Anyone got an error "Duplicate genetic element ID NIL"

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I am guessing you are not supplying a unique chromosome, plasmid or contig id for each of your genetic elements.

The underlying engine of Pathway Tools is built upon lisp. NIL is a default value of variables etc, analogous to NULL in C or undefined in other languages. It's probably failing to parse some of our input data and thus defaults to a NIL value. However to get a better idea, you'll need to submit more information such as a back trace or a log file for further investigation.