Lack of paired mate in BAM file

[PJohn]

Hello,

When I use BWA and samtools to align sequences to a reference host genome and extract the non-host DNA I get the following warning in some cases:

WARNING: Query HISEQ:218:C67H1ANXX:4:1214:15544:30005 is marked as paired, but its mate does not occur next to it in your BAM file. Skipping.

My next step is use again BWA to align the non-host DNA to a reference database looking for specific genes. My question is: is that warning important or can I ignore it?

Thanks!