Picard rmdup error

[kapoormanav]

Hi

I am getting problems in rmdup command in Piacrd tools. I am getting following error with picard while samtools rmdup is working fine..

[kapoorm@ewok picard-tools-1.29]$ java -jar MarkDuplicates.jar INPUT= ../merge3_4.bam OUTPUT= all_sorted_rmdup.bam METRICS_FILE= output
_metrics.txt REMOVE_DUPLICATES=True ASSUME_SORTED=True
[Tue Sep 07 11:16:09 EDT 2010] net.sf.picard.sam.MarkDuplicates INPUT=../merge3_4.bam OUTPUT=all_sorted_rmdup.bam METRICS_FILE=output_metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9][0-9]+)[0-9]+)[0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 TMP_DIR=/tmp/kapoorm VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
INFO 2010-09-07 11:16:09 MarkDuplicates Start of doWork freeMemory: 1998646216; totalMemory: 2009530368; maxMemory: 29822484480
INFO 2010-09-07 11:16:09 MarkDuplicates Reading input file and constructing read end information.
INFO 2010-09-07 11:16:09 MarkDuplicates Will retain up to 118343192 data points before spilling to disk.
INFO 2010-09-07 11:16:11 MarkDuplicates Assuming input is coordinate sorted.
[Tue Sep 07 11:16:11 EDT 2010] net.sf.picard.sam.MarkDuplicates done.
Runtime.totalMemory()=2956328960
Exception in thread "main" java.lang.RuntimeException: SAM validation error: ERROR: Record 5, Read name HWI-EAS440_0346_3_4_8506_17750#0, Mapped mate should have mate reference name
at net.sf.samtools.SAMUtils.processValidationErrors(SAMUtils.java:334)
at net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:449)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:430)
at net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:397)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:604)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:582)
at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:259)
at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:160)
at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93)


Can someone suggest me what should I do to correct this error or what this error exactly mean?

Manav

[mrawlins]

It looks like you've got mate pairs that don't have corresponding names. The way I read the file format specification is that every pair should have just one name, which is given to both the reads in the pair, and if they're different then Picard throws this error.

[kapoormanav]

Thanks! But can you suggest me some idea by which I can overcome this problem.