Hi Justine
Here is the full error traceback.
(base) -bash-4.2$ cat SpongeLarvae_Deblur-2051728.out
Traceback (most recent call last):
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/bin/deblur", line 684, in <module>
deblur_cmds()
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/click/core.py", line 764, in __call__
return self.main(*args, **kwargs)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/bin/deblur", line 632, in workflow
threads_per_sample=threads_per_sample)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/deblur/workflow.py", line 833, in launch_workflow
left_trim_len=left_trim_length):
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/deblur/workflow.py", line 130, in trim_seqs
for label, seq in input_seqs:
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/deblur/workflow.py", line 99, in sequence_generator
for record in skbio.read(input_fp, format=format, **kw):
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/skbio/io/registry.py", line 506, in <genexpr>
return (x for x in itertools.chain([next(gen)], gen))
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/skbio/io/registry.py", line 531, in _read_gen
yield from reader(file, **kwargs)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/skbio/io/registry.py", line 1008, in wrapped_reader
yield from reader_function(fhs[-1], **kwargs)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/skbio/io/format/fastq.py", line 344, in _fastq_to_generator
seq, qual_header = _parse_sequence_data(fh, seq_header)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/skbio/io/format/fastq.py", line 481, in _parse_sequence_data
_blank_error("before '+'")
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/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 "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/q2cli/commands.py", line 274, in __call__
results = action(**arguments)
File "</apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/decorator.py:decorator-gen-432>", line 2, in denoise_16S
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in _callable_executor_
output_views = self._callable(**view_args)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/q2_deblur/_denoise.py", line 96, in denoise_16S
hashed_feature_ids=hashed_feature_ids)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/site-packages/q2_deblur/_denoise.py", line 163, in _denoise_helper
subprocess.run(cmd, check=True)
File "/apps/pkg/qiime2/2019.1/rhel7_u5/gnu/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['deblur', 'workflow', '--seqs-fp', '/tmp/qiime2-archive-ntiq_i0w/d5f60d63-1a8b-44bc-bfcf-7a45e36acac7/data', '--output-dir', '/tmp/tmpnpsnjdgb', '--mean-error', '0.005', '--indel-prob', '0.01', '--indel-max', '3', '--trim-length', '100', '--min-reads', '1', '--min-size', '1', '--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-ntiq_i0w/d5f60d63-1a8b-44bc-bfcf-7a45e36acac7/data', '--output-dir', '/tmp/tmpnpsnjdgb', '--mean-error', '0.005', '--indel-prob', '0.01', '--indel-max', '3', '--trim-length', '100', '--min-reads', '1', '--min-size', '1', '--jobs-to-start', '1', '-w', '--keep-tmp-files']' returned non-zero exit status 1.
This all comes after 12+ hours of the code running successfully.
Regards,
Tyler