This indicates that set_meta is running locally, in the runner process. Can you make sure there's not a typo in your config? The other possibility is that external metadata setting failed and it's being retried internally (if that was true, you'd see messages indicated such in the server log).
I'm pretty sure there isn't a typo. Here is anything meta related (with
comment lines removed) in my universe_wsgi.*.ini files: [galaxy@bic galaxy-dist]$ grep set_meta *.ini universe_wsgi.ini:set_metadata_externally = True universe_wsgi.runner.ini:set_metadata_externally = True universe_wsgi.webapp.ini:set_metadata_externally = True [galaxy@bic galaxy-dist]$ grep meta *.ini universe_wsgi.ini:set_metadata_externally = True universe_wsgi.runner.ini:set_metadata_externally = True universe_wsgi.webapp.ini:set_metadata_externally = True I just tried it again on some BAM files, and nothing comes up in /var/log/messages or /var/log/httpd/error_log. Runner0.log also doesn't show anything except for the upload job being completed.