Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --cluster_size /tmp/tmpgm9lrl9r --id 0.99 --centroids /tmp/q2-DNAFASTAFormat-zdyznqtj --uc /tmp/tmpz0fek351 --qmask none --xsize --threads 6

vsearch v2.7.0_linux_x86_64, 31.1GB RAM, 8 cores
https://github.com/torognes/vsearch

Reading file /tmp/tmpgm9lrl9r 4%  

Fatal error: Invalid (zero) abundance annotation in FASTA file header
Traceback (most recent call last):
  File "/root/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py", line 327, in __call__
    results = action(**arguments)
  File "</root/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-121>", line 2, in cluster_features_de_novo
  File "/root/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
    output_types, provenance)
  File "/root/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/root/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_vsearch/_cluster_features.py", line 193, in cluster_features_de_novo
    run_command(cmd)
  File "/root/miniconda2/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_vsearch/_cluster_features.py", line 33, in run_command
    subprocess.run(cmd, check=True)
  File "/root/miniconda2/envs/qiime2-2019.7/lib/python3.6/subprocess.py", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['vsearch', '--cluster_size', '/tmp/tmpgm9lrl9r', '--id', '0.99', '--centroids', '/tmp/q2-DNAFASTAFormat-zdyznqtj', '--uc', '/tmp/tmpz0fek351', '--qmask', 'none', '--xsize', '--threads', '6']' returned non-zero exit status 1.

Plugin error from vsearch:

  Command '['vsearch', '--cluster_size', '/tmp/tmpgm9lrl9r', '--id', '0.99', '--centroids', '/tmp/q2-DNAFASTAFormat-zdyznqtj', '--uc', '/tmp/tmpz0fek351', '--qmask', 'none', '--xsize', '--threads', '6']' returned non-zero exit status 1.

vsearch --allpairs_global queries.fasta --acceptall --id 0.0 --blast6out out.bl6 --alnout out.aln --qmask none

self = <q2_vsearch.tests.test_join_pairs.MergePairsTests testMethod=test_join_pairs_alt_qminout>

    def test_join_pairs_alt_qminout(self):
        with redirected_stdio(stderr=os.devnull):
>           cmd, obs = _join_pairs_w_command_output(
                self.input_seqs, qminout=-1)

q2_vsearch/tests/test_join_pairs.py:276: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
q2_vsearch/_join_pairs.py:146: in _join_pairs_w_command_output
    run_command(cmd)
q2_vsearch/_cluster_features.py:33: in run_command
    subprocess.run(cmd, check=True)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

input = None, capture_output = False, timeout = None, check = True
popenargs = (['vsearch', '--fastq_mergepairs', '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/q2_v....dev0/.pybuild/cpython3_3.8/build/q2_vsearch/tests/data/demux-1/BAQ2687.1_3_L001_R2_001.fastq.gz', '--fastqout', ...],)
kwargs = {}, process = <subprocess.Popen object at 0x7ffb3af2a9a0>
stdout = None, stderr = None, retcode = 1

    def run(*popenargs,
            input=None, capture_output=False, timeout=None, check=False, **kwargs):
        """Run command with arguments and return a CompletedProcess instance.
    
        The returned instance will have attributes args, returncode, stdout and
        stderr. By default, stdout and stderr are not captured, and those attributes
        will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them.
    
        If check is True and the exit code was non-zero, it raises a
        CalledProcessError. The CalledProcessError object will have the return code
        in the returncode attribute, and output & stderr attributes if those streams
        were captured.
    
        If timeout is given, and the process takes too long, a TimeoutExpired
        exception will be raised.
    
        There is an optional argument "input", allowing you to
        pass bytes or a string to the subprocess's stdin.  If you use this argument
        you may not also use the Popen constructor's "stdin" argument, as
        it will be used internally.
    
        By default, all communication is in bytes, and therefore any "input" should
        be bytes, and the stdout and stderr will be bytes. If in text mode, any
        "input" should be a string, and stdout and stderr will be strings decoded
        according to locale encoding, or by "encoding" if set. Text mode is
        triggered by setting any of text, encoding, errors or universal_newlines.
    
