Hello- I am running qiime2-amplicon-2024.5
I am trying to run deblur denoise on CO1 sequence data and continue to get this error message
"Plugin error from deblur:
Command '['deblur', 'workflow', '--seqs-fp', '/tmp/qiime2/ajanosik/data/f4ed7265-dce0-4d25-9226-57540e4e29f0/data', '--output-dir', '/tmp/tmpnyxqf7dq', '--mean-error', '0.005', '--indel-prob', '0.01', '--indel-max', '3', '--trim-length', '230', '--left-trim-length', '50', '--min-reads', '10', '--min-size', '2', '--jobs-to-start', '8', '-w', '--pos-ref-fp', '/tmp/qiime2/ajanosik/data/9a769ac4-1d70-4fb9-9147-d42690c59091/data/dna-sequences.fasta']' returned non-zero exit status 1.
Debug info has been saved to /tmp/qiime2-q2cli-err-6a70l5ai.log"
These are the commands I have ran so far-
qiime tools import --type 'SampleData[SequencesWithQuality]'
--input-path /home/users/ajanosik/Jake_Roush/Full_Manifest.txt
--output-path single-end-demux.qza \
--input-format SingleEndFastqManifestPhred33V2
qiime quality-filter q-score
--i-demux single-end-demux.qza
--o-filtered-sequences single-end-demux-filtered.qza
--o-filter-stats single-end-demux-stats.qza
qiime deblur denoise-other
--i-demultiplexed-seqs single-end-demux-filtered.qza
--i-reference-seqs /home/users/ajanosik/Jake_Roush/References/reference_sequence_trim2.qza
--p-trim-length 230 \ (Tried 238,230,200 and it gave a "deblur plugin error" message
--p-left-trim-len 50\ (Tried trimming from the left to see if it work work also)
--o-representative-sequences rep-seqs.qza
--o-table table.qza
--p-sample-stats \ (I have tried command without this, incase memory storage was issue.)
--o-stats deblur-stats.qza
--p-jobs-to-start 8
When I ran the debug info this is what got kicked back- cat /tmp/qiime2-q2cli-err-6a70l5ai.log
/home/share/anaconda/envs/qiime2-amplicon-2024.5/bin/deblur:534: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
logger.warn('deblur version %s workflow started on %s' %
/home/share/anaconda/envs/qiime2-amplicon-2024.5/bin/deblur:536: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead
logger.warn('parameters: %s' % locals())
Traceback (most recent call last):
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/bin/deblur", line 687, in
deblur_cmds()
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/bin/deblur", line 664, in workflow
tmp_files = remove_artifacts_from_biom_table(output_fp, outputfasta_fp,
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/deblur/workflow.py", line 316, in remove_artifacts_from_biom_table
clean_fp, num_seqs_left, tmp_files = remove_artifacts_seqs(
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/deblur/workflow.py", line 466, in remove_artifacts_seqs
if (float(line[2]) >= sim_thresh) and
IndexError: list index out of range
Traceback (most recent call last):
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 581, in _execute_action
results = action(**arguments)
File "", line 2, in denoise_other
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 576, in callable_executor
output_views = self._callable(**view_args)
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_deblur/_denoise.py", line 120, in denoise_other
return _denoise_helper(
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/q2_deblur/_denoise.py", line 185, in _denoise_helper
subprocess.run(cmd, check=True)
File "/home/share/anaconda/envs/qiime2-amplicon-2024.5/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['deblur', 'workflow', '--seqs-fp', '/tmp/qiime2/ajanosik/data/f4ed7265-dce0-4d25-9226-57540e4e29f0/data', '--output-dir', '/tmp/tmpnyxqf7dq', '--mean-error', '0.005', '--indel-prob', '0.01', '--indel-max', '3', '--trim-length', '230', '--left-trim-length', '50', '--min-reads', '10', '--min-size', '2', '--jobs-to-start', '8', '-w', '--pos-ref-fp', '/tmp/qiime2/ajanosik/data/9a769ac4-1d70-4fb9-9147-d42690c59091/data/dna-sequences.fasta']' returned non-zero exit status 1.
I'm not sure how to interpret this or what my next steps should be. Please help me in fixing this.
Thank you!