SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   RNA Sequencing (http://seqanswers.com/forums/forumdisplay.php?f=26)
-   -   samtools index file error (http://seqanswers.com/forums/showthread.php?t=87778)

NDUFB11 02-19-2019 09:59 AM

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

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


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

GenoMax 02-19-2019 11:48 AM

Samtools 1.9 is the latest version.


All times are GMT -8. The time now is 10:20 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.