TESTING RDP-MULTICLASSIFER

First,
wget http://rdp.cme.msu.edu/download/rdp_multiclassifier.zip
Second,
unzip http://rdp.cme.msu.edu/download/rdp_multiclassifier.zip
cd rdp_multiclassifier

Third, get the input file,
grab a fasta to test, I grab ocular file.

Fourth,
Run the script
/scratch/cc0430/packages/jre1.6.0_20/bin/java -Xmx1g -jar /scratch/cc0430/rdp_multiclassifier/dist/multiclassifier.jar /scratch/cc0430/metagenome/Ocular/454/Fasta/V0021801ss_R1_trimmed.fasta > /scratch/cc0430/scripts/foooooo

the content of foooooo

taxid lineage name rank V0021801ss_R1_trimmed.fasta
0 null Root no rank 21920
1 Root;norank;Bacteria;domain; Bacteria domain 21916
61 Root;norank;Bacteria;domain;"Firmicutes";phylum; "Firmicutes" phylum 10225
62 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class; "Bacilli" class 10220
63 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order; Bacillales order 10216
140 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family; "Staphylococcaceae" family 10212
146 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family;Staphylococcus;genus; Staphylococcus genus 10210
-141 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family;unclassified_"Staphylococcaceae";; unclassified_"Staphylococcaceae" 2
-64 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;unclassified_Bacillales;; unclassified_Bacillales 4
160 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order; "Lactobacillales" order 3
203 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order;Streptococcaceae;family; Streptococcaceae family 3
206 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order;Streptococcaceae;family;Streptococcus;genus; Streptococcus genus 3
more....

Option

--conf= specifies the assignment confidence cutoff used to determine the assignment count in the hierarchical format. Range [0-1], Default is 0.8.

/scratch/cc0430/packages/jre1.6.0_20/bin/java -Xmx1g -jar /scratch/cc0430/rdp_multiclassifier/dist/multiclassifier.jar --conf=0.9 /scratch/cc0430/metagenome/Ocular/454/Fasta/V0021801ss_R1_trimmed.fasta > /scratch/cc0430/scripts/foooooo1

the content of foooooo1

taxid lineage name rank V0021801ss_R1_trimmed.fasta
0 null Root no rank 21920
1 Root;norank;Bacteria;domain; Bacteria domain 21915
61 Root;norank;Bacteria;domain;"Firmicutes";phylum; "Firmicutes" phylum 10221
62 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class; "Bacilli" class 10218
63 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order; Bacillales order 10211
140 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family; "Staphylococcaceae" family 10202
146 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family;Staphylococcus;genus; Staphylococcus genus 10196
-141 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;"Staphylococcaceae";family;unclassified_"Staphylococcaceae";; unclassified_"Staphylococcaceae" 6
-64 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;Bacillales;order;unclassified_Bacillales;; unclassified_Bacillales 9
160 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order; "Lactobacillales" order 3
203 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order;Streptococcaceae;family; Streptococcaceae family 3
206 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;"Lactobacillales";order;Streptococcaceae;family;Streptococcus;genus; Streptococcus genus 3
-63 Root;norank;Bacteria;domain;"Firmicutes";phylum;"Bacilli";class;unclassified_"Bacilli";; unclassified_"Bacilli" 4
653 Root;norank;Bacteria;domain;"Actinobacteria";phylum; "Actinobacteria" phylum 10452
654 Root;norank;Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class; Actinobacteria class 10452
666 Root;norank;Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Actinobacteridae;subclass; Actinobacteridae subclass 10452
667 Root;norank;Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Actinobacteridae;subclass;Actinomycetales;order; Actinomycetales order 10452
684 Root;norank;Bacteria;domain;"Actinobacteria";phylum;Actinobacteria;class;Actinobacteridae;subclass;Actinomycetales;order;Corynebacterineae;suborder; Corynebacterineae suborder 9700
more......


When we use --conf=0.9 the fifth value in every row is getting smaller.