masurca_error

(base) nakajima@nakajima-Precision-Tower-7910:~/biotools/MaSuRCA-3.3.3$ ./install.sh

+ pwd -P

+ ROOT=/home/nakajima/biotools/MaSuRCA-3.3.3

+ [ -z  ]

+ DEST=/home/nakajima/biotools/MaSuRCA-3.3.3

+ mkdir -p dist-bin

+ PATH=/home/nakajima/.rbenv/plugins/ruby-build/bin:/home/nakajima/.rbenv/shims:/home/nakajima/.rbenv/bin:/home/nakajima/biotools/Augustus/bin:/home/nakajima/anaconda3/bin:/home/nakajima/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/nakajima/biotools/salmon/bin:/home/nakajima/biotools/ont-guppy-cpu/bin/:/usr/include/string.h:/home/nakajima/biotools/MaSuRCA-3.3.3/dist-bin

+ which make

+ ln -sf /usr/bin/make /home/nakajima/biotools/MaSuRCA-3.3.3/dist-bin/gmake

+ ln -sf /home/nakajima/biotools/MaSuRCA-3.3.3/PkgConfig.pm /home/nakajima/biotools/MaSuRCA-3.3.3/dist-bin/pkg-config

+ grep -c ^processor /proc/cpuinfo

+ export NUM_THREADS=40

+ BINDIR=/home/nakajima/biotools/MaSuRCA-3.3.3/bin

+ LIBDIR=/home/nakajima/biotools/MaSuRCA-3.3.3/lib

+ export PKG_CONFIG_PATH=/home/nakajima/biotools/MaSuRCA-3.3.3/lib/pkgconfig:

+ cd global-1

+ ./configure --prefix=/home/nakajima/biotools/MaSuRCA-3.3.3 --bindir=/home/nakajima/biotools/MaSuRCA-3.3.3/bin --libdir=/home/nakajima/biotools/MaSuRCA-3.3.3/lib

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... no

checking for mawk... mawk

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

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/jellyfish' に入ります

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/jellyfish' に入ります

Makefile:1622: recipe for target 'swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo' failed

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/jellyfish' から出ます

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/jellyfish' から出ます

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/samtools' に入ります

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/samtools' に入ります

/bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/lib'

/bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/include/samtools/bcftools'

/bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/include/samtools'

/bin/bash ../libtool   --mode=install /usr/bin/install -c   libbam.la bcftools/libbcf.la '/home/nakajima/biotools/MaSuRCA-3.3.3/lib'

/usr/bin/install -c -m 644 bcftools/bcf.h bcftools/kmin.h bcftools/prob1.h '/home/nakajima/biotools/MaSuRCA-3.3.3/include/samtools/bcftools'

/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 '/home/nakajima/biotools/MaSuRCA-3.3.3/include/samtools'

 

flag during linking and do at least one of the following:

   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable

  - add LIBDIR to the `LD_RUN_PATH' environment variable

     during linking

   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag

 

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 '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'

  /bin/bash ../libtool   --mode=install /usr/bin/install -c samtools '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'

libtool: install: /usr/bin/install -c .libs/samtools /home/nakajima/biotools/MaSuRCA-3.3.3/bin/samtools

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/samtools' から出ます

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/samtools' から出ます

Making install in prepare pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/prepare' に入ります

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/prepare' に入ります

make[2]: 'install-data-am' に対して行うべき事はありません.

 /bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'

  /bin/bash ../libtool   --mode=install /usr/bin/install -c finalFusion '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'

libtool: install: /usr/bin/install -c finalFusion /home/nakajima/biotools/MaSuRCA-3.3.3/bin/finalFusion

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/prepare' から出ます

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/prepare' から出ます

Making install in ufasta pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' に入ります

make  install-am

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' に入ります

make[3]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' に入ります

make[3]: 'install-data-am' に対して行うべき事はありません.

