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  • NKAkers
    replied
    /home/local/bin/Rscript ./defuse-0.6.1//scripts/evaluate_fraglength_mean.R

    This is your problem, I believe. The double forward slash betweeen defuse-0.6.1 and scripts.

    Check your config.txt file to make sure you named your directories without a slash at the end. ie:

    /home/usr/defuse-0.6.1
    NOT:
    /home/usr/defuse-0.6.1/

    Leave a comment:


  • zslee
    started a topic Defuse Calculating spanning p-values Failure

    Defuse Calculating spanning p-values Failure

    Hey, could anyone help me with one problem:
    when I run defuse to find gene fusions based on fastq data (illumina HISEQ, paired-end, trimed by trimglore), the software goes well until Calculating spanning p-values:

    Importing fastq files
    Splitting fastq files
    Discordant alignments
    Read Stats
    Fragment mean 182.171678030117 stddev 43.6861609169054
    Read length min 20 max 100
    Generating discordant alignment clusters
    Remove mitochondrial-genomic clusters
    Generating maximum parsimony solution
    Selecting fusion clusters
    Preparing sequences for local realignment
    Performing local realignment
    Filtering concordant clusters
    Generating spanning alignment regions file
    Initializing split read alignments
    Calculating split read alignments
    Evaluating split reads
    Calculating spanning stats
    Calculating spanning p-values
    Failure for defuse command:
    /home/local/bin/Rscript ./defuse-0.6.1//scripts/evaluate_fraglength_mean.R ./temp/defuse/concordant.read.stats ./temp/defuse/spanlength.cov 50 ./temp/defuse/splitreads.span.stats ./temp/defuse/splitreads.span.pval.tmp
    Reason:
    Job command with nonzero return code
    Job output:
    Running on node4
    Rscript execution error: No such file or directory

    real 0m0.099s
    user 0m0.000s
    sys 0m0.003s
    Return codes: 255
    Commands failed after 1 seconds


    when I check I found there is no ./temp/defuse/splitreads.span.pval.tmp produced, what is the reason?
    thanks in advance for anyone's reply.

    code as bellow:
    ~/programs/defuse-0.6.1/scripts/defuse.pl -c ~/programs/defuse-0.6.1/scripts/config.txt -1 $inputdir/$file1 -2 $inputdir/$file2 -o $outputdir -p 24

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