I previously installed and ran PB Jelly. Despite no error messages being output, I noticed something odd during my quick post-assembly stats check: The PB Jelly numbers were identical to the input reference file. This seemed very strange and made me decide to look a bit deeper in the PB Jelly output files.

As it turns out, PB Jelly did not complete successfully! Here’s a look at one of the output files (notice the error messages!):

Looking around the internet seemed to suggest that the issue could be that the blasr program wasn’t in my system PATH (blasr is located in: /home/shared/bin). So, I updated that, since /home/shared/bin wasn’t in the system PATH!:

After doing this, I noticed that the PATH assignment in the /etc/environment file is incorrect – it has the $PATH variable appended to the front of the list. This results in the system PATH appending itself to itself over and over again, resulting in a ridiculously long list (like in the screen cap directly above this text). So, I removed that portion and re-sourced the /etc/environment file to tidy things up.

Fingers crossed this will resolve the issue…