 /bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'

  /bin/bash ../libtool   --mode=install /usr/bin/install -c ufasta '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'

libtool: install: /usr/bin/install -c ufasta /home/nakajima/biotools/MaSuRCA-3.3.3/bin/ufasta

make[3]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' から出ます

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' から出ます

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' から出ます

Making install in quorum pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/quorum' に入ります

make  install-am

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/quorum' に入ります

  CXX      src/error_correct_reads.o

  CXX      src/create_database.o

  CXX      src/merge_mate_pairs.o

  GEN      quorum

  CXXLD    split_mate_pairs

src/merge_mate_pairs.cc:4:10: fatal error: jellyfish/stream_manager.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/stream_manager.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

src/create_database.cc:23:10: fatal error: jellyfish/mer_dna.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/mer_dna.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:922: recipe for target 'src/merge_mate_pairs.o' failed

make[2]: *** [src/merge_mate_pairs.o] Error 1

make[2]: *** 未完了のジョブを待っています....

Makefile:922: recipe for target 'src/create_database.o' failed

make[2]: *** [src/create_database.o] Error 1

src/error_correct_reads.cc:25:10: fatal error: jellyfish/atomic_gcc.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/atomic_gcc.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:922: recipe for target 'src/error_correct_reads.o' failed

make[2]: *** [src/error_correct_reads.o] Error 1

/usr/bin/ld: cannot find -ljellyfish-2.0

collect2: error: ld returned 1 exit status

Makefile:862: recipe for target 'split_mate_pairs' failed

make[2]: *** [split_mate_pairs] Error 1

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/quorum' から出ます

Makefile:1257: recipe for target 'install' failed

make[1]: *** [install] Error 2

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/quorum' から出ます

Making install in SuperReads pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SuperReads' に入ります

make  install-am

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SuperReads' に入ります

  CXX      src/error_corrected2frg.o

  CXX      src/sorted_merge.o

  CXX      src/create_k_unitigs_large_k.o

  CXXLD    reverse_complement

  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

  CXXLD    reduce_sr

  CXXLD    homo_trim

  CXX      src2/findMatchesBetweenKUnitigsAndReads.o

  CXX      src2/createKUnitigMaxOverlaps.o

  CXX      src/read_parser.o

  CXXLD    samToDelta

  CXX      src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.o

  CXX      src2/getSuperReadInsertCountsFromReadPlacementFile.o

  CXX      src2/joinKUnitigs_v3.o

  CXXLD    createFastaSuperReadSequences

  CXXLD    eliminateBadSuperReadsUsingList

  CXXLD    outputRecordsNotOnList

  CXXLD    killBadKUnitigs

  CXXLD    makeAdjustmentFactorsForNumReadsForAStatBasedOnGC

  CXX      src2/collectReadSequencesForLocalGapClosing.o

  CXX      src2/runByDirectory.o

mkdir -p src/

  CXXLD    makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2

  CXXLD    create_sr_frg

  CXXLD    getATBiasInCoverageForIllumina_v2

  CXXLD    splitFileAtNs

sed -e 's,[@]bindir[@],/home/nakajima/biotools/MaSuRCA-3.3.3/bin,g' \

    -e 's,[@]libdir[@],/home/nakajima/biotools/MaSuRCA-3.3.3/lib,g' \

    -e 's,[@]PERL_EXT_DIR[@],/home/nakajima/biotools/MaSuRCA-3.3.3/lib/perl,g' < src/MasurcaPaths.pm.in > src/MasurcaPaths.pm

  CXXLD    extendSuperReadsForUniqueKmerNeighbors

  CXXLD    extendSuperReadsBasedOnUniqueExtensions

  CXXLD    addSurrogatesToFrgCtgFile

src2/findMatchesBetweenKUnitigsAndReads.cc:31:10: fatal error: jellyfish/mer_dna.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/mer_dna.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

chmod +x src/MasurcaPaths.pm

Makefile:1604: recipe for target 'src2/findMatchesBetweenKUnitigsAndReads.o' failed

make[2]: *** [src2/findMatchesBetweenKUnitigsAndReads.o] Error 1

make[2]: *** 未完了のジョブを待っています....

