deblur denoise-16S PACBIO

[coder]

environment : qiime2 2023.05 - docker-image
data:PACBIO sequel II
my command as follows:

qiime tools import           --type 'SampleData[SequencesWithQuality]'            --input-path ../input-path-list.tsv            --output-path ccs-data-demux.qza            --input-format SingleEndFastqManifestPhred33V2
qiime cutadapt trim-single --i-demultiplexed-sequences ../ccs-data-demux.qza --p-cores 4 --p-adapter RGYTACCTTGTTACGACTT --p-front AGRGTTYGATYMTGGCTCAG --o-trimmed-sequences ccs-data-cutadapt.qza --output-dir result
qiime deblur denoise-16S --i-demultiplexed-seqs ccs-data-cutadapt.qza --o-table deblur.table.qza --o-representative-sequences deblur.representative-sequences.qza --o-stats deblur.stat.qza --p-trim-length 10 --verbose

when i run those programm, something error information as follows:

File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/deblur/workflow.py", line 130, in trim_seqs
    for label, seq in input_seqs:
  File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/deblur/workflow.py", line 99, in sequence_generator
    for record in skbio.read(input_fp, format=format, **kw):
  File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/io/registry.py", line 506, in <genexpr>
    return (x for x in itertools.chain([next(gen)], gen))
  File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/io/registry.py", line 531, in _read_gen
    yield from reader(file, **kwargs)
  File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/io/registry.py", line 1008, in wrapped_reader
    yield from reader_function(fhs[-1], **kwargs)
  File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/io/format/fastq.py", line 351, in _fastq_to_generator
    phred_scores, seq_header = _parse_quality_scores(fh, len(seq),
  File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/io/format/fastq.py", line 522, in _parse_quality_scores
    _decode_qual_to_phred(chunk, variant=variant,
  File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/skbio/io/format/_base.py", line 34, in _decode_qual_to_phred
    raise ValueError("Decoded Phred score is out of range [%d, %d]."

this error information is ValueError: Decoded Phred score is out of range [0, 62] ,but data is correct when i import fastq data

[SoilRotifer (Mike Robeson)]

Hi @coder ,

I'll assume the first two commands ran successfully. I am also guessing that deblur is unable to handle PacBio data?

I'd suggest using the DADA2 CCS option, which is specific for denoising PacBio data:

qiime dada2 denoise-ccs ...