Thank you Douglas,
I am trying different ways to process data.
Now I have qiime2-2021.11 environment with picrust2 installed.
In main jupyter notebook, i call:
rep_seqs.export_data('test')
table.export_data('test')
from picrust2 import pipeline
from picrust2.default import (default_ref_dir, default_tables,
default_regroup_map, default_pathway_map)
pipeline_results = pipeline.full_pipeline(
input_table='test/feature-table.biom',
study_fasta='test/dna-sequences.fasta',
processes=128,
output_folder='jupyter_picrust',
placement_tool='epa-ng',
ref_dir=default_ref_dir,
in_traits='EC',
custom_trait_tables=None,
marker_gene_table=default_tables['16S'],
pathway_map=default_pathway_map,
rxn_func='EC',
no_pathways=False,
regroup_map=default_regroup_map,
no_regroup=False,
stratified=False,
max_nsti=2.0,
min_reads=1,
min_samples=1,
hsp_method='mp',
edge_exponent=0.5,
min_align=0.8,
skip_nsti=False,
skip_minpath=False,
no_gap_fill=False,
coverage=False,
per_sequence_contrib=False,
wide_table=False,
skip_norm=False,
remove_intermediate=False,
verbose='highly_verbose'
)
I feel there should be a way to run it with all default setting and feeding feature_table and rep_seqs directly without exporting but haven't figured out yet. Also not sure what is the right way to unpack results of function.