I get an error like "Encountered exception: Murasaki: Error creating System V IPC shared memory segment (size: 36.93 mb) for dna/human/chrX.fa.gz: Invalid argument" †

The default linux kernel only permits a total of 32mb of shared memory. Using System V IPC shared memory with murasaki and large sequences you'll quickly run into this limit. You can set a higher limit (say 6gb) by running "sysctl -w kernel.shmmax=6442450944" (or setting this in /etc/sysctl.conf).

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What's the -p (--pattern) argument? †

The -p parameter specifies the pattern used when creating seeds. While there's a number of posters for Murasaki, the journal paper is still in preparation, so it's rather hard to explain, but spaced seeds are a common feature now in homology search programs, and if you want some more information on them, you should check out the PatternHunter paper which introduced the idea. Basically a pattern is sequence which represents which bases in a seed must match and which can be mismatched. For example, for the pattern 101, "ATA" matches "AAA" but not "AAT". The -p argument can take a specific pattern like -p101, but in general we find that random patterns are generally acceptable, so we specify "random patterns" to Murasaki in the form of -p[weight:length] (the [ ] characters can be omitted) where "weight" represents the number of 1s in the pattern and "length" is the total length. The longer the pattern and the more 1s in it, the more specific but less sensitive it becomes.