I am finding it hard to understand why when loading the cutadapt it loads an older version.
I have put the relevant error stating something about a "VARIANT" here: https://gist.github.com/anonymous/0074fe513d72b8817d1649d1d27998d3. I create the job scripts via perl and then submit them. The errors one see's are result of using this method. If I submit the shell scripts directly in the command line, they run just fine.
The only way I can ensure I have the correct version of cutadapt running is if I preload it into the terminal before I run the perl script to create the shell.