Plugin error deblur

I was running deblur and I encountered the following error:
qiime deblur denoise-16S \

–i-demultiplexed-seqs demux-filtered.qza
–p-trim-length 259
–o-representative-sequences rep-seqs-deblur.qza
–o-table table-deblur.qza
–p-sample-stats
–o-stats deblur-stats.qza
–verbose
Traceback (most recent call last):
File “/home/basilin/miniconda3/envs/qiime2-2017.12/bin/deblur”, line 4, in
import(‘pkg_resources’).run_script(‘deblur==1.0.3’, ‘deblur’)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/pkg_resources/init.py”, line 750, in run_script
self.require(requires)[0].run_script(script_name, ns)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/pkg_resources/init.py”, line 1527, in run_script
exec(code, namespace, namespace)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/deblur-1.0.3-py3.5.egg-info/scripts/deblur”, line 684, in
deblur_cmds()
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 722, in call
return self.main(*args, **kwargs)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 697, in main
rv = self.invoke(ctx)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/click/core.py”, line 535, in invoke
return callback(*args, **kwargs)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/deblur-1.0.3-py3.5.egg-info/scripts/deblur”, line 632, in workflow
threads_per_sample=threads_per_sample)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/deblur/workflow.py”, line 832, in launch_workflow
left_trim_len=left_trim_length):
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/deblur/workflow.py”, line 130, in trim_seqs
for label, seq in input_seqs:
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/deblur/workflow.py”, line 99, in sequence_generator
for record in skbio.read(input_fp, format=format, **kw):
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/registry.py”, line 506, in
return (x for x in itertools.chain([next(gen)], gen))
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/registry.py”, line 531, in _read_gen
yield from reader(file, **kwargs)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/registry.py”, line 1008, in wrapped_reader
yield from reader_function(fhs[-1], **kwargs)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/format/fastq.py”, line 344, in _fastq_to_generator
seq, qual_header = _parse_sequence_data(fh, seq_header)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/format/fastq.py”, line 481, in _parse_sequence_data
_blank_error(“before ‘+’”)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/skbio/io/format/fastq.py”, line 473, in _blank_error
raise FASTQFormatError(error_string)
skbio.io._exception.FASTQFormatError: Found blank or whitespace-only line before ‘+’ in FASTQ file
Traceback (most recent call last):
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py”, line 224, in call
results = action(**arguments)
File “”, line 2, in denoise_16S
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 228, in bound_callable
output_types, provenance)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 363, in callable_executor
output_views = self._callable(**view_args)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_deblur/_denoise.py”, line 96, in denoise_16S
hashed_feature_ids=hashed_feature_ids)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_deblur/_denoise.py”, line 163, in _denoise_helper
subprocess.run(cmd, check=True)
File “/home/basilin/miniconda3/envs/qiime2-2017.12/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘deblur’, ‘workflow’, ‘–seqs-fp’, ‘/tmp/qiime2-archive-qbdmp7mr/95233b75-3c56-4bd4-b647-10d302273e93/data’, ‘–output-dir’, ‘/tmp/tmpovdhh13h’, ‘–mean-error’, ‘0.005’, ‘–indel-prob’, ‘0.01’, ‘–indel-max’, ‘3’, ‘–trim-length’, ‘259’, ‘–min-reads’, ‘10’, ‘–min-size’, ‘2’, ‘–jobs-to-start’, ‘1’, ‘-w’, ‘–keep-tmp-files’]’ returned non-zero exit status 1

Plugin error from deblur:

Command ‘[‘deblur’, ‘workflow’, ‘–seqs-fp’, ‘/tmp/qiime2-archive-qbdmp7mr/95233b75-3c56-4bd4-b647-10d302273e93/data’, ‘–output-dir’, ‘/tmp/tmpovdhh13h’, ‘–mean-error’, ‘0.005’, ‘–indel-prob’, ‘0.01’, ‘–indel-max’, ‘3’, ‘–trim-length’, ‘259’, ‘–min-reads’, ‘10’, ‘–min-size’, ‘2’, ‘–jobs-to-start’, ‘1’, ‘-w’, ‘–keep-tmp-files’]’ returned non-zero exit status 1

Any help would be greatly appreciated

Hi @basilin_benson,

Which version of Qiime2 are you running? Also, have you seen this post? It might help you.

Cheers,

I am currently running the version 2017.12.0

OK thanks.

Could you confirm that you have followed the instructions in the other post and have indexdb_rna? Also, how much RAM do you have in your machine?

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