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masurca_error

Hikik1225
Aug 23rd, 2019
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  1. (base) nakajima@nakajima-Precision-Tower-7910:~/biotools/MaSuRCA-3.3.3$ ./install.sh
  2. + pwd -P
  3. + ROOT=/home/nakajima/biotools/MaSuRCA-3.3.3
  4. + [ -z  ]
  5. + DEST=/home/nakajima/biotools/MaSuRCA-3.3.3
  6. + mkdir -p dist-bin
  7. + 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
  8. + which make
  9. + ln -sf /usr/bin/make /home/nakajima/biotools/MaSuRCA-3.3.3/dist-bin/gmake
  10. + ln -sf /home/nakajima/biotools/MaSuRCA-3.3.3/PkgConfig.pm /home/nakajima/biotools/MaSuRCA-3.3.3/dist-bin/pkg-config
  11. + grep -c ^processor /proc/cpuinfo
  12. + export NUM_THREADS=40
  13. + BINDIR=/home/nakajima/biotools/MaSuRCA-3.3.3/bin
  14. + LIBDIR=/home/nakajima/biotools/MaSuRCA-3.3.3/lib
  15. + export PKG_CONFIG_PATH=/home/nakajima/biotools/MaSuRCA-3.3.3/lib/pkgconfig:
  16. + cd global-1
  17. + ./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
  18. checking build system type... x86_64-unknown-linux-gnu
  19. checking host system type... x86_64-unknown-linux-gnu
  20. checking for a BSD-compatible install... /usr/bin/install -c
  21. checking whether build environment is sane... yes
  22. checking for a thread-safe mkdir -p... /bin/mkdir -p
  23. checking for gawk... no
  24. checking for mawk... mawk
  25. checking whether make sets $(MAKE)... yes
  26. checking whether make supports nested variables... yes
  27. checking whether make supports nested variables... (cached) yes
  28. checking how to print strings... printf
  29. checking for style of include used by make... GNU
  30. checking for gcc... gcc
  31. checking whether the C compiler works... yes
  32. checking for C compiler default output file name... a.out
  33. checking for suffix of executables...
  34. checking whether we are cross compiling... no
  35. checking for suffix of object files... o
  36. checking whether we are using the GNU C compiler... yes
  37. checking whether gcc accepts -g... yes
  38. checking for gcc option to accept ISO C89... none needed
  39. checking whether gcc understands -c and -o together... yes
  40. checking dependency style of gcc... gcc3
  41. checking for a sed that does not truncate output... /bin/sed
  42. checking for grep that handles long lines and -e... /bin/grep
  43. checking for egrep... /bin/grep -E
  44. checking for fgrep... /bin/grep -F
  45. checking for ld used by gcc... /usr/bin/ld
  46. checking if the linker (/usr/bin/ld) is GNU ld... yes
  47. checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
  48. checking the name lister (/usr/bin/nm -B) interface... BSD nm
  49. checking whether ln -s works... yes
  50. checking the maximum length of command line arguments... 1572864
  51. checking whether the shell understands some XSI constructs... yes
  52. checking whether the shell understands "+="... yes
  53. checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
  54. checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
  55. checking for /usr/bin/ld option to reload object files... -r
  56. checking for objdump... objdump
  57. checking how to recognize dependent libraries... pass_all
  58. checking for dlltool... no
  59. checking how to associate runtime and link libraries... printf %s\n
  60. checking for ar... ar
  61. checking for archiver @FILE support... @
  62. checking for strip... strip
  63. checking for ranlib... ranlib
  64. checking command to parse /usr/bin/nm -B output from gcc object... ok
  65. checking for sysroot... no
  66. checking for mt... mt
  67. checking if mt is a manifest tool... no
  68. checking how to run the C preprocessor... gcc -E
  69. checking for ANSI C header files... yes
  70. checking for sys/types.h... yes
  71. checking for sys/stat.h... yes
  72. checking for stdlib.h... yes
  73. checking for string.h... yes
  74. checking for memory.h... yes
  75. checking for strings.h... yes
  76. checking for inttypes.h... yes
  77. checking for stdint.h... yes
  78. checking for unistd.h... yes
  79. checking for dlfcn.h... yes
  80. checking for objdir... .libs
  81. checking if gcc supports -fno-rtti -fno-exceptions... no
  82. checking for gcc option to produce PIC... -fPIC -DPIC
  83. checking if gcc PIC flag -fPIC -DPIC works... yes
  84. checking if gcc static flag -static works... yes
  85. checking if gcc supports -c -o file.o... yes
  86. checking if gcc supports -c -o file.o... (cached) yes
  87. checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
  88. checking whether -lc should be explicitly linked in... no
  89. checking dynamic linker characteristics... GNU/Linux ld.so
  90. checking how to hardcode library paths into programs... immediate
  91. checking whether stripping libraries is possible... yes
  92. checking if libtool supports shared libraries... yes
  93. checking whether to build shared libraries... yes
  94. checking whether to build static libraries... yes
  95. checking for gcc... (cached) gcc
