Dear all,
I have paired end reads for which I merged using vsearch and removed primers using cutadapt (I had four base pair spike with NNNN that needed to be removed so I removed all primers). I then imported my data into qiime 2 and followed the "[Alternative methods of read-joining in QIIME 2](tutorial Alternative methods of read-joining in QIIME 2 — QIIME 2 2018.2.0 documentation)". However when I ran Deblur I had the following error message:
/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
from ._conv import register_converters as _register_converters
Traceback (most recent call last):
File "/home/mark/miniconda2/envs/deblurenv/bin/deblur", line 4, in <module>
__import__('pkg_resources').run_script('deblur==1.0.3', 'deblur')
File "/home/mark/miniconda2/envs/deblurenv/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/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/pkg_resources/__init__.py", line 1527, in run_script
exec(code, namespace, namespace)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/deblur-1.0.3-py3.5.egg-info/scripts/deblur", line 684, in <module>
deblur_cmds()
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/deblur-1.0.3-py3.5.egg-info/scripts/deblur", line 641, in workflow
neg_ref_db_fp, jobs_to_start)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/deblur/parallel_deblur.py", line 142, in parallel_deblur
es))
RuntimeError: stdout:
stderr: /home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/h5py/__init__.py:36: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
from ._conv import register_converters as _register_converters
Traceback (most recent call last):
File "/home/mark/miniconda2/envs/deblurenv/bin/deblur", line 4, in <module>
__import__('pkg_resources').run_script('deblur==1.0.3', 'deblur')
File "/home/mark/miniconda2/envs/deblurenv/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/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/pkg_resources/__init__.py", line 1527, in run_script
exec(code, namespace, namespace)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/deblur-1.0.3-py3.5.egg-info/scripts/deblur", line 684, in <module>
deblur_cmds()
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/mark/miniconda2/envs/deblurenv/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/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/deblur/workflow.py", line 832, in launch_workflow
left_trim_len=left_trim_length):
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/deblur/workflow.py", line 130, in trim_seqs
for label, seq in input_seqs:
File "/home/mark/miniconda2/envs/deblurenv/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/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/skbio/io/registry.py", line 506, in <genexpr>
return (x for x in itertools.chain([next(gen)], gen))
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/skbio/io/registry.py", line 531, in _read_gen
yield from reader(file, **kwargs)
File "/home/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/skbio/io/registry.py", line 1008, in wrapped_reader
yield from reader_function(fhs[-1], **kwargs)
File "/home/mark/miniconda2/envs/deblurenv/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/mark/miniconda2/envs/deblurenv/lib/python3.5/site-packages/skbio/io/format/fastq.py", line 481, in _parse_sequence_data
_blank_error("before '+'")
File "/home/mark/miniconda2/envs/deblurenv/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
exit: 1
Traceback (most recent call last):
File "/home/mark/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/commands.py", line 246, in __call__
results = action(**arguments)
File "<decorator-gen-344>", line 2, in denoise_16S
File "/home/mark/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/home/mark/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/mark/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_deblur/_denoise.py", line 96, in denoise_16S
hashed_feature_ids=hashed_feature_ids)
File "/home/mark/miniconda2/envs/qiime2-2018.2/lib/python3.5/site-packages/q2_deblur/_denoise.py", line 163, in _denoise_helper
subprocess.run(cmd, check=True)
File "/home/mark/miniconda2/envs/qiime2-2018.2/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['deblur', 'workflow', '--seqs-fp', '/tmp/qiime2-archive-ts48smgs/b2be2ea1-0067-4e1d-a22c-ed90fcb79087/data', '--output-dir', '/tmp/tmpx9g3ucks', '--mean-error', '0.005', '--indel-prob', '0.01', '--indel-max', '3', '--trim-length', '248', '--min-reads', '10', '--min-size', '2', '--jobs-to-start', '8', '-w', '--keep-tmp-files']' returned non-zero exit status 1
I aware of the following post which redirects me here, however reinstalling python 3.5 within a conda environment for Deblur did not solve my issues.
I would be grateful for any help!!! Thanks!!