paired: 0
    denovo: 0 (mapping=0, denovo=1)
    noshow: 0
    read trimming: 0 (off=0, on=1)
    kmer baiting: 31
    platform: SOLEXA
    clean: 0 (off=0, on=1)
    proofread: 0

    Starting MITObim

    ==============
    ITERATION 1
    ==============
    May 8 10:20:53


    recover backbone by running convert_project on maf file


    Parsing special MIRA parameters: SOLEXA_SETTINGS -CO:fnicpst=yes

    Ok.
    Loading from maf, saving to: fasta fastaqual
    First counting reads:
    [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.... [100%]
    Now loading and processing data:
    [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|.Localtime: Thu May 8 10:20:53 2014

    Generated 1692 unique template ids for 2548 valid reads.
    Localtime: Thu May 8 10:20:53 2014

    Seeing strain 1: "testpool"
    Seeing strain 2: "Salpinus-mt-genome"
    Generated 2 unique strain ids for 2548 reads.
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    makeIntelligentConsensus() complete calc
    ... [100%]

    Data conversion process finished, no obvious errors encountered.
    SC Read:: read name issorted (1) capacity 4294967295(4) size 1
    SC Read:: scf path name issorted (1) capacity 255(1) size 1
    SC Read:: exp path name issorted (1) capacity 255(1) size 1
    SC Read:: machine type issorted (1) capacity 255(1) size 1
    SC Read:: primer issorted (1) capacity 255(1) size 1
    SC Read:: strain issorted (1) capacity 255(1) size 3
    SC Read:: base caller issorted (1) capacity 255(1) size 1
    SC Read:: dye issorted (1) capacity 255(1) size 1
    SC Read:: process status issorted (1) capacity 255(1) size 1
    SC Read:: clone vector name issorted (1) capacity 65535(2) size 1
    SC Read:: sequencing vector name issorted (1) capacity 65535(2) size 1
    SC asped issorted (1) capacity 4294967295(4) size 1


    fishing readpool using mirabait (k = 31)



    mirabait seems to have failed - see detailed output above

  • #2
    See also this thread: http://seqanswers.com/forums/showthread.php?t=43064

    I suggest you email the authors or the mira_talk mailing list, and include links to these threads.

    Comment

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