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  • NDUFB11
    Member
    • Jul 2017
    • 34
    #1

    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
    Tags: None
  • NDUFB11
    Member
    • Jul 2017
    • 34
    #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


    samtools on macosx is incompatible with ncurses from defaults channel · Issue #13488 · bioconda/bioconda-recipes
    https://github.com/bioconda/bioconda-recipes/issues/13488
    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

    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #3
      Samtools 1.9 is the latest version.

      Comment

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