The first thing to do is when you see a QC metric warning or failure is to gain more information about the sample (read length, read quality, coverage, etc). Having more information makes it easier to diagnose the problem and make an informed decision about the required steps (e.g. full resequencing, resequencing from a specific step). Certain advanced analysis settings (e.g. processing more reads) can be used for compensating for some not too serious quality issues.