Picard MarkDuplicates /SAM validation error

Question

[whaiyu06]

Hello,everyone

I used Picardtools/MarkDuplicates as following:

java -jar picard.jar \
    INPUT=A01-2m-D6.sort.bam \
    OUTPUT=A01-2m-D6.bam \
        METRICS_FILE=A01-2m-D6.metrics CREATE_INDEX=true 2>A01-2m-D6.picard_MarkDuplicates.stderr

then I met thus error:

picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 2.38 minutes.
Runtime.totalMemory()=2058354688
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 78004, Read name E00477:238:hggvjccxy:8:2224:1519:63050, Zero-length read without FZ, CS or CQ tag
        at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:454)
        at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:812)
        at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:797)
        at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:765)
        at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:576)
        at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:548)
        at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:495)
        at picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:232)
        at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:269)
        at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
        at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

How can I deal with this problem ?Thanks

Answer 1

[Pierre Lindenbaum]

use https://broadinstitute.github.io/picard/command-line-overview.html#StandardOptions

VALIDATION_STRINGENCY=LENIENT

[andrew.phipps.00]

Thanks a heap Pierre!