Errors from Picard and GATK on a BWA paired-end BAM

[oiiio]

I have two samples with the following errors. One had an error in Picard MarkDuplicates. The other in GATK IndelRealigner. Both samples were mapped using BWA on paired-end data.

Does anyone know of a way to resolve these errors without removing reads from the sample? Any input at all is greatly appreciated

In Picard:

Exception in thread "main" net.sf.picard.PicardException: Value was put into PairInfoMap more than once.  2: foo:USI-EAS034_4_PE1_FC304CLAAXX:2:22:534:490
	at net.sf.picard.sam.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:124)
	at net.sf.picard.sam.CoordinateSortedPairInfoMap.remove(CoordinateSortedPairInfoMap.java:78)
	at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:61)
	at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:294)
	at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:117)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
	at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:101)

and in GATK:

##### ERROR MESSAGE: Exception when processing alignment for BAM index USI-EAS034_2_PE_FC307TBAAXX:3:79:1633:1917 2/2 45b aligned read.

[swbarnes2]

It would probably help if you showed all the .sam entries for reads with that name.

[oiiio]

I am searching for them, but these BAMs are quite large and it will require some time. In the meantime, do you have any thoughts on the problems?