src2/createKUnitigMaxOverlaps.cc:65:10: fatal error: jellyfish/err.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/err.hpp>

          ^~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1604: recipe for target 'src2/createKUnitigMaxOverlaps.o' failed

make[2]: *** [src2/createKUnitigMaxOverlaps.o] Error 1

src/filter_overlap_file.cc:23:10: fatal error: jellyfish/jellyfish.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/jellyfish.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1604: recipe for target 'src/filter_overlap_file.o' failed

make[2]: *** [src/filter_overlap_file.o] Error 1

src/rename_filter_fastq.cc:21:10: fatal error: jellyfish/err.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/err.hpp>

          ^~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1604: recipe for target 'src/rename_filter_fastq.o' failed

make[2]: *** [src/rename_filter_fastq.o] Error 1

src/bloom_query.cc:2:10: fatal error: jellyfish/mapped_file.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/mapped_file.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1604: recipe for target 'src/bloom_query.o' failed

make[2]: *** [src/bloom_query.o] Error 1

/usr/bin/ld: cannot find -ljellyfish-2.0

collect2: error: ld returned 1 exit status

src/error_corrected2frg.cc:24:10: fatal error: jellyfish/err.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/err.hpp>

          ^~~~~~~~~~~~~~~~~~~

compilation terminated.

/usr/bin/ld: cannot find -ljellyfish-2.0

collect2: error: ld returned 1 exit status

Makefile:1434: recipe for target 'reverse_complement' failed

make[2]: *** [reverse_complement] Error 1

Makefile:1422: recipe for target 'reduce_sr' failed

make[2]: *** [reduce_sr] Error 1

Makefile:1604: recipe for target 'src/error_corrected2frg.o' failed

make[2]: *** [src/error_corrected2frg.o] Error 1

/usr/bin/ld: cannot find -ljellyfish-2.0

collect2: error: ld returned 1 exit status

src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.cc:27:10: fatal error: jellyfish/err.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/err.hpp>

          ^~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1446: recipe for target 'samToDelta' failed

make[2]: *** [samToDelta] Error 1

/usr/bin/ld: cannot find -ljellyfish-2.0

Makefile:1604: recipe for target 'src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.o' failed

make[2]: *** [src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.o] Error 1

collect2: error: ld returned 1 exit status

In file included from ./include/jflib/multiplexed_parser.hpp:26:0,

                 from ./src/read_parser.hpp:24,

                 from src/read_parser.cc:19:

./include/jflib/pool.hpp:22:10: fatal error: jellyfish/circular_buffer.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/circular_buffer.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1416: recipe for target 'outputRecordsNotOnList' failed

make[2]: *** [outputRecordsNotOnList] Error 1

src/create_k_unitigs_large_k2.cc:24:10: fatal error: jellyfish/jellyfish.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/jellyfish.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

/usr/bin/ld: cannot find -ljellyfish-2.0

src2/runByDirectory.cc:20:10: fatal error: jellyfish/err.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/err.hpp>

          ^~~~~~~~~~~~~~~~~~~

compilation terminated.

collect2: error: ld returned 1 exit status

Makefile:1604: recipe for target 'src/read_parser.o' failed

make[2]: *** [src/read_parser.o] Error 1

src2/getSuperReadInsertCountsFromReadPlacementFile.cc:27:10: fatal error: jellyfish/err.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/err.hpp>

          ^~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1320: recipe for target 'create_sr_frg' failed

make[2]: *** [create_sr_frg] Error 1

In file included from src/create_k_unitigs_large_k.cc:25:0:

./src/create_k_unitigs_common.hpp:21:10: fatal error: jellyfish/thread_exec.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/thread_exec.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

/usr/bin/ld: cannot find -ljellyfish-2.0

/usr/bin/ld: cannot find -ljellyfish-2.0

/src2/collectReadSequencesForLocalGapClosing.cc:19:10: fatal error: jellyfish/err.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/err.hpp>

          ^~~~~~~~~~~~~~~~~~~

usr/bin/ld: cannot findcompilation terminated.

