Greeting Qiime hive mind,
I'm having an issue importing demultiplex reads using the fastq-manifest.
System: Ubuntu 20.04.6 LTS
Qiime Version: q2cli version 2023.5.1
Installed via conda
This is the command I was running
qiime tools import \
--type 'SampleData[SequencesWithQuality]' \
--input-path LS23-4703_pe-33-mainfest.txt \
--output-path paired-end-demux.qza \
--input-format PairedEndFastqManifestPhred33V2
this is the current format for the manifest file.
sample-id absolute-filepath direction
LS23-5403-1 $PWD/data/LS23-5403-1-16s_S1_L001_R1_001.fastq.gz forward
LS23-5403-1 $PWD/data/LS23-5403-1-16s_S1_L001_R2_001.fastq.gz reverse
I also tried with the forward-absolute-filepath and reverse-absolute-filepath format and received the same error.
error message:
Traceback (most recent call last):
File "/home/rnd/miniconda3/envs/qiime2-2023.5/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/rnd/miniconda3/envs/qiime2-2023.5/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/rnd/miniconda3/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/result.py", line 353, in _from_view
transformation = from_type.make_transformation(to_type,
File "/home/rnd/miniconda3/envs/qiime2-2023.5/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 did try to run this command with the --verbose flag but received an error saying no such option: --verbose
I'm not sure if the error is becasue it wants to make my paired end data single end and can't or (more likely) I choose the wrong option. I have tried using the more abstract FastqGZFormat as well and get the same error.
If anyone can point me in a direction I would appreciate it.
Thank you,
Sean