We associate a graph with a 1-safe Petri net and study the parameterized complexity of various problems with parameters derived from the graph. With treewidth as the parameter, we give W[1]-hardness results for many problems about 1-safe Petri nets. As a corollary, this proves a conjecture of Downey et. al. about the hardness of some graph pebbling problems. We consider the parameter benefit depth (that is known to be helpful in getting better algorithms for general Petri nets) and again give W[1]-hardness results for various problems on 1-safe Petri nets. We also consider the stronger parameter vertex cover number. Combining the well known automata-theoretic method and a powerful fixed parameter tractability (FPT) result about Integer Linear Programming, we give a FPT algorithm for model checking Monadic Second Order (MSO) formulas on 1-safe Petri nets, with parameters vertex cover number and the size of the formula.

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