Dada2 denoise-paired run time too long?

I am trying to run Dada2 denoise-paired for more than 12 hours using several theads with a subsample of 16 samples. My real set consists of 350 samples. currently using 425 % CPU :confused: I imported the demultiplexed files like this:

qiime tools import **

--type 'SampleData[PairedEndSequencesWithQuality]' **

--input-path “mypath” **

--output-path bobcat_sas_paired-end-demux.qza **

--source-format PairedEndFastqManifestPhred33

The 16 samples are ~4,5 Gb and the resulting .qza file is 981M.

I inspected the file:


And then ran

(qiime2-2018.6) ubuntu@aerosol0:~/mdw/Line_files$ qiime dada2 denoise-paired \

--i-demultiplexed-seqs bobcat_sas_paired-end-demux.qza \

--o-table bobcatsastable.qza \

--o-representative-sequences bobcatsas_rep-seqs.qza \

--o-denoising-stats bobcatsas_denoising-stats.qza

--verbose --p-n-threads 0 --p-trunc-len-r 0 --p-trunc-len-f 0

Unfortunately the remote conncetion broke, so I am not seeing any output from verbose, however dada2 is still running, based on other reports, it seems like the running time is unusually long. What can I expect for the run time for the large set of 350 samples? Could it be something with the import to qiime? any suggestions would be helpful.

An off-topic reply has been merged into an existing topic: Dada2 denoise-paired running time over 12 hours for 16 samples

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