From The Life of Mark Twain: The Early Years, 1835-1871, pp127-8

Sam's career on the river ended soon after the outbreak of the Civil War. He seems to have been largely oblivious to events that precipitated the conflict. He chewed the war talk without tasting it, as the saying went. Or, as Arthur Pettit has remarked, he “gave little thought or attention to the approaching collision between North and South or to his own position on the twin issues of slavery and sectionalism.” Sam was in New Orleans on January 26, 1861, when Louisiana seceded, and he remembered “Great rejoicing. Flags, Dixie, soldiers.” At Vicksburg en route to New Orleans on April 19, he heard about the firing on Fort Sumter the day before, and the crew of the Alonzo Child, on orders from its secessionist captain, David DeHaven, “hoisted the stars & bars & played Dixie” in celebration. While the gesture may seem innocuous enough, it was in fact an act of treason. According to Horace Bixby, who had by this time retired from the Alonzo Child, Sam “piloted .. . for the Confederacy between March and May 1861 before “he got through the lines and went home.” For many months as a pilot on the lower Mississippi, Sam had landed at no free port except those in southwestern Illinois such as Cairo, so the “Irrepressible Conflict” must have seemed Distant and/or Eminently Avoidable. The states of Arkansas, Louisiana, Mississippi, and Tennessee, all of which he passed every couple of weeks while piloting, seceded from the United States to join the Confederacy. Sam was earning $250 a month at a job for which he had been painstakingly trained, and the war seemed more a nuisance to him than a moral crusade. “I supposed—and hoped—that I was going to follow the river the rest of my days, and die at the wheel,” he wrote in Life on the Mississippi. Instead, he was bumped off his boat in New Orleans in mid-May 1861, nearly a month after the war began, because the owners of the Child had decided to sell it at nominal cost to the Confederate Navy. Its engines were removed and installed on the CSS Tennessee, an ironclad warship seized in February 1864 by the Union at the Battle of Mobile Bay. The shell of the Child was converted into a barge.