Error in the ./instaIl.sh process MaSuRCA3.3.3

Here is the full log:
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking how to print strings... printf
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for pthread_create in -lpthread... yes
checking for library containing clock_gettime... none required
checking for __int128... yes
checking for OpenMP flag of C++ compiler... -fopenmp
checking for Boost headers version >= 1.46.0... yes
checking for Boost's header version... 1_65_1
checking boost/icl/interval_set.hpp usability... yes
checking boost/icl/interval_set.hpp presence... yes
checking for boost/icl/interval_set.hpp... yes
checking for _NSGetExecutablePath... no
checking if std::thread::sleep_for is supported... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for mremap... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for zlibVersion in -lz... yes
checking bzlib.h usability... yes
checking bzlib.h presence... yes
checking for bzlib.h... yes
checking for BZ2_bzlibVersion in -lbz2... yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for __builtin_prefetch... yes
checking for architecture... Linux-amd64
checking for yaggo... false
checking for perl... /usr/bin/perl
checking for Perl prefix... /usr
checking for Perl extension include path... /usr/lib/x86_64-linux-gnu/perl/5.22/CORE
checking for Perl extension target directory... $(libdir)/perl
checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include
checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating jellyfish/jellyfish-2.0.pc
config.status: creating MUMmer/mummer.pc
config.status: creating samtools/Makefile
config.status: creating prepare/Makefile
config.status: creating ufasta/Makefile
config.status: creating quorum/Makefile
config.status: creating SuperReads/Makefile
config.status: creating SOAPdenovo2/Makefile
config.status: creating PacBio/Makefile
config.status: creating CA8/Makefile
config.status: creating jellyfish/Makefile
config.status: creating MUMmer/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
Making install in jellyfish pwd /usr/local/MaSuRCA-3.3.3/global-1
make[1]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/jellyfish'
make  install-am
make[2]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/jellyfish'
make[3]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/jellyfish'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libjellyfish-2.0.la '/usr/local/MaSuRCA-3.3.3/lib'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/include/jellyfish-1/jellyfish'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/share/man/man1'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/lib/perl'
 /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/usr/local/MaSuRCA-3.3.3/include/jellyfish-1/jellyfish'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/lib/perl'
 /usr/bin/install -c swig/perl5/jellyfish.pm '/usr/local/MaSuRCA-3.3.3/lib/perl'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   swig/perl5/jellyfish.la '/usr/local/MaSuRCA-3.3.3/lib/perl'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/lib/pkgconfig'
 /usr/bin/install -c -m 644 'doc/jellyfish.man' '/usr/local/MaSuRCA-3.3.3/share/man/man1/jellyfish.1'
 /usr/bin/install -c -m 644 jellyfish-2.0.pc '/usr/local/MaSuRCA-3.3.3/lib/pkgconfig'
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /usr/local/MaSuRCA-3.3.3/lib/libjellyfish-2.0.so.2.0.0
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/global-1/jellyfish; /bin/bash /usr/local/MaSuRCA-3.3.3/global-1/libtool  --silent --tag CXX --mode=relink g++ -DNDEBUG -std=c++0x -g -O2 -module -o swig/perl5/jellyfish.la -rpath /usr/local/MaSuRCA-3.3.3/lib/perl swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -lbz2 -lz -lpthread )
 /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/usr/local/MaSuRCA-3.3.3/include/jellyfish-1/jellyfish'
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; })
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; })
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /usr/local/MaSuRCA-3.3.3/lib/libjellyfish-2.0.la
libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /usr/local/MaSuRCA-3.3.3/lib/libjellyfish-2.0.a
libtool: install: chmod 644 /usr/local/MaSuRCA-3.3.3/lib/libjellyfish-2.0.a
libtool: install: ranlib /usr/local/MaSuRCA-3.3.3/lib/libjellyfish-2.0.a
libtool: finish: PATH="/home/gebarros/bin:/home/gebarros/.local/bin:/home/gebarros/miniconda3/condabin:/usr/local/meme_4.12.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/snap/bin:/opt/dell/srvadmin/bin:/usr/local/amos-3.1.0/bin:/usr/local/MaSuRCA-3.3.3/dist-bin:/sbin" ldconfig -n /usr/local/MaSuRCA-3.3.3/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/MaSuRCA-3.3.3/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c bin/jellyfish '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c bin/.libs/jellyfish /usr/local/MaSuRCA-3.3.3/bin/jellyfish
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /usr/local/MaSuRCA-3.3.3/lib/perl/jellyfish.so.0.0.0
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib/perl && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; })
