I am trying to run DADA2 using the below command, I have already run the previous step to get the demux-paired-end.qza, unfortunately I am stucked at the DADA2 and can not proceed, the system does not give me any error when I copy-paste the command, the curser blinks for few seconds and then stops... I waited for 10 hours because in my previous analysis (more than a year ago) this step took 9 hours on my mac. I uninstalled/installed Virtual box and qiime2 several times, freed space, etc... but nothing works..Please let me know if there is any solution to proceed. Thank you.
@salma_M,
can you save that log output and upload it so we can see it? You can use this command: cat /tmp/qiime2-q2cli-err-xo8m9xhw.log > ~/Desktop/dada2_error_log to save it to your desktop, and subsequently upload it.
You could also try running the command again with the --verbose flag set. But that might be a secondary step at this point. How big is your data? This is one of those operations that is dependent on the input dataset size, so sometimes it will just take a long time, which is not good if it is erroring out at the end .
@salma_M, can you run qiime info, conda list, and ls in the directory you are trying to run your commands + with your correct conda environment activated? It looks like it is having trouble finding your demultiplexed sequences and is spending a lot of time looking for them. Hopefully by letting QIIME 2 know exactly where they are we can get this working for you