Thanks a lot @SoilRotifer!
I think I'm moving forward...
So, I decide to use the manifest format to import the data, using SingleEndFastqManifestPhred33V2.
Here is my manifest.tsv file:
single-end PHRED 33 fastq manifest file for forward reads
sample-id absolute-filepath
sample-BB12S_69 gecele/sample-BB12S_69_R1.fastq.gz
sample-BB20S_53 gecele/sample-BB20S_53_R1.fastq.gz
sample-BB24S_55 gecele/sample-BB24S_55_R1.fastq.gz
sample-BB4S_65 gecele/sample-BB4S_65_R1.fastq.gz
sample-BB8S_47 gecele/sample-BB8S_47_R1.fastq.gz
sample-BB16S_38 gecele/sample-BB16S_38_R1.fastq.gz
sample-DE7S_32 gecele/sample-DE7S_32_R1.fastq.gz
sample-DM11S_36 gecele/sample-DM11S_36_R1.fastq.gz
sample-DM15S_49 gecele/sample-DM15S_49_R1.fastq.gz
sample-DM19S_52 gecele/sample-DM19S_52_R1.fastq.gz
sample-DM23S_40 gecele/sample-DM23S_40_R1.fastq.gz
sample-DM3S_42 gecele/sample-DM3S_42_R1.fastq.gz
The command I used was:
(qiime2-2021.11) [email protected]:~/projects/Microbioma/drive3$ qiime tools import \
--type 'SampleData[SequencesWithQuality]'
--input-path manifestbro1.tsv
--output-path solodemux.qza
--input-format SingleEndFastqManifestPhred33V2
And I got this...
Traceback (most recent call last):
File "/home/bio/software/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 157, in import_data
artifact = qiime2.sdk.Artifact.import_data(type, input_path,
File "/home/bio/software/miniconda3/envs/qiime2-2021.11/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 "/home/bio/software/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/result.py", line 305, in _from_view
result = transformation(view, validate_level)
File "/home/bio/software/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/home/bio/software/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_types/per_sample_sequences/_transformer.py", line 219, in _23
return _fastq_manifest_helper_partial(old_fmt, _copy_with_compression,
File "/home/bio/software/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_types/per_sample_sequences/_util.py", line 233, in _fastq_manifest_helper
input_manifest = _parse_and_validate_manifest(
File "/home/bio/software/miniconda3/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_types/per_sample_sequences/_util.py", line 108, in _parse_and_validate_manifest
raise ValueError('All paths provided in manifest must be '
ValueError: All paths provided in manifest must be absolute but found relative path: gecele/sample-BB12S_69_R1.fastq.gz
An unexpected error has occurred:
All paths provided in manifest must be absolute but found relative path: gecele/sample-BB12S_69_R1.fastq.gz
See above for debug info.
So, apparently, I have to adjust the filepath in my manifest file...
But how???
Thanks