DADA2 Denoise and dereplicate paired-end sequences

Running DADA2 on 16S HVR4 sequencing run (Illumina):

Files from all samples were imported into a single artifact using the following script in the CLI:
$qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path /home/qiime2/Desktop/Scowden/Fecal_analysis/
--source-format CasavaOneEightSingleLanePerSampleDirFmt --output-path Fecal-demux-paired-end.qza

Created a visualization (.qzv) from this - data looks ok

When I try and execute DADA2 through q2studio - it seems to hang. The zipped .qza file is ~128MB...total number of sequences across 9 libraries is ~430K. I let DADA2 chew on it for ~3 hours and then clicked on the link below 'Action' pictured below
image

The window brought up shows this:

This makes it look like my analysis is dead, but the ticker (Time Elapsed) on the Active Jobs keeps rolling. What's going on?

Thanks
S

Hey @Sausage_Mahoney,

I don’t think your job has failed yet, the denoising process can just take a while sometimes.

It should show up in the failed tab if something does go wrong. But your screenshots look normal to me. Outputs are null because they don’t exist yet, and you probably won’t see the stdout/stderr until the job finishes or fails.

You can ignore Job Code, that’s what’s actually running, and is kind of leftover from some much earlier ideas of how QIIME 2 would work.

2 Likes

Roger that - thanks for the quick reply!!

S

1 Like

Update here - script executed - required approximately 12 hours to complete…but it’s done!
Thanks again
S

2 Likes

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