I am having some trouble with importing my fastq files for dada2 denoising. I am able to create the “paired-end-demux.qza” file, but get an error message when working with this file. For example, when running “qiime demux summarize” I get the error: " ‘utf-8’ codec can’t decode byte 0xf8 in position 4099: invalid start byte" (full error message is pasted below). I see from the forum that this may have something to do with my manifest file, but I’m out of ideas with what it could be, and my manifest file was copied from a previous manifest file that worked fine. I have also tried removing all but one pair of fastq files (forward and reverse), to determine if it was an error with one of those files.
I tried running this in Qiime 2018-11 as well as 2018.8. I am using Virutal Box.
Thanks for an ideas.
Bill
Commands:
qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path pe-33-manifest.txt --output-path paired-end-demux.qza --input-format PairedEndFastqManifestPhred33
qiime demux summarize --i-data paired-end-demux.qza --o-visualization demux.qzv
Plugin error from demux:
‘utf-8’ codec can’t decode byte 0xf8 in position 4099: invalid start byte
Debug info has been saved to /tmp/qiime2-q2cli-err-_r505b82.log
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in summarize
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 424, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_demux/_summarize/_visualizer.py”, line 131, in summarize
for seq in _read_fastq_seqs(file):
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_demux/_demux.py”, line 34, in _read_fastq_seqs
for seq_header, seq, qual_header, qual in itertools.zip_longest(*[fh] * 4):
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/codecs.py”, line 321, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: ‘utf-8’ codec can’t decode byte 0xf8 in position 4099: invalid start byte