Exception "Inappropriate call if not paired read"

Dear colleagues,

I am running a third-party program that makes use of the htsjdk library.
For some of my samples (BWA alignments) it raises the following exception:

Exception in thread "Thread-5" java.lang.IllegalStateException: Inappropriate call if not paired read
at net.sf.samtools.SAMRecord.requireReadPaired(SAMRecord.java:655)
at net.sf.samtools.SAMRecord.getMateUnmappedFlag(SAMRecord.java:682)

It seems there may be some problem inside the BAM file. However, after running Picard's ValidateSamFile it only finds 1,155 INVALID_MAPPING_QUALITY errors (no errors related to mate reads).
Anyhow, I repaired the bam file using Picard's CleanSam and rerun the third-party program.
The "Inappropriate call if not paired read" error persisted.

How could I solve this, please?

Thanks in advance,
Federico

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