Can anyone help me in truncating sequences with qiime dada2 denoise-paired \?

Dear All,
After getting demux.qzv file and viewing the sequence quality at I tried to cut the sequences using the following message:

Qiime-dada2 denoise-paired
--i-demultiplexed-seqs aqleem12-paired-end-demux.qza
--o-table table
--o-representative-sequences rep-seqs
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 300
--p-trunc-len-r 300

However I got --o--denoising stats missing. I could not understand and solve the problem. Could anyone help me out? I also attached the error text with this message.

Aqleem Abbas

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Hi @Aqleem12,

The error seems to indicate that it is looking for you to direct it to a filepath for dada2 to store its stats summary artifact. Your 2 options are to include
--denoising-stats example/filepath
to your parameters list or include

--output-dir directoryname

instead of the individual

--o-table, --o-representative-sequences, and --odenoising-stats parameters


Thank you Mehrbod for correction. Could you also tell, how much time it will take for bacteria and fungi?

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Hi @Aqleem12,

Glad it was useful. It’s hard to predict dada2 run time as it depends on many factors including: how much memory you’ve dedicated to the task, how many cores are available, your processor speed, how many samples and reads are being denoised, how long the reads are etc. From personal experience for a small-medium data set, I would recommend dedicating a minimum of 6G memory, and 4 cores (use the --p-n-threads option), the more the better obviously. The process can still take a long time to complete however, I usually let this step run over night. Lower values may still work but then you run the risk of running into memory issues with dada2 which are frequently reported on the forum. Hope that helps!

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