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The French climber will not start the 13th stage at the Tour.
Arkéa-Samsic officials confirmed that the team’s other seven riders cleared health controls, and will continue in the race.
The 30-year-old Barguil was close to winning Wednesday’s 11th stage after riding into a long breakaway only to be caught on the upper reaches of the Col du Granon.
Also read: No regrets for Warren Barguil
Barguil won the day’s most aggressive prize for the effort.
On Thursday up Alpe d’Huez, teammate Nairo Quintana could not match his previous day’s effort when he was second at Granon, and struggled to 14th. Quintana dipped from fifth to sixth.
Arkéa-Samsic has never won a Tour stage in franchise history.
With Barguil’s DNS, some 158 riders remain in the 2022 Tour.