bin-contigs-metabat fails if no MAGs are formed for a sample

[gregcaporaso]

If no MAGs are formed for a sample, bin-contigs-metabat fails with a validation error:

[bam_sort_core] merging from 1 files and 1 in-memory blocks...
Output depth matrix to /tmp/tmpgg2uftbn/KS_depth.txt
jgi_summarize_bam_contig_depths 2.15 (Bioconda) 2020-01-04T21:10:40
Output matrix to /tmp/tmpgg2uftbn/KS_depth.txt
0: Opening bam: /tmp/tmpgg2uftbn/KS_alignment_sorted.bam
Processing bam files
Thread 0 finished: KS_alignment_sorted.bam with 3838648 reads and 219961 readsWellMapped
Creating depth matrix file: /tmp/tmpgg2uftbn/KS_depth.txt
Closing most bam files
Closing last bam file
Finished
MetaBAT 2 (2.15 (Bioconda)) using minContig 2500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=1680628081
0 bins (0 bases in total) formed.
Traceback (most recent call last):
  File "/home/gcaporaso/mambaforge/envs/q2-shotgun/lib/python3.8/site-packages/q2cli/commands.py", line 352, in __call__
    results = action(**arguments)
  File "<decorator-gen-40>", line 2, in bin_contigs_metabat
  File "/home/gcaporaso/mambaforge/envs/q2-shotgun/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/home/gcaporaso/mambaforge/envs/q2-shotgun/lib/python3.8/site-packages/qiime2/sdk/action.py", line 408, in _callable_executor_
    artifact = qiime2.sdk.Artifact._from_view(
  File "/home/gcaporaso/mambaforge/envs/q2-shotgun/lib/python3.8/site-packages/qiime2/sdk/result.py", line 349, in _from_view
    result = transformation(view, validate_level)
  File "/home/gcaporaso/mambaforge/envs/q2-shotgun/lib/python3.8/site-packages/qiime2/core/transform.py", line 68, in transformation
    self.validate(view, level=validate_level)
  File "/home/gcaporaso/mambaforge/envs/q2-shotgun/lib/python3.8/site-packages/qiime2/core/transform.py", line 143, in validate
    view.validate(level)
  File "/home/gcaporaso/mambaforge/envs/q2-shotgun/lib/python3.8/site-packages/qiime2/plugin/model/directory_format.py", line 177, in validate
    getattr(self, field)._validate_members(collected_paths, level)
  File "/home/gcaporaso/mambaforge/envs/q2-shotgun/lib/python3.8/site-packages/qiime2/plugin/model/directory_format.py", line 109, in _validate_members
    raise ValidationError(
qiime2.core.exceptions.ValidationError: Missing one or more files for MultiFASTADirectoryFormat: '.+\\.(fa|fasta)$'

Plugin error from moshpit:

  Missing one or more files for MultiFASTADirectoryFormat: '.+\\.(fa|fasta)$'

See above for debug info.
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: samtools sort /tmp/qiime2/gcaporaso/data/8a63aaeb-3bfc-4a2c-b3f3-6cfedfcf6a7a/data/KS_KS_All13-C0500000_alignment.bam -o /tmp/tmpgg2uftbn/KS_alignment_sorted.bam

Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: jgi_summarize_bam_contig_depths --outputDepth /tmp/tmpgg2uftbn/KS_depth.txt /tmp/tmpgg2uftbn/KS_alignment_sorted.bam

Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.

Command: metabat2 -i /tmp/qiime2/gcaporaso/data/c227e281-0838-4bfd-ac40-2d78f2e471e9/data/KS_KS_All13-C0500000_contigs.fa -a /tmp/tmpgg2uftbn/KS_depth.txt -o /tmp/tmpgg2uftbn/KS/bin --numThreads 40

I'm not sure what the right way to handle this internally is - e.g., the whole command fails, or no MAGs are provided for that sample - but we should catch and handle this case with a more informative error message.

UPDATE: This looks to actually be an issue with how the sample ids are obtained from the filenames, similar to what we discovered on bokulich-lab/q2-assembly#37. I am testing this now and will have a PR if it works.