Importing demultiplexed sequences in Casava format

User Support
1

Hi,
This was very useful, I'm trying to do something a little different.
A friend helped me join my R1 and R2 files using multiple_joint_ends and created for me files per sample called: 1_R1_join.fastq.
I renamed the files according to the casava format as: 1_01_L001_R1_001.fastq and saved all the files in the same folder called casava.
Is casava only for non-joint files?
I´m not sure what´s wrong:

(qiime2) MacBook-Pro-de-Malena-2:FirstHS mae$ qiime tools import   --type 'SampleData[SequencesWithQuality]'   --input-path casava   --source-format CasavaOneEightSingleLanePerSampleDirFmt   --output-path demux.qza
Traceback (most recent call last):
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/q2cli-0.0.6-py3.5.egg/q2cli/tools.py", line 62, in import_data
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/qiime-2.0.6-py3.5.egg/qiime/sdk/result.py", line 191, in import_data
    return cls._from_view(type_, view, view_type, provenance_capture)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/qiime-2.0.6-py3.5.egg/qiime/sdk/result.py", line 216, in _from_view
    result = transformation(view)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/qiime-2.0.6-py3.5.egg/qiime/core/transform.py", line 57, in transformation
    self.validate(view)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/qiime-2.0.6-py3.5.egg/qiime/core/transform.py", line 114, in validate
    view.validate()
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/qiime-2.0.6-py3.5.egg/qiime/plugin/model/directory_format.py", line 168, in validate
    getattr(self, field)._validate_members(collected_paths)
  File "/Users/mae/Desktop/Shell/ENTER/envs/qiime2/lib/python3.5/site-packages/qiime-2.0.6-py3.5.egg/qiime/plugin/model/directory_format.py", line 104, in _validate_members
    self.pathspec))
ValueError: Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\\.fastq\\.gz'

Thanks for your help!

2

Hi @malenaamer! As of the latest 2017.2 release, we support importing single- and paired-end demultiplexed sequences in the Casava format. I highly recommend upgrading to 2017.2 if you're not already using that.

For examples of importing these types of sequence data, check out the importing tutorial. Since you joined the reads using an external program, you'll want to import your sequences as single-end (since QIIME 2 doesn't know any better).

However, if you plan to denoise your data with dada2 (e.g. qiime dada2 denoise-single or qiime dada2 denoise-paired), you'll get better results by not joining your reads. Instead, you'll want to import your unjoined reads using the paired-end Casava format, then denoise them using qiime dada2 denoise-paired.

Let us know if you're still having issues importing your data after checking out that tutorial and deciding whether you want to import joined or unjoined reads.

3

Thanks!
What is the difference between upgrading and updating?

4

That's described in the first paragraph of the doc I linked to. Please be sure to read the resources we link to before posting additional questions.