BUG: classify-kraken2 fails when trying to process empty fastq files.

[mikerobeson]

Describe the bug
I would not necessarily consider this a BUG per se, but when I ran moshpit classify-kraken2 on our data, it turned out that some of our samples did not sequence and consisted of empty fastq files. I removed the empty sample files, everything appears to be running smoothly for the moment.

To Reproduce
Steps to reproduce the behavior:

1. Run moshpit classify-kraken2 on any empty fastq files.

Expected behavior
I would expect that empty files would be logged to a file and skipped during processing.

Error output log

Running qiime moshpit classify-kraken2 ...
/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/numpy/core/fromnumeric.py:59: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead.
return bound(*args, **kwds)
Loading database information... done.
24964735 sequences (6605.33 Mbp) processed in 4064.781s (368.5 Kseq/m, 97.50 Mbp/m).
12785302 sequences classified (51.21%)
12179433 sequences unclassified (48.79%)
Loading database information... done.
0 sequences (0.00 Mbp) processed in 0.741s (0.0 Kseq/m, 0.00 Mbp/m).
0 sequences classified (-nan%)
0 sequences unclassified (-nan%)
Traceback (most recent call last):
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/q2_types/kraken2/_format.py", line 52, in validate
df, COLUMNS = self._to_dataframe()
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/q2_types/kraken2/_format.py", line 39, in _to_dataframe
df = pd.read_csv(self.path, sep='\t', header=None)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 620, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1620, in init
self._engine = self._make_engine(f, self.engine)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine
return mapping[engine](f, **self.options)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in init
self._reader = parsers.TextReader(src, **kwds)
File "parsers.pyx", line 581, in pandas._libs.parsers.TextReader.cinit
pandas.errors.EmptyDataError: No columns to parse from file
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/plugin/model/file_format.py", line 26, in validate
self.validate(level)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/q2_types/kraken2/_format.py", line 58, in validate
raise ValidationError(
qiime2.core.exceptions.ValidationError: An error occurred when reading in the Kraken2 report file
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 520, in call
results = self._execute_action(
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/q2cli/commands.py", line 586, in _execute_action
results = action(**arguments)
File "", line 2, in classify_kraken2
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 657, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/q2_moshpit/kraken2/classification.py", line 99, in classify_kraken2
(kraken2_report, kraken2_output) = _classify_kraken2(
File "", line 2, in _classify_kraken2
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/sdk/context.py", line 143, in deferred_action
return action_obj._bind(
File "", line 2, in _classify_kraken2
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 342, in bound_callable
outputs = self.callable_executor(
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/sdk/action.py", line 593, in callable_executor
self.signature.coerce_given_outputs(output_views, output_types,
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 493, in coerce_given_outputs
output = self._create_output_artifact(
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/core/type/signature.py", line 517, in _create_output_artifact
artifact = qiime2.sdk.Artifact._from_view(
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/sdk/result.py", line 360, in _from_view
result = transformation(view, validate_level)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/core/transform.py", line 68, in transformation
self.validate(view, level=validate_level)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/core/transform.py", line 143, in validate
view.validate(level)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/plugin/model/directory_format.py", line 177, in validate
getattr(self, field)._validate_members(collected_paths, level)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/plugin/model/directory_format.py", line 107, in _validate_members
self.format(path, mode='r').validate(level)
File "/home/.../qiime2-metagenome-2024.5/lib/python3.9/site-packages/qiime2/plugin/model/file_format.py", line 28, in validate
raise ValidationError(
qiime2.core.exceptions.ValidationError: /home/.../tmp/q2-Kraken2ReportDirectoryFormat-f7b5ug6y/S10.report.txt is not a(n) Kraken2ReportFormat file:
An error occurred when reading in the Kraken2 report file
Plugin error from moshpit:
/home/.../tmp/q2-Kraken2ReportDirectoryFormat-f7b5ug6y/S10.report.txt is not a(n) Kraken2ReportFormat file:
An error occurred when reading in the Kraken2 report file
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: kraken2 --threads 56 --confidence 0.6 --minimum-base-quality 20 --minimum-hit-groups 2 --report-minimizer-data --db cache/data/40fe59c3-e5ed-40a6-a405-8c22407495d8/data --paired --report /home/.../tmp/q2-Kraken2ReportDirectoryFormat-h45l0b1k/S1.report.txt --output /home/.../tmp/q2-Kraken2OutputDirectoryFormat-z1xdkzbx/S1.output.txt cache/data/293caa72-5433-40d9-a81d-8a68044248ca/data/S1_40_L001_R1_001.fastq.gz cache/data/293caa72-5433-40d9-a81d-8a68044248ca/data/S1_88_L001_R2_001.fastq.gz
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: kraken2 --threads 56 --confidence 0.6 --minimum-base-quality 20 --minimum-hit-groups 2 --report-minimizer-data --db cache/data/40fe59c3-e5ed-40a6-a405-8c22407495d8/data --paired --report /home/.../tmp/q2-Kraken2ReportDirectoryFormat-f7b5ug6y/S10.report.txt --output /home/.../tmp/q2-Kraken2OutputDirectoryFormat-yrhq93zn/S10.output.txt cache/data/f6faa848-fe19-4432-9fe0-2be68994eb29/data/S10_15_L001_R1_001.fastq.gz cache/data/f6faa848-fe19-4432-9fe0-2be68994eb29/data/S10_63_L001_R2_001.fastq.gz

Please complete the following information:

• OS: Our HPC runs CentOS Linux v7
• QIIME 2 version: qiime2-metagenome-2024.5