I encountered this issue when importing the manifest file in jupyter notebook:
!qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]'
--input-path [email protected]_manifest.csv
There was a problem importing [email protected]_manifest.csv: /tmp/q2-SingleLanePerSamplePairedEndFastqDirFmt-413rrait is not a(n) SingleLanePerSamplePairedEndFastqDirFmt: Contains a subdirectory: O148
I have a folder contains 16s reads and ITS reads together. I created a qiime2_pipeline folder with 2 sub directories for storing the output file. 2 manifest files for each 16s and ITS. They look as below.
[email protected]_manifest.csv (21.4 KB)
not sure why the format is not correct and why it says containing a subdirectory. Maybe I should separate the reads into two folders?