ERROR in QIIME

Question

[dpc]

Hi I want to merge some biom tables within qiime conda environment with script merge_otu_tables.py. When I use following commands, it shows following error:

COMMAND:

qiime merge_otu_tables.py -i *biom -o merge.biom
  

ERROR:

Error: QIIME 2 has no plugin/command named 'merge_otu_tables.py'.
  

Again, for the following command, following error was received:

COMMAND:

python merge_otu_tables.py -i *.biom -o merge.biom
  

ERROR:

Traceback (most recent call last):
  File "merge_otu_tables.py", line 16, in <module>
    from qiime.util import (parse_command_line_parameters, make_option,
ModuleNotFoundError: No module named 'qiime'
  

Can anyone please help me?

[gb]

Think you are mixing qiime and qiime2.

https://docs.qiime2.org/2020.6/plugins/available/feature-table/merge/?highlight=merge

[dpc]

so, are you suggesting to install qiime version 1?

[gb]

No, you can install qiime and use qiime or you can install qiime2 and use qiime2. My suggestion is to use the merge from qiime2 instead of qiime because you already installed that one. See the earlier posted link for the merge script in qiime2.

[dpc]

Thanks gb. The question is why I want to use the script? Because, I have several .biom outputs from MetaPhlAn 3.0. For each of the sample, I have one biom output. Now, I want to merge all these outputs into a single file so that I can feed into any R package. From the merge option you shared, is it possible to merge those biom output files generated from MetPhlAn 3.0?

[gb]

Sorry, I don't know that. I only gave the comment for you to help solve the error itself. Maybe some one else will give an answer to that. Because the title of your post is now "ERROR in QIIME" you may need to create a new one with this specific question. Good luck!