I am having trouble with the qiime feature-table merge command, and I can’t figure out what the problem is. Terminal keeps giving me the output “-bash: qiime feature-table: command not found”, even though clearly the command is there (see the --help output below). Other qiime2 commands (like qiime diversity core-metrics-phylogenetic) are currently working. Any help would be much appreciated… thanks!
$ qiime feature-table merge
-bash: qiime feature-table: command not found
However, when I type: (qiime2) $ qiime feature-table merge --help
I get the following output, indicating that the function is there…
Usage: qiime feature-table merge [OPTIONS]
Combines feature tables using the
–i-tables MULTIPLE ARTIFACT PATH List[FeatureTable[Frequency]]
The collection of feature tables to be
Method for handling overlapping ids.
–o-merged-table ARTIFACT PATH FeatureTable[Frequency]
The resulting merged feature table.
[required if not passing --output-dir]
–output-dir DIRECTORY Output unspecified results to a directory
–cmd-config PATH Use config file for command options
–verbose Display verbose output to stdout and/or
stderr during execution of this action.
–quiet Silence output if execution is successful
(silence is golden). [default: False]
–help Show this message and exit.