  96. checking whether we are using the GNU C compiler... (cached) yes
  97. checking whether gcc accepts -g... (cached) yes
  98. checking for gcc option to accept ISO C89... (cached) none needed
  99. checking whether gcc understands -c and -o together... (cached) yes
  100. checking dependency style of gcc... (cached) gcc3
  101. checking for g++... g++
  102. checking whether we are using the GNU C++ compiler... yes
  103. checking whether g++ accepts -g... yes
  104. checking dependency style of g++... gcc3
  105. checking how to run the C++ preprocessor... g++ -E
  106. checking for ld used by g++... /usr/bin/ld -m elf_x86_64
  107. checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
  108. checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
  109. checking for g++ option to produce PIC... -fPIC -DPIC
  110. checking if g++ PIC flag -fPIC -DPIC works... yes
  111. checking if g++ static flag -static works... yes
  112. checking if g++ supports -c -o file.o... yes
  113. checking if g++ supports -c -o file.o... (cached) yes
  114. checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
  115. checking dynamic linker characteristics... (cached) GNU/Linux ld.so
  116. checking how to hardcode library paths into programs... immediate
  117. checking for pthread_create in -lpthread... yes
  118. checking for library containing clock_gettime... none required
  119. checking for __int128... yes
  120. checking for OpenMP flag of C++ compiler... -fopenmp
  121. checking for Boost headers version >= 1.46.0... yes
  122. checking for Boost's header version... 1_65_1
  123. checking boost/icl/interval_set.hpp usability... yes
  124. checking boost/icl/interval_set.hpp presence... yes
  125. checking for boost/icl/interval_set.hpp... yes
  126. checking for _NSGetExecutablePath... no
  127. checking if std::thread::sleep_for is supported... yes
  128. checking for stdlib.h... (cached) yes
  129. checking for unistd.h... (cached) yes
  130. checking for sys/param.h... yes
  131. checking for getpagesize... yes
  132. checking for working mmap... yes
  133. checking for mremap... yes
  134. checking zlib.h usability... yes
  135. checking zlib.h presence... yes
  136. checking for zlib.h... yes
  137. checking for zlibVersion in -lz... yes
  138. checking bzlib.h usability... yes
  139. checking bzlib.h presence... yes
  140. checking for bzlib.h... yes
  141. checking for BZ2_bzlibVersion in -lbz2... yes
  142. checking for pkg-config... /usr/bin/pkg-config
  143. checking pkg-config is at least version 0.9.0... yes
  144. checking for __builtin_prefetch... yes
  145. checking for architecture... Linux-amd64
  146. checking for yaggo... false
  147. checking for perl... /home/nakajima/anaconda3/bin/perl
  148. checking for Perl prefix... .../..
  149. checking for Perl extension include path... /home/nakajima/anaconda3/lib/5.26.2/x86_64-linux-thread-multi/CORE
  150. checking for Perl extension target directory... $(libdir)/perl
  151. checking for Perl extensions C preprocessor flags... --sysroot=/tmp/build/80754af9/perl_1527832170752/_build_env/x86_64-conda_cos6-linux-gnu/sysroot -D_REENTRANT -D_GNU_SOURCE --sysroot=/tmp/build/80754af9/perl_1527832170752/_build_env/x86_64-conda_cos6-linux-gnu/sysroot -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong
  152. checking for Perl extensions linker flags... -shared -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,-rpath,/home/nakajima/anaconda3/lib -L/home/nakajima/anaconda3/lib --sysroot /tmp/build/80754af9/perl_1527832170752/_build_env/x86_64-conda_cos6-linux-gnu/sysroot -fstack-protector-strong
  153. checking that generated files are newer than configure... done
  154. configure: creating ./config.status
  155. config.status: creating Makefile
  156. config.status: creating jellyfish/jellyfish-2.0.pc
  157. config.status: creating MUMmer/mummer.pc
  158. config.status: creating samtools/Makefile
  159. config.status: creating prepare/Makefile
  160. config.status: creating ufasta/Makefile
  161. config.status: creating quorum/Makefile
  162. config.status: creating SuperReads/Makefile
  163. config.status: creating SOAPdenovo2/Makefile
  164. config.status: creating PacBio/Makefile
  165. config.status: creating CA8/Makefile
  166. config.status: creating jellyfish/Makefile
  167. config.status: creating MUMmer/Makefile
  168. config.status: creating config.h
  169. config.status: config.h is unchanged
  170. config.status: executing depfiles commands
  171. config.status: executing libtool commands
  172. + make -j 40 install-special
  173. Making install in jellyfish pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1
  174. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/jellyfish' に入ります
  175. make  install-am
  176. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/jellyfish' に入ります
  177.  CXX      swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo
  178. swig/perl5/swig_wrap.cpp:322:10: fatal error: string.h: No such file or directory
  179. #include <string.h>
  180.          ^~~~~~~~~~
  181. compilation terminated.
