Importing demultiplexed fastq data into qiime2 and --source-format error

[Daniela_Vargas (Daniela Vargas Robles)]

Hello to all,
I am trying to import my demultiplexed fastq data into qiime2. However, I am having troubles.

My sequences format:

>@M01380:50:000000000-AV1DH:1:1101:8541:2802 1:N:0:871:16S_V1V3 TTCTGCCT|0|ACTGCATA|0 CS1_534R_Chl_for|1|28|
GACGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAGCGAGTCTGCCTTGAAGATCGGAGTGCTTGCACTCTGTGAAACAAGATACAGGCTAGCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCCAAGAGATCGGGATAACACCTGGAAACAGATGCTAATACCGGATAACAACAGATGATGCCTATCAACTGTTTAAAAGATGGTTCTGCTATCACTCTTGGATGGACCTGCGGTGCATTAGCTAGTTGGTAGGGTAACGGCCTAC
+
GGGEGGG+7FCCGGEGDGEEGGGGGFGGGGGGGGGGDGGGGGEGGGGGGGGCFG,,5CCFFEEGGGGGGGGGGGG9E9EFGGGGGGGGGGFGGGGGGGGGEGGGEGGGGGGGGGGGGCEFGGGGGGGCC7<FCAFGGFGGGGE77CFGGGGGFFFF?FGGCGEFGGGGCFEGGGGC6FGFFGGFFGGC+<<@C?+<89C?+7?FF?CGFGDCD7=77DC7@GGCG>>=6609376@**8>DEDB96@4@:66)76B72<21340:?016(84)

Manifest csv file for :

311,Users/xx/xx/pe-manifest/311-r1.fastq,forward
311,Users/xx/xx/pe-manifest/311-r2.fastq,reverse
...

Used script:

> qiime tools import \
>   --type SampleData[PairedEndSequencesWithQuality] \
>   --input-path pe-manifest1.csv \
>   --output-path paired-end-demux.qza \
>   --source-format PairedEndFastqManifestPhred64

Yielded error:

Traceback (most recent call last):
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/bin/qiime", line 6, in <module>
    sys.exit(q2cli.__main__.qiime())
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/q2cli/tools.py", line 111, in import_data
    view_type=source_format)
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/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/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/sdk/result.py", line 217, in _from_view
    result = transformation(view)
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/core/transform.py", line 57, in transformation
    self.validate(view)
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/core/transform.py", line 131, in validate
    view.validate()
  File "/Users/danielavargasrobles/miniconda3/envs/qiime2-2017.6/lib/python3.5/site-packages/qiime2/plugin/model/file_format.py", line 31, in validate
    % (self.path, self.__class__.__name__))
ValueError: InPath('pe-manifest1.csv') is not formatted as a PairedEndFastqManifestPhred64 file.

I also tried with Phred33 format since I am not sure which one is mine.

I can’t find the error with the format I am using…

Thanks for your help!

Daniela

[ebolyen (Evan Bolyen)]

Hey @Daniela_Vargas,

I think you may just be missing your header line. Make sure the first line of your .csv file matches:

sample-id,absolute-filepath,direction

[Daniela_Vargas (Daniela Vargas Robles)]

Thanks @ebolyen for your response

I actually did not have the appropriated header however fixing it did not solved it. I get the sale error

Any other idea?

Thanks for trying!

[thermokarst]

@Daniela_Vargas: it looks like your filepaths are not absolute filepaths, that might be the problem!

Example:

Users/xx/xx/pe-manifest/311-r1.fastq

change to

/Users/xx/xx/pe-manifest/311-r1.fastq

Note the / at the beginning of the path. Hope that helps!