Update reference files

Makefile

@@ -29,32 +29,32 @@ print-%:
 
 # We want the latest greatest reference alignment and the SILVA reference
 # alignment is the best reference alignment on the market. This version is from
-# v123 and described at http://blog.mothur.org/2015/12/03/SILVA-v123-reference-files/
-# We will use the SEED v. 123, which contain 12,083 bacterial sequences. This
+# 132 and described at http://blog.mothur.org/2018/01/10/SILVA-v132-reference-files/
+# We will use the SEED v. 132, which contain 12,083 bacterial sequences. This
 # also contains the reference taxonomy. We will limit the databases to only
 # include bacterial sequences.
 
 $(REFS)/silva.seed.align :
-	wget -N http://mothur.org/w/images/1/15/Silva.seed_v123.tgz
-	tar xvzf Silva.seed_v123.tgz silva.seed_v123.align silva.seed_v123.tax
-	mothur "#get.lineage(fasta=silva.seed_v123.align, taxonomy=silva.seed_v123.tax, taxon=Bacteria);degap.seqs(fasta=silva.seed_v123.pick.align, processors=8)"
-	mv silva.seed_v123.pick.align $(REFS)/silva.seed.align
-	rm Silva.seed_v123.tgz silva.seed_v123.*
+	wget -N https://mothur.org/w/images/7/71/Silva.seed_v132.tgz
+	tar xvzf Silva.seed_v132.tgz silva.seed_v132.align silva.seed_v132.tax
+	mothur "#get.lineage(fasta=silva.seed_v132.align, taxonomy=silva.seed_v132.tax, taxon=Bacteria);degap.seqs(fasta=silva.seed_v132.pick.align, processors=8)"
+	mv silva.seed_v132.pick.align $(REFS)/silva.seed.align
+	rm Silva.seed_v132.tgz silva.seed_v132.*
 
 $(REFS)/silva.v4.align : $(REFS)/silva.seed.align
 	mothur "#pcr.seqs(fasta=$(REFS)/silva.seed.align, start=11894, end=25319, keepdots=F, processors=8)"
 	mv $(REFS)/silva.seed.pcr.align $(REFS)/silva.v4.align
 
 # Next, we want the RDP reference taxonomy. The current version is v10 and we
 # use a "special" pds version of the database files, which are described at
-# http://blog.mothur.org/2014/10/28/RDP-v10-reference-files/
+# http://blog.mothur.org/2017/03/15/RDP-v16-reference_files/
 
-$(REFS)/trainset14_032015.% :
-	wget -N http://www.mothur.org/w/images/8/88/Trainset14_032015.pds.tgz
-	tar xvzf Trainset14_032015.pds.tgz trainset14_032015.pds
-	mv trainset14_032015.pds/* $(REFS)/
-	rm -rf trainset14_032015.pds
-	rm Trainset14_032015.pds.tgz
+$(REFS)/trainset16_022016.% :
+	wget -N https://www.mothur.org/w/images/c/c3/Trainset16_022016.pds.tgz
+	tar xvzf Trainset16_022016.pds.tgz trainset16_022016.pds
+	mv trainset16_022016.pds/* $(REFS)/
+	rm -rf trainset16_022016.pds
+	rm Trainset16_022016.pds.tgz
 
 ################################################################################
 #
@@ -76,8 +76,8 @@ BASIC_STEM = data/mothur/stability.trim.contigs.good.unique.good.filter.unique.p
 # Edit code/get_good_seqs.batch to include the proper name of your *files file
 $(BASIC_STEM).denovo.uchime.pick.pick.count_table $(BASIC_STEM).pick.pick.fasta $(BASIC_STEM).pick.pds.wang.pick.taxonomy : code/get_good_seqs.batch\
 					data/references/silva.v4.align\
-					data/references/trainset14_032015.pds.fasta\
-					data/references/trainset14_032015.pds.tax
+					data/references/trainset16_022016.pds.fasta\
+					data/references/trainset16_022016.pds.tax
 	mothur code/get_good_seqs.batch;\
 	rm data/mothur/*.map