DADA2 error (return code -9) and (return code 1)


(Sin Li Jiao) #1

Hi,

I am using QIIME2 2019.1 on virtualbox.
I was running DADA2 when I encountered the following errors:

qiime dada2 denoise-paired \

–i-demultiplexed-seqs demux-paired-end.qza
–p-trim-left-f 6
–p-trim-left-r 6
–p-trunc-len-f 200
–p-trunc-len-r 220
–o-table table-dada2.qza
–o-representative-sequences rep-seqs-dada2.qza
–o-denoising-stats denoising-stats.qza
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-_kcduaha.log

After which I tried to run it again with different p-trim-left values.

qiime dada2 denoise-paired \

–i-demultiplexed-seqs demux-paired-end.qza
–p-trim-left-f 0
–p-trim-left-r 0
–p-trunc-len-f 200
–p-trunc-len-r 220
–o-table table-dada2.qza
–o-representative-sequences rep-seqs-dada2.qza
–o-denoising-stats denoising-stats.qza
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-oog8x06p.log

Does anyone know what is causing these errors?


(Nicholas Bokulich) #2

@LiJiao,
Return code -9 is a memory error — your computer is running out of memory and you will need to find a more powerful machine.

Return code -1 can mean a variety of things and you will need to provide the full error message to learn more (use the --verbose flag when you run your command to see the full error log).

Both of these errors have been reported frequently and you can troubleshoot by searching the forum archive. For example, see:

Good luck!