length of deletions called by Pindel

Question

[hnmcy11]

I am calling deletions using Pindel, in my script, I set the parameter -x 6. However,the length of some deletions I called is much larger than that threshold(129,472).In fact, the largest deletion I called is as long as 2 million bp, that is too weird. Can anyone help me with that?

I am dealing with DGRP data, here is my script:

./pindel -f dmel-all-chromosome-r6.03.fasta -i configuration_file -o ./output -x 6 -d 20

and I use novoalign to produce the bam file.