Manifest importing issue


(Xio Lee) #1


I encountered this issue when importing the manifest file in jupyter notebook:

!qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’
–input-path [email protected]_manifest.csv
–output-path qiime2_pipeline/16s/micro_16s_sequences.qza
–input-format PairedEndFastqManifestPhred33

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?

Many Thanks.

(Xio Lee) #2

I figured out. The sample id can not contain “/”, so I changed it to underscore. It is working now.