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/tmphhzdymj7/input.tsv.biom /tmp/tmphhzdymj7/input.map.txt Type 128 t all /tmp/tmphhzdymj7/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" Error in aldex.clr.function(as.data.frame(reads), conds, mc.samples, denom, : not all reads are integers Calls: aldex -> aldex.clr -> aldex.clr -> aldex.clr.function Execution halted Traceback (most recent call last): File "/home/server-mk/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_aldex2/_method.py", line 59, in aldex2 run_commands([cmd]) File "/home/server-mk/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 "/home/server-mk/miniconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['run_aldex2.R', '/tmp/tmphhzdymj7/input.tsv.biom', '/tmp/tmphhzdymj7/input.map.txt', 'Type', '128', 't', 'all', '/tmp/tmphhzdymj7/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/server-mk/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in __call__ results = action(**arguments) File "", line 2, in aldex2 File "/home/server-mk/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable output_types, provenance) File "/home/server-mk/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 "/home/server-mk/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.