songbird troubleshooting


I am trying to run explore if there are any differences between taxonomy between two clinical groups (weight gain and weight loss). I read the songbird tutorial on github but not sure I fully understand what to write for the command as it’s not working.
I’m using QIIME2-2020.2

This is the command I’m writing (please see my questions after the ## for each of the lines):

qiime songbird multinomial \
    --i-table filtered-allpaired.qza \  (### *that is my feature table after I filtered low abundance features)*
    --m-metadata-file  metadata.tsv \ *(## can my metadata contain blanks for the WeightChangeCategory column or do I need to filter in advance)*
    --p-formula "Wt_chng_category" \  (*### As I said, I'm tying to explore whether taxons differ between the two weight change cateogries. Is that where I enter this variable)*
    --p-epochs 10000 \ (*## do I change this number?Not sure I really understand what this represents?? I know that this number means how long I need to run Songbird, but again not sure I grasp the meaning for this)*
    --p-differential-prior 0.5 \ *(### again not sure I know what that means and if I need to change it?)*
    --p-summary-interval 1 \ (### again not sure I know what that means and if I need to change it?)
    --p-training-column Training \
    --o-differentials differentials.qza \
    --o-regression-stats regression-stats.qza \
    --o-regression-biplot regression-biplot.qza

Thank you so much in advance!

Hi @rnasrah,
I’ve moved your post to community plugin support, because q2-songbird is a community plugin. I haven’t used songbird and may not be able to help here. In order for anyone to respond to an error message question, you’ll need to include a complete copy-paste of the error message.

It seems like many of your questions are general questions about what parameters are and how they work. Have you read the songbird paper or readme?

Chris :honeybee:

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.