7 hour vs 21 minute runtime for snippy on usegalaxy.eu

As part of preparing a video for Galaxy Smörgåsbord, I ran snippy on a M. tuberculosis sample against the M. tuberculosis reference genome (4.4 MB). The history is history ID 892dbfe970f1b275. The first time I ran this process it ran for 7 hours and 29 minutes (history content ID 11ac94870d0bb33ab4c15a5f44a50587). The second time I ran it, it ran for a more usual 21 minutes (history content API ID 11ac94870d0bb33a6be2899d512a2697). Examining the log, the bulk of the runtime was spent on running bwa-mem, which is known to be an I/O intensive process.

I’m reporting this in case investigation shows something useful about usegalaxy.eu configuration.


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Thanks, Peter, for reporting it.
Last week, we fixed several tools that were monopolizing computing nodes. Hope this helps to normalize the computing times.

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