Error message using ReorderSam

JuttaJutta Bonn, GermanyMember

Dear GATK team,

I am still following the Best practice guide for SNP calling of RNA-seq data.
For one of my samples, I obtained the following error message when applying the following program code:

java -jar /opt/picard/picard.jar ReorderSam I=sample_dedupped.bam O=sample_reordered.bam R=Zea_mays.AGPv3.31.dna.genome.edit.fa CREATE_INDEX=TRUE

For all my other samples this program code worked fine, and I treaded all the samples similar in any previous steps.

...
INFO 2016-12-19 16:03:33 ReorderSam Processing 7
INFO 2016-12-19 16:04:03 ReorderSam Wrote 2554799 reads
INFO 2016-12-19 16:04:03 ReorderSam Processing 5
INFO 2016-12-19 16:04:44 ReorderSam Wrote 3838774 reads
INFO 2016-12-19 16:04:44 ReorderSam Processing 3
[Mon Dec 19 16:04:47 CET 2016] picard.sam.ReorderSam done. Elapsed time: 3,19 minutes.
Runtime.totalMemory()=796393472
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 228651, Read name K00114:299:H5Y5TBBXX:6:1202:27407:1508, bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned
at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:441)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:665)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:650)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:620)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:853)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:843)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:809)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:545)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:519)
at picard.sam.ReorderSam.writeReads(ReorderSam.java:170)
at picard.sam.ReorderSam.doWork(ReorderSam.java:125)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

I had a look at several websites, but I couldn't find any solution for this problem.
So, I would be very happy, if there are any suggestions how to solve this error?

Greetings Jutta

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