DADA2 in R (return code 1) error

[Nicholas_Bokulich]

Hi @joe0750,
Here is the key line in the error message:

@joe0750

system call failed: Cannot allocate memory

Have you searched the archive for this error message or just for return code 1? Search results for 'system call failed: Cannot allocate memory' - QIIME 2 Forum

I recommend reading over those topics. This is almost always a hardware issue, though you may be able to mitigate in some ways, e.g., see here:

DADA2 Issue with R

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, …

DADA2 error : Cannot allocate memory error in denoising step

How many samples are in this dataset? And what is the sequencing technology? My suspicion is that one very large or very noisy (or both) sample is exceeding the 16GB of memory even when dereplicated. This can happen when there are a very large number of unique sequences, as it is that number, not the raw number of reads, that controls the peak memory requirements.