read_name is not in your group file

mothur bugs
1

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

2

I suspect it’s in the “tweak” you did. Some things off the top of my head to ask about include whether you replaced the colons in the sequence names with underscores and whether any of your group names have spaces in them.