make compiles some programs every time, even if they are just compiled - makefile

Question

I have a Makefile below. Whenever I run make clean and then make everything is compiled again. But just after that if I run make again a subset of programs: convert_genomes, align_bs and methyl_extract are compiled again, which is strange since they have just compiled.
I have tested this in different operating systems, and the result is the same. Do you have any ideas?
EDIT
When I changed convert-genomes to convert_genomes (and similarly for the two other programs) the problem got solved, but I have still no idea what is the different between - and _ in Makefile that results in my problem
CC= gcc
CXX= g++
CFLAGS= -Wall -Wno-unused-function -O2
CXXFLAGS= -Wall -Wno-unused-function -O2
OBJS= QSufSort.o bwt_gen.o utils.o bwt.o bwtaln.o bwa2.o bwtgap.o sam.o hash.o smith.o aligner.o fa2bin.o \
is.o bntseq.o bwtindex.o ksw.o stdaln.o simple_dp.o \
bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o \
bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
bwtsw2_chain.o bamlite.o bwtsw2_pair.o bwt2.o bwa.o
PROG= aryana
INCLUDES=
LIBS= -lm -lz -lpthread
SUBDIRS= .
debug: CFLAGS += -DDEBUG -g3 -O0
debug: CXXFLAGS += -DDEBUG -g3 -O0
.SUFFIXES:.c .o .cc
.c.o:
$(CC) -c $(CFLAGS) $(INCLUDES) $< -o $#
.cc.o:
$(CXX) -c $(CXXFLAGS) $(INCLUDES) $< -o $#
all: $(PROG) aryana convert-genomes align-bs methyl-extract read_simul SamAnalyzer fastaseq bwtcheck SamToNormWig
debug: all
aryana:$(OBJS) aryana_main.o
$(CC) $(CFLAGS) $(OBJS) aryana_main.o -o aryana $(LIBS)
convert-genomes:
$(CXX) $(CXXFLAGS) convert_genomes.cpp -o convert_genomes
align-bs:
$(CXX) $(CXXFLAGS) align_bs.cpp -o align_bs
methyl-extract:
$(CXX) $(CXXFLAGS) methyl_extract.cpp -o methyl_extract
read_simul:
$(CXX) $(CXXFLAGS) read_simul.cpp -o read_simul
SamAnalyzer:
$(CXX) $(CXXFLAGS) SamAnalyzer.cpp -o SamAnalyzer
SamToNormWig:
$(CXX) $(CXXFLAGS) SamToNormWig.cpp -o SamToNormWig
fastaseq:
$(CXX) $(CXXFLAGS) fastaseq.cpp -o fastaseq
bwtcheck:
$(CXX) $(CXXFLAGS) bwtcheck.cpp -o bwtcheck
QSufSort.o:QSufSort.h
bwt.o:bwt.h
bwt2.o:bwt.h
bwtaln.o:bwt.h bwtaln.h kseq.h bwa2.h
bwt1away.o:bwt.h bwtaln.h
bwt2fmv.o:bwt.h
bntseq.o:bntseq.h
bwtgap.o:bwtgap.h bwtaln.h bwt.h
aligner.o: aligner.h bwt.h hash.h smith.h
fa2bin.o: fa2bin.h
hash.o: hash.h
bwa2.o: bwa2.h sam.h aligner.h bwt.h
sam.o: sam.h bwt.h
smith.o: smith.h bwt.h
bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h stdaln.h
bwtsw2_main.o:bwtsw2.h
bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h kstring.h malloc_wrap.h kvec.h
aryana_main.o: aryana_main.h aryana_args.h bwt.h bwtaln.h kseq.h bwa2.h
clean:
rm -f gmon.out *.o a.out $(PROG) *~ *.a aryana align_bs methyl_extract convert_genomes read_simul SamAnalyzer bwtcheck fastaseq SamToNormWig

Answer 1

If your target is convert-genomes but the program is convert_genomes, then every time you try to make convert-genomes, the file convert-genomes does not exist, so it is out of date, and the rules to 'build it' are run once more, recreating convert_genomes instead of create-genomes.
make makes files. If you tell make 'this rule will make a file F' and actually the rule creates some other file G, then make will never find that F is up to date — as you carefully demonstrated, albeit by accident.