  182. Makefile:1622: recipe for target 'swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo' failed
  183. make[2]: *** [swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo] Error 1
  184. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/jellyfish' から出ます
  185. Makefile:2398: recipe for target 'install' failed
  186. make[1]: *** [install] Error 2
  187. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/jellyfish' から出ます
  188. Making install in samtools pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1
  189. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/samtools' に入ります
  190. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/samtools' に入ります
  191. /bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/lib'
  192. /bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/include/samtools/bcftools'
  193. /bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/include/samtools'
  194. /bin/bash ../libtool   --mode=install /usr/bin/install -c   libbam.la bcftools/libbcf.la '/home/nakajima/biotools/MaSuRCA-3.3.3/lib'
  195. /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'
  196. /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'
  197. libtool: install: /usr/bin/install -c .libs/libbam.so.0.0.0 /home/nakajima/biotools/MaSuRCA-3.3.3/lib/libbam.so.0.0.0
  198. libtool: install: (cd /home/nakajima/biotools/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; }; })
  199. libtool: install: (cd /home/nakajima/biotools/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; }; })
  200. libtool: install: /usr/bin/install -c .libs/libbam.lai /home/nakajima/biotools/MaSuRCA-3.3.3/lib/libbam.la
  201. libtool: install: /usr/bin/install -c bcftools/.libs/libbcf.so.0.0.0 /home/nakajima/biotools/MaSuRCA-3.3.3/lib/libbcf.so.0.0.0
  202. libtool: install: (cd /home/nakajima/biotools/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; }; })
  203. libtool: install: (cd /home/nakajima/biotools/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; }; })
  204. libtool: install: /usr/bin/install -c bcftools/.libs/libbcf.lai /home/nakajima/biotools/MaSuRCA-3.3.3/lib/libbcf.la
  205. libtool: install: /usr/bin/install -c .libs/libbam.a /home/nakajima/biotools/MaSuRCA-3.3.3/lib/libbam.a
  206. libtool: install: chmod 644 /home/nakajima/biotools/MaSuRCA-3.3.3/lib/libbam.a
  207. libtool: install: ranlib /home/nakajima/biotools/MaSuRCA-3.3.3/lib/libbam.a
  208. libtool: install: /usr/bin/install -c bcftools/.libs/libbcf.a /home/nakajima/biotools/MaSuRCA-3.3.3/lib/libbcf.a
  209. libtool: install: chmod 644 /home/nakajima/biotools/MaSuRCA-3.3.3/lib/libbcf.a
  210. libtool: install: ranlib /home/nakajima/biotools/MaSuRCA-3.3.3/lib/libbcf.a
  211. libtool: finish: 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:/sbin" ldconfig -n /home/nakajima/biotools/MaSuRCA-3.3.3/lib
  212. ----------------------------------------------------------------------
  213. Libraries have been installed in:
  214.   /home/nakajima/biotools/MaSuRCA-3.3.3/lib
  215.  
  216. If you ever happen to want to link against installed libraries
  217. in a given directory, LIBDIR, you must either use libtool, and
  218. specify the full pathname of the library, or use the `-LLIBDIR'
  219. flag during linking and do at least one of the following:
  220.    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
  221.     during execution
  222.   - add LIBDIR to the `LD_RUN_PATH' environment variable
  223.      during linking
  224.    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
  225.   - have your system administrator add LIBDIR to `/etc/ld.so.conf'
  226.  
  227. See any operating system documentation about shared libraries for
  228. more information, such as the ld(1) and ld.so(8) manual pages.
  229. ----------------------------------------------------------------------
  230.  /bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'
  231.   /bin/bash ../libtool   --mode=install /usr/bin/install -c samtools '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'
  232. libtool: install: /usr/bin/install -c .libs/samtools /home/nakajima/biotools/MaSuRCA-3.3.3/bin/samtools
  233. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/samtools' から出ます
  234. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/samtools' から出ます
  235. Making install in prepare pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1
  236. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/prepare' に入ります
  237. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/prepare' に入ります
  238. make[2]: 'install-data-am' に対して行うべき事はありません.
  239.  /bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'
  240.   /bin/bash ../libtool   --mode=install /usr/bin/install -c finalFusion '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'
  241. libtool: install: /usr/bin/install -c finalFusion /home/nakajima/biotools/MaSuRCA-3.3.3/bin/finalFusion
  242. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/prepare' から出ます
  243. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/prepare' から出ます
  244. Making install in ufasta pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1
  245. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' に入ります
  246. make  install-am
  247. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' に入ります
  248. make[3]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' に入ります
  249. make[3]: 'install-data-am' に対して行うべき事はありません.
  250.  /bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'
  251.   /bin/bash ../libtool   --mode=install /usr/bin/install -c ufasta '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'
  252. libtool: install: /usr/bin/install -c ufasta /home/nakajima/biotools/MaSuRCA-3.3.3/bin/ufasta
  253. make[3]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' から出ます
  254. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' から出ます
  255. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/ufasta' から出ます
  256. Making install in quorum pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1
  257. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/quorum' に入ります
  258. make  install-am
  259. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/quorum' に入ります
  260.   CXX      src/error_correct_reads.o
  261.   CXX      src/create_database.o
  262.   CXX      src/merge_mate_pairs.o
  263.   GEN      quorum
  264.   CXXLD    split_mate_pairs
  265. 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
  266.  #include <jellyfish/stream_manager.hpp>
  267.           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  268. compilation terminated.
  269. 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
  270.  #include <jellyfish/mer_dna.hpp>
  271.           ^~~~~~~~~~~~~~~~~~~~~~~
  272. compilation terminated.
  273. Makefile:922: recipe for target 'src/merge_mate_pairs.o' failed
  274. make[2]: *** [src/merge_mate_pairs.o] Error 1
  275. make[2]: *** 未完了のジョブを待っています....