        The other arguments are the same as for the Popen constructor.
        """
        if input is not None:
            if kwargs.get('stdin') is not None:
                raise ValueError('stdin and input arguments may not both be used.')
            kwargs['stdin'] = PIPE
    
        if capture_output:
            if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
                raise ValueError('stdout and stderr arguments may not be used '
                                 'with capture_output.')
            kwargs['stdout'] = PIPE
            kwargs['stderr'] = PIPE
    
        with Popen(*popenargs, **kwargs) as process:
            try:
                stdout, stderr = process.communicate(input, timeout=timeout)
            except TimeoutExpired as exc:
                process.kill()
                if _mswindows:
                    # Windows accumulates the output in a single blocking
                    # read() call run on child threads, with the timeout
                    # being done in a join() on those threads.  communicate()
                    # _after_ kill() is required to collect that and add it
                    # to the exception.
                    exc.stdout, exc.stderr = process.communicate()
                else:
                    # POSIX _communicate already populated the output so
                    # far into the TimeoutExpired exception.
                    process.wait()
                raise
            except:  # Including KeyboardInterrupt, communicate handled that.
                process.kill()
                # We don't call process.wait() as .__exit__ does that for us.
                raise
            retcode = process.poll()
            if check and retcode:
>               raise CalledProcessError(retcode, process.args,
                                         output=stdout, stderr=stderr)
E               subprocess.CalledProcessError: Command '['vsearch', '--fastq_mergepairs', '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/q2_vsearch/tests/data/demux-1/BAQ2687.1_3_L001_R1_001.fastq.gz', '--reverse', '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/q2_vsearch/tests/data/demux-1/BAQ2687.1_3_L001_R2_001.fastq.gz', '--fastqout', '/tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-uv9jfa6y/BAQ2687.1_0_L001_R1_001.fastq', '--fastq_ascii', '33', '--fastq_minlen', '1', '--fastq_minovlen', '10', '--fastq_maxdiffs', '10', '--fastq_qmin', '0', '--fastq_qminout', '-1', '--fastq_qmax', '41', '--fastq_qmaxout', '41', '--minseqlength', '1', '--fasta_width', '0', '--threads', '1']' returned non-zero exit status 1.

/usr/lib/python3.8/subprocess.py:512: CalledProcessError
----------------------------- Captured stdout call -----------------------------
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: vsearch --fastq_mergepairs /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/q2_vsearch/tests/data/demux-1/BAQ2687.1_3_L001_R1_001.fastq.gz --reverse /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8/build/q2_vsearch/tests/data/demux-1/BAQ2687.1_3_L001_R2_001.fastq.gz --fastqout /tmp/q2-SingleLanePerSampleSingleEndFastqDirFmt-uv9jfa6y/BAQ2687.1_0_L001_R1_001.fastq --fastq_ascii 33 --fastq_minlen 1 --fastq_minovlen 10 --fastq_maxdiffs 10 --fastq_qmin 0 --fastq_qminout -1 --fastq_qmax 41 --fastq_qmaxout 41 --minseqlength 1 --fasta_width 0 --threads 1

----------------------------- Captured stderr call -----------------------------
Fatal error: Invalid options to command fastq_mergepairs
Invalid option(s): --fastq_qminout --minseqlength
The valid options for the fastq_mergepairs command are: --bzip2_decompress --eeout --eetabbedout --fasta_width --fastaout --fastaout_notmerged_fwd --fastaout_notmerged_rev --fastq_allowmergestagger --fastq_ascii --fastq_eeout --fastq_maxdiffpct --fastq_maxdiffs --fastq_maxee --fastq_maxlen --fastq_maxmergelen --fastq_maxns --fastq_minlen --fastq_minmergelen --fastq_minovlen --fastq_nostagger --fastq_qmax --fastq_qmaxout --fastq_qmin --fastq_truncqual --fastqout --fastqout_notmerged_fwd --fastqout_notmerged_rev --gzip_decompress --label_suffix --log --no_progress --quiet --relabel --relabel_keep --relabel_md5 --relabel_self --relabel_sha1 --reverse --sizein --sizeout --threads --xee --xsize