Hi there!
I’m having the same issue and ran the standalone ITSxpress; however, I cannot seem to get the file back into qiime2 now.
I did the following: exported my demultiplexed data from qiime2 >> merged the sample by sample files with a cat command >> ran ITSxpress on the merged file, but now I get error after error when trying to import. What import-format and type did you specify to get the file back into qiime2?
Thanks!
Take care,
Molly