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

Join Date: Feb 2008
Posts: 6,975
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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 reformat.sh took out some of the reads so the problem reads have been hopefully addressed.
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