PacBio Data Import PHRED

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.

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?


This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.