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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