What are defects in approximation? What are the disadvantages to using defect mode?

[sclamons]

A common error I've encountered when using preseq is "ERROR: too many defects in the approximation, consider running in defect mode". I have a few questions about this for which I haven't found answers in the docs:

• What does this mean, exactly? What is a defect in this context?
• What are the downsides of running in defect mode?
• Should we trust the answers that come out of a defect mode run less?

Any help with this would be appreciated.

[andrewdavidsmith]

@sclamons I can't answer in detail right now.

Yes. In the context of preseq, having a defect means the predictions might not be as reliable.

But I suggest you run in defect mode, which might actually work out for you. Then plot the output as a graph (e.g., with R or whatever you use). If your plot looks like it's somewhat smooth, at least enough for you to feel like you can visually interpret it, then it should be fine. If not, then share a screen capture here. And if you don't want to share the image here, feel free to email me directly.