I have run it both with and without & on the end. Every time I have run it either way, I have only gotten the table.qza output. While it is running, I have been able to see that it is running using the top command but once the table appears in my directory, top no longer shows any qiime2 command running. It seems like the command is stopping after generating the table.qza. How can I get the full command to run?
My system versions are the following:
Python version: 3.6.7
QIIME 2 release: 2019.7
QIIME 2 version: 2019.7.0
q2cli version: 2019.7.0
Thank you for your time and attention to this!
I ran the same command with verbose and it ended up running just fine and created all three outputs. I haven’t figured out why this made any difference but if people have ideas, please let me know. I’d like to understand what happened and it may be helpful if someone has this issue again at some point.
Thanks for following up! The addition of the --verbose flag almost certainly had no bearing on the results. My best guess is that something “interrupted” the process the first time you ran it, and so the command was terminated before all the outputs were written. Just a theory at this point.