/home/sdegregori/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/gemelli/preprocessing.py:423: RuntimeWarning: divide by zero encountered in log
mat = np.log(matrix_closure(matrix_closure(mat) * branch_lengths))
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 2.57 TiB for an array with shape (594002, 594002) and data type float64
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/sdegregori/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in __call__
results = self._execute_action(
File "/home/sdegregori/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 539, in _execute_action
results = action(**arguments)
File "<decorator-gen-76>", line 2, in phylogenetic_rpca_with_taxonomy
File "/home/sdegregori/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self._callable_executor_(
File "/home/sdegregori/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/sdegregori/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/gemelli/rpca.py", line 88, in phylogenetic_rpca_with_taxonomy
output = phylogenetic_rpca(table=table,
File "/home/sdegregori/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/gemelli/rpca.py", line 267, in phylogenetic_rpca
ord_res, dist_res = optspace_helper(rclr_table, fids, table.ids(),
File "/home/sdegregori/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/gemelli/rpca.py", line 514, in optspace_helper
u, s, v = svd(X)
File "/home/sdegregori/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/scipy/linalg/_decomp_svd.py", line 127, in svd
u, s, v, info = gesXd(a1, compute_uv=compute_uv, lwork=lwork,
TypeError: __init__() missing 1 required positional argument: 'dtype'
Plugin error from gemelli:
__init__() missing 1 required positional argument: 'dtype'
See above for debug info.
Are my file sizes too big? I am running this on a large microbiome table that has thousands of samples. Only using about 50% of the memory I requested on my server when I run it. Any help would be appreciated!
pip install gemelli
qiime dev refresh-cache
qiime gemelli phylogenetic-rpca-with-taxonomy \
--i-table ~/TOL/minich/GMTOLsong_table2024_N20_f2all_V4.qza \
--i-phylogeny ~/TOL/minich/GMTOLsong_rooted_tree2024f2.qza \
--m-taxonomy-file ~/TOL/minich/merged_GMTOL_taxonomy2024_N20all_f2_V4.qza \
--p-min-feature-count 10 \
--p-min-sample-count 500 \
--o-biplot ~/TOL/minich/GMTOLsong_rpca_biplot.qza \
--o-distance-matrix ~/TOL/minich/GMTOLsong_rpca_distance_matrix.qza \
--o-counts-by-node-tree ~/TOL/minich/GMTOLsong_rpca_counts_by_node_tree.qza \
--o-counts-by-node ~/TOL/minich/GMTOLsong_rpca_counts_by_node_phylotable.qza \
--o-t2t-taxonomy ~/TOL/minich/GMTOLsong_rpca_taxonomy.qza \
--verbose
Hi,
Trying to use gemelli as a qiime2 plugin and I get the following error:
Are my file sizes too big? I am running this on a large microbiome table that has thousands of samples. Only using about 50% of the memory I requested on my server when I run it. Any help would be appreciated!
Also here is the original code I ran:
Cheers,
Sam