Here’s the [Meraculous manual (PDF)(https://1ofdmq2n8tc36m6i46scovo2e.wpengine.netdna-cdn.com/wp-content/uploads/2014/12/Manual.pdf).
After a bunch of various issues (running out of hard drive space - multiple times, config file issues, typos), I’ve finally given up on running meraculous. It failed, again, saying it couldn’t find a file in a directory that meraculous created! I’ve emailed the authors and if they have an easy fix, I’ll implement it and see what happens.
Anyway, it’s all documented in the Jupyter Notebook below.
One good thing came out of all of it is that I had to run kmergenie to identify an appopriate kmer size to use for assembly, as well as estimated genome size (this info is needed for both meraculous and SOAPdeNovo (which I’ll be trying next)):
kmergenie output folder: https://owl.fish.washington.edu/Athaliana/20180125_geoduck_novaseq/20180206_kmergenie/ kmergenie HTML report (doesn’t display histograms for some reason): 20180206_kmergenie/histograms_report.html kmer size: 117 Est. genome size: 2.17Gbp
Jupyter Notebook (GitHub): 20180205_roadrunner_meraculous_geoduck_novaseq.ipynb