Question: Can't get samtools version: "unrecognized command"
0
gravatar for ariel.balter
2.6 years ago by
ariel.balter140
ariel.balter140 wrote:

The docs say to use --version, but I'm getting uncrecognized command

balter@exalab3:~$ which samtools
/usr/local/bin/samtools
balter@exalab3:~$ samtools --version
[main] unrecognized command '--version'
balter@exalab3:~$ samtools --version-only
[main] unrecognized command '--version-only'
samtools • 2.4k views
ADD COMMENTlink modified 2.6 years ago by Brice Sarver2.6k • written 2.6 years ago by ariel.balter140
3

You probably have an older version of samtools (likely v.0.1.1x) otherwise you should see this with newer samtools

$ samtools --version
samtools 1.3.1
Using htslib 1.3.1
Copyright (C) 2016 Genome Research Ltd.

You can confirm this by using @Brice's method below.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax65k

Indeed. Understanding --version and --version-only was something we added on the way from 0.1.19 to 1.0 (in c4d398b9).

ADD REPLYlink written 2.6 years ago by John Marshall1.5k
4
gravatar for Brice Sarver
2.6 years ago by
Brice Sarver2.6k
United States
Brice Sarver2.6k wrote:

Type samtools without any arguments. It will display the version at the top.

ADD COMMENTlink written 2.6 years ago by Brice Sarver2.6k

Bingo! Version: 0.1.19

ADD REPLYlink written 2.6 years ago by ariel.balter140
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