I got the following error message when I try to run the script. I am new to PICRUSt2 and not sure what I need to do to solve this problem.
Thank you!
qiime picrust2 custom-tree-pipeline \
--i-table table.qza \ --i-tree output_directory/tree.qza \ --output-dir q2-picrust2_output \ --p-threads 1 \ --p-hsp-method pic \ --p-max-nsti 2 \ --verbose
Running the below commands:
hsp.py -i 16S -t /tmp/tmp13btt4an/placed_seqs.tre -p 1 -n -o /tmp/tmp13btt4an/picrust2_out/16S_predicted.tsv.gz -m pic -e 0.5
hsp.py -i EC -t /tmp/tmp13btt4an/placed_seqs.tre -p 1 -n -o /tmp/tmp13btt4an/picrust2_out/EC_predicted.tsv.gz -m pic -e 0.5
hsp.py -i KO -t /tmp/tmp13btt4an/placed_seqs.tre -p 1 -n -o /tmp/tmp13btt4an/picrust2_out/KO_predicted.tsv.gz -m pic -e 0.5
Error running this command:
hsp.py -i KO -t /tmp/tmp13btt4an/placed_seqs.tre -p 1 -n -o /tmp/tmp13btt4an/picrust2_out/KO_predicted.tsv.gz -m pic -e 0.5
Standard error of the above failed command:
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2021.2/bin/hsp.py", line 145, in
main()
File "/home/qiime2/miniconda/envs/qiime2-2021.2/bin/hsp.py", line 136, in main
verbose=args.verbose)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/wrap_hsp.py", line 35, in castor_hsp_workflow
trait_tab = pd.read_csv(trait_table_path, sep="\t", dtype={'assembly': str})
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pandas/io/parsers.py", line 688, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pandas/io/parsers.py", line 460, in _read
data = parser.read(nrows)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pandas/io/parsers.py", line 1213, in read
df = DataFrame(col_dict, columns=columns, index=index)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pandas/core/frame.py", line 468, in init
mgr = init_dict(data, index, columns, dtype=dtype)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pandas/core/internals/construction.py", line 283, in init_dict
return arrays_to_mgr(arrays, data_names, index, columns, dtype=dtype)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pandas/core/internals/construction.py", line 93, in arrays_to_mgr
return create_block_manager_from_arrays(arrays, arr_names, axes)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pandas/core/internals/managers.py", line 1692, in create_block_manager_from_arrays
blocks = form_blocks(arrays, names, axes)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pandas/core/internals/managers.py", line 1762, in form_blocks
int_blocks = _multi_blockify(items_dict["IntBlock"])
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pandas/core/internals/managers.py", line 1844, in _multi_blockify
values, placement = _stack_arrays(list(tup_block), dtype)
File "/home/qiime2/miniconda/envs/qiime2-2021.2/lib/python3.6/site-packages/pandas/core/internals/managers.py", line 1872, in _stack_arrays
stacked = np.empty(shape, dtype=dtype)
numpy.core._exceptions.MemoryError: Unable to allocate 1.57 GiB for an array with shape (10543, 20000) and data type int64