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  • mmcniu
    Junior Member
    • Aug 2013
    • 1
    #1

    Ask for help for running Trans-abyss 1.3.5

    Dear sir/madam；
    I'm trying to locally run Trans-ABySS version_1.3.5. The first time I run the stage 0 separately, the code and the output showed as follow:

    <TOPDIR>:/home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST
    <INPUT>:/home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1
    <ASSEMBLY>:/home/wangsheng/rnaseq/ABYSS_LIB
    <LIBRARY>:ABYSS_LIB
    <YOUR_PROJECT_NAME>:ABYSS_TEST1

    STAGE 0

    STEP1：
    INPUT:
    /home/wangsheng/rnaseq/trans-ABySS-v1.3.5
    wrappers/setup.pl /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1 -make_dir
    OUTPUT:
    /home/wangsheng/rnaseq/trans-ABySS-v1.3.5
    topdir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB; reference: none
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Reads_to_genome
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
    ln -s abyss-1.3.5 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/current
    ln -s /home/wangsheng/rnaseq/ABYSS_LIB /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/source
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k52
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k54
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k58
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k62
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k64
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge/cluster
    chmod a+w /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge/cluster
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/fusions
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/tracks
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/reads_to_contigs
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/novelty
    mkdir -m 2775 /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/snv


    STEP2:
    INPUT:
    [~/rnaseq/trans-ABySS-v1.3.5]
    wangsheng@Venus $ wrappers/setup.pl /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1 -get_reads
    OUTPUT:
    /home/wangsheng/rnaseq/trans-ABySS-v1.3.5
    topdir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB; reference: none
    Reads files are ready.


    STEP3:
    ~/rnaseq/trans-ABySS-v1.3.5/wrappers/setup.pl /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1 -fem
    INPUT:
    [~/rnaseq/trans-ABySS-v1.3.5]
    wangsheng@Venus $ wrappers/setup.pl /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1 -fem
    OUTPUT:
    ……
    Venus
    ====================================
    library: ABYSS_LIB
    kmer size: 52
    island size: 151
    working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
    input dir: /home/wangsheng/rnaseq/ABYSS_LIB/k52
    output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k52
    output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k52/ABYSS_LIB-contigs.fa
    task: Extend junction contigs and indel-bubbles.
    ====================================
    ====================================
    library: ABYSS_LIB
    kmer size: 54
    island size: 151
    working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
    input dir: /home/wangsheng/rnaseq/ABYSS_LIB/k54
    output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k54
    output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k54/ABYSS_LIB-contigs.fa
    task: Extend junction contigs and indel-bubbles.
    ====================================
    ====================================
    library: ABYSS_LIB
    kmer size: 58
    island size: 151
    working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
    input dir: /home/wangsheng/rnaseq/ABYSS_LIB/k58
    output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k58
    output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k58/ABYSS_LIB-contigs.fa
    task: Extend junction contigs and indel-bubbles.
    ====================================
    ====================================
    library: ABYSS_LIB
    kmer size: 62
    island size: 151
    working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
    input dir: /home/wangsheng/rnaseq/ABYSS_LIB/k62
    output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k62
    output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k62/ABYSS_LIB-contigs.fa
    task: Extend junction contigs and indel-bubbles.
    ====================================
    ====================================
    library: ABYSS_LIB
    kmer size: 64
    island size: 151
    working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
    input dir: /home/wangsheng/rnaseq/ABYSS_LIB/k64
    output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k64
    output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/k64/ABYSS_LIB-contigs.fa
    task: Extend junction contigs and indel-bubbles.
    ====================================
    ====================================
    library: ABYSS_LIB
    input: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
    input type: DIR
    working dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5
    output dir: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge
    threads: 8
    output file: /home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge/ABYSS_LIB-contigs.fa
    task: Merge both contigs and indel-bubbles.
    but when I try to run stage 2 the programme it shows me the following:
    INPUT:
    /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/wrappers/trans-abyss.sh -i /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1 -2
    OUTPUT:
    input: /home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1
    Option cluster requires an argument
    input:/home/wangsheng/rnaseq/trans-ABySS-v1.3.5/input/ABYSS_TEST1
    ABYSS_LIB
    sh: 1: source: not found
    ERROR: Cannot find contigs fasta file, /home/wangsheng/rnaseq/ABYSS_ABYSS_LIB/TOPDIR_TEST/ABYSS_ABYSS_LIB/Assembly/abyss-1.3.5/merge/ABYSS_ABYSS_LIB-contigs.fa

    I think it try to find the contigs fasta file in a wrong path, the correct path should be “/home/wangsheng/rnaseq/ABYSS_LIB/TOPDIR_TEST/ABYSS_LIB/Assembly/abyss-1.3.5/merge/ABYSS_LIB-contigs.fa” instead of “/home/wangsheng/rnaseq/ABYSS_ABYSS_LIB/TOPDIR_TEST/ABYSS_ABYSS_LIB/Assembly/abyss-1.3.5/merge/ABYSS_ABYSS_LIB-contigs.fa”. I don’t how could it happened and what should I do to correct the path.

    Moreover, there is another warning “sh: 1: source: not found” appeared. Would you please tell me what does this warning mean? And does it matter?

    I really hope you could help.

    Best regards

    Wangsheng
    2013-08-09
    Tags: trans-abyss 1.3.5
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