I'm doing metagenomic pacbio data assembly using canu. I have tried a few runs with different parameters to see what N50 I would get and estimate a good k-mer size.
Each run has lasted for approx. 3-4 hours, as long as the set k-mer size was below 50. In the last run I have brought the k-mer size to 101 and it has been going on for what are now 4 days and it still is at the "meryl" step, which I suppose is where it counts k-mers and their occurrences.
Now, I know that assemblies take long but could it be that canu is for some reason idling at the meryl step? Did anybody experience this in their work already?