PacBio Data Import PHRED

import

#1

Dear QIIME2 team,

I have a problem importing my PacBio fastq files into qiime2. I am trying with the manifest format, but whenever I run the command:

qiime tools import
–type ‘SampleData[SequencesWithQuality]’
–input-path /***/_test/se-64-manifest.gz
–output-path /***/_test/single-end-demux64.qza
–input-format SingleEndFastqManifestPhred64

I get a long error message, at the end saying:

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.

Any ideas how I can solve this problem? I would really love to try and analyze my data with qiime2. I am grateful for any support.


(Devon O'rourke) #2

My first thought is that it’s not a Phred64 encoding, but Phred33. Having not used PacBio data before I could be totally wrong, but this thread from my first Google search indicates that might be where you’re getting stuck?