Samtool merge problem

[kapoormanav]

Hi

I am trying to merge two bam files using samtools merge and its giving me error message

"Truncated file"
It completes the merging but when I do the samtools flagstat, It again gives me message truncated file, and its even not giving me full flagstat. When I tried to sort the merged file (which given me truncate message) it just generated the temp files but while merging the temp files it given the segmentation fault and stopped. It never happened with previous alignments.

I have used novo2sam.pl for sam file conversion. Even when I am using picard tools for merge it says that header of two mates don't match and truncate the merging.

Any suggestion will be helpful to me.

Thanks

Manav