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Thanks. So, this is what I did (if anybody else is curious) to make it run successfully:
xvfb-run ebook-convert /usr/share/calibre/recipes/san_fran_chronicle.recipe todays_sfgate.mobi
Note the command xvfb-run at the beginning, which ran ebook-convert with X support (as I understand it). It successfully produced the mobi file I wanted and now I can automate this all with cron.
Thanks!
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