  276. Makefile:922: recipe for target 'src/create_database.o' failed
  277. make[2]: *** [src/create_database.o] Error 1
  278. 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
  279.  #include <jellyfish/atomic_gcc.hpp>
  280.           ^~~~~~~~~~~~~~~~~~~~~~~~~~
  281. compilation terminated.
  282. Makefile:922: recipe for target 'src/error_correct_reads.o' failed
  283. make[2]: *** [src/error_correct_reads.o] Error 1
  284. /usr/bin/ld: cannot find -ljellyfish-2.0
  285. collect2: error: ld returned 1 exit status
  286. Makefile:862: recipe for target 'split_mate_pairs' failed
  287. make[2]: *** [split_mate_pairs] Error 1
  288. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/quorum' から出ます
  289. Makefile:1257: recipe for target 'install' failed
  290. make[1]: *** [install] Error 2
  291. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/quorum' から出ます
  292. Making install in SuperReads pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1
  293. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SuperReads' に入ります
  294. make  install-am
  295. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SuperReads' に入ります
  296.   CXX      src/error_corrected2frg.o
  297.   CXX      src/sorted_merge.o
  298.   CXX      src/create_k_unitigs_large_k.o
  299.   CXXLD    reverse_complement
  300.   CXX      src/create_k_unitigs_large_k2.o
  301.   CXX      src/bloom_query.o
  302.   CXX      src/filter_overlap_file.o
  303.   CXX      src/rename_filter_fastq.o
  304.   CXXLD    reduce_sr
  305.   CXXLD    homo_trim
  306.   CXX      src2/findMatchesBetweenKUnitigsAndReads.o
  307.   CXX      src2/createKUnitigMaxOverlaps.o
  308.   CXX      src/read_parser.o
  309.   CXXLD    samToDelta
  310.   CXX      src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.o
  311.   CXX      src2/getSuperReadInsertCountsFromReadPlacementFile.o
  312.   CXX      src2/joinKUnitigs_v3.o
  313.   CXXLD    createFastaSuperReadSequences
  314.   CXXLD    eliminateBadSuperReadsUsingList
  315.   CXXLD    outputRecordsNotOnList
  316.   CXXLD    killBadKUnitigs
  317.   CXXLD    makeAdjustmentFactorsForNumReadsForAStatBasedOnGC
  318.   CXX      src2/collectReadSequencesForLocalGapClosing.o
  319.   CXX      src2/runByDirectory.o
  320. mkdir -p src/
  321.   CXXLD    makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2
  322.   CXXLD    create_sr_frg
  323.   CXXLD    getATBiasInCoverageForIllumina_v2
  324.   CXXLD    splitFileAtNs
  325. sed -e 's,[@]bindir[@],/home/nakajima/biotools/MaSuRCA-3.3.3/bin,g' \
  326.     -e 's,[@]libdir[@],/home/nakajima/biotools/MaSuRCA-3.3.3/lib,g' \
  327.     -e 's,[@]PERL_EXT_DIR[@],/home/nakajima/biotools/MaSuRCA-3.3.3/lib/perl,g' < src/MasurcaPaths.pm.in > src/MasurcaPaths.pm
  328.   CXXLD    extendSuperReadsForUniqueKmerNeighbors
  329.   CXXLD    extendSuperReadsBasedOnUniqueExtensions
  330.   CXXLD    addSurrogatesToFrgCtgFile
  331. 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
  332.  #include <jellyfish/mer_dna.hpp>
  333.           ^~~~~~~~~~~~~~~~~~~~~~~
  334. compilation terminated.
  335. chmod +x src/MasurcaPaths.pm
  336. Makefile:1604: recipe for target 'src2/findMatchesBetweenKUnitigsAndReads.o' failed
  337. make[2]: *** [src2/findMatchesBetweenKUnitigsAndReads.o] Error 1
  338. make[2]: *** 未完了のジョブを待っています....
  339. 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
  340.  #include <jellyfish/err.hpp>
  341.           ^~~~~~~~~~~~~~~~~~~
  342. compilation terminated.
  343. Makefile:1604: recipe for target 'src2/createKUnitigMaxOverlaps.o' failed
  344. make[2]: *** [src2/createKUnitigMaxOverlaps.o] Error 1
  345. 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
  346.  #include <jellyfish/jellyfish.hpp>
  347.           ^~~~~~~~~~~~~~~~~~~~~~~~~
  348. compilation terminated.
  349. Makefile:1604: recipe for target 'src/filter_overlap_file.o' failed
  350. make[2]: *** [src/filter_overlap_file.o] Error 1
  351. 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
  352.  #include <jellyfish/err.hpp>
  353.           ^~~~~~~~~~~~~~~~~~~
  354. compilation terminated.
  355. Makefile:1604: recipe for target 'src/rename_filter_fastq.o' failed
  356. make[2]: *** [src/rename_filter_fastq.o] Error 1
  357. 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
  358.  #include <jellyfish/mapped_file.hpp>
  359.           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
  360. compilation terminated.