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib/perl && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; })
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /usr/local/MaSuRCA-3.3.3/lib/perl/jellyfish.la
libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /usr/local/MaSuRCA-3.3.3/lib/perl/jellyfish.a
libtool: install: chmod 644 /usr/local/MaSuRCA-3.3.3/lib/perl/jellyfish.a
libtool: install: ranlib /usr/local/MaSuRCA-3.3.3/lib/perl/jellyfish.a
libtool: finish: PATH="/home/gebarros/bin:/home/gebarros/.local/bin:/home/gebarros/miniconda3/condabin:/usr/local/meme_4.12.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/snap/bin:/opt/dell/srvadmin/bin:/usr/local/amos-3.1.0/bin:/usr/local/MaSuRCA-3.3.3/dist-bin:/sbin" ldconfig -n /usr/local/MaSuRCA-3.3.3/lib/perl
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/MaSuRCA-3.3.3/lib/perl

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[3]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/jellyfish'
make[2]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/jellyfish'
make[1]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/jellyfish'
Making install in samtools pwd /usr/local/MaSuRCA-3.3.3/global-1
make[1]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/samtools'
make[2]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/samtools'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/lib'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/include/samtools/bcftools'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libbam.la bcftools/libbcf.la '/usr/local/MaSuRCA-3.3.3/lib'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/include/samtools'
 /usr/bin/install -c -m 644 bam.h bam2bcf.h bam_endian.h bgzf.h errmod.h faidx.h kaln.h khash.h klist.h knetfile.h kprobaln.h kseq.h ksort.h kstring.h razf.h sam.h sam_header.h sample.h bam_tview.h '/usr/local/MaSuRCA-3.3.3/include/samtools'
 /usr/bin/install -c -m 644 bcftools/bcf.h bcftools/kmin.h bcftools/prob1.h '/usr/local/MaSuRCA-3.3.3/include/samtools/bcftools'
libtool: install: /usr/bin/install -c .libs/libbam.so.0.0.0 /usr/local/MaSuRCA-3.3.3/lib/libbam.so.0.0.0
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib && { ln -s -f libbam.so.0.0.0 libbam.so.0 || { rm -f libbam.so.0 && ln -s libbam.so.0.0.0 libbam.so.0; }; })
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib && { ln -s -f libbam.so.0.0.0 libbam.so || { rm -f libbam.so && ln -s libbam.so.0.0.0 libbam.so; }; })
libtool: install: /usr/bin/install -c .libs/libbam.lai /usr/local/MaSuRCA-3.3.3/lib/libbam.la
libtool: install: /usr/bin/install -c bcftools/.libs/libbcf.so.0.0.0 /usr/local/MaSuRCA-3.3.3/lib/libbcf.so.0.0.0
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib && { ln -s -f libbcf.so.0.0.0 libbcf.so.0 || { rm -f libbcf.so.0 && ln -s libbcf.so.0.0.0 libbcf.so.0; }; })
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib && { ln -s -f libbcf.so.0.0.0 libbcf.so || { rm -f libbcf.so && ln -s libbcf.so.0.0.0 libbcf.so; }; })
libtool: install: /usr/bin/install -c bcftools/.libs/libbcf.lai /usr/local/MaSuRCA-3.3.3/lib/libbcf.la
libtool: install: /usr/bin/install -c .libs/libbam.a /usr/local/MaSuRCA-3.3.3/lib/libbam.a
libtool: install: chmod 644 /usr/local/MaSuRCA-3.3.3/lib/libbam.a
libtool: install: ranlib /usr/local/MaSuRCA-3.3.3/lib/libbam.a
libtool: install: /usr/bin/install -c bcftools/.libs/libbcf.a /usr/local/MaSuRCA-3.3.3/lib/libbcf.a
libtool: install: chmod 644 /usr/local/MaSuRCA-3.3.3/lib/libbcf.a
libtool: install: ranlib /usr/local/MaSuRCA-3.3.3/lib/libbcf.a
libtool: finish: PATH="/home/gebarros/bin:/home/gebarros/.local/bin:/home/gebarros/miniconda3/condabin:/usr/local/meme_4.12.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/snap/bin:/opt/dell/srvadmin/bin:/usr/local/amos-3.1.0/bin:/usr/local/MaSuRCA-3.3.3/dist-bin:/sbin" ldconfig -n /usr/local/MaSuRCA-3.3.3/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/MaSuRCA-3.3.3/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c samtools '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c .libs/samtools /usr/local/MaSuRCA-3.3.3/bin/samtools
make[2]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/samtools'
make[1]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/samtools'
Making install in prepare pwd /usr/local/MaSuRCA-3.3.3/global-1
make[1]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/prepare'
make[2]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/prepare'
make[2]: Nothing to be done for 'install-data-am'.
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c finalFusion '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c finalFusion /usr/local/MaSuRCA-3.3.3/bin/finalFusion
make[2]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/prepare'
make[1]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/prepare'
Making install in ufasta pwd /usr/local/MaSuRCA-3.3.3/global-1
make[1]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/ufasta'
make  install-am
make[2]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/ufasta'
make[3]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/ufasta'
make[3]: Nothing to be done for 'install-data-am'.
