I am having an issue with importing my fastq data. I am using the 2017.7 form of QIIME 2.
I am using this as a practice run for when I have the full of my data. My files are under a directory still in their .gz format. The command I have been using to import them is
qiime tools import \ --type SampleData[PairedEndSequencesWithQuality]' \ --input-path import_file_fastq.txt \ --output-path paired-end-demux.qza \ --source-format PairedEndFastqManifestPhred33
However I am not sure if it is the correct one to use.
The error I have been receiving is:
return cls._from_view(type_, view, view_type, provenance_capture) File "/mnt/lustre/software/anaconda/colsa/envs/qiime2-2017.7/lib/python3.5/site-packages/qiime2/sdk/$ result = transformation(view) File "/mnt/lustre/software/anaconda/colsa/envs/qiime2-2017.7/lib/python3.5/site-packages/qiime2/core$ self.validate(view) File "/mnt/lustre/software/anaconda/colsa/envs/qiime2-2017.7/lib/python3.5/site-packages/qiime2/core$ view.validate() File "/mnt/lustre/software/anaconda/colsa/envs/qiime2-2017.7/lib/python3.5/site-packages/qiime2/plug$ % (self.path, self.__class__.__name__)) ValueError: InPath('import_file_fastq.txt') is not formatted as a PairedEndFastqManifestPhred33 file.
I have followed how to do the manifest file form the importing tutorial, but I am unsure of what I am doing wrong. Attached is the file I am currently using. It's written through excel-->notepad. Import_file_fastq.txt (4.0 KB)
It's a .txt file and I don't know if that's the reason it's not being formatted correctly, but I have also tried a .csv file and it did not work either. Any help is appreciated.