Hi. I am running adonis with qiime2-2019.7. I have run the lines below:
$ qiime diversity adonis \
--i-distance-matrix beta-gut-uw-5per.qza
--m-metadata-file metadata-gut-5per.csv
--p-formula Diet
--o-visualization permanova-gut-uw-5per-diet.qzv
--verbose
But I am receiving this common error, and the log file says:
Error in G * t(hat) : non-conformable arrays
Calls: adonis -> sapply -> lapply -> FUN
Execution halted
Traceback (most recent call last):
File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in call
results = action(**arguments)
File "</home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-432>", line 2, in adonis
File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 445, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_diversity/_beta/_visualizer.py", line 367, in adonis
_run_command(cmd)
File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_diversity/_beta/_visualizer.py", line 393, in _run_command
subprocess.run(cmd, check=True)
File "/home/allio/bin/anaconda2/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_adonis.R', '/tmp/tmpzlvn8ktm/dm.tsv', '/tmp/tmpzlvn8ktm/md.tsv', 'Diet', '999', '1', '/tmp/qiime2-temp-fxgvmtum/adonis.tsv']' returned non-zero exit status 1.
I've verified my metadata with Keemei and found no problems. I'm also using the 1st column and row name as "SampleID". How do I solve this problem to run adonis without this error?
Thank you in advance!
If it helps, I've attached the 2 input files:
beta-gut-uw-5per.qza (7.2 MB)
metadata-gut-5per.csv (126.0 KB)