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Restarting plants even under the best conditions can take a week or more.

Scene from the Harvey flood in Houston. "Roof is sinking due to Hurricane Harvey dumping heavy and large amounts of rainfall in short period of time".

Earlier on Tuesday, Motiva Enterprises said that its refinery in Port Arthur, Texas - the biggest in the U.S. - had cut output to 40 percent.

Other refineries on the Gulf Coast have reported no major damage so far.

The refinery shutdowns have caused a quick spike in gasoline prices, both in futures markets as well as at the retail level, especially in and around Houston.

One accident happened at Exxon's Beaumont petrochemical refinery. After all, it seems like nearly everybody was flaring or just releasing all kinds of chemicals.

"Any release of carcinogens (like benzene, 1,3-butadiene) adds to the increased cancer risk for those living near these plants", Metzger said in an email.

Damage to floating roofs is becoming a common theme for refiners in the rain-drenched Houston area.

Exxon said it would "conduct an assessment to determine the impact of the storm once it's safe to do so", the Washington Post reports.

As of Tuesday afternoon, Exxon's Baton Rouge facilities were operating as normal, the company said in its latest safety and operations update on Hurricane Harvey.

Colonial Pipeline, the key artery sending gasoline up the East Coast, was still shipping barrels there but had faced flooding at origination points in Texas.

"Excess emissions occurred during an upset on the Sulfur Plant Thermal Oxidizer", Exxon said in the report. "The unit was stabilized". The Cedar Bayou chemical plant, for instance, exceeded permitted limits for several kinds of hazardous pollutants, including 1,3-butadiene, benzene and ethylene, during shutdown procedures. ExxonMobil said it had flared hazardous materials at its Baytown refinery Sunday and Monday.

Companies are now working to clean up the mess as best they can, with Pasadena Terminal saying it is "taking all necessary steps to prevent or minimize any increased risk to human health and safety and to the environment" in its damage report. USA traded crude-oil futures were off 0.5% at $47.42 a barrel. Based on operator reports, 19.1 percent of the natural gas production in the Gulf of Mexico was shut-in as of yesterday evening.

CNBC estimates the port closures cost roughly $350 million a day. The oil giant also has halted operations at its Pasadena facility.

Gas prices across the United States have already risen to a two-year high, with the increase likely to hit consumers at the pump in a week.