Question: Picard MarkDuplicates /SAM validation error
gravatar for whaiyu06
9 months ago by
whaiyu0620 wrote:


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.
To get help, see
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(
        at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(
        at htsjdk.samtools.BAMFileReader$
        at htsjdk.samtools.BAMFileReader$
        at htsjdk.samtools.SamReader$
        at htsjdk.samtools.SamReader$
        at picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(
        at picard.sam.markduplicates.MarkDuplicates.doWork(
        at picard.cmdline.CommandLineProgram.instanceMain(
        at picard.cmdline.PicardCommandLine.instanceMain(
        at picard.cmdline.PicardCommandLine.main(

How can I deal with this problem ?Thanks

sequencing alignment • 750 views
ADD COMMENTlink modified 9 months ago by Pierre Lindenbaum115k • written 9 months ago by whaiyu0620
gravatar for Pierre Lindenbaum
9 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum115k wrote:


ADD COMMENTlink written 9 months ago by Pierre Lindenbaum115k

Thanks a heap Pierre!

ADD REPLYlink written 9 months ago by andrew.phipps.000
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2147 users visited in the last hour