  361. Makefile:1604: recipe for target 'src/bloom_query.o' failed
  362. make[2]: *** [src/bloom_query.o] Error 1
  363. /usr/bin/ld: cannot find -ljellyfish-2.0
  364. collect2: error: ld returned 1 exit status
  365. 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
  366.  #include <jellyfish/err.hpp>
  367.           ^~~~~~~~~~~~~~~~~~~
  368. compilation terminated.
  369. /usr/bin/ld: cannot find -ljellyfish-2.0
  370. collect2: error: ld returned 1 exit status
  371. Makefile:1434: recipe for target 'reverse_complement' failed
  372. make[2]: *** [reverse_complement] Error 1
  373. Makefile:1422: recipe for target 'reduce_sr' failed
  374. make[2]: *** [reduce_sr] Error 1
  375. Makefile:1604: recipe for target 'src/error_corrected2frg.o' failed
  376. make[2]: *** [src/error_corrected2frg.o] Error 1
  377. /usr/bin/ld: cannot find -ljellyfish-2.0
  378. collect2: error: ld returned 1 exit status
  379. 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
  380.  #include <jellyfish/err.hpp>
  381.           ^~~~~~~~~~~~~~~~~~~
  382. compilation terminated.
  383. Makefile:1446: recipe for target 'samToDelta' failed
  384. make[2]: *** [samToDelta] Error 1
  385. /usr/bin/ld: cannot find -ljellyfish-2.0
  386. Makefile:1604: recipe for target 'src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.o' failed
  387. make[2]: *** [src2/getSuperReadInsertCountsFromReadPlacementFileTwoPasses.o] Error 1
  388. collect2: error: ld returned 1 exit status
  389. In file included from ./include/jflib/multiplexed_parser.hpp:26:0,
  390.                  from ./src/read_parser.hpp:24,
  391.                  from src/read_parser.cc:19:
  392. ./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
  393.  #include <jellyfish/circular_buffer.hpp>
  394.           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  395. compilation terminated.
  396. Makefile:1416: recipe for target 'outputRecordsNotOnList' failed
  397. make[2]: *** [outputRecordsNotOnList] Error 1
  398. 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
  399.  #include <jellyfish/jellyfish.hpp>
  400.           ^~~~~~~~~~~~~~~~~~~~~~~~~
  401. compilation terminated.
  402. /usr/bin/ld: cannot find -ljellyfish-2.0
  403. 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
  404.  #include <jellyfish/err.hpp>
  405.           ^~~~~~~~~~~~~~~~~~~
  406. compilation terminated.
  407. collect2: error: ld returned 1 exit status
  408. Makefile:1604: recipe for target 'src/read_parser.o' failed
  409. make[2]: *** [src/read_parser.o] Error 1
  410. 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
  411.  #include <jellyfish/err.hpp>
  412.           ^~~~~~~~~~~~~~~~~~~
  413. compilation terminated.
  414. Makefile:1320: recipe for target 'create_sr_frg' failed
  415. make[2]: *** [create_sr_frg] Error 1
  416. In file included from src/create_k_unitigs_large_k.cc:25:0:
  417. ./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
  418.  #include <jellyfish/thread_exec.hpp>
  419.           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
  420. compilation terminated.
  421. /usr/bin/ld: cannot find -ljellyfish-2.0
  422. /usr/bin/ld: cannot find -ljellyfish-2.0
  423. /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
  424.  #include <jellyfish/err.hpp>
  425.           ^~~~~~~~~~~~~~~~~~~
  426. usr/bin/ld: cannot findcompilation terminated.
  427.  -ljellyfish-2.0
  428. /usr/bin/ld: cannot find -ljellyfish-2.0
  429. /usr/bin/ld: cannot find -ljellyfish-2.0
  430. /usr/bin/ld: cannot find -ljellyfish-2.0
  431. 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
  432.  #include <jellyfish/err.hpp>
  433.           ^~~~~~~~~~~~~~~~~~~
  434. compilation terminated.
  435. /usr/bin/ld: cannot find -ljellyfish-2.0
  436. /usr/bin/ld: cannot find -ljellyfish-2.0
  437. 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
  438.  #include <jellyfish/err.hpp>
  439.           ^~~~~~~~~~~~~~~~~~~
  440. compilation terminated.
