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Failed to run the jobs #6

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ma-tongji opened this issue Jan 15, 2021 · 0 comments
Open

Failed to run the jobs #6

ma-tongji opened this issue Jan 15, 2021 · 0 comments

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@ma-tongji
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Here's my command, and ${i} is the fastq file

erv_genome.pl -stage 1 -stage2 6 -fastq /${i}.fastq.gz

And the software prints

Usage:
    erv_se_genome_v2.pl [options]

       Options:
        -h, -? --help            brief help message
        -t, --test               print out commands without run
        --btrim                  path to btrim (http://graphics.med.yale.edu/trim/)
        --tophat                 path to tophat
        --bwa                    path to bwa
        --samtools               path to samtools
        --filter                 path to filter (parse_bam.pl)
        --bedtools               path to bedtools

        --genome                 path to bwa human genome index
        --genome_Bowtie2         path to Bowtie2 human genome index
        --bed                    path to bed file of ERVs
        --genomefile             path to genome size file
        --gtf                    path to gtf file of human gene annotation
        --transcriptome          path to known transcriptome, used by tophat2
        --adaptor                path to adaptor files, used by btrim (http://graphics.med.yale.edu/trim/)

        --fastq                  fastq file
        --stage                  start stage (see below)
        --stage2                 end stage (see below)


        Stages:
          1                      trim adaptors and low quality regions
          2                      map reads using bwa
          3                      sort bam file
          4                      count reads mapped to ERVs
          5                      map reads using  tophat2
          6                      counts reads mapped to genes

Any idea on this?

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