1. Have you change minReadLength( default 1000)? I suggest you to have a look at your reads distribution ,maybe many of your reads are too short. Read length below 1000bp will be discarded.Please read the canu document canu questions carefully .That will be helpful.
2. In the assembly step,you can change correctedErrorRate according to your coverage:

1. For low coverage: For less than 30X coverage, increase the alllow difference in overlaps by a few percent (from 4.5%to 8.5% (or more) with correctedErrorRate=0.105 for PacBio and from 14.4% to 16% (or more) correctedErrorRate=0.16 for Nanopore), to adjust for inferior read correction.Canu will automatically reduce corMinCoverageto zero to correct as many reads as possible.
2. For high coverage: For more than 60X coverage, decrease the allowed difference in overlaps (from 4.5% to 4.0% with correctedErrorRate=0.040 for PacBio, from 14.4% to 12% with correctedErrorRate=0.12 for Nanopore), so that only the better corrected reads are used.This is primarily an optimization for speed and generally does not change assembly continuity.