Hi @Mehrbod_Estaki!
Thank you for your support. I am using qiime2-2019.7. The command that I am running is:
qiime diversity adonis --i-distance-matrix Core_Metric_Results_Bsal_Newts_5000/jaccard_distance_matrix.qza --m-metadata-file Metadata_Hyliolas4.txt --p-formula SiteName+Vegetation --o-visualization Adonis_Results_SiteName_Vegetation.qzv --verbose
The full error message is:
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: run_adonis.R /tmp/tmp5yqfz4w1/dm.tsv /tmp/tmp5yqfz4w1/md.tsv SiteName+Vegetation 999 1 /tmp/qiime2-temp-s0f4pta4/adonis.tsv
R version 3.5.1 (2018-07-02)
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-5
Error in read.table(file = args[[2]], sep = “\t”, header = TRUE, fill = TRUE, :
more columns than column names
Ejecución interrumpida
Traceback (most recent call last):
File “/home/delibasanta/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</home/delibasanta/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-432>”, line 2, in adonis
File “/home/delibasanta/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/delibasanta/miniconda/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/delibasanta/miniconda/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_diversity/_beta/_visualizer.py”, line 367, in adonis
_run_command(cmd)
File “/home/delibasanta/miniconda/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/delibasanta/miniconda/envs/qiime2-2019.7/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_adonis.R’, ‘/tmp/tmp5yqfz4w1/dm.tsv’, ‘/tmp/tmp5yqfz4w1/md.tsv’, ‘SiteName+Vegetation’, ‘999’, ‘1’, ‘/tmp/qiime2-temp-s0f4pta4/adonis.tsv’]’ returned non-zero exit status 1.
Plugin error from diversity:
Command ‘[‘run_adonis.R’, ‘/tmp/tmp5yqfz4w1/dm.tsv’, ‘/tmp/tmp5yqfz4w1/md.tsv’, ‘SiteName+Vegetation’, ‘999’, ‘1’, ‘/tmp/qiime2-temp-s0f4pta4/adonis.tsv’]’ returned non-zero exit status 1.
See above for debug info.
Thank you very much,
Delia