Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • 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
    Previous template Next

    Latest Articles

    Collapse
    • kinpict.com
      Reply to 16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
      by kinpict.com
      The part about this topic feels surprisingly grounded, and the details on the page is the bit that made me slow down. I’d keep <a href="https://kinpict.com/">ai family photo generator</a> bookmarked for later.
      Today, 06:37 PM
    • SEQadmin2
      16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
      by SEQadmin2





      NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...
      10-30-2026, 06:46 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    Gene Copies Once Dismissed as Junk DNA Shape Animal Adaptation and Human Disease by SEQadmin2
    Started by SEQadmin2, 11-12-2026, 07:59 AM
    0 responses
    27 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    11-12-2026, 07:59 AM  
    WashU Medicine Study Verifies Methods for Tracking Genetic Mosaicism by SEQadmin2
    Started by SEQadmin2, 11-05-2026, 09:25 AM
    0 responses
    35 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    11-05-2026, 09:25 AM  
    HuBMAP Portal Offers Free Access to Single-Cell Data from Healthy Human Tissues by SEQadmin2
    Started by SEQadmin2, 11-03-2026, 11:54 AM
    2 responses
    56 views
    0 reactions
    		 Last Post kinpict.com
    by kinpict.com
    Today, 06:49 PM  
    Genome Sequencing Reveals Large, Repeat-Rich DNA in Trapdoor Spider Named for Stephen Colbert by SEQadmin2
    Started by SEQadmin2, 10-28-2026, 09:57 AM
    0 responses
    175 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    10-28-2026, 09:57 AM  
    View All
    Working...