qiime feature-classifier classify-consensus-vsearch \
--i-query RepresenDenoisedmcrSeasalt1.2.qza
--i-reference-reads RefSequencesmcrA.qza
--i-reference-taxonomy Reftaxonomy.qza
--p-strand 'plus'
--p-unassignable-label Unassigned
--o-classification VsearchtaxonomyformcrA.qza
--verbose
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command: vsearch --usearch_global /tmp/qiime2-archive-w3_9bk2z/5782004b-c1e9-4e21-90ad-53cc5fdfc30a/data/dna-sequences.fasta --id 0.8 --query_cov 0.8 --strand plus --maxaccepts 10 --maxrejects 0 --output_no_hits --db /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/data/dna-sequences.fasta --threads 1 --blast6out /tmp/tmpt9p5k3yc
vsearch v2.7.0_linux_x86_64, 15.5GB RAM, 4 cores
Reading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file 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/tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/dReading file /tmp/qiime2-archive-kpqzgysv/516e5207-bffe-496c-915d-56816664acae/data/dna-sequences.fasta 100%
3603404 nt in 8135 seqs, min 390, max 471, avg 443
Masking 100%
Counting k-mers 100%
Creating k-mer index 100%
Searching 100%
Matching query sequences: 992 of 2222 (44.64%)
Traceback (most recent call last):
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 4381, in get_value
return libindex.get_value_box(s, key)
File "pandas/_libs/index.pyx", line 52, in pandas._libs.index.get_value_box
File "pandas/_libs/index.pyx", line 48, in pandas._libs.index.get_value_at
File "pandas/_libs/util.pxd", line 113, in pandas._libs.util.get_value_at
File "pandas/_libs/util.pxd", line 98, in pandas._libs.util.validate_indexer
TypeError: 'str' object cannot be interpreted as an integer
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_feature_classifier/_consensus_assignment.py", line 104, in import_blast_format_assignments
t = ref_taxa[id]
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/pandas/core/series.py", line 868, in getitem
result = self.index.get_value(self, key)
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 4389, in get_value
raise e1
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 4375, in get_value
tz=getattr(series.dtype, 'tz', None))
File "pandas/_libs/index.pyx", line 81, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 89, in pandas._libs.index.IndexEngine.get_value
File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: '173'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py", line 311, in call
results = action(**arguments)
File "</home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/decorator.py:decorator-gen-355>", line 2, in classify_consensus_vsearch
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in callable_executor
output_views = self._callable(**view_args)
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_feature_classifier/_vsearch.py", line 37, in classify_consensus_vsearch
unassignable_label=unassignable_label)
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_feature_classifier/_consensus_assignment.py", line 29, in _consensus_assignments
output.name, ref_taxa, unassignable_label=unassignable_label)
File "/home/mpi/miniconda3/envs/qiime2-2019.4/lib/python3.6/site-packages/q2_feature_classifier/_consensus_assignment.py", line 109, in import_blast_format_assignments
'taxonomy.').format(str(id)))
KeyError: 'Identifier 173 was reported in taxonomic search results, but was not present in the reference taxonomy.'
Plugin error from feature-classifier:
'Identifier 173 was reported in taxonomic search results, but was not present in the reference taxonomy.'