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US General John Allen, who just wrapped up a tour as commander in Afghanistan, said Tuesday he will retire instead of accepting the top job at NATO, citing his wife's health problems.
Allen's departure comes weeks after a Pentagon investigation cleared him of any wrongdoing in a drama over emails to a Florida socialite, and he told the Washington Post the highly-publicized case did not influence his decision.
Speculation had been rife for weeks that Allen, who led the war effort in Afghanistan for 19 months, would not take up Obama's offer to serve as the alliance's supreme commander due to the fallout from the email drama.
"Today, I met with General John Allen and accepted his request to retire from the military so that he can address health issues within his family," Obama said in a written statement.
Obama praised the Marine Corps general for presiding over "significant growth" in Afghanistan's security forces and a "further degradation" of Al-Qaeda.
In a statement, Allen said his decision to retire from the military after 38 years was the "only choice" due to his wife's illness.
"The reasons for my decision are personal. I did not come to it lightly or quickly, but given the considerations behind it, I recognized in the end it was the only choice I could make," he said.
"While I won't go into the details, my primary concern is for the health of my wife, who has sacrificed so much for so long."
The four-star general said his family had stood by him throughout his career and now it was his turn "to be there for them when they need me most."
Allen told the Washington Post in an interview published Tuesday that he wanted to focus on helping his wife, Kathy, who has chronic health problems including autoimmune disorder.
"Right now, I've just got to get her well," Allen said. "It's time to take care of my family."
He said his decision was not related to the episode over his email exchanges with the Florida socialite, Jill Kelley. The Pentagon inspector general investigated the correspondence but concluded Allen had not violated rules on conduct "unbecoming of an officer," including adultery.
The probe stemmed from a scandal that forced David Petraeus to resign as CIA director over an extramarital affair with his biographer, Paula Broadwell.
Kelley had complained to the FBI about harassing emails that turned out to be written by Broadwell, who allegedly warned Kelley away from Petraeus.
The investigation not only uncovered the affair between Petraeus and Broadwell, but it also revealed emails between Allen and Kelley that were described by defense officials as potentially "inappropriate."
Allen's supporters have expressed anger over how the case was handled, saying the general suffered from unfair treatment and that the Pentagon should not have launched a probe in the first place.
During his time in Afghanistan, Allen presided over a shift from counter-insurgency operations led by large numbers of US troops to advising the Afghan security forces to take the lead.
Allen, who took over from Petraeus as commander in Afghanistan, oversaw the withdrawal of about 33,000 American troops, with the current US force there at about 66,000.
Defense Secretary Leon Panetta heaped praise on Allen, saying history would judge him as a pivotal commander in the war against the Taliban insurgency.
"General John Allen has proven himself to be one of the United States military's most outstanding battlefield leaders, a brilliant strategist, and an exemplary Marine, and I am deeply grateful for his many years of dedicated service to our country," he said.
The Pentagon chief said the strategy Allen helped shape and carry out "has put us on the right path towards completing this mission, with Afghan forces now on track to step into the lead for security nationwide this spring and to assume full security responsibility by the end of next year."
The United States and its NATO allies have committed to withdrawing almost all combat troops by the end of 2014, when Afghan army and police will take over responsibility for security for the whole country.