Hi there,
I've been trying to run diversity analyses on a dataset but keep geeting the following error:
Plugin error from diversity:
array must not contain infs or NaNs
The dataset is a filtered table and alpha diversity runs smoothly. Below the commands:
#filter-table by samples of interest
qiime feature-table filter-samples \
--i-table table-many-samples.qza \
--m-metadata-file smp_ID \
--p-min-features 2 \
--o-filtered-table table.ftd.qza
(I then filtred-out Unassigned reads...)
qiime taxa filter-table --i-table table.ftd.qza --i-taxonomy taxonomy.qza --p-exclude Unassigned --o-filtered-table table.ftd.noUnassigned.qza
... and got a file containing the rep-seqs...
qiime feature-table filter-seqs --i-data rep-seqs.full.qza --i-table table.ftd.noUnassigned.qza --o-filtered-data rep-seqs.ftd.noUnassigned.qza
... and aligned the rep-seqs...
qiime phylogeny align-to-tree-mafft-fasttree --p-n-threads 15 --i-sequences rep-seqs.ftd.noUnassigned.qza --o-alignment aligned.qza --o-masked-alignment masked.qza --o-tree unrooted.qza --o-rooted-tree rooted.qza
...and run core-metrics-phylogeny
qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.ftd.noUnassigned.qza --p-sampling-depth 20000 --m-metadata-file metadata3 --output-dir core-metrics-output --p-n-jobs 7
Then the error
/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/sklearn/utils/validation.py:475: DataConversionWarning: Data with inp
ut dtype float64 was converted to bool by check_pairwise_arrays.
warnings.warn(msg, DataConversionWarning)
/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/ordination/_utils.py:186: RuntimeWarning: overflow encoun
tered in multiply
return distance_matrix * distance_matrix / -2
/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/ordination/_utils.py:198: RuntimeWarning: invalid value e
ncountered in subtract
return E_matrix - row_means - col_means + matrix_mean
/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/ordination/_utils.py:198: RuntimeWarning: invalid value e
ncountered in add
return E_matrix - row_means - col_means + matrix_mean
Traceback (most recent call last):
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in core_metrics_phylogenetic
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 455, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_diversity/_core_metrics.py", line 65, in core_metrics_phyl
ogenetic
pcoas += pcoa(distance_matrix=dm)
File "", line 2, in pcoa
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in callable_executor
output_views = self._callable(**view_args)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/q2_diversity/_ordination.py", line 18, in pcoa
inplace=False)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/skbio/stats/ordination/_principal_coordinate_analysis.py", li
ne 126, in pcoa
eigvals, eigvecs = eigh(matrix_data)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/scipy/linalg/decomp.py", line 327, in eigh
a1 = _asarray_validated(a, check_finite=check_finite)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/scipy/_lib/_util.py", line 238, in _asarray_validated
a = toarray(a)
File "/home/leonardo.alves/miniconda2/envs/qiime2-2018.11/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
A similar error was reported here Qiime diversity beta-phylogenetic Data must be symmetric and cannot contain NaNs error
but I've checked and there are no samples with 0 observations in the table.
qiime feature-table summarize --i-table table.ftd.noUnassigned.qza --o-visualization table.ftd.noUnassigned.qzv
table.filtered.qzv (430.6 KB) table.ftd.noUnassigned.qzv (430.1 KB) rep-seqs.ftd.noUnassigned.qza (163.4 KB) rooted.qza (132.4 KB) metadata3.tsv (82 Bytes)
It seems the error has something related to a filtered table, but I don't know what.
Could you guys help me on that?
Cheers
Update:
I am not sure what's happenig, but I was able to access Unifrac and PCoA plotting by running standalone commands:
qiime feature-table rarefy --i-table table.ftd.noUnassigned.qza --p-sampling-depth 20000 --o-rarefied-table table.ftd.noUnassigned.rarefied.qza
qiime diversity beta-phylogenetic --i-table table.ftd.noUnassigned.rarefied.qza --p-metric weighted_unifrac --i-phylogeny rooted.qza --o-distance-matrix w_unifrac_matrix.qza
qiime diversity pcoa --i-distance-matrix w_unifrac_matrix.qza --o-pcoa _unifrac_pcoa.qzv
qiime emperor plot --i-pcoa w_unifrac_pcoa.qzv.qza --m-metadata-file metadata3 --o-visualization w_unifrac_emperor