Hi, I'm now trying the above instructions.
I'm doing a gradient-clustering analysis with gneiss, and I found the following error after running this comand:
qiime gneiss gradient-clustering --i-table /home/qiime2/C-table.qza --m-gradient-file sample-metadata1.tsv --m-gradient-column Accumulatedscore --o-clustering gradient-hierarchy.qza --verbose
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__
results = action(**arguments)
File "<decorator-gen-288>", line 2, in gradient_clustering
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_gneiss/cluster/_cluster.py", line 94, in gradient_clustering
t = gradient_linkage(table, c, method='average')
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/gneiss-0.4.4-py3.5.egg/gneiss/cluster/_pba.py", line 203, in gradient_linkage
t = rank_linkage(mean_X)
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/gneiss-0.4.4-py3.5.egg/gneiss/cluster/_pba.py", line 125, in rank_linkage
dm = DistanceMatrix.from_iterable(r, euclidean)
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 778, in from_iterable
key, keys)
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/skbio/stats/distance/_base.py", line 159, in from_iterable
dm[i, j] = metric(a, b)
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/scipy/spatial/distance.py", line 433, in euclidean
dist = norm(u - v)
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/scipy/linalg/misc.py", line 129, in norm
a = np.asarray_chkfinite(a)
File "/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/numpy/lib/function_base.py", line 1215, in asarray_chkfinite
"array must not contain infs or NaNs")
ValueError: array must not contain infs or NaNs
I think that there is something wrong with my feature table, because if I run the command with the tutorial files, it works fine.
I hope we could fine the source of the error.
Thanks
C-table.qza (166.7 KB)
sample-metadata1.tsv (2.5 KB)