Can anyone tell me what the following error means?
My metadata only has two levels (MOR and VEH) so I don't understand what it is asking me?
(qiime2-2019.7) hharder@ni-murn8c9-p915:~$ qiime aldex2 aldex2 --i-table table.qza --m-metadata-file metadata_corrected_2.tsv --m-metadata-column Txt --output-dir Txt-test --verbose
/home/hharder/ENTER/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_aldex2/_method.py:39: FutureWarning:
Passing list-likes to .loc or [] with any missing label will raise
KeyError in the future, you can use .reindex() as an alternative.
See the documentation here:
https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike
meta = meta.loc[list(table.index)]
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 /tmp/tmprwe2bv59/input.tsv.biom /tmp/tmprwe2bv59/input.map.txt Txt 128 t all /tmp/tmprwe2bv59/output.summary.txt
R version 3.5.1 (2018-07-02)
[1] "aldex.clr: generating Monte-Carlo instances and clr values"
[1] "operating in serial mode"
[1] "computing center with all features"
[1] "aldex.ttest: doing t-test"
Error in aldex.ttest(x, conditions, paired.test = FALSE) :
only two condition levels are currently supported
Calls: aldex -> aldex.ttest
Execution halted
Traceback (most recent call last):
File "/home/hharder/ENTER/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_aldex2/_method.py", line 59, in aldex2
run_commands([cmd])
File "/home/hharder/ENTER/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_aldex2/_method.py", line 21, in run_commands
subprocess.run(cmd, check=True)
File "/home/hharder/ENTER/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_aldex2.R', '/tmp/tmprwe2bv59/input.tsv.biom', '/tmp/tmprwe2bv59/input.map.txt', 'Txt', '128', 't', 'all', '/tmp/tmprwe2bv59/output.summary.txt']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/hharder/ENTER/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in call
results = action(**arguments)
File "</home/hharder/ENTER/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-481>", line 2, in aldex2
File "/home/hharder/ENTER/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/hharder/ENTER/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 "/home/hharder/ENTER/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.