Hi, I am importing a single sample from a pair end shotgun sequencing run. I managed to import without error using the following code, however, in the files generated in the cache I cannot find any qza files with which I can continue the pipeline (ie, check quality and trim reads ect.) Specifically, the next steps use ./cache:reads but I can't see that among the files generated during import.
Just an FYI, if you work via the cache system, no QZAs will be made. The idea is to avoid zipping and unzipping large files, every time a command is run. This can waste a lot of time. So the cache system allows you to work quickly by bypassing this step for all your analyses. You can of course export any of the cached files to a qza files. See the actions within mosh tools cache-fetch ... and the other cache-* actions.
Thanks for the information. I didn't explain myself well - I don't necessarily need qza files, I'm just trying to follow the moshpit docs with my own data. I figured out why my reads where not showing up in the imported data, it's because I used the wrong key. I should have used --key reads
Once I fixed that, it worked fine.