Hello, everyone,
I started analysis on qiime2 but I have problems with qiime dada2 denoise-paired (cmd=qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --o-table table.qza --o-representative-sequences rep-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 200 --p-trunc-len-r 200), after running for about 2hours, this error presented itself:
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-wk2njlcu.log
I use qiime2 2018.2 on virtualbox.
Help me please.
Thanks
Thank you for your assistance,
The file /tmp/qiime2-q2cli-err-wk2njlcu.log? does not exist.
Then I re-run the command as you suggest.
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --o-table table.qza --o-representative-sequences rep-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 200 --p-trunc-len-r 200 --verbose
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
That error code indicates that your machine is running out of memory, causing dada2 to fail. Please see here or search the forum archive for some more details on alternative approaches.
Sorry I can't give a more satisfying answer! Memory issues can be difficult to overcome but in this case is an issue with the hardware, not the software.