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`
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!
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` ```
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. ```
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.
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
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
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)?
