Ive been using what you suggested to use for creating OTU table in Qiime2 and yesterday I had an error msg that says:
(1/2) Missing option ‘–o-collapsed-table’. ("–output-dir" may also be
(2/2) Got unexpected extra argument ( )
/var/lib/slurmd/job2227746/slurm_script: line 22: --output-dir: command not found
my script was:
qiime taxa collapse
I also switched --output-dir dada2_trial/ to --o-collapsed-table dada2_trial.qza
it gave me similar results as missing options… so I really don’t know what is wrong??