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c ufasta '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c ufasta /usr/local/MaSuRCA-3.3.3/bin/ufasta
make[3]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/ufasta'
make[2]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/ufasta'
make[1]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/ufasta'
Making install in quorum pwd /usr/local/MaSuRCA-3.3.3/global-1
make[1]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/quorum'
make  install-am
make[2]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/quorum'
  CXX      src/error_correct_reads.o
  CXX      src/create_database.o
  CXX      src/merge_mate_pairs.o
  GEN      quorum
  CXXLD    merge_mate_pairs
  CXXLD    quorum_create_database
  CXXLD    quorum_error_correct_reads
make[3]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/quorum'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/share'
 /usr/bin/install -c -m 644 data/adapter.jf '/usr/local/MaSuRCA-3.3.3/share'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c quorum_error_correct_reads quorum_create_database merge_mate_pairs split_mate_pairs '/usr/local/MaSuRCA-3.3.3/bin'
 /usr/bin/install -c .libs/quorum '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c quorum_error_correct_reads /usr/local/MaSuRCA-3.3.3/bin/quorum_error_correct_reads
libtool: install: /usr/bin/install -c quorum_create_database /usr/local/MaSuRCA-3.3.3/bin/quorum_create_database
libtool: install: /usr/bin/install -c merge_mate_pairs /usr/local/MaSuRCA-3.3.3/bin/merge_mate_pairs
libtool: install: /usr/bin/install -c split_mate_pairs /usr/local/MaSuRCA-3.3.3/bin/split_mate_pairs
make[3]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/quorum'
make[2]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/quorum'
make[1]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/quorum'
Making install in SuperReads pwd /usr/local/MaSuRCA-3.3.3/global-1
make[1]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/SuperReads'
make  install-am
make[2]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/SuperReads'
  CXX      src/error_corrected2frg.o
  CXX      src/sorted_merge.o
  CXX      src/create_k_unitigs_large_k.o
  CXX      src/create_k_unitigs_large_k2.o
  CXX      src/bloom_query.o
  CXX      src/filter_overlap_file.o
  CXX      src/rename_filter_fastq.o
  CXX      src2/createKUnitigMaxOverlaps.o
  CXX      src/read_parser.o
  CXX      src2/getSuperReadInsertCountsFromReadPlacementFile.o
  CXX      src2/joinKUnitigs_v3.o
  CXX      src2/findMatchesBetweenKUnitigsAndReads.o
  CXX      src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.o
mkdir -p src/
  CXX      src2/collectReadSequencesForLocalGapClosing.o
  CXX      src2/runByDirectory.o
sed -e 's,[@]bindir[@],/usr/local/MaSuRCA-3.3.3/bin,g' \
    -e 's,[@]libdir[@],/usr/local/MaSuRCA-3.3.3/lib,g' \
    -e 's,[@]PERL_EXT_DIR[@],/usr/local/MaSuRCA-3.3.3/lib/perl,g' < src/MasurcaPaths.pm.in > src/MasurcaPaths.pm
chmod +x src/MasurcaPaths.pm
  CXXLD    rename_filter_fastq
  CXXLD    error_corrected2frg
  CXXLD    bloom_query
  CXXLD    sorted_merge
  CXXLD    getSuperReadInsertCountsFromReadPlacementFile
  CXXLD    createKUnitigMaxOverlaps
  CXXLD    getSuperReadInsertCountsFromReadPlacementFileTwoPasses
  CXXLD    runByDirectory
  CXXLD    collectReadSequencesForLocalGapClosing
  CXXLD    findMatchesBetweenKUnitigsAndReads
  CXXLD    create_k_unitigs_large_k
  CXXLD    filter_overlap_file
  CXXLD    create_k_unitigs_large_k2
  CXXLD    joinKUnitigs_v3
