Hi @ameliak
I have a completed history here with the tutorial data here run through the tutorial’s workflow. Maybe you can compare the usage and notice where things are different?
- https://usegalaxy.org/u/jen-galaxyproject/h/training-16s-rrna-sequencing-with-mothur-main-tutorial-5
This is the filter step to help you navigate the history.
These are the statistics from the log.
Length of filtered alignment: 376
Number of columns removed: 13049
Length of the original alignment: 13425
Number of sequences used to construct filter: 16298
As a pure guess, you could seems to be based on the number of 16s reads that are used with this pipeline, not the smaller list of assemblies from the earlier steps (mothur align.seqs output).
Hope this helps! 