 -ljellyfish-2.0

/usr/bin/ld: cannot find -ljellyfish-2.0

/usr/bin/ld: cannot find -ljellyfish-2.0

/usr/bin/ld: cannot find -ljellyfish-2.0

src/sorted_merge.cc:29:10: fatal error: jellyfish/err.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/err.hpp>

          ^~~~~~~~~~~~~~~~~~~

compilation terminated.

/usr/bin/ld: cannot find -ljellyfish-2.0

/usr/bin/ld: cannot find -ljellyfish-2.0

src2/joinKUnitigs_v3.cc:48:10: fatal error: jellyfish/err.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/err.hpp>

          ^~~~~~~~~~~~~~~~~~~

compilation terminated.

/usr/bin/ld: cannot find -ljellyfish-2.0

/usr/bin/ld: cannot find -ljellyfish-2.0

/usr/bin/ld: cannot find -ljellyfish-2.0

Makefile:1604: recipe for target 'src/create_k_unitigs_large_k2.o' failed

make[2]: *** [src/create_k_unitigs_large_k2.o] Error 1

Makefile:1604: recipe for target 'src2/runByDirectory.o' failed

make[2]: *** [src2/runByDirectory.o] Error 1

collect2: error: ld returned 1 exit status

collect2: error: ld returned 1 exit status

collect2: error: ld returned 1 exit status

collect2: error: ld returned 1 exit status

collect2: error: ld returned 1 exit status

collect2: error: ld returned 1 exit status

collect2: error: ld returned 1 exit status

collect2: error: ld returned 1 exit status

collect2: error: ld returned 1 exit status

Makefile:1604: recipe for target 'src2/getSuperReadInsertCountsFromReadPlacementFile.o' failed

make[2]: *** [src2/getSuperReadInsertCountsFromReadPlacementFile.o] Error 1

Makefile:1604: recipe for target 'src/create_k_unitigs_large_k.o' failed

make[2]: *** [src/create_k_unitigs_large_k.o] Error 1

collect2: error: ld returned 1 exit status

collect2: error: ld returned 1 exit status

Makefile:1604: recipe for target 'src2/collectReadSequencesForLocalGapClosing.o' failed

make[2]: *** [src2/collectReadSequencesForLocalGapClosing.o] Error 1

Makefile:1604: recipe for target 'src/sorted_merge.o' failed

make[2]: *** [src/sorted_merge.o] Error 1

Makefile:1604: recipe for target 'src2/joinKUnitigs_v3.o' failed

make[2]: *** [src2/joinKUnitigs_v3.o] Error 1

Makefile:1326: recipe for target 'eliminateBadSuperReadsUsingList' failed

make[2]: *** [eliminateBadSuperReadsUsingList] Error 1

Makefile:1386: recipe for target 'homo_trim' failed

make[2]: *** [homo_trim] Error 1

Makefile:1458: recipe for target 'splitFileAtNs' failed

make[2]: *** [splitFileAtNs] Error 1

Makefile:1338: recipe for target 'extendSuperReadsBasedOnUniqueExtensions' failed

make[2]: *** [extendSuperReadsBasedOnUniqueExtensions] Error 1

Makefile:1366: recipe for target 'getATBiasInCoverageForIllumina_v2' failed

make[2]: *** [getATBiasInCoverageForIllumina_v2] Error 1

Makefile:1404: recipe for target 'makeAdjustmentFactorsForNumReadsForAStatBasedOnGC' failed