make[3]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/SuperReads'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c error_corrected2frg reverse_complement reduce_sr sorted_merge create_k_unitigs_large_k create_k_unitigs_large_k2 homo_trim bloom_query filter_overlap_file rename_filter_fastq samToDelta createFastaSuperReadSequences findMatchesBetweenKUnitigsAndReads createKUnitigMaxOverlaps eliminateBadSuperReadsUsingList getSuperReadInsertCountsFromReadPlacementFile getSuperReadInsertCountsFromReadPlacementFileTwoPasses joinKUnitigs_v3 outputRecordsNotOnList killBadKUnitigs makeAdjustmentFactorsForNumReadsForAStatBasedOnGC makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2 create_sr_frg splitFileAtNs getATBiasInCoverageForIllumina_v2 collectReadSequencesForLocalGapClosing runByDirectory extendSuperReadsForUniqueKmerNeighbors extendSuperReadsBasedOnUniqueExtensions addSurrogatesToFrgCtgFile '/usr/local/MaSuRCA-3.3.3/bin'
 /usr/bin/install -c src/MasurcaPaths.pm '/usr/local/MaSuRCA-3.3.3/bin'
 /usr/bin/install -c src/getNumBasesPerReadInFastaFile.perl src/create_end_pairs.pl src/close_gaps.sh src/compute_sr_cov.pl src/create_sr_frg.pl src2/compute_sr_cov.revisedForGCContig.pl src/extractreads.pl src/extract_unjoined_pairs.pl src/fasta2frg.pl src/filter_library.sh src/fix_unitigs.sh src/recompute_astat_superreads.sh src/runSRCA.pl src/extractreads_not.pl src/run_ECR.sh src/filter_alt.pl src/rename_filter_fastq.pl src/filter_redundancy.pl src/expand_fastq src/sample_mate_pairs.pl src/fasta2frg_m.pl src/splitFileByPrefix.pl src/restore_ns.pl src/masurca-superreads src/splitLongKUnitigs.pl src/masurca src/MasurcaConf.pm src/MasurcaCommon.pm src/MasurcaCelera.pm src/MasurcaSoap.pm src/MasurcaSuperReads.pm src2/getLengthStatisticsForKUnitigsFile.perl src2/createSuperReadsForDirectory.perl src2/add_missing_mates.pl src2/outputAlekseysJellyfishReductionFile.perl src2/translateReduceFile.perl src/mergeSuperReadsUniquely.pl src2/closeGapsInScaffFastaFile.perl src2/getGCBiasStatistics.perl src2/getSuperReadPlacements.perl '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c error_corrected2frg /usr/local/MaSuRCA-3.3.3/bin/error_corrected2frg
libtool: install: /usr/bin/install -c reverse_complement /usr/local/MaSuRCA-3.3.3/bin/reverse_complement
libtool: install: /usr/bin/install -c reduce_sr /usr/local/MaSuRCA-3.3.3/bin/reduce_sr
 /usr/bin/install -c src2/getMeanAndStdevByGCCount.perl src2/closeGaps.perl src2/getEndSequencesOfContigs.perl src2/create_end_pairs.perl src2/outputJoinedPairs.perl src2/getSequenceForClosedGaps.perl src2/closeGapsLocally.perl src2/closeGaps.oneDirectory.perl src2/closeGaps.oneDirectory.fromMinKmerLen.perl src2/extractJoinableAndNextPassReadsFromJoinKUnitigs.perl src2/getSequenceForLocallyClosedGaps.perl src2/getMeanAndStdevForGapsByGapNumUsingCeleraTerminatorDirectory.perl src2/createSuperReadSequenceAndPlacementFileFromCombined.perl src2/getMeanAndStdevForGapsByGapNumUsingCeleraAsmFile.perl src2/addSurrogatesToFrgctg.perl src2/getUnitigTypeFromAsmFile.perl '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c sorted_merge /usr/local/MaSuRCA-3.3.3/bin/sorted_merge
libtool: install: /usr/bin/install -c create_k_unitigs_large_k /usr/local/MaSuRCA-3.3.3/bin/create_k_unitigs_large_k
libtool: install: /usr/bin/install -c create_k_unitigs_large_k2 /usr/local/MaSuRCA-3.3.3/bin/create_k_unitigs_large_k2
libtool: install: /usr/bin/install -c homo_trim /usr/local/MaSuRCA-3.3.3/bin/homo_trim
libtool: install: /usr/bin/install -c bloom_query /usr/local/MaSuRCA-3.3.3/bin/bloom_query
libtool: install: /usr/bin/install -c filter_overlap_file /usr/local/MaSuRCA-3.3.3/bin/filter_overlap_file
