The company said in an update on its Facebook page at 8:55 p.m. that employees had stopped the flaring, but intermittent flaring could still occur as the refinery is brought back up to full production.
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Thick black smoke could be seen billowing from the refinery on Monday afternoon starting at about 4:15 p.m.
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No evacuations were issued and teams from Contra Costa County Health's hazmat unit, the Richmond Fire Department, and the Bay Area Air Quality Management District were called to the refinery to measure air quality levels.
A Community Warning System level 1 warning was issued by the refinery because of the visibility of the smoke. A level 1 warning does not require any action by the public.
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To view real-time air quality data, click here.