System locale settings and q2cli

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Interesting! Are you changing between different terminal applications (e.g. Apple Terminal vs iTerm) between running those commands?

Another factor that comes to mind is if you have any internationalization helpers enabled on your computer (I am assuming it is a Mac, given the filepaths in your snippet above) --- this could look like alternative language support, or some other keyboard switcher (on the macs i have used, this looks like a little country flag in the task bar up top to let me know what language is enabled on the system).

Either way, something else on your computer seems to be toggling your language/locale settings (QIIME 2 doesn't know how to change those settings, so it seems unlikely that it would be the culprit here...), so you should be able to get around this by manually setting those values when you execute a QIIME 2 command:

$ source activate qiime2-2017.10
$ export LC_ALL=en_US.UTF-8
$ export LANG=en_US.UTF-8
$ qiime tools import \
  --input-path /Users/Paige/WorkFolder_NBZLJBA6E8Z5_R1clean/otu_table_halandmock_meta_filtered.biom \
  --output-path /Users/Paige/qiime2-testing/out_hal.gza \
  --type FeatureTable[Frequency]

or alternatively:

$ LC_ALL=C.UTF-8 LANG=C.UTF-8 qiime tools import \
  --input-path /Users/Paige/WorkFolder_NBZLJBA6E8Z5_R1clean/otu_table_halandmock_meta_filtered.biom \
  --output-path /Users/Paige/qiime2-testing/out_hal.gza \
  --type FeatureTable[Frequency]

which will only temporarily set those values for you. Give one or both of the options a shot and let us know how it goes!

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