libtool: install: /usr/bin/install -c rename_filter_fastq /usr/local/MaSuRCA-3.3.3/bin/rename_filter_fastq
libtool: install: /usr/bin/install -c samToDelta /usr/local/MaSuRCA-3.3.3/bin/samToDelta
libtool: install: /usr/bin/install -c createFastaSuperReadSequences /usr/local/MaSuRCA-3.3.3/bin/createFastaSuperReadSequences
libtool: install: /usr/bin/install -c findMatchesBetweenKUnitigsAndReads /usr/local/MaSuRCA-3.3.3/bin/findMatchesBetweenKUnitigsAndReads
libtool: install: /usr/bin/install -c createKUnitigMaxOverlaps /usr/local/MaSuRCA-3.3.3/bin/createKUnitigMaxOverlaps
libtool: install: /usr/bin/install -c eliminateBadSuperReadsUsingList /usr/local/MaSuRCA-3.3.3/bin/eliminateBadSuperReadsUsingList
libtool: install: /usr/bin/install -c getSuperReadInsertCountsFromReadPlacementFile /usr/local/MaSuRCA-3.3.3/bin/getSuperReadInsertCountsFromReadPlacementFile
libtool: install: /usr/bin/install -c getSuperReadInsertCountsFromReadPlacementFileTwoPasses /usr/local/MaSuRCA-3.3.3/bin/getSuperReadInsertCountsFromReadPlacementFileTwoPasses
libtool: install: /usr/bin/install -c joinKUnitigs_v3 /usr/local/MaSuRCA-3.3.3/bin/joinKUnitigs_v3
libtool: install: /usr/bin/install -c outputRecordsNotOnList /usr/local/MaSuRCA-3.3.3/bin/outputRecordsNotOnList
libtool: install: /usr/bin/install -c killBadKUnitigs /usr/local/MaSuRCA-3.3.3/bin/killBadKUnitigs
libtool: install: /usr/bin/install -c makeAdjustmentFactorsForNumReadsForAStatBasedOnGC /usr/local/MaSuRCA-3.3.3/bin/makeAdjustmentFactorsForNumReadsForAStatBasedOnGC
libtool: install: /usr/bin/install -c makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2 /usr/local/MaSuRCA-3.3.3/bin/makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2
libtool: install: /usr/bin/install -c create_sr_frg /usr/local/MaSuRCA-3.3.3/bin/create_sr_frg
libtool: install: /usr/bin/install -c splitFileAtNs /usr/local/MaSuRCA-3.3.3/bin/splitFileAtNs
libtool: install: /usr/bin/install -c getATBiasInCoverageForIllumina_v2 /usr/local/MaSuRCA-3.3.3/bin/getATBiasInCoverageForIllumina_v2
libtool: install: /usr/bin/install -c collectReadSequencesForLocalGapClosing /usr/local/MaSuRCA-3.3.3/bin/collectReadSequencesForLocalGapClosing
libtool: install: /usr/bin/install -c runByDirectory /usr/local/MaSuRCA-3.3.3/bin/runByDirectory
libtool: install: /usr/bin/install -c extendSuperReadsForUniqueKmerNeighbors /usr/local/MaSuRCA-3.3.3/bin/extendSuperReadsForUniqueKmerNeighbors
libtool: install: /usr/bin/install -c extendSuperReadsBasedOnUniqueExtensions /usr/local/MaSuRCA-3.3.3/bin/extendSuperReadsBasedOnUniqueExtensions
libtool: install: /usr/bin/install -c addSurrogatesToFrgCtgFile /usr/local/MaSuRCA-3.3.3/bin/addSurrogatesToFrgCtgFile
make[3]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/SuperReads'
make[2]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/SuperReads'
make[1]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/SuperReads'
Making install in SOAPdenovo2 pwd /usr/local/MaSuRCA-3.3.3/global-1
make[1]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/SOAPdenovo2'
  CC       standardPregraph/libstandard63_a-readseq1by1.o
  CXX      sparsePregraph/libsparse63_a-io_func.o
  CXX      sparsePregraph/libsparse63_a-build_preArc.o
  CXX      sparsePregraph/libsparse127_a-build_preArc.o
  CXX      sparsePregraph/libsparse127_a-io_func.o
  CC       standardPregraph/libstandard127_a-readseq1by1.o
  AR       libstandard127.a
  AR       libstandard63.a
  AR       libsparse127.a
  AR       libsparse63.a
  GEN      SOAPdenovo-127mer
  GEN      SOAPdenovo-63mer
make[2]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/SOAPdenovo2'
make[2]: Nothing to be done for 'install-data-am'.
