Very long time importing fastq files with Phred64

#1

Hi,

I am trying to import my data with phred64 offset, however, it is taking a very long time even when I try with just two files (forward and reverse). I have attached my manifest file and shared the link for the mentioned fastq files.

I am using qiime2-2019.7, with this command :

qiime tools import
–type 'SampleData[PairedEndSequencesWithQuality]
–input-path manifest_toy.tsv
–output-path paired-end-demux_toy.qza
–input-format PairedEndFastqManifestPhred64V2

manifest_toy.tsv (104 Bytes)
files : https://drive.google.com/open?id=1I6EmDhfmHP5eEg1J-yIW9yY6oQB-WJvC

I was wondering if this is expected?

Thanks in advance,
Parizad

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#2

Yep, I think so! This is a pretty intensive process, since the import converts from PHRED 64 to PHRED 33. Just let it cook for a while :stew:!

:t_rex:

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#3

Alright! :slight_smile:
Would it be help if I convert Phred64 to 33 before importing or will it be basically the same thing?
I was also curious if working on cluster would increase the speed of this process?

#4

It will be exactly the same thing.

No, I doubt it — this process can’t be parallelized (yet) in QIIME 2. Just let it cook.

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