remove.lineage -not removing lineages

Commands in mothur
1

HI,
using Mothur v 1.36
commands
classify.seqs(fasta=mander.final.fasta,template=gg.fasta, taxonomy=gg.tax, cutoff=80, processors=8, group=mander.final.groups)

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 mander.final.fasta.
Reading template taxonomy… DONE.
Reading template probabilities… DONE.
It took 45 seconds get probabilities.
Classifying sequences from mander.final.fasta …
[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: mander.final.gg.wang.taxonomy mander.final.gg.wang.tax.summary
mothur > remove.lineage(taxonomy=mander.final.gg.wang.taxonomy, name=mander.final.names, group=mander.final.groups, fasta=mander.final.fasta, taxon=k__Bacteria;p__Cyanobacteria;c__Chloroplast;-k__Archaea-k_Bacteria;unclassified;-unknown, dups=T)

Output File Names:
mander.final.gg.wang.pick.taxonomy
mander.final.pick.names
mander.final.pick.fasta
mander.final.pick.groups

All fine but actually mander.final.gg.wang.pick.taxonomy 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’ mander.final.gg.wang.pick.taxonomy -P.
also the sequences bac27#FL2ME8Y01EKRUV,bac19#FL2ME8Y01ESSJF (mentioned in the error message of clasify seqs),
remain fine in the mander.final.pick.fasta.

Is there something wrong with my commands or what?

2

Self -reply seems to be that the trouble might come from not finishing the classifications with semicolon in classify.seqs command.
remove.lineage(taxonomy=mander.final.gg.wang.taxonomy, name=mander.final.names, group=mander.final.groups, fasta=mander.final.fasta, 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?

3

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:
    k__Bacteria;p__Cyanobacteria;c__Chloroplast;
    k__Archaea
    k_Bacteria;unclassified;
    unknown;

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

k__Bacteria(97);unclassified;unclassified;unclassified;unclassified;unclassified;unclassified;
k_Bacteria;unclassified;

Kindly,
Sarah