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c SOAPdenovo-63mer SOAPdenovo-127mer '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c SOAPdenovo-63mer /usr/local/MaSuRCA-3.3.3/bin/SOAPdenovo-63mer
libtool: install: /usr/bin/install -c SOAPdenovo-127mer /usr/local/MaSuRCA-3.3.3/bin/SOAPdenovo-127mer
make[2]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/SOAPdenovo2'
make[1]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/SOAPdenovo2'
Making install in PacBio pwd /usr/local/MaSuRCA-3.3.3/global-1
make[1]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/PacBio'
make  install-am
make[2]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/PacBio'
  CXX      src_jf_aligner/jf_aligner.o
  CXX      src_jf_aligner/pb_aligner.o
  CXX      src_jf_aligner/coarse_aligner.o
  CXX      src_jf_aligner/superread_parser.o
  CXX      src_jf_aligner/fine_aligner.o
  CXX      src_jf_aligner/create_mega_reads.o
  CXX      src_jf_aligner/overlap_graph.o
  CXX      src_jf_aligner/longest_path_overlap_graph2.o
  CXX      src_jf_aligner/coords_parsing.o
  CXX      src_jf_aligner/merge_coords.o
  CXXLD    bin/merge_coords
  CXXLD    bin/longest_path
  CXXLD    bin/jf_aligner
  CXXLD    bin/create_mega_reads
make[3]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/PacBio'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c bin/jf_aligner bin/create_mega_reads bin/longest_path bin/merge_coords bin/findGapsInCoverageOfPacbios bin/get_super_read_sizes '/usr/local/MaSuRCA-3.3.3/bin'
 /usr/bin/install -c src_mega_reads/mega_reads_assemble_nomatch.sh src_mega_reads/mega_reads_assemble_cluster.sh src_mega_reads/make_mr_frg.pl src_mega_reads/fastqToFasta.pl src_mega_reads/reconciliate_mega_reads.maximal.nucmer.pl src_mega_reads/join_mega_reads_trim.onepass.nomatch.pl src_mega_reads/join_mega_reads_trim.onepass.pl src_mega_reads/make_mate_frg.pl src_mega_reads/determineUnjoinablePacbioSubmegas.perl src_ref/join_mega_reads_trim.onepass.ref.pl src_mega_reads/refine.sh src_mega_reads/refine_alignments.pl src_mega_reads/split_matches_file.pl src_ref/mega_reads_assemble_ref.sh src_reconcile/reconcile_matches.pl src_reconcile/merge_contigs.sh src_reconcile/merge_scaffolds.sh src_reconcile/output_reconciled_scaffolds.pl src_reconcile/merge_matches_and_tile_coords_file.pl src_mega_reads/reconcile_alignments.sh src_mega_reads/split_long_unitigs.pl src_mega_reads/recover_scaffolds.pl src_mega_reads/trim_by_kunitigs.pl src_mega_reads/trim_mega_reads.pl src_reconcile/compute_coverage.pl src_reconcile/evaluate_splits.pl src_reconcile/evaluate_consensus_error_rate.sh src_reconcile/extract_single_best_match_coords_file.pl src_reconcile/chromosome_scaffolder.sh src_reconcile/break_contigs.pl src_reconcile/merge_sequences_simple.pl src_mega_reads/get_super_read_sizes.pl src_mega_reads/translate_reduced_reads.pl src_ref/recompute_astat_superreads_CA8.sh src_mega_reads/add_pb_seq.pl src_mega_reads/deduplicate_unitigs.sh src_mega_reads/deduplicate_contigs.sh src_mega_reads/parallel_delta-filter.sh src_reconcile/polish_with_illumina_assembly.sh src_reconcile/extract_merges.pl '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c bin/jf_aligner /usr/local/MaSuRCA-3.3.3/bin/jf_aligner
libtool: install: /usr/bin/install -c bin/create_mega_reads /usr/local/MaSuRCA-3.3.3/bin/create_mega_reads
libtool: install: /usr/bin/install -c bin/longest_path /usr/local/MaSuRCA-3.3.3/bin/longest_path
 /usr/bin/install -c src_reconcile/merge_contigs.pl src_reconcile/create_merged_sequences.pl src_mega_reads/find_contained_reads.pl src_reconcile/reconcile_consensus.pl src_mega_reads/fragScaff.sh src_mega_reads/fragScaff.pl src_mega_reads/blast_self_alignment_filter.pl src_mega_reads/fasta_make_Nbase_bed.pl src_mega_reads/create_merged_mega-reads.pl src_mega_reads/extract_merges_mega-reads.pl src_mega_reads/merge_mega-reads.pl src_mega_reads/split_reads_to_join.pl src_mega_reads/filter_delta_file_for_qrys.pl src_mega_reads/process_scaffold_gaps.pl src_mega_reads/splitScaffoldsAtNs.pl src_trio/classify_reads.pl src_trio/resolve_trio.sh src_mega_reads/extract_unique_mega-reads.pl '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c bin/merge_coords /usr/local/MaSuRCA-3.3.3/bin/merge_coords
libtool: install: /usr/bin/install -c bin/findGapsInCoverageOfPacbios /usr/local/MaSuRCA-3.3.3/bin/findGapsInCoverageOfPacbios
libtool: install: /usr/bin/install -c bin/get_super_read_sizes /usr/local/MaSuRCA-3.3.3/bin/get_super_read_sizes
make[3]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/PacBio'
