Hello,
I was running vsearch open reference otu which uses a database which we have curated using the following script:
declare -a arr=(“v2” “v3” “v4” “v67” “v8” “v9”)
REGION={arr[{SLURM_ARRAY_TASK_ID}-1]}
echo “$REGION”
intableqza=…/analysis/A04-workflow-v2/merged-$REGION-table.qza
inrepsqza=…/analysis/A04-workflow-v2/merged-$REGION-rep-seqs.qza
echo “$intableqza”
echo “$inrepsqza”
qiime vsearch cluster-features-open-reference
–i-table $intableqza
–i-sequences $inrepsqza
–i-reference-sequences /path/db_v4.0.fasta.qza
–p-perc-identity 0.99
–p-strand plus
–p-threads 4
–o-clustered-table $outDir/$REGION/otu-table.qza
–o-clustered-sequences $outDir/$REGION/otu-rep-seqs.qza
–o-new-reference-sequences $outDir/$REGION/otu-new-ref-seqs.qza
My array works for 4 of my 6 regions, however I get a similar error for region v2 and region v9 which states:
“Plugin error from vsearch:
‘db16c939e7d01eaf1a3554820a848d44’ (this is diff bw v2 and v9)
Debug info has been saved to /tmp/qiime2-q2cli-err-55fzxzyt.log”
This is the information that is contained in the log:
"vsearch v2.7.0_linux_x86_64, 125.5GB RAM, 24 cores
Reading file /tmp/qiime2-archive-hta8hld1/e2641e45-f8eb-4865-99fc-1e4f999cbc6f/data/dna-sequences.fasta 100%
105012606 nt in 72682 seqs, min 900, max 2200, avg 1445
Masking 100%
Counting k-mers 100%
Creating k-mer index 100%
Searching 100%
Matching query sequences: 1090 of 3099 (35.17%)
vsearch v2.7.0_linux_x86_64, 125.5GB RAM, 24 cores
Reading file /tmp/tmpo_m_cxfp 100%
440560 nt in 2009 seqs, min 21, max 310, avg 219
Getting sizes 100%
Sorting 100%
Median abundance: 27
Writing output 100%
vsearch v2.7.0_linux_x86_64, 125.5GB RAM, 24 cores
Reading file /tmp/tmpuq4x0ruu 100%
440539 nt in 2008 seqs, min 39, max 310, avg 219
minseqlength 32: 1 sequence discarded.
Sorting by abundance 100%
Counting k-mers 100%
Clustering 100%
Sorting clusters 100%
Writing clusters 100%
Clusters: 1250 Size min 1, max 10, avg 1.6
Singletons: 862, 42.9% of seqs, 69.0% of clusters
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/tmpeikkpvjc --id 0.99 --db /tmp/qiime2-archive-hta8hld1/e2641e45-f8eb-4865-99fc-1e4f999cbc6f/data/dna-sequences.fasta --uc /tmp/tmpqlwer7vq --strand plus --qmask none --notmatched /tmp/tmpo_m_cxfp --threads 4
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 --sortbysize /tmp/tmpo_m_cxfp --xsize --output /tmp/q2-DNAFASTAFormat-q8u2szxs
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/tmpuq4x0ruu --id 0.99 --centroids /tmp/q2-DNAFASTAFormat-fi1gqdmv --uc /tmp/tmpbsyzyr6g --qmask none --xsize --threads 4
Traceback (most recent call last):
File “/home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-126>”, line 2, in cluster_features_open_reference
File “/home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 484, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File “/home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_vsearch/_cluster_features.py”, line 338, in cluster_features_open_reference
perc_identity=perc_identity, threads=threads)
File “</home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-479>”, line 2, in cluster_features_de_novo
File “/home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_vsearch/cluster_features.py", line 201, in cluster_features_de_novo
include_collapsed_metadata=False)
File “/home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/biom/table.py”, line 2604, in collapse
for part, table in self.partition(f, axis=axis):
File “/home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/biom/table.py”, line 2310, in partition
part = f(id, md)
File "/home-3/[email protected]/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_vsearch/cluster_features.py", line 100, in collapse_f
return id_to_centroid[id]
KeyError: ‘db16c939e7d01eaf1a3554820a848d44’ "
Do you have suggestions for fixing this error?
Thank you!
Lauren
