"--i-tables" command not found

User Support
1

Continuing the discussion from Merge feature-table list example?:
Hello
I am trying to merge several feature tables using the qiime feature-table merge command as describe in the FMT tutorial and the linked conversation, but I keep getting this same error:
`Usage: qiime feature-table merge [OPTIONS]
Try "qiime feature-table merge --help" for help.

Error: Got unexpected extra argument ( )
/var/spool/torque/mom_priv/jobs/454600.pitzer-batch.ten.osc.edu.SC: line 33: --i-tables: command not found
/var/spool/torque/mom_priv/jobs/454600.pitzer-batch.ten.osc.edu.SC: line 34: --i-tables: command not found`

qiime feature-table merge --i-tables Lane_1/16s-filtered-table.qza --i-tables Lane_2/16s-filtered-table.qza --i-tables Lane_3/16s-filtered-table.qza --i-tables Lane_4/16s-filtered-table.qza \ --p-overlap-method sum --o-merged-data 16s-merged-table.qza

Is this an internal problem (ie a problem with the server) or am I doing something wrong? Any advice is appreciated!

Thanks
Laura

2

Hello Laura,

I think you are on the right track here. That command looks OK to me, but let's explore this a bit.

What does the output of qiime feature-table merge --help show you?

Also, could you post your full error and input command again, and this time using the little ``` tick marks ``` (key above the tab with the ~tilda~ on it) to show your code blocks? This will help format the code so it's more clear.

So if you post this...

```bash
qiime feature-table merge ...
```

... then it will be easier for us to hunt for clues!

Thanks!
Colin

3

Hi Colin
Sorry for the super slow response, and thanks for your very quick one!
Command:
qiime feature-table merge --i-tables Lane_1/16s-filtered-table.qza --p-overlap-method sum --o-merged-data 16s-merged-table.qza

Error:

Try “qiime feature-table merge --help” for help.

Error: Got unexpected extra argument ( ) 
/var/spool/torque/mom_priv/jobs/454600.pitzer-batch.ten.osc.edu.SC: line 33: --i-tables: command not found
/var/spool/torque/mom_priv/jobs/454600.pitzer-batch.ten.osc.edu.SC: line 34: --i-tables: command not found` ```
4

This is what I get when I look into the help command. Any advice is appreciated!

*continued from post above:

Usage: qiime feature-table merge [OPTIONS]
  Combines feature tables using the `overlap_method` provided.
Options:
  --i-tables MULTIPLE ARTIFACT PATH List[FeatureTable[Frequency]]
                                  The collection of feature tables to be
                                  merged.  [required]
  --p-overlap-method [error_on_overlapping_feature|error_on_overlapping_sample|sum]
                                  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 FILE               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]
  --citations                     Show citations and exit.
  --help                          Show this message and exit. ```
5

@LauraMason,

It sounds like there may be an invisible character lurking in your command! Instead of copying/pasting, please try typing out the full command to see if you get this same error.

6

Hello Laura,

In this command, you can pass --i-tables multiple times, once for each table you want to merge.

Like this

qiime feature-table merge \
  --i-tables table-1.qza \
  --i-tables table-2.qza \
  --p-overlap-method sum \
  --o-merged-table table.qza

Or you can do it on one line:
qiime feature-table merge --i-tables table-1.qza --i-tables table-2.qza --p-overlap-method sum --o-merged-table table.qza

Let me know what you find.

Colin
P.S. Nice code formatting :+1:

8

Hey there!
Looks like that worked! Thanks for your help @colinbrislawn and @Nicholas_Bokulich !
I'll keep an eye out for errors like that in the future - seems like an easy fix

9

Glad it worked @LauraMason!

Just for posterity, can you tell us which fix worked? using --i-tables multiple times or typing out the command (to avoid copying an invisible character)?

10

Hey
I re-typed the whole command and used --i-tables multiple times

Here's my full command (8 tables)

qiime feature-table merge \
--i-tables Lane_1/16s-filtered-table.qza \
--i-tables Lane_2/16s-filtered-table.qza \
--i-tables Lane_3/16s-filtered-table.qza \
--i-tables Lane_4/16s-filtered-table.qza \
--i-tables Lane_5/16s-filtered-table.qza \
--i-tables Lane_6/16s-filtered-table.qza \
--i-tables Lane_7/16s-filtered-table.qza \
--i-tables Lane_8/16s-filtered-table.qza \
--p-overlap-method sum \
--o-merged-table 16s-merged-table.qza