sort --stable (-s) doesn't appear to work on my system

[Terry Farrah]

I have a tab-separated file that I think is already sorted on the first 3 columns. Here is a 2-line sample in a file named foo:

chr10   60379   60380   10:60380-60380  T/T

chr10   60379   60380   10:60380-60380  G/T

I try checking it with

sort -s -k1,1V -k2,2n -k3,3n -c foo

but the check fails:

sort: foo:2: disorder: chr10      60379   60380   10:60380-60380  G/T

If I sort it using the above key specification, it swaps the order of the lines:

sort -s -k1,1V -k2,2n -k3,3n foo

chr10   60379   60380   10:60380-60380  G/T

chr10   60379   60380   10:60380-60380  T/T

Here it is with --debug:

$ sort -s -k1,1V -k2,2n -k3,3n --debug foo

sort: using ‘en_US.UTF-8’ sorting rules

sort: leading blanks are significant in key 1; consider also specifying 'b'

chr10>60379>60380>10:60380-60380>G/T

_____

      _____

            _____

chr10>60379>60380>10:60380-60380>T/T

_____

      _____

            _____

Here is some info about what I'm running:

$ sort --version

sort (GNU coreutils) 8.22

$ more /etc/*-release

::::::::::::::

/etc/oracle-release

::::::::::::::

Oracle Linux Server release 7.1

$ uname -r

3.8.13-68.1.2.el7uek.x86_64

Many thanks for your help!

Terry

--------

Terry Farrah
Bioinformatics Scientist

Institute for Systems Biology
206-732-1348