I'm trying to import 102 standard, paired end fastq.gz files into the latest version in a MacOS environment. I've created my manifest file and I'm using the code below:
qiime tools import \
--type 'SampleData[SequencesWithQuality]’ \
--input-path manifest.tsv \
--output-path paired-end-demux.qza \
--input-format PairedEndFastqManifestPhred33V2
I get no error messages, everything appears to be running smoothly, but it never finishes. I've stopped and restarted is several times, let it run over night but nothing. When I check the activity monitor on my computer it appears that terminal is not using any CPUs either, regardless of if I just started the process or it's been several hours.
I re-ran some steps on an already analyzed dataset to make sure other parts of qiime2 were working and that ran perfectly fine.
Thanks for your help Colin. I replaced the curly quote and got an error message, which is progress, I guess?
None of the fastq files are empty and my manifest file is in the correct format.
Here is the new error message:
Traceback (most recent call last):
File "/Users/jenniferbell/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 156, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/Users/jenniferbell/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 277, in import_data
return cls.from_view(type, view, view_type, provenance_capture,
File "/Users/jenniferbell/miniconda3/envs/qiime2-2021.8/lib/python3.8/site-packages/qiime2/sdk/result.py", line 303, in _from_view
transformation = from_type.make_transformation(to_type,
File "/Users/jenniferbell/miniconda3/envs/qiime2-2021.8/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'>
I updated my conda environment and installed the newest version of qiime2 three days ago. Do you think I should uninstall and re-install? There were no installation errors.
Here's the issue: --type 'SampleData[SequencesWithQuality]' is for single-end reads, however you are listing the input format as PairedEndFastqManifestPhred33V2 which is for paired-end reads.
Check out the examples in the importing docs, and try something like