Warning error for PE

[Anne Van Arsdale]

Hi Tobias-

Have there been any issues with any version of delly giving a warning that the paired end reads are non default? 

I have been using delly successfully for awhile with PE sequencing and alignment with bwa, however it is now giving me this warning everytime and thus not calculating the PE support for the SV. 

I thought maybe it was on the alignment side and tried some alternative aligners as well like bowtie, but I'm getting the same thing. 

Thanks!

Anne