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The president made the comments during an interview with Steve Harvey on his radio program.
"If you don't vote, that's a vote for Trump," he told Harvey. "If you vote for a 3rd party candidate that's a vote for Trump."
Johnson, the Libertarian nominee, and Stein, the Green Party nominee, are garnering 7.4% and 2.4% in the RealClearPolitics 4-way race polling average.
Both candidates were not included in the first debate after not meeting the necessary polling threshold.