/usr/bin/c++    -Wall -Wextra -Wunused -Wno-long-long -Wsign-compare -Wpointer-arith -Wno-unused-parameter  -pedantic  -O2 -g   CMakeFiles/phageAlign.dir/phageAlign.cpp.o  -o phageAlign -rdynamic ../lib/smallRna/libcasava_smallRna.a ../lib/kagu/libcasava_kagu.a ../lib/eland_ms/libcasava_eland_ms.a ../lib/SamMD2Export/libcasava_SamMD2Export.a ../lib/SamMD/libcasava_SamMD.a ../lib/statistics/libcasava_statistics.a ../lib/demultiplex/libcasava_demultiplex.a ../lib/applications/libcasava_applications.a ../lib/variance/libcasava_variance.a ../lib/assembly/libcasava_assembly.a ../lib/basecalling/libcasava_basecalling.a ../lib/alignment/libcasava_alignment.a ../lib/io/libcasava_io.a ../lib/common/libcasava_common.a ../lib/starling/libcasava_starling.a ../lib/blt/libcasava_blt.a ../lib/blt_common/libcasava_blt_common.a ../lib/blt_util/libcasava_blt_util.a ../../opt/samtools-0.1.8/libbam.a ../../opt/bootstrap/lib/libboost_date_time.a ../../opt/bootstrap/lib/libboost_filesystem.a ../../opt/bootstrap/lib/libboost_iostreams.a ../../opt/bootstrap/lib/libboost_program_options.a ../../opt/bootstrap/lib/libboost_regex.a ../../opt/bootstrap/lib/libboost_serialization.a ../../opt/bootstrap/lib/libboost_system.a ../../opt/bootstrap/lib/libboost_thread.a -lxml2 -lz -lbz2 -lpthread