@isaacovercast: I tried two different assembly methods, using the same data set and the version [v.0.6.11] of ipyrad. All parameters were the same in the params file (except the ones referring to the assembly method. The run using denovo-reference is running normally in step 3 but the one using reference gives the following message in ipyrad_log.txt (attached)
Merging reads 100% Fatal error: More reverse reads than forward reads Any advise would be much appreciated
@R2C2_Lab_twitter The denovo-reference assembly is running ok because it's the reference mapping part that's causing problems, so denovo-reference does the mapping, but then throws out the mapped reads, so no problems.