Hey Hua,
the error message has a link to getting help, and the problem you are
having is described in the FAQ (search for "MAPQ"):
http://broadinstitute.github.io/picard/faq.html. Please send further
questions here. Thank-you,
N
On Tue, Jan 27, 2015 at 8:53 PM, 黄桦 <huangh...@mail2.sysu.edu.cn> wrote:
> Hi All
> I am getting the following error when I run picard.
> picard version:1.128
> java version:1.6.0_33
> root@ubuntu:/home/dell/ruanjian/picard/picard-tools-1.128# java -Xmx10g
> -jar picard.jar SortSam INPUT=BZ69-R162N-69831_AGTCAA_L003_R_001.bam
> OUTPUT=BZ69-R162N-69831_AGTCAA_L003_R_001.sort.bam SORT_ORDER=coordinate
> [Tue Jan 27 22:39:58 CST 2015] picard.sam.SortSam
> INPUT=BZ69-R162N-69831_AGTCAA_L003_R_001.bam
> OUTPUT=BZ69-R162N-69831_AGTCAA_L003_R_001.sort.bam SORT_ORDER=coordinate
> VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5
> MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
> [Tue Jan 27 22:39:58 CST 2015] Executing as root@ubuntu on Linux
> 3.11.0-26-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_33-b33; Picard
> version: 1.128(c8e12338d226532b30e9ecdbf33180a073c3ffc7_1421081159)
> IntelDeflater
> [Tue Jan 27 22:40:10 CST 2015] picard.sam.SortSam done. Elapsed time: 0.19
> minutes.
> Runtime.totalMemory()=1274740736
> To get help, see
> http://broadinstitute.github.io/picard/index.html#GettingHelp
> Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM
> validation error: ERROR: Record 918149, Read name
> HWI-ST1033:89:C0JT0ACXX:3:1101:20187:194779, MAPQ should be 0 for unmapped
> read.
> at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:439)
> at
> htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:643)
> at
> htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:628)
> at
> htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:598)
> at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:515)
> at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:489)
> at picard.sam.SortSam.doWork(SortSam.java:81)
> at
> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
> at
> picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
> at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
> Would you please tell me what I should do? In addition, I wonder if there
> is any test data and result for users to check whether picard work normally
> or not.
> Thank you for your attention. I am looking forward to hearing from you.
>
> Hua
>
>
>
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leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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