My computer has a icore 7 processor, and an 8GB RAM, even though I try to run the DADA2 program with the following command:
$ qiime dada2 denoise-paired
–i-demultiplexed-seqs 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 280
–p-trunc-len-r 260
–p-n-threads 0
It locks
Hi @Nasute,
Can you clarify what you mean by “It locks”? Does the computer freeze or do you just mean the operation seems to take a long time. It’s hard to answer exactly how long DADA2 takes or how much RAM it needs but from experience, 8Gig should be enough for most general projects, unless you’re analyzing a massive dataset. Even then I imagine you wouldn’t run into any problems other than it might just take a very long time.
A few additional questions, are you using a VirtualBox to run an image of qiime2? If so you want to check how much of your system’s memory is dedicated to the VM, so while you may have 8 Gig in your actual computer, you might allocating a lot less RAM (and maybe limited cores) to the VM itself.
How big is the file you are trying to denoise? How many reads and how many samples?
Lastly, I would try running your command with the “–verbose” tag to see if the program is running or it has indeed for some reason locked, as you suggested.
DADA2 can take a very long time depending on many factors, so you should anticipate some long wait times.
Thank you very much for your answer
Responding to your previous message
Can you clarify what you mean by “It locks”? Basically the machine goes into suspension with the screen on, that is, I can not execute any other activity while the computer is running the DADA2 program
Are you using a VirtualBox to run an image of qiime2? No, I’m using Ubuntu and I run the analyzes through a command line.
How big is the file you are trying to denoise? The summary that showed me the subsequent visualization to use the function “Demultiplexing sequences” was about 230000 sequences.
How many reads and how many samples? I am trying to process a raw database that comes from a MiSeq analysis with illumina and I throw a forward of 300 bp and Reverse of 300 bp, for a total of 4 samples
I will try to execute the last command that you suggest
Hi @Nasute,
That’s actually a fairly small dataset you are trying to denoise so it shouldn’t take too long… of course that’s dependent on your processor, how many cores you have available on your system etc.
What you are describing as ‘locked up’ is actually normal. As long as the last operation you entered is still running you won’t be able to run any other. With the --verbose tag you’ll see some more information as DADA2 is running but you still won’t be able to perform any other operations (again, totally normal). Just let it run until it completes or perhaps you’ll get an error which then we can trouble-shoot further.
Good luck!
2 off-topic replies have been split into a new topic: Memory considerations
Please keep replies on-topic in the future.
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.