MAFFT's usage of stdout + direct file handle redirection in `run_command` doesn't play nicely with some environments

Bug Description mafft stdout/stderr implementation does not work in a Jupyterhub deployment.

Screenshots

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: mafft --preservecase --inputorder --thread 1 /tmp/qiime2-archive-xr3zed18/1fe37b20-35c7-4a07-b0d7-f9e7a3d6b30f/data/dna-sequences.fasta

/home/jorden/dev/mc3/envs/biota/lib/python3.5/site-packages/skbio/io/registry.py:548: FormatIdentificationWarning: <_io.BufferedReader name='/tmp/q2-AlignedDNAFASTAFormat-4i04u915'> does not look like a fasta file
  % (file, fmt), FormatIdentificationWarning)

---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-5-59f24acdb7a5> in <module>()
----> 1 biota.util.make_tree(f.DenoisedSequenceVariant)

~/dev/biota_code/biota/util.py in make_tree(seqs, tree_path, overwrite, n_threads)
    347     if not os.path.isfile(tree_path) or overwrite:
    348         q_seqs = qiime2.Artifact.import_data("FeatureData[Sequence]", seqs)
--> 349         aligned_seqs, = alignment.methods.mafft(q_seqs, n_threads=n_threads)
    350         filtered_aligned_seqs, = alignment.methods.mask(aligned_seqs)
    351         tree, = fasttree(filtered_aligned_seqs, n_threads=n_threads)

<decorator-gen-410> in mafft(sequences, n_threads)

~/dev/mc3/envs/biota/lib/python3.5/site-packages/qiime2/sdk/action.py in bound_callable(*args, **kwargs)
    226                 # Execute
    227                 outputs = self._callable_executor_(scope, callable_args,
--> 228                                                    output_types, provenance)
    229 
    230                 if len(outputs) != len(self.signature.outputs):

~/dev/mc3/envs/biota/lib/python3.5/site-packages/qiime2/sdk/action.py in _callable_executor_(self, scope, view_args, output_types, provenance)
    361 
    362     def _callable_executor_(self, scope, view_args, output_types, provenance):
--> 363         output_views = self._callable(**view_args)
    364         output_views = tuplize(output_views)
    365 

~/dev/caporasolab/q2-alignment/q2_alignment/_mafft.py in mafft(sequences, n_threads)
     68     # while aligning, which would be a bug on mafft's end. This is just a
     69     # sanity check and is not expected to trigger in practice.
---> 70     assert len(ids) == len(msa)
     71     for id, seq in zip(ids, msa):
     72         seq.metadata['id'] = id

AssertionError:

Comments Changing to subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE...) resolves the issue.

qiime2 / q2-alignment

MAFFT's usage of stdout + direct file handle redirection in `run_command` doesn't play nicely with some environments #42