Hello, I am getting the same error message that was discussed here: Denoising and trimming already demultiplexed paired end data1
The error says:
Exception: No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>
However, I have tried creating a new manifest file in excel and I still get the same error when using [SequencesWithQuality]. When I try using [PairedEndSequencesWithQuality] I get a different error saying my manifest.csv file is not formatted as a PairedEndFastqManifestPhred33 file. The first few lines of my manifest file are:
sample-id absolute-filepath direction
27 /data/Desktop/mv_abund/QIIME2_babypoop/fastq/27_S25_L001_R1_001.fastq.gz forward
27 /data/Desktop/mv_abund/QIIME2_babypoop/fastq/27_S25_L001_R2_001.fastq.gz reverse
28 /data/Desktop/mv_abund/QIIME2_babypoop/fastq/28_S26_L001_R1_001.fastq.gz forward
28 /data/Desktop/mv_abund/QIIME2_babypoop/fastq/28_S26_L001_R2_001.fastq.gz reverse
I am using:
qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path manifest.csv --output-path paired-end-demux.qza --source-format PairedEndFastqManifestPhred33
Any feedback would be greatly appreciated.
Thank you,