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NDUFB11 02-19-2019 09:59 AM

samtools index file error

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,


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


NDUFB11 02-19-2019 10:15 AM

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

GenoMax 02-19-2019 11:48 AM

Samtools 1.9 is the latest version.

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