I am trying to cluster my samples @97% using vsearch cluster-features-de-novo but it's giving me an error.
I'm using qiime2 version 2019.10
my command is:
qiime vsearch cluster-features-de-novo
--i-sequences $projID-rep-seqs.qza
--i-table $projID-DADA2-table.qza
--p-perc-identity 0.97
--p-threads 75
--o-clustered-table $projID-RepTbl-clustered.qza
--o-clustered-sequences $projID-RepSeqs-clustered.qza
--verbose
here is the output:
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 --cluster_size /tmp/tmpoenbe0b2 --id 0.97 --centroids /tmp/q2-DNAFASTAFormat-oh_ukntc --uc /tmp/tmprsr5qvfs --qmask none --xsize --threads 75
vsearch v2.7.0_linux_x86_64, 377.4GB RAM, 88 cores
Reading file /tmp/tmpoenbe0b2 100%
756563 nt in 3696 seqs, min 32, max 440, avg 205
minseqlength 32: 2 sequences discarded.
Sorting by abundance 100%
Counting k-mers 100%
Clustering 100%
Sorting clusters 100%
Writing clusters 100%
Clusters: 2876 Size min 1, max 12, avg 1.3
Singletons: 2457, 66.5% of seqs, 85.4% of clusters
Traceback (most recent call last):
File "/home/AnalysisTools/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</home/AnalysisTools/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-121>", line 2, in cluster_features_de_novo
File "/home/AnalysisTools/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/AnalysisTools/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in callable_executor
output_views = self._callable(**view_args)
File "/home/AnalysisTools/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_vsearch/cluster_features.py", line 201, in cluster_features_de_novo
include_collapsed_metadata=False)
File "/home/AnalysisTools/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/biom/table.py", line 2589, in collapse
for part, table in self.partition(f, axis=axis):
File "/home/AnalysisTools/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/biom/table.py", line 2295, in partition
part = f(id, md)
File "/home/AnalysisTools/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_vsearch/cluster_features.py", line 100, in collapse_f
return id_to_centroid[id]
KeyError: 'bc581ce18c66116833d712e4076a8b63'