make[2]: *** [makeAdjustmentFactorsForNumReadsForAStatBasedOnGC] Error 1

Makefile:1398: recipe for target 'killBadKUnitigs' failed

make[2]: *** [killBadKUnitigs] Error 1

Makefile:1410: recipe for target 'makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2' failed

make[2]: *** [makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2] Error 1

Makefile:1344: recipe for target 'extendSuperReadsForUniqueKmerNeighbors' failed

make[2]: *** [extendSuperReadsForUniqueKmerNeighbors] Error 1

Makefile:1296: recipe for target 'createFastaSuperReadSequences' failed

make[2]: *** [createFastaSuperReadSequences] Error 1

Makefile:1214: recipe for target 'addSurrogatesToFrgCtgFile' failed

make[2]: *** [addSurrogatesToFrgCtgFile] Error 1

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SuperReads' から出ます

Makefile:2285: recipe for target 'install' failed

make[1]: *** [install] Error 2

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SuperReads' から出ます

Making install in SOAPdenovo2 pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SOAPdenovo2' に入ります

  CC       standardPregraph/libstandard63_a-readseq1by1.o

  CXX      sparsePregraph/libsparse63_a-build_preArc.o

  CXX      sparsePregraph/libsparse63_a-io_func.o

  CC       standardPregraph/libstandard127_a-readseq1by1.o

  CXX      sparsePregraph/libsparse127_a-build_preArc.o

  CXX      sparsePregraph/libsparse127_a-io_func.o

standardPregraph/readseq1by1.c: In function ‘read1seqfq’:

standardPregraph/readseq1by1.c:425:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]

    fgets ( str, lineLen, fp ); // pass quality value line

    ^~~~~~~~~~~~~~~~~~~~~~~~~~

standardPregraph/readseq1by1.c: In function ‘read1seqfq’:

standardPregraph/readseq1by1.c:425:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]

    fgets ( str, lineLen, fp ); // pass quality value line

    ^~~~~~~~~~~~~~~~~~~~~~~~~~

  AR       libstandard127.a

ar: `u' modifier ignored since `D' is the default (see `U')

ar: `u' modifier ignored since `D' is the default (see `U')

In file included from sparsePregraph/build_preArc.cpp:46:0:

./sparsePregraph/inc/sparse_kmer.h: In function ‘void printKmer(const kmer_t2*, FILE*)’:

./sparsePregraph/inc/sparse_kmer.h:307:121: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]

  fprintf ( fp, "%llx %llx %llx %llx,\n", ( kmer->kmer ) [0], ( kmer->kmer ) [1], ( kmer->kmer ) [2], ( kmer->kmer ) [3] );

                                          ~~~~~~~~~~~~~~~~~~                                                             ^

./sparsePregraph/inc/sparse_kmer.h:307:121: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]

./sparsePregraph/inc/sparse_kmer.h:307:121: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]

./sparsePregraph/inc/sparse_kmer.h:307:121: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]

sparsePregraph/build_preArc.cpp: In function ‘void build_vertexes(vertex_hash2*, int, char*)’:

sparsePregraph/build_preArc.cpp:132:128: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 4 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

             & ( from_kmer.kmer ) [0], & ( from_kmer.kmer ) [1], & ( from_kmer.kmer ) [2], & ( from_kmer.kmer ) [3],

             ~~~~~~~~~~~~~~~~~~~~~~~~                                                                                            

             & ( to_kmer.kmer ) [0], & ( to_kmer.kmer ) [1], & ( to_kmer.kmer ) [2], & ( to_kmer.kmer ) [3], str, &cvg, &bal_ed ); // from_kmer to_kmer is of no use here

