mate alignment error when running ValidateSamFile in Picard

[slowsmile]

Dear All
I am trying to identify snps using GATK tool. Their manual suggested that I shall try to validate my bam files before entering the analytic pipeline.

My samples are 100 nucleotides long (first 3 sites trimmed) paired reads.

I generated bam files for each sample using tophat 1.33 and I sorted each bam file (one file per sample) using picard ReorderSam.jar,

After that I added read group information using Picard AddOrReplaceReadGroups.jar.

Then I ran a ValidateSamFile.jar to check whether these bam files are suitable in GATK pipeline. However, I got a lot of errors like this.

ERROR: Record 21368, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate alignment does not match alignment start of mate
ERROR: Record 21368, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate negative strand flag does not match read negative strand flag of mate
ERROR: Record 21377, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate alignment does not match alignment start of mate
ERROR: Record 21377, Read name HWI-ST978:1370AHMACXX:5:1308:13890:200017, Mate negative strand flag does not match read negative strand flag of mate
ERROR: Record 21477, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate alignment does not match alignment start of mate
ERROR: Record 21477, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate negative strand flag does not match read negative strand flag of mate
ERROR: Record 21481, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate alignment does not match alignment start of mate
ERROR: Record 21481, Read name HWI-ST978:1370AHMACXX:5:1306:2629:199972, Mate reference index (MRNM) does not match reference index of mate
ERROR: Record 21490, Read name HWI-ST978:1370AHMACXX:5:2108:3190:30134, Mate alignment does not match alignment start of mate
ERROR: Record 21490, Read name HWI-ST978:1370AHMACXX:5:2108:3190:30134, Mate negative strand flag does not match read negative strand flag of mate

Can anyone tell me where the problem is? Why do I have so many unmatched pairs identified at this step. Should I delete them before the analysis?

Thanks a lot.

[gormleymp]

I am seeing the same errors. Does anyone have any insight into this?

[sciencewu]

I also encounter this problem, and now I am using the picard/FixMateInformation.jar to fix it, maybe you can try

[tatumdmortimer]

I am also seeing these errors. I tried using Picard's FixMateInformation, but it did not resolve the errors. They seem to be appearing after I use Picard's MarkDuplicates. Is anyone else having this problem/know how to fix it?

[yeyeming]

I am also seeing these errors. I tried using Picard's FixMateInformation, but it did not resolve the errors. They seem to be appearing after I use Picard's MarkDuplicates. Is anyone else having this problem/know how to fix it?

I ValidateSamFile before MarkDuplicates, these errors still occur.

Has anyone solved this problem?

[raphael123]

Same

I have the exact same problem tat I can't solve ...
Maybe it have a link but I also have an exception when trying the CollectGcBiasMetrics command

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 142549452
	at net.sf.picard.analysis.CollectGcBiasMetrics.doWork(CollectGcBiasMetrics.java:152)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
	at net.sf.picard.analysis.CollectGcBiasMetrics.main(CollectGcBiasMetrics.java:95)