  441. /usr/bin/ld: cannot find -ljellyfish-2.0
  442. /usr/bin/ld: cannot find -ljellyfish-2.0
  443. /usr/bin/ld: cannot find -ljellyfish-2.0
  444. Makefile:1604: recipe for target 'src/create_k_unitigs_large_k2.o' failed
  445. make[2]: *** [src/create_k_unitigs_large_k2.o] Error 1
  446. Makefile:1604: recipe for target 'src2/runByDirectory.o' failed
  447. make[2]: *** [src2/runByDirectory.o] Error 1
  448. collect2: error: ld returned 1 exit status
  449. collect2: error: ld returned 1 exit status
  450. collect2: error: ld returned 1 exit status
  451. collect2: error: ld returned 1 exit status
  452. collect2: error: ld returned 1 exit status
  453. collect2: error: ld returned 1 exit status
  454. collect2: error: ld returned 1 exit status
  455. collect2: error: ld returned 1 exit status
  456. collect2: error: ld returned 1 exit status
  457. Makefile:1604: recipe for target 'src2/getSuperReadInsertCountsFromReadPlacementFile.o' failed
  458. make[2]: *** [src2/getSuperReadInsertCountsFromReadPlacementFile.o] Error 1
  459. Makefile:1604: recipe for target 'src/create_k_unitigs_large_k.o' failed
  460. make[2]: *** [src/create_k_unitigs_large_k.o] Error 1
  461. collect2: error: ld returned 1 exit status
  462. collect2: error: ld returned 1 exit status
  463. Makefile:1604: recipe for target 'src2/collectReadSequencesForLocalGapClosing.o' failed
  464. make[2]: *** [src2/collectReadSequencesForLocalGapClosing.o] Error 1
  465. Makefile:1604: recipe for target 'src/sorted_merge.o' failed
  466. make[2]: *** [src/sorted_merge.o] Error 1
  467. Makefile:1604: recipe for target 'src2/joinKUnitigs_v3.o' failed
  468. make[2]: *** [src2/joinKUnitigs_v3.o] Error 1
  469. Makefile:1326: recipe for target 'eliminateBadSuperReadsUsingList' failed
  470. make[2]: *** [eliminateBadSuperReadsUsingList] Error 1
  471. Makefile:1386: recipe for target 'homo_trim' failed
  472. make[2]: *** [homo_trim] Error 1
  473. Makefile:1458: recipe for target 'splitFileAtNs' failed
  474. make[2]: *** [splitFileAtNs] Error 1
  475. Makefile:1338: recipe for target 'extendSuperReadsBasedOnUniqueExtensions' failed
  476. make[2]: *** [extendSuperReadsBasedOnUniqueExtensions] Error 1
  477. Makefile:1366: recipe for target 'getATBiasInCoverageForIllumina_v2' failed
  478. make[2]: *** [getATBiasInCoverageForIllumina_v2] Error 1
  479. Makefile:1404: recipe for target 'makeAdjustmentFactorsForNumReadsForAStatBasedOnGC' failed
  480. make[2]: *** [makeAdjustmentFactorsForNumReadsForAStatBasedOnGC] Error 1
  481. Makefile:1398: recipe for target 'killBadKUnitigs' failed
  482. make[2]: *** [killBadKUnitigs] Error 1
  483. Makefile:1410: recipe for target 'makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2' failed
  484. make[2]: *** [makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2] Error 1
  485. Makefile:1344: recipe for target 'extendSuperReadsForUniqueKmerNeighbors' failed
  486. make[2]: *** [extendSuperReadsForUniqueKmerNeighbors] Error 1
  487. Makefile:1296: recipe for target 'createFastaSuperReadSequences' failed
  488. make[2]: *** [createFastaSuperReadSequences] Error 1
  489. Makefile:1214: recipe for target 'addSurrogatesToFrgCtgFile' failed
  490. make[2]: *** [addSurrogatesToFrgCtgFile] Error 1
  491. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SuperReads' から出ます
  492. Makefile:2285: recipe for target 'install' failed
  493. make[1]: *** [install] Error 2
  494. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SuperReads' から出ます
  495. Making install in SOAPdenovo2 pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1
  496. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SOAPdenovo2' に入ります
  497.   CC       standardPregraph/libstandard63_a-readseq1by1.o
  498.   CXX      sparsePregraph/libsparse63_a-build_preArc.o
  499.   CXX      sparsePregraph/libsparse63_a-io_func.o
  500.   CC       standardPregraph/libstandard127_a-readseq1by1.o
  501.   CXX      sparsePregraph/libsparse127_a-build_preArc.o
  502.   CXX      sparsePregraph/libsparse127_a-io_func.o
  503. standardPregraph/readseq1by1.c: In function ‘read1seqfq’:
  504. standardPregraph/readseq1by1.c:425:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  505.     fgets ( str, lineLen, fp ); // pass quality value line
  506.     ^~~~~~~~~~~~~~~~~~~~~~~~~~
  507. standardPregraph/readseq1by1.c: In function ‘read1seqfq’:
  508. standardPregraph/readseq1by1.c:425:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  509.     fgets ( str, lineLen, fp ); // pass quality value line
  510.     ^~~~~~~~~~~~~~~~~~~~~~~~~~
  511.   AR       libstandard127.a
  512. ar: `u' modifier ignored since `D' is the default (see `U')
  513.  AR       libstandard63.a
  514. ar: `u' modifier ignored since `D' is the default (see `U')
  515. In file included from sparsePregraph/build_preArc.cpp:46:0:
  516. ./sparsePregraph/inc/sparse_kmer.h: In function ‘void printKmer(const kmer_t2*, FILE*)’:
  517. ./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=]
  518.   fprintf ( fp, "%llx %llx %llx %llx,\n", ( kmer->kmer ) [0], ( kmer->kmer ) [1], ( kmer->kmer ) [2], ( kmer->kmer ) [3] );
  519.                                           ~~~~~~~~~~~~~~~~~~                                                             ^
  520. ./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=]
  521. ./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=]
  522. ./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=]
  523. sparsePregraph/build_preArc.cpp: In function ‘void build_vertexes(vertex_hash2*, int, char*)’:
  524. 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=]
  525.              & ( from_kmer.kmer ) [0], & ( from_kmer.kmer ) [1], & ( from_kmer.kmer ) [2], & ( from_kmer.kmer ) [3],
  526.              ~~~~~~~~~~~~~~~~~~~~~~~~                                                                                            
  527.              & ( 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
  528.                                                                                                                                 ^
