Qiime feature-table merge not working


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
–i-tables Nereo_Temporal-filtered-table.qza
–i-tables Temporal-Nereo-base-200-seqs.qza
–o-merged-table Temporal_blade_tip_seawater_table.qza

-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 overlap_method provided.

–i-tables MULTIPLE ARTIFACT PATH List[FeatureTable[Frequency]]
The collection of feature tables to be
merged. [required]
–p-overlap-method [sum|error_on_overlapping_sample|error_on_overlapping_feature]
Method for handling overlapping ids.
[default: error_on_overlapping_sample]
–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.
[default: False]
–quiet Silence output if execution is successful
(silence is golden). [default: False]
–help Show this message and exit.

Hi @Brooke,

This looks a bit odd, but we’ll figure it out!
You mentioned that QIIME2 produces an output when you type qiime feature-table merge --help. Does it also work when you type qiime feature-table --help?

Also, could you paste the code you’re trying to run verbatim in a code field provided by the editor, so that I can test it out?


Hi Tomasz,

I figured it out eventually… for some reason, the code that I was copy-pasting into the terminal from text edit had some strange formatting. When I started using text wrangler and copy-pasting QIIME commands from there, everything worked! I am still not sure exactly what was wrong, but it is recognizing the commands now. You can close this topic.


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