Error with Snippy and Prokka


#1

Hello

I am trying to run Prokka and Snippy and I get this error.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Can’t build a GFF object with the unknown version 3
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/ubuntu/cgview_comparison_tool/lib/bioperl-1.2.3/Bio/Root/Root.pm:342
STACK: Bio::tools::GFF::new /home/ubuntu/cgview_comparison_tool/lib/bioperl-1.2.3/Bio/Tools/GFF.pm:115
STACK: /home/linuxbrew/.linuxbrew/bin/snippy:128

A few days back, I installed cgview comparison tool but I am not sure how it can affect these programs.

Any help is welcome!

Thank you!

Anu


#2

The problem is likely cause by this part of the cgview installation:

export CCT_HOME="/path/to/cgview_comparison_tool"
export PATH="$PATH":"${CCT_HOME}/scripts":/path/to/blast-2.2.26/bin
export PERL5LIB="${CCT_HOME}"/lib/bioperl-1.2.3:"${CCT_HOME}"/lib/perl_modules:"$PERL5LIB"

Which installs an ancient release of bioperl (pre-GFF3!), then gives it precedence on your PERL5LIB, resulting in anything that uses a modern release of bioperl failing with the above message.

My suggested fix is to remove the above lines from your bashrc and add them to a new file called something like ~/cgview.env, then logout and log back in again.

Then, whenever you want to use cgview, all you need to do is

source ~/cgview.env

which will setup the ancient perl modules for you, remembering that if you want to use anything depending on modern bioperl, you’ll need to log out and back in again to clear your environment.


#3

Thanks a lot Matt. It seems to be working now!.. :slight_smile: