I decided to use other assembly method and tweak their output to be readable for mothur. I also made the “groupfile” as mothur makes.
however, now when I am running count.seqs(name=stability.trim.contigs.good.names, group=stability.contigs.good.groups)
I get a bunch of “read_name is not in your group file” for many reads.
however when I check using greb command
“grep -e “MISEQ-2_111_000000000-A9PNR_1_2114_3887_13191” …/output/stability.contigs.good.groups”
I see that the read_name exists inside the group file !
The “.names” file I use, is generated by “unique.seqs” and the group file is a tab generated file.
I tried make.table command and it works on this “name” file and it works without any complains
I appreciate your comments on this