Problem when runnin classify-consensus-blast

[Cesar_Alejandro (Cesar Alejandro Perez Fernandez)]

Greetings,

I am trying to classify some 16S sequences with the SILVA database, For this I am running the next command using the feature-classifier module:

qiime feature-classifier classify-consensus-blast
--i-query 04_Deblur/Featured_Data.qza
--i-reference-reads SILVA_138/silva-138-99-seqs.qza
--i-reference-taxonomy SILVA_138/silva-138-99-tax.qza
--o-classification 05_Taxonomic/Classified.qza

I received the next error:
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-drr5i1f1/c740bc5f-413e-4eb2-8109-964ea9eb00ab/data/dna-sequences.fasta -evalue 0.001 -strand both -outfmt 7 -subject /tmp/qiime2-archive-l0bxvjzl/a7432d0f-b5f7$

Traceback (most recent call last):
File "/home/capfz200/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in classify_consensus_blast
File "/home/capfz200/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 244, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/capfz200/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/capfz200/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_feature_classifier/_blast.py", line 44, in classify_consensus_blast
consensus = _consensus_assignments(
File "/home/capfz200/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_feature_classifier/_consensus_assignment.py", line 28, in _consensus_assignments
_run_command(cmd)
File "/home/capfz200/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_feature_classifier/_consensus_assignment.py", line 74, in _run_command
subprocess.run(cmd, check=True)
File "/home/capfz200/anaconda3/envs/qiime2-2021.4/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['blastn', '-query', '/tmp/qiime2-archive-drr5i1f1/c740bc5f-413e-4eb2-8109-964ea9eb00ab/data/dna-sequences.fasta', '-evalue', '0.001', '-strand', 'both', '-outfmt$

I am not sure what it is about, maybe memory? It seems like the process stopped suddenly.

Cesar

[lizgehret]

Hi @Cesar_Alejandro,

Welcome to the forum!

Can you share how you have QIIME 2 installed on your machine? Conda, virtualbox, WSL, etc.

That aside, a good first step here will be to make sure you have the latest version of QIIME 2 Installed - you can get that updated here, after which I'd recommend re-running your same command again, but also including the --verbose flag (which will provide us with some additional error messaging, if you run into this problem after updating QIIME 2). If you do run into this error again, please copy/paste the entire message you receive from your terminal window, and we'll go from there.

Thanks!

[Cesar_Alejandro (Cesar Alejandro Perez Fernandez)]

Hi !lizgehret,

I installed qiime2 in a conda environment, I update it to the version 2022.2 and try the same command adding the --verbose. It shows the next error:

Command: blastn -query /tmp/qiime2-archive-qo_juqfe/c740bc5f-413e-4eb2-8109-964ea9eb00ab/data/dna-sequences.fasta -evalue 0.001 -strand both -outfmt 7 -subject /tmp/qiime2-archive-1dggqzu6/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta -perc_identity 80.0 -qcov_hsp_perc 80.0 -max_target_seqs 10 -out /tmp/tmpx8hy5q1y

Traceback (most recent call last):
File "/home/capfz200/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in classify_consensus_blast
File "/home/capfz200/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/capfz200/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in callable_executor
output_views = self._callable(**view_args)
File "/home/capfz200/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_feature_classifier/_blast.py", line 44, in classify_consensus_blast
consensus = _consensus_assignments(
File "/home/capfz200/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_feature_classifier/_consensus_assignment.py", line 28, in _consensus_assignments
_run_command(cmd)
File "/home/capfz200/anaconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_feature_classifier/_consensus_assignment.py", line 74, in _run_command
subprocess.run(cmd, check=True)
File "/home/capfz200/anaconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['blastn', '-query', '/tmp/qiime2-archive-qo_juqfe/c740bc5f-413e-4eb2-8109-964ea9eb00ab/data/dna-sequences.fasta', '-evalue', '0.001', '-strand', 'both', '-outfmt', '7', '-subject', '/tmp/qiime2-archive-1dggqzu6/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta', '-perc_identity', '80.0', '-qcov_hsp_perc', '80.0', '-max_target_seqs', '10', '-out', '/tmp/tmpx8hy5q1y']' died with <Signals.SIGKILL: 9>.

Plugin error from feature-classifier:

Command '['blastn', '-query', '/tmp/qiime2-archive-qo_juqfe/c740bc5f-413e-4eb2-8109-964ea9eb00ab/data/dna-sequences.fasta', '-evalue', '0.001', '-strand', 'both', '-outfmt', '7', '-subject', '/tmp/qiime2-archive-1dggqzu6/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta', '-perc_identity', '80.0', '-qcov_hsp_perc', '80.0', '-max_target_seqs', '10', '-out', '/tmp/tmpx8hy5q1y']' died with <Signals.SIGKILL: 9>.

See above for debug info.

Kinda regards,
Cesar

[lizgehret]

Hi @Cesar_Alejandro,

Thanks for your patience here! The <Signals.SIGKILL: 9> code indicates that this process was killed - which is typically due to a memory issue on your machine. Check out some of the other forum posts related to this issue - this should provide you with a few ways to sort this out!

Cheers