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lbcb-sci / graphmap2

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1
MIT License
66 stars 6 forks source link

make installation error #18

Open ksahlin opened 3 years ago

ksahlin commented 3 years ago

Hi,

I am trying to install graphmap2 on a Linux server (see details below). After successfully executing the make modules, it failed on make step. Log pasted below.

Best, Kristoffer

gcc details

(base) [kris@rackham3 graphmap2]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)

Server details

(base) [kris@rackham3 graphmap2]$ uname -a
Linux rackham3.uppmax.uu.se 3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

Log

(base) [kris@rackham3 graphmap2]$ make
mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.cpp
mkdir -p obj_linux/codebase/gindex/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/main.o codebase/gindex/src/main.cc
mkdir -p obj_linux/codebase/argumentparser/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/argumentparser/src/example.o codebase/argumentparser/src/example.cc
mkdir -p obj_linux/codebase/argumentparser/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/argumentparser/src/argparser.o codebase/argumentparser/src/argparser.cc
mkdir -p obj_linux/codebase/seqlib/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/test.o codebase/seqlib/src/test.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/experimental.o codebase/gindex/src/minimizer_index/experimental.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/compiled_shape.o codebase/gindex/src/minimizer_index/compiled_shape.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/seed.o codebase/gindex/src/minimizer_index/seed.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o codebase/gindex/src/minimizer_index/minimizer_index.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o codebase/gindex/src/minimizer_index/minimizer_generator.cc
mkdir -p obj_linux/codebase/gindex/src/minimizer_index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/gindex/src/minimizer_index/index_pos.o codebase/gindex/src/minimizer_index/index_pos.cc
mkdir -p obj_linux/codebase/seqlib/src/utility/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/utility/utility_general.o codebase/seqlib/src/utility/utility_general.cc
mkdir -p obj_linux/codebase/seqlib/src/utility/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/utility/tictoc.o codebase/seqlib/src/utility/tictoc.cc
mkdir -p obj_linux/codebase/seqlib/src/utility/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/utility/evalue_constants.o codebase/seqlib/src/utility/evalue_constants.cc
mkdir -p obj_linux/codebase/seqlib/src/utility/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/utility/evalue.o codebase/seqlib/src/utility/evalue.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o codebase/seqlib/src/sequences/sequence_gfa_test.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/sequence_file.o codebase/seqlib/src/sequences/sequence_file.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o codebase/seqlib/src/sequences/sequence_alignment.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o codebase/seqlib/src/sequences/sequence_gfa.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o codebase/seqlib/src/sequences/sequence_alignment_test.cc
mkdir -p obj_linux/codebase/seqlib/src/sequences/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/sequences/single_sequence.o codebase/seqlib/src/sequences/single_sequence.cc
mkdir -p obj_linux/codebase/seqlib/src/log_system/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/log_system/log_system.o codebase/seqlib/src/log_system/log_system.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/edlib.o codebase/seqlib/src/libs/edlib.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/edlibcigar.o codebase/seqlib/src/libs/edlibcigar.cc
mkdir -p obj_linux/codebase/seqlib/src/libs/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/codebase/seqlib/src/libs/opal.o codebase/seqlib/src/libs/opal.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/alignment.o src/alignment/alignment.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/semiglobal.o src/alignment/semiglobal.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/cigargen.o src/alignment/cigargen.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/transcriptome_mod.o src/alignment/transcriptome_mod.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/anchored.o src/alignment/anchored.cc
mkdir -p obj_linux/src/alignment/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/alignment/alignment_wrappers.o src/alignment/alignment_wrappers.cc
mkdir -p obj_linux/src/ksw2/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/ksw2_exts2_sse.o src/ksw2/ksw2_exts2_sse.cc
mkdir -p obj_linux/src/ksw2/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/ksw2_extz2_sse.o src/ksw2/ksw2_extz2_sse.cc
mkdir -p obj_linux/src/ksw2/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/ksw2_extd2_sse.o src/ksw2/ksw2_extd2_sse.cc
mkdir -p obj_linux/src/ksw2/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/kalloc.o src/ksw2/kalloc.cc
mkdir -p obj_linux/src/ksw2/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/ksw2/ksw2_ll_sse.o src/ksw2/ksw2_ll_sse.cc
mkdir -p obj_linux/src/index/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/index/index_util.o src/index/index_util.cc
mkdir -p obj_linux/src/aligner/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/aligner/aligner_ksw2.o src/aligner/aligner_ksw2.cc
