Samtools import problem

[karl.d]

Hello all, I am working with some CHIP-seq paired-end data from our Solexa machine, using BWA and Samtools. The first few lanes have gone smoothly up to the pileup step but now on my current lane samtools is giving me an error. When I try to import the sam file it says this: (after a few minutes)

[sam_header_read2] 117 sequences loaded
Parse error at line 10884530: sequence and quality are inconsistent
Abort

Has anyone ran into a similar problem or at least know what the issue is? Thanks in advance.

-karl