Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • 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

            Previous template Next

            Latest Articles

            Collapse
            • SEQadmin2
              Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
              by SEQadmin2



              Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

              Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating              ...
              10-14-2026, 09:55 AM
            • SEQadmin2
              New Genomics Technologies Take Aim at Long-Standing Limits
              by SEQadmin2


              Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

              We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing              ...
              09-28-2026, 10:25 AM
            View All

            ad_right_rmr

            Collapse

            News

            Collapse
            Topics Statistics Last Post
            Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
            Started by SEQadmin2, 10-22-2026, 11:13 AM
            0 responses
            23 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            10-22-2026, 11:13 AM  
            Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
            Started by SEQadmin2, 10-22-2026, 10:48 AM
            0 responses
            20 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            10-22-2026, 10:48 AM  
            Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2
            Started by SEQadmin2, 10-15-2026, 10:52 AM
            0 responses
            36 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            10-15-2026, 10:52 AM  
            Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2
            Started by SEQadmin2, 10-14-2026, 05:39 AM
            0 responses
            42 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            10-14-2026, 05:39 AM  
            View All
            Working...