only table.qza after dada2

[ljy0676 (fairy)]

Hi all,
I used this command below to control quality of my 24 samples (including 16s and ITS):

qiime dada2 denoise-paired
–i-demultiplexed-seqs paired-end-demux.qza
–p-trunc-len-f 240 --p-trunc-len-r 240 --p-trim-left-f 20 --p-trim-left-r 20
–o-representative-sequences rep-seqs-dada2.qza
–o-table table-dada2.qza
–o-denoising-stats stats-dada2.qza

But I only got “table-dada2.qza” after the command finished. There were no "rep-seqs-dada2.qza "
and “stats-dada2.qza” file.

However, after that I only choose 2 from 24 samples , used same command to control quality . This time, all the files are avaliable in the end, including table.qza, rep-seqs.qza et al…
I do not know which step is fault.

Thank you so much for your answer.

[Nicholas_Bokulich]

Hi @ljy0676,
We have seen this reported just a couple times before — not sure why it occurs, but it sounds like sometimes q2-dada2 crashes between outputting the first and second files.

See here for some info and steps to troubleshoot:

Missing dada2 Output with and without &

Hello, I have read through a previous post with a similar topic name but didn’t find how the issue was resolved. I have tried to run dada2 several times using the following: qiime dada2 denoise-paired –i-demultiplexed-seqs seqs.qza –p-trim-left-f 0 –p-trim-left-r 0 –p-trunc-len-f 299 –p-trunc-len-r 256 –o-table table.qza –o-representative-sequences rep_seqs.qza –o-denoising-stats denoising_stats.qza I have run it both with and without & on the end. Every time I have run it eith…

Let us know if that helps!