mkdir -p obj_linux/src/aligner/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/aligner/aligner_util.o src/aligner/aligner_util.cc
mkdir -p obj_linux/src/aligner/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/aligner/anchor_aligner.o src/aligner/anchor_aligner.cc
mkdir -p obj_linux/src/aligner/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/aligner/sam_parser.o src/aligner/sam_parser.cc
mkdir -p obj_linux/src/containers/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/containers/path_graph_entry.o src/containers/path_graph_entry.cc
mkdir -p obj_linux/src/containers/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/containers/mapping_data.o src/containers/mapping_data.cc
mkdir -p obj_linux/src/containers/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/containers/vertices.o src/containers/vertices.cc
mkdir -p obj_linux/src/containers/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/containers/region.o src/containers/region.cc
mkdir -p obj_linux/src/containers/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/containers/score_registry.o src/containers/score_registry.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/experimental.o src/graphmap/experimental.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/lcs_anchored.o src/graphmap/lcs_anchored.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/region_selection.o src/graphmap/region_selection.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/process_read.o src/graphmap/process_read.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/rna.o src/graphmap/rna.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/transcriptome.o src/graphmap/transcriptome.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/lcs_semiglobal.o src/graphmap/lcs_semiglobal.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/filter_anchors.o src/graphmap/filter_anchors.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/graphmap.o src/graphmap/graphmap.cc
mkdir -p obj_linux/src/graphmap/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/graphmap/core_graphmap.o src/graphmap/core_graphmap.cc
mkdir -p obj_linux/src/owler/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/owler/owler.o src/owler/owler.cc
mkdir -p obj_linux/src/owler/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/owler/lcsk.o src/owler/lcsk.cc
mkdir -p obj_linux/src/owler/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/owler/process_read.o src/owler/process_read.cc
mkdir -p obj_linux/src/owler/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/owler/owler_experimental.o src/owler/owler_experimental.cc
mkdir -p obj_linux/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/program_parameters.o src/program_parameters.cc
mkdir -p obj_linux/src/
g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -g -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread  -o obj_linux/src/main.o src/main.cc
mkdir -p ./bin/Linux-x64/
g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/Linux-x64/graphmap2 ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o ./obj_linux/codebase/gindex/src/main.o ./obj_linux/codebase/argumentparser/src/example.o ./obj_linux/codebase/argumentparser/src/argparser.o ./obj_linux/codebase/seqlib/src/test.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o ./obj_linux/codebase/gindex/src/minimizer_index/experimental.o ./obj_linux/codebase/gindex/src/minimizer_index/compiled_shape.o ./obj_linux/codebase/gindex/src/minimizer_index/seed.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o ./obj_linux/codebase/gindex/src/minimizer_index/index_pos.o ./obj_linux/codebase/seqlib/src/utility/utility_general.o ./obj_linux/codebase/seqlib/src/utility/tictoc.o ./obj_linux/codebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/seqlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/sequence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_linux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edlibcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/src/alignment/alignment.o ./obj_linux/src/alignment/semiglobal.o ./obj_linux/src/alignment/cigargen.o ./obj_linux/src/alignment/transcriptome_mod.o ./obj_linux/src/alignment/anchored.o ./obj_linux/src/alignment/alignment_wrappers.o ./obj_linux/src/ksw2/ksw2_exts2_sse.o ./obj_linux/src/ksw2/ksw2_extz2_sse.o ./obj_linux/src/ksw2/ksw2_extd2_sse.o ./obj_linux/src/ksw2/kalloc.o ./obj_linux/src/ksw2/ksw2_ll_sse.o ./obj_linux/src/index/index_util.o ./obj_linux/src/aligner/aligner_ksw2.o ./obj_linux/src/aligner/aligner_util.o ./obj_linux/src/aligner/anchor_aligner.o ./obj_linux/src/aligner/sam_parser.o ./obj_linux/src/containers/path_graph_entry.o ./obj_linux/src/containers/mapping_data.o ./obj_linux/src/containers/vertices.o ./obj_linux/src/containers/region.o ./obj_linux/src/containers/score_registry.o ./obj_linux/src/graphmap/experimental.o ./obj_linux/src/graphmap/lcs_anchored.o ./obj_linux/src/graphmap/region_selection.o ./obj_linux/src/graphmap/process_read.o ./obj_linux/src/graphmap/rna.o ./obj_linux/src/graphmap/transcriptome.o ./obj_linux/src/graphmap/lcs_semiglobal.o ./obj_linux/src/graphmap/filter_anchors.o ./obj_linux/src/graphmap/graphmap.o ./obj_linux/src/graphmap/core_graphmap.o ./obj_linux/src/owler/owler.o ./obj_linux/src/owler/lcsk.o ./obj_linux/src/owler/process_read.o ./obj_linux/src/owler/owler_experimental.o ./obj_linux/src/program_parameters.o ./obj_linux/src/main.o -lpthread -lgomp -lm -lz
/usr/bin/ld: cannot find -lstdc++
collect2: error: ld returned 1 exit status
make: *** [linux] Error 1