/hpc-home/USER/miniconda3/envs/qiime2-2021.4/bin/deblur:531: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead logger.warn('deblur version %s workflow started on %s' % /hpc-home/USER/miniconda3/envs/qiime2-2021.4/bin/deblur:533: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead logger.warn('parameters: %s' % locals()) Traceback (most recent call last): File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/bin/deblur", line 684, in deblur_cmds() File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 829, in __call__ return self.main(*args, **kwargs) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/bin/deblur", line 640, in workflow parallel_deblur(input_file_list, sys.argv, pos_ref_db_fp, File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/deblur/parallel_deblur.py", line 140, in parallel_deblur raise RuntimeError("stdout: %s\nstderr: %s\nexit: %d" % (stdout, RuntimeError: stdout: stderr: /hpc-home/USER/miniconda3/envs/qiime2-2021.4/bin/deblur:531: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead logger.warn('deblur version %s workflow started on %s' % /hpc-home/USER/miniconda3/envs/qiime2-2021.4/bin/deblur:533: DeprecationWarning: The 'warn' method is deprecated, use 'warning' instead logger.warn('parameters: %s' % locals()) Traceback (most recent call last): File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/bin/deblur", line 684, in deblur_cmds() File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 829, in __call__ return self.main(*args, **kwargs) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/bin/deblur", line 625, in workflow deblurred_file_name = launch_workflow( File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/deblur/workflow.py", line 830, in launch_workflow for label, seq in trim_seqs( File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/deblur/workflow.py", line 130, in trim_seqs for label, seq in input_seqs: File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/deblur/workflow.py", line 99, in sequence_generator for record in skbio.read(input_fp, format=format, **kw): File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/skbio/io/registry.py", line 506, in return (x for x in itertools.chain([next(gen)], gen)) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/skbio/io/registry.py", line 531, in _read_gen yield from reader(file, **kwargs) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/skbio/io/registry.py", line 1008, in wrapped_reader yield from reader_function(fhs[-1], **kwargs) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/skbio/io/format/fastq.py", line 344, in _fastq_to_generator seq, qual_header = _parse_sequence_data(fh, seq_header) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/skbio/io/format/fastq.py", line 481, in _parse_sequence_data _blank_error("before '+'") File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/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 "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 329, in __call__ results = action(**arguments) File "", line 2, in denoise_other File "/hpc-home/USER/miniconda3/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 "/hpc-home/USER/miniconda3/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 "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_deblur/_denoise.py", line 118, in denoise_other return _denoise_helper( File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_deblur/_denoise.py", line 180, in _denoise_helper subprocess.run(cmd, check=True) File "/hpc-home/USER/miniconda3/envs/qiime2-2021.4/lib/python3.8/subprocess.py", line 516, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['deblur', 'workflow', '--seqs-fp', '/tmp/qiime2-archive-0bqcac9s/0219a9da-b09d-41af-b101-7e53e3029021/data', '--output-dir', '/tmp/tmp50kege8y', '--mean-error', '0.005', '--indel-prob', '0.01', '--indel-max', '3', '--trim-length', '238', '--left-trim-length', '0', '--min-reads', '10', '--min-size', '2', '--jobs-to-start', '24', '-w', '--pos-ref-fp', '/tmp/qiime2-archive-7_lkp0px/630d0d6d-f4df-40a0-afac-4f3bb8bd2b1a/data/dna-sequences.fasta']' returned non-zero exit status 1. Plugin error from deblur: Command '['deblur', 'workflow', '--seqs-fp', '/tmp/qiime2-archive-0bqcac9s/0219a9da-b09d-41af-b101-7e53e3029021/data', '--output-dir', '/tmp/tmp50kege8y', '--mean-error', '0.005', '--indel-prob', '0.01', '--indel-max', '3', '--trim-length', '238', '--left-trim-length', '0', '--min-reads', '10', '--min-size', '2', '--jobs-to-start', '24', '-w', '--pos-ref-fp', '/tmp/qiime2-archive-7_lkp0px/630d0d6d-f4df-40a0-afac-4f3bb8bd2b1a/data/dna-sequences.fasta']' returned non-zero exit status 1. See above for debug info.