Importing fastq files

[marymary (Mary)]

Hi. I am trying to import paired end reads into QIIME2. My files are in name.fz.bz2 format, so I unzipped them and inserted them in the folder /project-1-reads/ as project1_R1.fastq and project1_R2.fastq. My manifest file (project-1-manifest.csv), which I generated in excel as a csv file is

sample-id,absolute-filepath,direction
project-1,$PWD/project-1-reads/project1_R1.fastq,forward
project-1,$PWD/project-1-reads/project1_R2.fastq,reverse

I also unzipped my barcodes file and saved it as barcodes.fastq

My code in the terminal is:

qiime tools import \
  --type 'SampleData[SequencesWithQuality]' \
  --input-path project-1-manifest.csv \
  --output-path paired-end-demux.qza \
  --source-format PairedEndFastqManifestPhred33

I am getting the following error:
An unexpected error has occurred:

  No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>

Can you help me figure out what I did wrong?
Thanks!

[Mehrbod_Estaki]

Hi @marymary,
It looks like you are trying to import paired end reads but your input command is referring to a single-end type.
Try changing your
--type 'SampleData[SequencesWithQuality]'
to
--type 'SampleData[PairedEndSequencesWithQuality]'

I’m thinking that will do the trick?

[marymary (Mary)]

Thank you. That solved the problem.