Closed BanaIbrahim closed 8 months ago
After looking into the source code, it seemed that renkonen_distance_df is not being filled within the for loop of replicates. Eventually, there were some issues with my sortedinfo.tsv, now it's working. Thank you
I'll close this issue.
I ran filter variant step as described in the documentation.
vtam filter --params params.yml --db db.sqlite --sortedinfo sorted/sortedinfo.tsv --sorteddir sorted/ --asvtable asvtable_default.tsv -v --log vtam.log
However, I keep getting the following error:
I don't know how feasible is this, but it would be easier to customize and troubleshoot if I can skip any step in filter, as currently, it's only implemented for filter_indel and filter_codon_stop. I even tried with --until and --since to skip the FilterRenkonen step, but it seems they are connected.