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Old 06-13-2019, 08:16 AM   #226
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,975

Have you tried adding "VALIDATION_STRINGENCY=LENIENT" to your picard command? Default value is STRICT and sometime it leads to picard throwing errors like this.

It does looks like took out some of the reads so the problem reads have been hopefully addressed.
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