aldex2 error in QIIME2 2019.7

(qiime2-2019.7) Jinbings-iMac:fatigue jinbingbai$ qiime aldex2 aldex2 --i-table table.qza --m-metadata-file sample-metadata.tsv --m-metadata-column Fatigue2 --output-dir fatigue2 --verbose
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: run_aldex2.R /var/folders/sd/vlrr9d916gg5qj3yzzf3srfw0000gn/T/tmpkz449n84/input.tsv.biom /var/folders/sd/vlrr9d916gg5qj3yzzf3srfw0000gn/T/tmpkz449n84/input.map.txt Fatigue2 128 t all /var/folders/sd/vlrr9d916gg5qj3yzzf3srfw0000gn/T/tmpkz449n84/output.summary.txt

R version 3.5.1 (2018-07-02)
Error: package or namespace load failed for ‘ALDEx2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Execution halted
Traceback (most recent call last):
File “/Users/jinbingbai/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_aldex2/_method.py”, line 59, in aldex2
run_commands([cmd])
File “/Users/jinbingbai/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_aldex2/_method.py”, line 21, in run_commands
subprocess.run(cmd, check=True)
File “/Users/jinbingbai/miniconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_aldex2.R’, ‘/var/folders/sd/vlrr9d916gg5qj3yzzf3srfw0000gn/T/tmpkz449n84/input.tsv.biom’, ‘/var/folders/sd/vlrr9d916gg5qj3yzzf3srfw0000gn/T/tmpkz449n84/input.map.txt’, ‘Fatigue2’, ‘128’, ‘t’, ‘all’, ‘/var/folders/sd/vlrr9d916gg5qj3yzzf3srfw0000gn/T/tmpkz449n84/output.summary.txt’]’ returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/Users/jinbingbai/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</Users/jinbingbai/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-485>”, line 2, in aldex2
File “/Users/jinbingbai/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/Users/jinbingbai/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/Users/jinbingbai/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_aldex2/_method.py”, line 63, in aldex2
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running ALDEx2 in R (return code 1), please inspect stdout and stderr to learn more.

Plugin error from aldex2:

An error was encountered while running ALDEx2 in R (return code 1), please inspect stdout and stderr to learn more.

See above for debug info.
(qiime2-2019.7) Jinbings-iMac:fatigue jinbingbai$

1 Like

HI @Bing,
Looks like your installation is incomplete (you are missing at least one dependency):

I am cc:ing @dgiguer to see if he can help troubleshoot.

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Hi @Bing,

The likely way to fix this would be to install any dependencies that pop up. To fix this, do BiocManager::install("GenomeInfoDbData"). You may need to do this for other dependencies as well!

Cheers,

Dan

I am confused about this R installation. If I am in QIIME2 env. How can install this?

Thanks

1 Like

@Bing

In your conda environment, you can access R from the command line (terminal on Mac). For me:

# activate my conda environment using an alias i have set up
# it's important to ensure you activate the qiime environment first because you may have multiple versions of R on your computer. 

Daniels-MacBook-Pro:~ dan$ qiime-activate 
(qiime2-2019.7) Daniels-MacBook-Pro:~ dan$

# now im in the conda environment. I can start R with the following command:
R

# now that you are in R, you can install the required dependencies.
BiocManager::install("GenomeInfoDbData")

Check out the installation page for Bioconductor for more instructions.

Cheers,

Dan

1 Like

Thanks @dgiguer. It works now yay!!

1 Like