Hi,
I am running qiime2 version 2021.2 in a conda environment
I am trying to run feature-classifier for taxonomic assignments of ASVs created with DADA2 in qiime2. The reference data files imported nicely.
This is the command with the error message:
(qiime2-2021.2) Ingas-iMac:DADA2 inga$ qiime feature-classifier classify-consensus-vsearch --i-query denoiseSeqs180.qza --i-reference-reads Refseq.qza --i-reference-taxonomy Reftax.qza --o-classification Class-DADA2-180-98.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 /var/folders/y5/2wrthn7s40l3q1f43wfbtz100000gn/T/qiime2-archive-5z_u0uu4/e1b2b1aa-ee63-4dc2-86fc-1873aa55fb2d/data/dna-sequences.fasta --id 0.8 --query_cov 0.8 --strand both --maxaccepts 10 --maxrejects 0 --db /var/folders/y5/2wrthn7s40l3q1f43wfbtz100000gn/T/qiime2-archive-r3mibele/7794c726-a931-4ff8-8756-b8909fcbde17/data/dna-sequences.fasta --threads 1 --output_no_hits --blast6out /var/folders/y5/2wrthn7s40l3q1f43wfbtz100000gn/T/tmpib716o0u
vsearch v2.7.0_macos_x86_64, 8.0GB RAM, 4 cores
Unable to read from file (/var/folders/y5/2wrthn7s40l3q1f43wfbtz100000gn/T/qiime2-archive-r3mibele/7794c726-a931-4ff8-8756-b8909fcbde17/data/dna-sequences.fasta)
Traceback (most recent call last):
File "/Users/inga/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in classify_consensus_vsearch
File "/Users/inga/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/Users/inga/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/Users/inga/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_feature_classifier/_vsearch.py", line 64, in classify_consensus_vsearch
unassignable_label=unassignable_label)
File "/Users/inga/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_feature_classifier/_consensus_assignment.py", line 28, in _consensus_assignments
_run_command(cmd)
File "/Users/inga/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_feature_classifier/_consensus_assignment.py", line 74, in _run_command
subprocess.run(cmd, check=True)
File "/Users/inga/miniconda3/envs/qiime2-2021.2/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['vsearch', '--usearch_global', '/var/folders/y5/2wrthn7s40l3q1f43wfbtz100000gn/T/qiime2-archive-5z_u0uu4/e1b2b1aa-ee63-4dc2-86fc-1873aa55fb2d/data/dna-sequences.fasta', '--id', '0.8', '--query_cov', '0.8', '--strand', 'both', '--maxaccepts', '10', '--maxrejects', '0', '--db', '/var/folders/y5/2wrthn7s40l3q1f43wfbtz100000gn/T/qiime2-archive-r3mibele/7794c726-a931-4ff8-8756-b8909fcbde17/data/dna-sequences.fasta', '--threads', '1', '--output_no_hits', '--blast6out', '/var/folders/y5/2wrthn7s40l3q1f43wfbtz100000gn/T/tmpib716o0u']' returned non-zero exit status 1.
Plugin error from feature-classifier:
Command '['vsearch', '--usearch_global', '/var/folders/y5/2wrthn7s40l3q1f43wfbtz100000gn/T/qiime2-archive-5z_u0uu4/e1b2b1aa-ee63-4dc2-86fc-1873aa55fb2d/data/dna-sequences.fasta', '--id', '0.8', '--query_cov', '0.8', '--strand', 'both', '--maxaccepts', '10', '--maxrejects', '0', '--db', '/var/folders/y5/2wrthn7s40l3q1f43wfbtz100000gn/T/qiime2-archive-r3mibele/7794c726-a931-4ff8-8756-b8909fcbde17/data/dna-sequences.fasta', '--threads', '1', '--output_no_hits', '--blast6out', '/var/folders/y5/2wrthn7s40l3q1f43wfbtz100000gn/T/tmpib716o0u']' returned non-zero exit status 1.
See above for debug info.
The exported dna-sequences.fasta of --i-query denoiseSeqs180.qza file looks like you would expect a fasta file to look like like:
85ecdf4a3e2813dc5239fdf9d759e5aa
CGCAGCCTGCTAAATAATCACAACAATGATTTTTCATTGCTGATGGTTTCTTAGAGGGACATGTAGTATAAAACTACAGGAAGATTGCGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGAACCGCACGCGTGTTACACTGACGCAATCAACGAGCATATAACCTTAGCCGAGAGGCTTGGGCAATCTTGTTAACCTGCGTCGTGATAGGGATAGATTATTGCAATTATTAATCTT
0e058910a64cf7d1b679b035e1e67b1c
TCCAACCTACTAACTAGTGGGCGAATCTTTCTGTTCGCGACACTTCTTAGAGGGATAGGTGACTTTTAGTCACATGAGAAGGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCGGGGCTGCACGCGCGCTACACTGAAAGAATCAGCGTGCCAGAAAACCTTGCTTGACATGGCTAGGTAACCCGTTGAAAATCTTTCGTGATTGGGATCGGGACTTGCAAATGTGTCCCTT
...
It feels silly but I do not even have any idea where to start looking for a solution. Why can't the file be read?