mothur

Help with get.lineage

#1

I have a large dataset for which I want bins for the Cyanobacteria. I have completed the following steps.

mothur >
get.oturep(column=JL_16S.full.dist, list=JL_16S.full.list, fasta=JL_16S.full.fasta, count=JL_16S.full.count_table, label=0.01)
0.01 228863

Output File Names:
JL_16S.full.0.01.rep.count_table
JL_16S.full.0.01.rep.fasta

mothur >
create.database(list=JL_16S.full.list, label=0.01, repfasta=JL_16S.full.0.01.rep.fasta, count=JL_16S.full.0.01.rep.count_table, constaxonomy=JL_16S.full.0.01.cons.taxonomy)

Output File Names:
JL_16S.full.database

Within the database, Otu000002 is a Cyanobacteria, as are several others. I want to run bin.seqs on these so I want to run the following.

get.lineage(fasta=JL_16S.full.fasta, list=JL_16S.full.list, taxon=Cyanobacteria, taxonomy=JL_16S.full.taxonomy, count=JL_16S.full.count_table)
rename.file(fasta=current, list=current, count=current, taxonomy=current, prefix=JL_16S_cyano)
bin.seqs(fasta=current, list=current, count=current, label=0.01)
rename.file(fasta=current, prefix=JL_16S_cyano.bin)

When I run the first line, however, I get the following:

mothur >
get.lineage(fasta=JL_16S.full.fasta, list=JL_16S.full.list, taxon=Cyanobacteria, taxonomy=JL_16S.full.taxonomy, count=JL_16S.full.count_table)
[WARNING]: You did not provide a label, I will use the first label in your inputfile.

[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.

Your file contains does not contain any sequences from Cyanobacteria.

Removing group: DNA_JL1001 because all sequences have been removed.

Removing group: DNA_JL1178 because all sequences have been removed.
Your file contains does not contain any sequences from Cyanobacteria.
Your file contains does not contain any sequences from Cyanobacteria.

Output File Names:
JL_16S.full.pick.taxonomy
JL_16S.full.pick.fasta
JL_16S.full.pick.count_table
JL_16S.full.0.01.pick.list

Since I created the database file based on the the same fasta, dist, count_table,and list that I’m using for get.lineages, I don’t understand why it doesn’t see the Cyanobacteria.

#2

Can you post the taxonomy string for the OTU that you think is a Cyano?

#3

From JL_16S.full.taxonomy:

Otu000002 195776 Bacteria(100);Cyanobacteria(100);Oxyphotobacteria(100);Synechococcales(100);Cyanobiaceae(100);Cyanobium_PCC-6307(100);

#4

Could you send your input files and logfile to mothur.bugs@gmail.com?

closed #5

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