                                                                                                                                ^

sparsePregraph/build_preArc.cpp:132:128: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 5 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

sparsePregraph/build_preArc.cpp:132:128: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 6 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

sparsePregraph/build_preArc.cpp:132:128: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 7 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

sparsePregraph/build_preArc.cpp:132:128: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 8 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

sparsePregraph/build_preArc.cpp:132:128: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 9 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

sparsePregraph/build_preArc.cpp:132:128: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 10 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

sparsePregraph/build_preArc.cpp:132:128: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 11 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

sparsePregraph/build_preArc.cpp:132:128: warning: format ‘%d’ expects argument of type ‘int*’, but argument 14 has type ‘bool*’ [-Wformat=]

sparsePregraph/build_preArc.cpp: In function ‘void output_preArcs(preArc_array*, char*)’:

sparsePregraph/build_preArc.cpp:637:26: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]

    fprintf ( fp, "%u", i );

                          ^

sparsePregraph/build_preArc.cpp:649:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]

      fprintf ( fp, "%u", i );

                            ^

sparsePregraph/build_preArc.cpp: In function ‘void process_1read_preArc(preArc_array*, pthread_spinlock_t*, int, vertex_hash2*, int, int, const char*)’:

sparsePregraph/build_preArc.cpp:785:93: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]

        fprintf ( stderr, "ERROR: left edge id found already !new found id %llu \n", left_id );

                                                                                             ^

sparsePregraph/build_preArc.cpp:860:96: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]

        fprintf ( stderr, "ERROR: right edge id found already, new found id %llu !\n", right_id );

                                                                                                ^

In file included from sparsePregraph/build_preArc.cpp:46:0:

./sparsePregraph/inc/sparse_kmer.h: In function ‘void printKmer(const kmer_t2*, FILE*)’:

./sparsePregraph/inc/sparse_kmer.h:304:72: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]

  fprintf ( fp, "%llx %llx ,\n", ( kmer->kmer ) [0], ( kmer->kmer ) [1] );

                                 ~~~~~~~~~~~~~~~~~~                     ^

./sparsePregraph/inc/sparse_kmer.h:304:72: warning: format ‘%llx’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘uint64_t {aka long unsigned int}’ [-Wformat=]

sparsePregraph/build_preArc.cpp: In function ‘void build_vertexes(vertex_hash2*, int, char*)’:

sparsePregraph/build_preArc.cpp:127:132: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 4 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

             & ( from_kmer.kmer ) [0], & ( from_kmer.kmer ) [1], & ( to_kmer.kmer ) [0], & ( to_kmer.kmer ) [1], str, &cvg, &bal_ed ); // from_kmer to_kmer is of no use here

             ~~~~~~~~~~~~~~~~~~~~~~~~                                                                                               ^

sparsePregraph/build_preArc.cpp:127:132: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 5 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

sparsePregraph/build_preArc.cpp:127:132: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 6 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

sparsePregraph/build_preArc.cpp:127:132: warning: format ‘%llx’ expects argument of type ‘long long unsigned int*’, but argument 7 has type ‘uint64_t* {aka long unsigned int*}’ [-Wformat=]

sparsePregraph/build_preArc.cpp:127:132: warning: format ‘%d’ expects argument of type ‘int*’, but argument 10 has type ‘bool*’ [-Wformat=]

sparsePregraph/build_preArc.cpp: In function ‘void output_preArcs(preArc_array*, char*)’:

sparsePregraph/build_preArc.cpp:637:26: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]

    fprintf ( fp, "%u", i );

                          ^

sparsePregraph/build_preArc.cpp:649:28: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]

      fprintf ( fp, "%u", i );

                            ^

sparsePregraph/build_preArc.cpp: In function ‘void process_1read_preArc(preArc_array*, pthread_spinlock_t*, int, vertex_hash2*, int, int, const char*)’:

sparsePregraph/build_preArc.cpp:785:93: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]

        fprintf ( stderr, "ERROR: left edge id found already !new found id %llu \n", left_id );

                                                                                             ^

sparsePregraph/build_preArc.cpp:860:96: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘size_t {aka long unsigned int}’ [-Wformat=]

        fprintf ( stderr, "ERROR: right edge id found already, new found id %llu !\n", right_id );

                                                                                                ^

  AR       libsparse127.a

ar: `u' modifier ignored since `D' is the default (see `U')

ar: `u' modifier ignored since `D' is the default (see `U')

  GEN      SOAPdenovo-63mer

  GEN      SOAPdenovo-127mer

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SOAPdenovo2' に入ります

make[2]: 'install-data-am' に対して行うべき事はありません.

