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Old 04-26-2011, 02:19 PM   #3
Richard Finney
Senior Member
 
Location: bethesda

Join Date: Feb 2009
Posts: 700
Default Validation_stringency=lenient

Try VALIDATION_STRINGENCY=LENIENT in the java invocation.

Example:

java-Xmx67T -jar wherever/SamTowhatevernameis.jar \
VALIDATION_STRINGENCY=LENIENT \ INPUT=uncle.sam O=nephew.sam


That might shut up the error message and get Picard to accept the input.
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