  529. 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=]
  530. 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=]
  531. 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=]
  532. 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=]
  533. 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=]
  534. 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=]
  535. 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=]
  536. sparsePregraph/build_preArc.cpp:132:128: warning: format ‘%d’ expects argument of type ‘int*’, but argument 14 has type ‘bool*’ [-Wformat=]
  537. sparsePregraph/build_preArc.cpp: In function ‘void output_preArcs(preArc_array*, char*)’:
  538. 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=]
  539.     fprintf ( fp, "%u", i );
  540.                           ^
  541. 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=]
  542.       fprintf ( fp, "%u", i );
  543.                             ^
  544. sparsePregraph/build_preArc.cpp: In function ‘void process_1read_preArc(preArc_array*, pthread_spinlock_t*, int, vertex_hash2*, int, int, const char*)’:
  545. 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=]
  546.         fprintf ( stderr, "ERROR: left edge id found already !new found id %llu \n", left_id );
  547.                                                                                              ^
  548. 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=]
  549.         fprintf ( stderr, "ERROR: right edge id found already, new found id %llu !\n", right_id );
  550.                                                                                                 ^
  551. In file included from sparsePregraph/build_preArc.cpp:46:0:
  552. ./sparsePregraph/inc/sparse_kmer.h: In function ‘void printKmer(const kmer_t2*, FILE*)’:
  553. ./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=]
  554.   fprintf ( fp, "%llx %llx ,\n", ( kmer->kmer ) [0], ( kmer->kmer ) [1] );
  555.                                  ~~~~~~~~~~~~~~~~~~                     ^
  556. ./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=]
  557. sparsePregraph/build_preArc.cpp: In function ‘void build_vertexes(vertex_hash2*, int, char*)’:
  558. 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=]
  559.              & ( 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
  560.              ~~~~~~~~~~~~~~~~~~~~~~~~                                                                                               ^
  561. 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=]
  562. 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=]
  563. 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=]
  564. sparsePregraph/build_preArc.cpp:127:132: warning: format ‘%d’ expects argument of type ‘int*’, but argument 10 has type ‘bool*’ [-Wformat=]
  565. sparsePregraph/build_preArc.cpp: In function ‘void output_preArcs(preArc_array*, char*)’:
  566. 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=]
  567.     fprintf ( fp, "%u", i );
  568.                           ^
  569. 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=]
  570.       fprintf ( fp, "%u", i );
  571.                             ^
  572. sparsePregraph/build_preArc.cpp: In function ‘void process_1read_preArc(preArc_array*, pthread_spinlock_t*, int, vertex_hash2*, int, int, const char*)’:
  573. 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=]
  574.         fprintf ( stderr, "ERROR: left edge id found already !new found id %llu \n", left_id );
  575.                                                                                              ^
  576. 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=]
  577.         fprintf ( stderr, "ERROR: right edge id found already, new found id %llu !\n", right_id );
  578.                                                                                                 ^
  579.   AR       libsparse127.a
  580. ar: `u' modifier ignored since `D' is the default (see `U')
  581.  AR       libsparse63.a
  582. ar: `u' modifier ignored since `D' is the default (see `U')
  583.   GEN      SOAPdenovo-63mer
  584.   GEN      SOAPdenovo-127mer
  585. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SOAPdenovo2' に入ります
  586. make[2]: 'install-data-am' に対して行うべき事はありません.
  587.  /bin/mkdir -p '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'
  588.   /bin/bash ../libtool   --mode=install /usr/bin/install -c SOAPdenovo-63mer SOAPdenovo-127mer '/home/nakajima/biotools/MaSuRCA-3.3.3/bin'
  589. libtool: install: /usr/bin/install -c SOAPdenovo-63mer /home/nakajima/biotools/MaSuRCA-3.3.3/bin/SOAPdenovo-63mer
  590. libtool: install: /usr/bin/install -c SOAPdenovo-127mer /home/nakajima/biotools/MaSuRCA-3.3.3/bin/SOAPdenovo-127mer
  591. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SOAPdenovo2' から出ます
  592. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/SOAPdenovo2' から出ます
  593. Making install in PacBio pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1
  594. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/PacBio' に入ります
  595. make  install-am
  596. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/PacBio' に入ります
  597.   CXX      src_jf_aligner/jf_aligner.o
  598.   CXX      src_jf_aligner/pb_aligner.o
  599.   CXX      src_jf_aligner/superread_parser.o
  600.   CXX      src_jf_aligner/coarse_aligner.o
  601.   CXX      src_jf_aligner/fine_aligner.o
  602.   CXX      src_jf_aligner/overlap_graph.o
  603.   CXX      src_jf_aligner/create_mega_reads.o
  604.   CXX      src_jf_aligner/merge_coords.o
  605.   CXX      src_jf_aligner/longest_path_overlap_graph2.o
  606.   CXX      src_jf_aligner/coords_parsing.o
  607.   CXXLD    bin/get_super_read_sizes
  608.   CXXLD    bin/findGapsInCoverageOfPacbios
  609. In file included from src_jf_aligner/jf_aligner.cc:8:0:
  610. ./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
  611.  #include <jellyfish/mer_dna.hpp>
  612.           ^~~~~~~~~~~~~~~~~~~~~~~
  613. compilation terminated.