 /bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'

  /bin/bash ../libtool   --mode=install /usr/bin/install -c SOAPdenovo-63mer SOAPdenovo-127mer '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'

libtool: install: /usr/bin/install -c SOAPdenovo-63mer /home/nakajima/biotools/MaSuRCA-3.3.3/bin/SOAPdenovo-63mer

libtool: install: /usr/bin/install -c SOAPdenovo-127mer /home/nakajima/biotools/MaSuRCA-3.3.3/bin/SOAPdenovo-127mer

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SOAPdenovo2' から出ます

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SOAPdenovo2' から出ます

Making install in PacBio pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/PacBio' に入ります

make  install-am

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/PacBio' に入ります

  CXX      src_jf_aligner/jf_aligner.o

  CXX      src_jf_aligner/pb_aligner.o

  CXX      src_jf_aligner/superread_parser.o

  CXX      src_jf_aligner/coarse_aligner.o

  CXX      src_jf_aligner/fine_aligner.o

  CXX      src_jf_aligner/overlap_graph.o

  CXX      src_jf_aligner/create_mega_reads.o

  CXX      src_jf_aligner/merge_coords.o

  CXX      src_jf_aligner/longest_path_overlap_graph2.o

  CXX      src_jf_aligner/coords_parsing.o

  CXXLD    bin/get_super_read_sizes

  CXXLD    bin/findGapsInCoverageOfPacbios

In file included from src_jf_aligner/jf_aligner.cc:8:0:

./src_jf_aligner/superread_parser.hpp:8:10: fatal error: jellyfish/mer_dna.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/mer_dna.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

In file included from src_jf_aligner/superread_parser.cc:6:0:

./src_jf_aligner/superread_parser.hpp:8:10: fatal error: jellyfish/mer_dna.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/mer_dna.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1249: recipe for target 'src_jf_aligner/jf_aligner.o' failed

make[2]: *** [src_jf_aligner/jf_aligner.o] Error 1

make[2]: *** 未完了のジョブを待っています....

Makefile:1249: recipe for target 'src_jf_aligner/superread_parser.o' failed

make[2]: *** [src_jf_aligner/superread_parser.o] Error 1

In file included from ./src_jf_aligner/fine_aligner.hpp:7:0,

                 from src_jf_aligner/fine_aligner.cc:4:

./src_jf_aligner/jf_aligner.hpp:14:10: fatal error: jellyfish/mer_dna.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/mer_dna.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1249: recipe for target 'src_jf_aligner/fine_aligner.o' failed

make[2]: *** [src_jf_aligner/fine_aligner.o] Error 1

In file included from ./include/jflib/multiplexed_parser.hpp:26:0,

                 from ./src_jf_aligner/coords_parsing.hpp:10,

                 from src_jf_aligner/coords_parsing.cc:4:

./include/jflib/pool.hpp:22:10: fatal error: jellyfish/circular_buffer.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/circular_buffer.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1249: recipe for target 'src_jf_aligner/coords_parsing.o' failed

make[2]: *** [src_jf_aligner/coords_parsing.o] Error 1

In file included from src_jf_aligner/create_mega_reads.cc:8:0:

./src_jf_aligner/superread_parser.hpp:8:10: fatal error: jellyfish/mer_dna.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/mer_dna.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

In file included from ./include/jflib/multiplexed_parser.hpp:26:0,

                 from ./src_jf_aligner/coords_parsing.hpp:10,

                 from src_jf_aligner/merge_coords.cc:7:

