Dear all,
I am excited about the plugin aldex2, however, I am experiencing the next error. Could anybody help me?
(qiime2-2019.7) mbp-de-isabel:~ Isa$ qiime aldex2 aldex2 --i-table /Users/Isa/Downloads/archivos/sleeve-table-final.qza --m-metadata-file /Users/Isa/Downloads/archivos/sleeve_map_final.txt --m-metadata-column Treatment --output-dir /Users/Isa/Downloads/archivos/aldex2 --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/4m/y_fd8knd03sgjw5llgpmv7pc0000gn/T/tmp4lq44rvj/input.tsv.biom /var/folders/4m/y_fd8knd03sgjw5llgpmv7pc0000gn/T/tmp4lq44rvj/input.map.txt Treatment 128 t all /var/folders/4m/y_fd8knd03sgjw5llgpmv7pc0000gn/T/tmp4lq44rvj/output.summary.txt
R version 3.5.1 (2018-07-02)
Error in library(ALDEx2) : there is no package called ‘ALDEx2’
Ejecución interrumpida
Traceback (most recent call last):
File “/Users/Isa/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_aldex2/_method.py”, line 59, in aldex2
run_commands([cmd])
File “/Users/Isa/miniconda2/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/Isa/miniconda2/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/4m/y_fd8knd03sgjw5llgpmv7pc0000gn/T/tmp4lq44rvj/input.tsv.biom’, ‘/var/folders/4m/y_fd8knd03sgjw5llgpmv7pc0000gn/T/tmp4lq44rvj/input.map.txt’, ‘Treatment’, ‘128’, ‘t’, ‘all’, ‘/var/folders/4m/y_fd8knd03sgjw5llgpmv7pc0000gn/T/tmp4lq44rvj/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/Isa/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</Users/Isa/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-485>”, line 2, in aldex2
File “/Users/Isa/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/Users/Isa/miniconda2/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/Isa/miniconda2/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.
thanks in advance,
Isabel