Importing Illumina 1.9 data to qiime2


(raw937) #1

Hello,

I have tested both commands:
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path pe_manifest --output-path pe_test.qza --input-format PairedEndFastqManifestPhred33

Hangs!

qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path pe_manifest --output-path pe_test.qza --input-format PairedEndFastqManifestPhred64

error

/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py:344: 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)
/opt/apps/conda/envs/qiime2/lib/python3.5/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 “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/q2cli/tools.py”, line 140, in import_data
view_type=input_format)
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 240, in import_data
return cls.from_view(type, view, view_type, provenance_capture)
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 265, in _from_view
result = transformation(view)
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/qiime2/core/transform.py”, line 70, in transformation
new_view = transformer(view)
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 346, in _9
single_end=False)
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 288, in _fastq_manifest_helper
fastq_copy_fn(input_fastq_fp, str(output_fastq_fp))
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/q2_types/per_sample_sequences/_transformer.py”, line 313, in _write_phred64_to_phred33
variant=‘illumina1.3’):
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/skbio/io/registry.py”, line 1161, in read
**kwargs)
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/skbio/io/registry.py”, line 506, in read
return (x for x in itertools.chain([next(gen)], gen))
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/skbio/io/registry.py”, line 531, in _read_gen
yield from reader(file, **kwargs)
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/skbio/io/registry.py”, line 1008, in wrapped_reader
yield from reader_function(fhs[-1], **kwargs)
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/skbio/io/format/fastq.py”, line 354, in _fastq_to_generator
qual_header)
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/skbio/io/format/fastq.py”, line 523, in _parse_quality_scores
phred_offset=phred_offset))
File “/opt/apps/conda/envs/qiime2/lib/python3.5/site-packages/skbio/io/format/_base.py”, line 34, in _decode_qual_to_phred
% (phred_range[0], phred_range[1]))
ValueError: Decoded Phred score is out of range [0, 62].

I think it is a newer 1.9 format? I can’t figure out why it isn’t importing.
pe_manifest paths are correct.

Help?


(Matthew Ryan Dillon) #2

What do you mean by this? This step can take a long time, depending on the size of your dataset. How long did you let it run?

This error means you are trying to import Phred33 offset data as Phred64 offset data in QIIME 2.

If you waited less than one hour importing the Phred33 data please try again and let us know! :qiime2: :t_rex: