DADA2 Issue with R

[basilin_benson]

I tried running DADA2 but keeps throwing me the error stated below:
Plugin error from dada2:

An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

Debug info has been saved to /tmp/qiime2-q2cli-err-e4i52m_r.log

I have attached the error log filedebug.txt (2.4 KB)
Help would be appreciated

[colinbrislawn (Colin J Brislawn)]

Good afternoon,

Thanks for posting your log file! Inside, I found these important lines:

2) Learning Error Rates
Error: cannot allocate vector of size 11.7 Gb
Execution halted
Warning message:
system call failed: Cannot allocate memory 

It looks like you don’t have enough RAM / memory to run this command.

My first suggestion would be to run this command with a smaller value for --p-n-reads-learn (it’s 1000000 by default). This could let you get through this step.

Let me know if that helps,
Colin

[jairideout (Jai Ram Rideout)]

Hi @basilin_benson! Adding to @colinbrislawn's reply, you might take a look at @thermokarst's suggestions here for getting access to more system memory:

DADA2 paired end denoising step error

Hi @slh277! As the error says, it looks like your machine is running out of memory. Unfortunately, there aren’t many other options in this situation other than somewhere procuring more memory. If you are running this on an institutional cluster, perhaps you can request a node with more memory. If you are running in a Virtualbox VM you could try increasing the allocated RAM to the VM. If you don’t have any machines available to you with more memory, you can always check out our QIIME 2 AWS Mach…

Could you also share the exact command you're running? That might shed some light on why you're running out of memory. Thanks!

[basilin_benson]

Hi,
Thank you for the prompt reply. As said above my my system did not have enough memory to run so I will be running it on an institutional cluster soon. Will update on the status soon.