Manifest Import Issue

[Biancabrown]

Hello,

I have an issue with importing my fastq files into the qiime format using the manifest option. .

Error Message

module: loading 'anaconda/3-4.4.0'
Traceback (most recent call last):
  File "/users/bbrown3/anaconda/qiime2-2017.8/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/users/bbrown3/anaconda/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 "/users/bbrown3/anaconda/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 "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/q2cli/tools.py", line 111, in import_data
    view_type=source_format)
  File "/users/bbrown3/anaconda/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 "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/result.py", line 217, in _from_view
    result = transformation(view)
  File "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/qiime2/core/transform.py", line 59, in transformation
    new_view = transformer(view)
  File "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py", line 336, in _8
    single_end=False)
  File "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py", line 266, in _fastq_manifest_helper
    absolute=True)
  File "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py", line 156, in _parse_and_validate_manifest
    _validate_paired_end_fastq_manifest_directions(manifest)
  File "/users/bbrown3/anaconda/qiime2-2017.8/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py", line 209, in _validate_paired_end_fastq_manifest_directions
    '"reverse", but observed: %s' % direction)
ValueError: Directions can only be "forward" or "reverse", but observed: reverse`Preformatted text`

Qiime code:

qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path $PWD/scripts/pe-33-manifest.txt --source-format PairedEndFastqManifestPhred33 --output-path $PWD/demux-paired-end.qza 

Below is the text file that that I use:

sample-id,absolute-filepath,direction
BB1,fastq/BB1_01_L001_R1_001.fastq,forward
BB1,fastq/BB1_01_L001_R2_001.fastq,reverse
BB10,/fastq/BB10_06_L001_R1_001.fastq,forward
BB10,/fastq/BB10_06_L001_R2_001.fastq,reverse

Any suggestions on how to fix this?

[thermokarst]

Hi @Biancabrown!

The error message you provided above says that in the last column it observed a value of

reverse`Preformatted text`

It looks to me like one of your entries in your manifest might not be reverse or forward in the direction column.

Would it be possible for you to copy-and-paste or attach your complete manifest file here? The sample you provided is invalid, too, but for different reasons (there are relative filepaths listed there, instead of absolute filepaths).

Thanks!

[Biancabrown]

Hi @thermokarst this worked great. I had black a space at the end of one of the reverse.
Thanks!