make[2]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/PacBio'
make[1]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/PacBio'
Making install in MUMmer pwd /usr/local/MaSuRCA-3.3.3/global-1
make[1]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/MUMmer'
make  install-am
make[2]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/MUMmer'
make[3]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/MUMmer'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libumdmummer.la '/usr/local/MaSuRCA-3.3.3/lib'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/include/mummer-1'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/libexec/global'
 /usr/bin/install -c .libs/mummerplot .libs/dnadiff .libs/promer .libs/exact-tandems '/usr/local/MaSuRCA-3.3.3/bin'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/lib/perl'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/lib/perl'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/lib/pkgconfig'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   swig/perl5/mummer.la '/usr/local/MaSuRCA-3.3.3/lib/perl'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include/mt_skip_list'
 /usr/bin/install -c -m 644  include/mt_skip_list/common.hpp include/mt_skip_list/set.hpp '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include/mt_skip_list'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c mgaps postnuc prepro postpro '/usr/local/MaSuRCA-3.3.3/libexec/global'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/lib/global'
 /usr/bin/install -c -m 644 mummer.pc '/usr/local/MaSuRCA-3.3.3/lib/pkgconfig'
 /usr/bin/install -c swig/perl5/mummer.pm '/usr/local/MaSuRCA-3.3.3/lib/perl'
 /usr/bin/install -c scripts/Foundation.pm scripts/tandem-repeat.awk '/usr/local/MaSuRCA-3.3.3/lib/global'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include/compactsufsort'
 /usr/bin/install -c -m 644  include/compactsufsort/compactsufsort.hpp include/compactsufsort/const_iterator_traits.hpp include/compactsufsort/said_traits.hpp include/compactsufsort/trsort_imp.hpp include/compactsufsort/compactsufsort_imp.hpp include/compactsufsort/divsufsort_private.h include/compactsufsort/sssort_imp.hpp '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include/compactsufsort'
libtool: install: /usr/bin/install -c .libs/libumdmummer.so.0.0.0 /usr/local/MaSuRCA-3.3.3/lib/libumdmummer.so.0.0.0
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include/mummer'
 /usr/bin/install -c -m 644  include/mummer/sparseSA.hpp include/mummer/fasta.hpp include/mummer/postnuc.hh include/mummer/translate.hh include/mummer/sw_align.hh include/mummer/tigrinc.hh include/mummer/nucmer.hpp include/mummer/mgaps.hh include/mummer/delta.hh include/mummer/sw_alignscore.hh include/mummer/sparseSA_imp.hpp include/mummer/timer.hpp include/mummer/48bit_index.hpp include/mummer/48bit_iterator.hpp include/mummer/const_iterator_traits.hpp include/mummer/dset.hpp include/mummer/openmp_qsort.hpp include/mummer/redirect_to_pager.hpp '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include/mummer'
libtool: install: /usr/bin/install -c .libs/mgaps /usr/local/MaSuRCA-3.3.3/libexec/global/mgaps
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/global-1/MUMmer; /bin/bash /usr/local/MaSuRCA-3.3.3/global-1/libtool  --silent --tag CXX --mode=relink g++ -std=c++11 -std=c++0x -fopenmp -DNDEBUG -std=c++0x -g -O2 -module -o swig/perl5/mummer.la -rpath /usr/local/MaSuRCA-3.3.3/lib/perl swig/perl5/swig_perl5_mummer_la-swig_wrap.lo libumdmummer.la -lbz2 -lz -lpthread )
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib && { ln -s -f libumdmummer.so.0.0.0 libumdmummer.so.0 || { rm -f libumdmummer.so.0 && ln -s libumdmummer.so.0.0.0 libumdmummer.so.0; }; })
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib && { ln -s -f libumdmummer.so.0.0.0 libumdmummer.so || { rm -f libumdmummer.so && ln -s libumdmummer.so.0.0.0 libumdmummer.so; }; })
libtool: install: /usr/bin/install -c .libs/libumdmummer.lai /usr/local/MaSuRCA-3.3.3/lib/libumdmummer.la
libtool: install: /usr/bin/install -c .libs/libumdmummer.a /usr/local/MaSuRCA-3.3.3/lib/libumdmummer.a
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include'
 /usr/bin/install -c -m 644  include/thread_pipe.hpp '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include'
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include/thread_pipe'
 /usr/bin/install -c -m 644  include/thread_pipe/circular_buffer.hpp include/thread_pipe/cooperative_pool2.hpp include/thread_pipe/divisor.hpp include/thread_pipe/traits.hpp '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include/thread_pipe'
