Following run did not write results
docker run --rm -it -u $(id -u):$(id -g) -v $(pwd):/data qiime2/core:2019.4 qiime feature-classifier classify-sklearn --i-classifier silva-132-99-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy1.qza --verbose
No error log or verbose comment generated as the run completed.
While the same command run natively (qiime2-2019.4) generates results.
qiime feature-classifier classify-sklearn --i-classifier silva-132-99-nb-classifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza --verbose
Saved FeatureData[Taxonomy] to: taxonomy.qza
Please let me know if you need more information about this run?
It sounds to me like maybe you didn't let the command run to completion - have you had any success with other QIIME 2 commands run in docker? The command you shared above can take quite a long time to complete, and might not be representative of the "usual" runtime of things.
Thanks. I did let it complete and it ran for over a little more than an hour. Had only tried it running with the commands mentioned previously (with docker and natively). Haven’t tried it running inside the docker container.
Yesterday after receiving your reply, I re-ran it and this time it wrote the results as expected. Seems in previous instance my system, docker environment and resources prevented it from writing the results.