./include/jflib/pool.hpp:22:10: fatal error: jellyfish/circular_buffer.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/circular_buffer.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1249: recipe for target 'src_jf_aligner/create_mega_reads.o' failed

make[2]: *** [src_jf_aligner/create_mega_reads.o] Error 1

Makefile:1249: recipe for target 'src_jf_aligner/merge_coords.o' failed

make[2]: *** [src_jf_aligner/merge_coords.o] Error 1

In file included from src_jf_aligner/longest_path_overlap_graph2.cc:9:0:

./src_jf_aligner/output_file.hpp:9:10: fatal error: jellyfish/err.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/err.hpp>

          ^~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1249: recipe for target 'src_jf_aligner/longest_path_overlap_graph2.o' failed

make[2]: *** [src_jf_aligner/longest_path_overlap_graph2.o] Error 1

In file included from ./src_jf_aligner/pb_aligner.hpp:12:0,

                 from src_jf_aligner/pb_aligner.cc:8:

./src_jf_aligner/jf_aligner.hpp:14:10: fatal error: jellyfish/mer_dna.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/mer_dna.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1249: recipe for target 'src_jf_aligner/pb_aligner.o' failed

make[2]: *** [src_jf_aligner/pb_aligner.o] Error 1

In file included from ./src_jf_aligner/pb_aligner.hpp:12:0,

                 from ./src_jf_aligner/overlap_graph.hpp:9,

                 from src_jf_aligner/overlap_graph.cc:4:

./src_jf_aligner/jf_aligner.hpp:14:10: fatal error: jellyfish/mer_dna.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/mer_dna.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1249: recipe for target 'src_jf_aligner/overlap_graph.o' failed

make[2]: *** [src_jf_aligner/overlap_graph.o] Error 1

In file included from ./src_jf_aligner/pb_aligner.hpp:12:0,

                 from ./src_jf_aligner/coarse_aligner.hpp:10,

                 from src_jf_aligner/coarse_aligner.cc:4:

./src_jf_aligner/jf_aligner.hpp:14:10: fatal error: jellyfish/mer_dna.hpp: そのようなファイルやディレクトリはありません

 #include <jellyfish/mer_dna.hpp>

          ^~~~~~~~~~~~~~~~~~~~~~~

compilation terminated.

Makefile:1249: recipe for target 'src_jf_aligner/coarse_aligner.o' failed

make[2]: *** [src_jf_aligner/coarse_aligner.o] Error 1

/usr/bin/ld: cannot find -ljellyfish-2.0

collect2: error: ld returned 1 exit status

Makefile:1087: recipe for target 'bin/findGapsInCoverageOfPacbios' failed

make[2]: *** [bin/findGapsInCoverageOfPacbios] Error 1

/usr/bin/ld: cannot find -ljellyfish-2.0

collect2: error: ld returned 1 exit status

Makefile:1094: recipe for target 'bin/get_super_read_sizes' failed

make[2]: *** [bin/get_super_read_sizes] Error 1

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/PacBio' から出ます

Makefile:1613: recipe for target 'install' failed

make[1]: *** [install] Error 2

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/PacBio' から出ます

Making install in MUMmer pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/MUMmer' に入ります

make  install-am

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/MUMmer' に入ります

  CXX      swig/perl5/swig_perl5_mummer_la-swig_wrap.lo

swig/perl5/swig_wrap.cpp:322:10: fatal error: string.h: No such file or directory

 #include <string.h>

          ^~~~~~~~~~

compilation terminated.

Makefile:1830: recipe for target 'swig/perl5/swig_perl5_mummer_la-swig_wrap.lo' failed

make[2]: *** [swig/perl5/swig_perl5_mummer_la-swig_wrap.lo] Error 1

make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/MUMmer' から出ます

Makefile:2418: recipe for target 'install' failed

make[1]: *** [install] Error 2

make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/MUMmer' から出ます

Makefile:847: recipe for target 'install-special' failed

make: *** [install-special] Error 2