Hello! I ran the following command
qiime feature-classifier classify-consensus-blast \
--i-query OTUs/rep-seqs.qza \
--i-reference-reads Classifier/silva-138-99-seqs.qza \
--i-reference-taxonomy Classifier/silva-138-99-tax.qza \
--o-classification Taxonomy/taxonomy.qza \
--verbose
rep-seqs.qza (431.3 KB)
and received the following error message
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: blastn -query /tmp/qiime2-archive-x_41oylq/86175dbd-b53d-4936-bc87-c583edef5175/data/dna-sequences.fasta -evalue 0.001 -strand both -outfmt 7 -subject /tmp/qiime2-archive-e__3v_y9/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta -perc_identity 80.0 -qcov_hsp_perc 80.0 -max_target_seqs 10 -out /tmp/tmpg1gbf89t
Traceback (most recent call last):
File "/home/macgregor/anaconda3/envs/qiime2/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__
results = action(**arguments)
File "<decorator-gen-359>", line 2, in classify_consensus_blast
File "/home/macgregor/anaconda3/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/macgregor/anaconda3/envs/qiime2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/macgregor/anaconda3/envs/qiime2/lib/python3.6/site-packages/q2_feature_classifier/_blast.py", line 47, in classify_consensus_blast
exp_seq_ids=seqs_fp)
File "/home/macgregor/anaconda3/envs/qiime2/lib/python3.6/site-packages/q2_feature_classifier/_consensus_assignment.py", line 28, in _consensus_assignments
_run_command(cmd)
File "/home/macgregor/anaconda3/envs/qiime2/lib/python3.6/site-packages/q2_feature_classifier/_consensus_assignment.py", line 74, in _run_command
subprocess.run(cmd, check=True)
File "/home/macgregor/anaconda3/envs/qiime2/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['blastn', '-query', '/tmp/qiime2-archive-x_41oylq/86175dbd-b53d-4936-bc87-c583edef5175/data/dna-sequences.fasta', '-evalue', '0.001', '-strand', 'both', '-outfmt', '7', '-subject', '/tmp/qiime2-archive-e__3v_y9/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta', '-perc_identity', '80.0', '-qcov_hsp_perc', '80.0', '-max_target_seqs', '10', '-out', '/tmp/tmpg1gbf89t']' died with <Signals.SIGKILL: 9>.
Plugin error from feature-classifier:
Command '['blastn', '-query', '/tmp/qiime2-archive-x_41oylq/86175dbd-b53d-4936-bc87-c583edef5175/data/dna-sequences.fasta', '-evalue', '0.001', '-strand', 'both', '-outfmt', '7', '-subject', '/tmp/qiime2-archive-e__3v_y9/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta', '-perc_identity', '80.0', '-qcov_hsp_perc', '80.0', '-max_target_seqs', '10', '-out', '/tmp/tmpg1gbf89t']' died with <Signals.SIGKILL: 9>.
See above for debug info.
Looking at another post, it seems that "died with <Signals.SIGKILL: 9>" indicates that something shut down the Qiime plugin while it was running. However, I'm not working on any shared server/cluster, and I've ran the same command on the same inputs multiple times before with no issue.
The solution on said post seemed to be modifying the original command to be less computationally intensive(?). However, I get the same error if I instead run
!qiime feature-classifier classify-consensus-blast \
--i-query OTUs/rep-seqs.qza \
--i-reference-reads Classifier/silva-138-99-seqs.qza \
--i-reference-taxonomy Classifier/silva-138-99-tax.qza \
--p-maxaccepts 2 \
--p-perc-identity 0.7 \
--p-query-cov 0.7 \
--o-classification Taxonomy/taxonomy.qza \
--verbose
Could anyone clue me in as to what might be causing this?
!