while running dada 2 denoise paired, after houres i got this error message:
An error was encountered while running DADA in R (retutn code -9) please inspect stdout and stderr to learn more.
Debug info has been saved to/tmp/qiime2-q2cli-err-tqlt65uy.log
What @Deni_Ribicic meant was that you need to show us the contents of the debug file.
When your run failed, a log file was created “Debing info has been saved to /tmp/qiime2-q2cli-err-tqlt65uy.log”.
Run the command (without the quotations) “cat /tmp/qiime2-q2cli-err-tqlt65uy.log”, it should print everything in the log file on your screen and post the results so we can have a better idea of what went wrong.
As a side note, @Zeina, details on what operating system and what version of QIIME 2 you’re using often helps people diagnose issues. Looks like that screen capture is from q2-2019.4 running on a linux machine?
@Zeina, I had this issue a while ago when I first started using Qiime2. Basically, your computer is running out of memory while Dada2 is denoising the sequences. This can happen if you are trying to work on a large dataset, or your computer has a small amount of RAM. How are you running Qiime2? If it is through Docker, you may need to give it more of your RAM to use. If not, you may have to find a different computer to analyze your data with.
Alternatively, you could break your data up into smaller chunks and analyze a handful of samples at one time (instead of all at once). The authors of Dada2 claim you can do this without losing meaningful sensitivity, but I’m not sure if this has been directly tested. Someone with more working knowledge on this particular topic is welcome to correct me.