Qiime2 seems to have hung up when trying to generate the ancom file… can anyone see anything wrong with the code?
I first tried it with the original table, but got an error, so I tried the previous code to generate a composition table first; it seemed to have worked, but it hung for about an hour on this code without generating any output. I then just Ctrl + C to cancel.
This is kind of important for measuring differential abundance in my project.
I think ANCOM is a fairly computationally expensive algorithm. It’s possible that it can take over an hour to run. Do you have reason to believe that it should complete in under an hour? I would suggest allowing to job to run for longer before canceling it unless you are absolutely sure that it shouldn’t take that long.
Aside, from that, in your screen shot, I notice what appears to be some rogue text: table co> on the second line after qiime composition ancom. That looks like a typo to me.
Hi @dvdharkin ,
Runtime for ancom, like many things, really depends on much more than hardware specs — it is really quite difficult to predict.
As @andrewsanchez already pointed out, ancom can be quite computationally intensive if you have many features and/or samples. Issues with runtime have been reported a lot on this forum, so you could search the archives for different ways to address this, e.g., the advice in this post still stands:
Other than that, the best system spec for using ancom is a bit of patience