Qiime dada2 denoise Error

User Support
1

Hi,everyone,i have some ploblems in qiime2 dada2 denoise-paired, i ran the following command

qiime dada2 denoise-paired
 --i-demultiplexed-seqs  Filename.qza 
--p-trunc-len-f 0 
--p-trunc-len-r 220 
--p-trim-left-f 18 
--p-trim-left-r 20 
--p-trunc-q 5 
--p-n-threads 3 
--o-table  Filename-table.qza
--o-representative-sequences  Filename-rep-seqs.qza 
--o-denoising-stats  Filename-denoisings-stats.qza

i had this error:
There was a problem with the command:
(1/1?) No such option: --p- (Possible options: --p-allow-one-off,
--p-chimera-method, --p-hashed-feature-ids, --p-max-ee-f, ...)

As i need to follow the workflow and proceed the taxonomic analysis, how can i fix this error ? Any idea
Thank you

2

Hi @Zeina,
it looks like there was a sneaky 'enter' or newline character between you --p- and one of your parameters?

would you mind re-typing the command and trying to run it again? If the error persists let me know!

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3

Thank you very much, it was like that.
Zeina

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4

Awesome! Glad we were able to figure it out!

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5

How long will this step take ? ?

6

Hi @Zeina,

Can you provide more context for your question (i.e. how long has the command been running, how much memory do you have on your machine, etc)? DADA2 runtimes will vary depending on the size of your dataset and the machine you're running QIIME 2 on.

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7

Hi, I executed the above command 2 days ago, I work on a server. I don't have big dataset ( 30 samples) .

I had this error :

Plugin error from dada2:

An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.

Debug info has been saved to /tmp/qiime2-q2cli-err-mfmailvp.log

8

This is a Linux code meaning a process was 'killed' or 'canceled' by the OS.

This often happens when there's not enough memory / RAM required to run a program.
This can also happen when a program uses more time than it was allocated in the queue.

Cool!

How much RAM was allocated to the DADA2 job?
How much time was allocated to the DADA2 job?

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9

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