I get an error message when using the chimera.vsearch command, which points to specific sequences that either have a value of zero or are absent in the count_table file generated from the pre.cluster command I used in the previous step. I have re-run the pre.cluster command with different diff values (1,2,3 …) but to no avail.
May I know why I am getting this error message in the chimera.vsearch step?
PS: I do not run the filter.seqs command. Is this a possible reason?