I was trying to import my fastq reads through a manifest file in WSL, q2cli version 2023.7.0
This is my manifest file
"sample-id forward-absolute-filepath reverse-absolute-filepath
E1T1 /home/alfa_ley/TFG/qiimefile/manifest_seqs/T1R1_1.fastq.gz /home/alfa_ley/TFG/qiimefile/manifest_seqs/T1R1_2.fastq.gz
E2T1 /home/alfa_ley/TFG/qiimefile/manifest_seqs/T1R2_1.fastq.gz /home/alfa_ley/TFG/qiimefile/manifest_seqs/T1R2_2.fastq.gz
E3T1 /home/alfa_ley/TFG/qiimefile/manifest_seqs/T1R3_1.fastq.gz /home/alfa_ley/TFG/qiimefile/manifest_seqs/T1R3_2.fastq.gz
E1T2 /home/alfa_ley/TFG/qiimefile/manifest_seqs/T2R1_1.fastq.gz /home/alfa_ley/TFG/qiimefile/manifest_seqs/T2R1_2.fastq.gz
E2T2 /home/alfa_ley/TFG/qiimefile/manifest_seqs/T2R2_1.fastq.gz /home/alfa_ley/TFG/qiimefile/manifest_seqs/T2R2_2.fastq.gz
E3T3 /home/alfa_ley/TFG/qiimefile/manifest_seqs/T2R3_1.fastq.gz /home/alfa_ley/TFG/qiimefile/manifest_seqs/T2R3_2.fastq.gz"
This is the command I ran
"qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path manifest_file.tsv --output-path single-end-demux.qza --input-format PairedEndFastqManifestPhred33V2"
And this is the error message I got
" File "/home/alfa_ley/miniconda3/envs/qiime2-OG/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 266, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/home/alfa_ley/miniconda3/envs/qiime2-OG/lib/python3.8/site-packages/qiime2/sdk/result.py", line 327, in import_data
return cls.from_view(type, view, view_type, provenance_capture,
File "/home/alfa_ley/miniconda3/envs/qiime2-OG/lib/python3.8/site-packages/qiime2/sdk/result.py", line 353, in _from_view
transformation = from_type.make_transformation(to_type,
File "/home/alfa_ley/miniconda3/envs/qiime2-OG/lib/python3.8/site-packages/qiime2/core/transform.py", line 58, in make_transformation
raise Exception("No transformation from %r to %r" %
Exception: No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33V2'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>
An unexpected error has occurred:
No transformation from <class 'q2_types.per_sample_sequences._format.PairedEndFastqManifestPhred33V2'> to <class 'q2_types.per_sample_sequences._format.SingleLanePerSampleSingleEndFastqDirFmt'>
See above for debug info."
I have checked the reads have a 33 Phred offset because they have ascii characters that are out of the range of 64 Phred offset. I am using differentiated forward and reverse reads. I am not sure what this error message means, so all help is welcome.