Brian Walenz

How was meryl-lookup installed? What version is this (`meryl-lookup --version`)? What is the command line? Have you tried the latest release?

That will work. You might want to limit memory and thread usage with `memory=` and `threads=`. By default, it will use as much memory as it wants and all the...

Thanks, Mikko. It's not just an empty first file that causes trouble. The 'compress' flag is reset after EACH file. The workaround is simple but annoying: add 'compress' before each...

Sorry about that. I just pushed a rewrite of that piece that should resolve the compile errors.

That seems to be the same as in https://github.com/marbl/merqury/issues/98. The resolution there was to compile `meryl` from either the `master` or `v1.4-maintenance` branch (both have the bugfix). Holler if you...

You want to use Canu. If you include the '-haplotype' option Canu will only do the read partitioning. meryl is (mostly) the same between the two repos; the trio partitioning...

You can cheat a little bit and get the next Canu release (expected next week) with: ``` git clone [email protected]:marbl/canu cd canu git checkout v1.9 ``` marbl/meryl is intended to...

Try reducing the number of threads to 16 or even 8. I can't advise more without knowing the command line.

The script feature is described in https://github.com/snakemake/snakemake/pull/1821 from Aug 22 and appears in release 7.14.0 from Aug 27. It requires bash, while verkko is happy with generic sh. It allows...

The code looks like it should be requesting additional memory on the second retry, but, indeed, cluster logs show two jobs with the same memory request. Advise manually increasing the...