`qiime diversity core-metrics`, empty output-dir

Following was creating an empty output folder with no Error:

qiime diversity core-metrics \
  --i-phylogeny rooted-tree.qza \
  --i-table table.qza \
  --p-sampling-depth 1441 \
  --output-dir cm1441 \

--verbose showed:

Intel MKL FATAL ERROR: Cannot load libmkl_avx2.so or libmkl_def.so.

Solved with:

conda install nomkl

Only a problem with one of our 2017.2 installations. Posting in case anyone else encounters it.


Thanks for posting your fix @Perugolate! To my knowledge, we haven’t seen this issue before. What platform/OS/architecture did you install QIIME 2 on?

1 Like

Sorry this was on Ubuntu 16.04 x86_64 4.4.0-66-generic. I don’t have the issue on any other xenial installs. Mysterious.


Solution (not able to mark the first post in a topic as the solution):

Thanks @Perugolate!

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