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  • Bowtie2 'Could not open alignment output file' error

    Hi,
    here is my command line :
    test is a directory that contains my index (genome.1.bt2 etc), and the two fastq files.

    /usr/bin/bowtie2 -x genome -1 12344_TGACCA_L007_R1_001.fq -2 12344_TGACCA_L007_R2_001.fq -S /Documents/tests/test.sam

    And the error message I get :

    Error: Could not open alignment output file /Documents/tests/test.sam
    Error: Encountered internal Bowtie 2 exception (#1)
    Command: /usr/bin/bowtie2-align --wrapper basic-0 -x genome -S /Documents/tests/test.sam -1 12344_TGACCA_L007_R1_001.fq -2 12344_TGACCA_L007_R2_001.fq

    If you see what's wrong with my code please help me !
    Thks

  • #2
    Does your account have write permissions to the /Documents/tests directory?

    Comment

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