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  • alebueno
    Junior Member
    • Dec 2014
    • 4

    #1

    IMAGE in closing gaps

    Hi everyone. I am using the PAGIT software in order to generate a final contig from my scaffolds. When trying to use IMAGE to close gaps this messages pops up and we get no further. Anyone of you could figure out what is happening and what am I possibly doing wrong?

    root@lgmmicrorganismo-To-be-filled-by-O-E-M:/home/lgmmicrorganismo/Programas_Análise/PAGIT/PAGIT/IMAGE# perl image.pl -scaffolds /home/lgmmicrorganismo/Projeto_Cviolaceum/runabacas2/runImage/mappunmapp.fasta -prefix /home/lgmmicrorganismo/Projeto_Cviolaceum/runabacas2/runImage/Bac5_S5_L001_R2_001.fastq /home/lgmmicrorganismo/Projeto_Cviolaceum/runabacas2/runImage/Bac5_S5_L001_R2_001.fastq -iteration 1 -all_iteration 9 -dir_prefix ite -kmer 55
    mv: impossível obter estado de “/home/lgmmicrorganismo/Projeto_Cviolaceum/runabacas2/runImage/mappunmapp.fasta”: Arquivo ou diretório não encontrado
    Can't exec "/get_fasta_containNs_toIMAGE_format.pl": Arquivo ou diretório não encontrado at image.pl line 169.
    ln: falhou ao criar link simbólico “read.placed.original”: Arquivo existe
    ln: falhou ao criar link simbólico “contigs.fa.original”: Arquivo existe

    ------------------------------------------------
    IMAGE parameters


    Process ID = 3817
    directory prefix = ite

    reference = contigs.fa
    solexa_prefix = /home/lgmmicrorganismo/Projeto_Cviolaceum/runabacas2/runImage/Bac5_S5_L001_R2_001.fastq
    insert size = 600
    toignore = 10
    overhang = 50
    velvet ins_len = 500
    velvet kmer = 55

    current iteration = 1
    iteration left = 9
    ------------------------------------------------

    WHAT DID I JUST DO (compulsory parameters) :
    checking all the paths..
    /ssaha2 path not found!

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