remove.lineage -not removing lineages

using Mothur v 1.36
classify.seqs(,template=gg.fasta,, cutoff=80, processors=8,

Using 8 processors.
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is mander.trim.unique.good.filter.unique.precluster.pick.names which seems to match
Reading template taxonomy… DONE.
Reading template probabilities… DONE.
It took 45 seconds get probabilities.
Classifying sequences from …
[WARNING]: bac27#FL2ME8Y01EKRUV could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.
[WARNING]: bac19#FL2ME8Y01ESSJF could not be classified. You can use the remove.lineage command with taxon=unknown; to remove such sequences.

It took 587 secs to classify 29891 sequences.

It took 2 secs to create the summary file for 29891 sequences.
Output File Names:
mothur > remove.lineage(,,,, taxon=k__Bacteria;p__Cyanobacteria;c__Chloroplast;-k__Archaea-k_Bacteria;unclassified;-unknown, dups=T)

Output File Names:

All fine but actually is chock full of lineages it should have gotten rid of with remove.lineage command.
Fore example…
bac17#FL2ME8Y01BU9SZ k__Bacteria(97);unclassified;unclassified;unclassified;unclassified;unclassified;unclassified;
bac17#FL2ME8Y01BRLQZ k__Bacteria(99);unclassified;unclassified;unclassified;unclassified;unclassified;unclassified;
bac17#FL2ME8Y01B6CYE k__Bacteria(98);unclassified;unclassified;unclassified;unclassified;unclassified;unclassified;
bac17#FL2ME8Y01AZW9R k__Bacteria(99);unclassified;unclassified;unclassified;unclassified;unclassified;unclassified;
bac17#FL2ME8Y01AGCZ5 k__Bacteria(99);unclassified;unclassified;unclassified;unclassified;unclassified;unclassified;
bac17#FL2ME8Y01AF1SE k__Bacteria(97);unclassified;unclassified;unclassified;unclassified;unclassified;unclassified;

are just some of the 750 - results for grep ‘k__Bacteria.\d\d.;unclassified’ -P.
also the sequences bac27#FL2ME8Y01EKRUV,bac19#FL2ME8Y01ESSJF (mentioned in the error message of clasify seqs),
remain fine in the

Is there something wrong with my commands or what?

Self -reply seems to be that the trouble might come from not finishing the classifications with semicolon in classify.seqs command.
remove.lineage(,,,, taxon=k__Bacteria;p__Cyanobacteria;c__Chloroplast;-k__Archaea-k_Bacteria;unclassified;-unknown, dups=T)
I think the command tries to remove taxon “k__Archaea-k_Bacteria;unclassified” instead of taxon k_Archaea and taxon k_Bacteria;unclassified etc?

In your example: taxon=k__Bacteria;p__Cyanobacteria;c__Chloroplast;-k__Archaea-k_Bacteria;unclassified;-unknown;.

  1. Mothur divides the taxons by the ‘-’ character first. Taxons to remove:

Looking closely at the sequences that weren’t removed and the taxons listed, it appears to be a typo.