libtool: install: /usr/bin/install -c .libs/postnuc /usr/local/MaSuRCA-3.3.3/libexec/global/postnuc
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include/jellyfish'
 /usr/bin/install -c -m 644  include/jellyfish/circular_buffer.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/cpp_array.hpp include/jellyfish/divisor.hpp include/jellyfish/stream_manager.hpp include/jellyfish/whole_sequence_parser.hpp '/usr/local/MaSuRCA-3.3.3/include/mummer-1/include/jellyfish'
libtool: install: /usr/bin/install -c .libs/prepro /usr/local/MaSuRCA-3.3.3/libexec/global/prepro
libtool: install: chmod 644 /usr/local/MaSuRCA-3.3.3/lib/libumdmummer.a
libtool: install: ranlib /usr/local/MaSuRCA-3.3.3/lib/libumdmummer.a
libtool: install: /usr/bin/install -c .libs/postpro /usr/local/MaSuRCA-3.3.3/libexec/global/postpro
libtool: finish: PATH="/home/gebarros/bin:/home/gebarros/.local/bin:/home/gebarros/miniconda3/condabin:/usr/local/meme_4.12.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/snap/bin:/opt/dell/srvadmin/bin:/usr/local/amos-3.1.0/bin:/usr/local/MaSuRCA-3.3.3/dist-bin:/sbin" ldconfig -n /usr/local/MaSuRCA-3.3.3/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/MaSuRCA-3.3.3/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/usr/local/MaSuRCA-3.3.3/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c mummer show-coords show-aligns show-snps show-tiling show-diff repeat-match annotate combineMUMs delta-filter nucmer '/usr/local/MaSuRCA-3.3.3/bin'
libtool: install: /usr/bin/install -c .libs/mummer /usr/local/MaSuRCA-3.3.3/bin/mummer
libtool: install: /usr/bin/install -c .libs/show-coords /usr/local/MaSuRCA-3.3.3/bin/show-coords
libtool: install: /usr/bin/install -c swig/perl5/.libs/mummer.so.0.0.0T /usr/local/MaSuRCA-3.3.3/lib/perl/mummer.so.0.0.0
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib/perl && { ln -s -f mummer.so.0.0.0 mummer.so.0 || { rm -f mummer.so.0 && ln -s mummer.so.0.0.0 mummer.so.0; }; })
libtool: install: (cd /usr/local/MaSuRCA-3.3.3/lib/perl && { ln -s -f mummer.so.0.0.0 mummer.so || { rm -f mummer.so && ln -s mummer.so.0.0.0 mummer.so; }; })
libtool: install: /usr/bin/install -c swig/perl5/.libs/mummer.lai /usr/local/MaSuRCA-3.3.3/lib/perl/mummer.la
libtool: install: /usr/bin/install -c .libs/show-aligns /usr/local/MaSuRCA-3.3.3/bin/show-aligns
libtool: install: /usr/bin/install -c swig/perl5/.libs/mummer.a /usr/local/MaSuRCA-3.3.3/lib/perl/mummer.a
libtool: install: /usr/bin/install -c .libs/show-snps /usr/local/MaSuRCA-3.3.3/bin/show-snps
libtool: install: chmod 644 /usr/local/MaSuRCA-3.3.3/lib/perl/mummer.a
libtool: install: ranlib /usr/local/MaSuRCA-3.3.3/lib/perl/mummer.a
libtool: install: /usr/bin/install -c .libs/show-tiling /usr/local/MaSuRCA-3.3.3/bin/show-tiling
libtool: finish: PATH="/home/gebarros/bin:/home/gebarros/.local/bin:/home/gebarros/miniconda3/condabin:/usr/local/meme_4.12.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/snap/bin:/opt/dell/srvadmin/bin:/usr/local/amos-3.1.0/bin:/usr/local/MaSuRCA-3.3.3/dist-bin:/sbin" ldconfig -n /usr/local/MaSuRCA-3.3.3/lib/perl
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/MaSuRCA-3.3.3/lib/perl

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
libtool: install: /usr/bin/install -c .libs/show-diff /usr/local/MaSuRCA-3.3.3/bin/show-diff
libtool: install: /usr/bin/install -c .libs/repeat-match /usr/local/MaSuRCA-3.3.3/bin/repeat-match
libtool: install: /usr/bin/install -c .libs/annotate /usr/local/MaSuRCA-3.3.3/bin/annotate
libtool: install: /usr/bin/install -c .libs/combineMUMs /usr/local/MaSuRCA-3.3.3/bin/combineMUMs
libtool: install: /usr/bin/install -c .libs/delta-filter /usr/local/MaSuRCA-3.3.3/bin/delta-filter
libtool: install: /usr/bin/install -c .libs/nucmer /usr/local/MaSuRCA-3.3.3/bin/nucmer
make[3]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/MUMmer'
make[2]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/MUMmer'
make[1]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/MUMmer'
Making install in CA8
make[1]: Entering directory '/usr/local/MaSuRCA-3.3.3/global-1/CA8'
  CXXLD    bin/meryl
  CXXLD    bin/merTrim
  CXXLD    bin/overmerry
Makefile:3344: recipe for target 'bin/meryl' failed
Makefile:3453: recipe for target 'bin/overmerry' failed
Makefile:3324: recipe for target 'bin/merTrim' failed
make[1]: Leaving directory '/usr/local/MaSuRCA-3.3.3/global-1/CA8'
Makefile:847: recipe for target 'install-special' failed
alekseyzimin / masurca

Error in the ./instaIl.sh process MaSuRCA3.3.3 #125

--
