Missing feature in feature-table filter-seqs output

[jairideout (Jai Ram Rideout)]

@Nicholas_Bokulich

It looks like the issue is that your features-to-retain.tsv file contains a # character at the start of the header line. This causes that line to be interpreted as a comment line instead of a header, and hence it is ignored; the next line (the missing feature!) winds up being interpreted as the header line, and hence is not retained in your filtered sequences! Remove the # in the first line and all is well.

Ouch, it looks like @steff1088 ran into the same metadata filtering issue reported here (other users have also run into this problem):

Possible to provide warning when metadata doesn't have a header?

In my rush to try out the new filter-seqs command I made a bit of a headache for myself by not having a header line in my metadata and losing my first sequence. I wasn't using a where clause, so just using the first column as ids. In this case, would it be possible to test the header line to see if it is a valid id in the data to be filtered and either retain it (perhaps too clever) or throw a warning? Thanks!

The issue stems from the fact that QIIME 2 doesn't have a required header for metadata files, making it impossible to detect and correct from the situation @steff1088 and @Chris_Hemmerich ran into I am working on overhauling metadata this month (including the file format), and this issue will be addressed then (no more unexpected filtering behavior!). I'll follow up here when the issue is fixed in the 2017.12 release!