Hello. I am also having difficulty with the import of the fastq (not fastq.gz) files using the manifest approach. I am using the manifest approach since the fastq file names are changed when the sequencing facility runs their in-house script. Indeed, the file names do have underscores, which may play into this issue. I checked my manifest file for trailing spaces and correct headers. I am running qiime2 in VB.
My qiime script :
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path /media/sf_qiime/MMPC/Berryman/pe-33-manifest.csv \
--output-path /media/sf_qiime/MMPC/Berryman/paired-end-demux.qza \
--source-format PairedEndFastqManifestPhred33`
example of portion of my mainfest file:
sample-id,absolute-filepath,direction
G691,/media/sf_qiime/MMPC/Berryman/TKnotts0517_G691_1.fastq,forward
G693,/media/sf_qiime/MMPC/Berryman/TKnotts0517_G693_1.fastq,forward
G725,/media/sf_qiime/MMPC/Berryman/TKnotts0517_G725_1.fastq,forward
G691,/media/sf_qiime/MMPC/Berryman/TKnotts0517_G691_2.fastq,reverse
G693,/media/sf_qiime/MMPC/Berryman/TKnotts0517_G693_2.fastq,reverse
G725,/media/sf_qiime/MMPC/Berryman/TKnotts0517_G725_2.fastq,reverse
Error message seems to be similar to what others have reported.
'/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/skbio/io/registry.py:922: FormatIdentificationWarning: '_fastq_sniffer' has encountered a problem.
Please send the following to our issue tracker at
https://github.com/biocore/scikit-bio/issues
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/skbio/io/registry.py", line 914, in wrapped_sniffer
return sniffer(fh)
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/skbio/io/format/fastq.py", line 320, in _fastq_sniffer
if split_length == 10 and description[1] in 'YN':
IndexError: list index out of range
FormatIdentificationWarning)
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2017.8/bin/qiime", line 6, in <module>
sys.exit(q2cli.__main__.qiime())
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/tools.py", line 111, in import_data
view_type=source_format)
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/result.py", line 192, in import_data
return cls._from_view(type_, view, view_type, provenance_capture)
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/result.py", line 217, in _from_view
result = transformation(view)
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/core/transform.py", line 62, in transformation
other.validate(new_view)
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/core/transform.py", line 131, in validate
view.validate()
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/plugin/model/directory_format.py", line 168, in validate
getattr(self, field)._validate_members(collected_paths)
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/plugin/model/directory_format.py", line 100, in _validate_members
self.format(path, mode='r').validate()
File "/home/qiime2/miniconda/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/plugin/model/file_format.py", line 31, in validate
% (self.path, self.__class__.__name__))
ValueError: InPath('/tmp/q2-SingleLanePerSamplePairedEndFastqDirFmt-wvek0f3l/G860_38_L001_R2_001.fastq.gz') is not formatted as a FastqGzFormat file.'
Please let me know if you need further information to help troubleshoot this issue.
Thanks!
Trina