samtools index file error

NDUFB11 · 02-19-2019, 10:59 AM

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

NDUFB11 · 02-19-2019, 11:15 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

https://github.com/bioconda/bioconda...s/issues/13488

GenoMax · 02-19-2019, 12:48 PM

Samtools 1.9 is the latest version.

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02-19-2019, 10:59 AM	#1
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	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

02-19-2019, 11:15 AM	#2
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	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 https://github.com/bioconda/bioconda...s/issues/13488

02-19-2019, 12:48 PM	#3
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	Samtools 1.9 is the latest version.