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  • samtools index file error

    Hello,

    I have to post process the outcome STAR file .bam but when I go to create an index for it I have an error with samtools,


    Code:
    Patrizios-MBP:star patrizio$ samtools index SRR359063.bam
    dyld: Symbol not found: _stdscr
      Referenced from: /Users/patrizio/anaconda3/bin/samtools
      Expected in: /Users/patrizio/anaconda3/bin/../lib/libncursesw.6.dylib
     in /Users/patrizio/anaconda3/bin/samtools
    Abort trap: 6

    I read online and seems to be related with anaconda but I don't know how to fix it, anyone experienced that?

    thank you


    -P

  • #2
    ok probably I solved the problem by using this line command to install a older version of samtools

    conda install -c bioconda samtools=1.9=h8ee4bcc_1


    from this forum discussion


    I'm getting: dyld: Symbol not found: _stdscr Referenced from: /opt/conda/miniconda3/envs/test/bin/samtools Expected in: /opt/conda/miniconda3/envs/test/bin/../lib/libncursesw.6.dylib in /opt/conda/...

    Comment


    • #3
      Samtools 1.9 is the latest version.

      Comment

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