Hi,
I am trying to import data.
Unfortunately, I’ve run into an issue and I’m not sure how to deal with it.
I’m running qiime2-2020.2.
The details are as follows:
nohup qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /mnt/weicai/workplace-life/QIIME2/sequences/manifest --output-path /mnt/weicai/workplace-life/QIIME2/Artifact/paired-end-demux.qza --input-format PairedEndFastqManifestPhred64V2 &
/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py:451: UserWarning: Importing of PHRED 64 data is slow as it is converted internally to PHRED
33. Working with the imported data will not be slower than working with PHRED 33 data.
warnings.warn(_phred64_warning)
/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/io/registry.py:557: ArgumentOverrideWarning: Best guess was: variant='illumina1.8', continuing with user supplied: 'illumina1.3'
ArgumentOverrideWarning)
Traceback (most recent call last):
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 158, in import_data
view_type=input_format)
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/result.py", line 241, in import_data
validate_level='max')
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/result.py", line 267, in _from_view
result = transformation(view, validate_level)
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py", line 454, in _26
single_end=False)
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py", line 299, in _fastq_manifest_helper
fastq_copy_fn(input_fastq_fp, str(output_fastq_fp))
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_types/per_sample_sequences/_transformer.py", line 324, in _write_phred64_to_phred33
variant='illumina1.3'):
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/io/registry.py", line 1161, in read
**kwargs)
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/io/registry.py", line 506, in read
return (x for x in itertools.chain([next(gen)], gen))
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/io/registry.py", line 531, in _read_gen
yield from reader(file, **kwargs)
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/io/registry.py", line 1008, in wrapped_reader
yield from reader_function(fhs[-1], **kwargs)
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/io/format/fastq.py", line 354, in _fastq_to_generator
qual_header)
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/io/format/fastq.py", line 523, in _parse_quality_scores
phred_offset=phred_offset))
File "/home/weicai/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/skbio/io/format/_base.py", line 35, in _decode_qual_to_phred
% (phred_range[0], phred_range[1]))
ValueError: Decoded Phred score is out of range [0, 62].
An unexpected error has occurred:
Decoded Phred score is out of range [0, 62].
See above for debug info.
Thank you for your help.