  614. In file included from src_jf_aligner/superread_parser.cc:6:0:
  615. ./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
  616.  #include <jellyfish/mer_dna.hpp>
  617.           ^~~~~~~~~~~~~~~~~~~~~~~
  618. compilation terminated.
  619. Makefile:1249: recipe for target 'src_jf_aligner/jf_aligner.o' failed
  620. make[2]: *** [src_jf_aligner/jf_aligner.o] Error 1
  621. make[2]: *** 未完了のジョブを待っています....
  622. Makefile:1249: recipe for target 'src_jf_aligner/superread_parser.o' failed
  623. make[2]: *** [src_jf_aligner/superread_parser.o] Error 1
  624. In file included from ./src_jf_aligner/fine_aligner.hpp:7:0,
  625.                  from src_jf_aligner/fine_aligner.cc:4:
  626. ./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
  627.  #include <jellyfish/mer_dna.hpp>
  628.           ^~~~~~~~~~~~~~~~~~~~~~~
  629. compilation terminated.
  630. Makefile:1249: recipe for target 'src_jf_aligner/fine_aligner.o' failed
  631. make[2]: *** [src_jf_aligner/fine_aligner.o] Error 1
  632. In file included from ./include/jflib/multiplexed_parser.hpp:26:0,
  633.                  from ./src_jf_aligner/coords_parsing.hpp:10,
  634.                  from src_jf_aligner/coords_parsing.cc:4:
  635. ./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
  636.  #include <jellyfish/circular_buffer.hpp>
  637.           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  638. compilation terminated.
  639. Makefile:1249: recipe for target 'src_jf_aligner/coords_parsing.o' failed
  640. make[2]: *** [src_jf_aligner/coords_parsing.o] Error 1
  641. In file included from src_jf_aligner/create_mega_reads.cc:8:0:
  642. ./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
  643.  #include <jellyfish/mer_dna.hpp>
  644.           ^~~~~~~~~~~~~~~~~~~~~~~
  645. compilation terminated.
  646. In file included from ./include/jflib/multiplexed_parser.hpp:26:0,
  647.                  from ./src_jf_aligner/coords_parsing.hpp:10,
  648.                  from src_jf_aligner/merge_coords.cc:7:
  649. ./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
  650.  #include <jellyfish/circular_buffer.hpp>
  651.           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  652. compilation terminated.
  653. Makefile:1249: recipe for target 'src_jf_aligner/create_mega_reads.o' failed
  654. make[2]: *** [src_jf_aligner/create_mega_reads.o] Error 1
  655. Makefile:1249: recipe for target 'src_jf_aligner/merge_coords.o' failed
  656. make[2]: *** [src_jf_aligner/merge_coords.o] Error 1
  657. In file included from src_jf_aligner/longest_path_overlap_graph2.cc:9:0:
  658. ./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
  659.  #include <jellyfish/err.hpp>
  660.           ^~~~~~~~~~~~~~~~~~~
  661. compilation terminated.
  662. Makefile:1249: recipe for target 'src_jf_aligner/longest_path_overlap_graph2.o' failed
  663. make[2]: *** [src_jf_aligner/longest_path_overlap_graph2.o] Error 1
  664. In file included from ./src_jf_aligner/pb_aligner.hpp:12:0,
  665.                  from src_jf_aligner/pb_aligner.cc:8:
  666. ./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
  667.  #include <jellyfish/mer_dna.hpp>
  668.           ^~~~~~~~~~~~~~~~~~~~~~~
  669. compilation terminated.
  670. Makefile:1249: recipe for target 'src_jf_aligner/pb_aligner.o' failed
  671. make[2]: *** [src_jf_aligner/pb_aligner.o] Error 1
  672. In file included from ./src_jf_aligner/pb_aligner.hpp:12:0,
  673.                  from ./src_jf_aligner/overlap_graph.hpp:9,
  674.                  from src_jf_aligner/overlap_graph.cc:4:
  675. ./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
  676.  #include <jellyfish/mer_dna.hpp>
  677.           ^~~~~~~~~~~~~~~~~~~~~~~
  678. compilation terminated.
  679. Makefile:1249: recipe for target 'src_jf_aligner/overlap_graph.o' failed
  680. make[2]: *** [src_jf_aligner/overlap_graph.o] Error 1
  681. In file included from ./src_jf_aligner/pb_aligner.hpp:12:0,
  682.                  from ./src_jf_aligner/coarse_aligner.hpp:10,
  683.                  from src_jf_aligner/coarse_aligner.cc:4:
  684. ./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
  685.  #include <jellyfish/mer_dna.hpp>
  686.           ^~~~~~~~~~~~~~~~~~~~~~~
  687. compilation terminated.
  688. Makefile:1249: recipe for target 'src_jf_aligner/coarse_aligner.o' failed
  689. make[2]: *** [src_jf_aligner/coarse_aligner.o] Error 1
  690. /usr/bin/ld: cannot find -ljellyfish-2.0
  691. collect2: error: ld returned 1 exit status
  692. Makefile:1087: recipe for target 'bin/findGapsInCoverageOfPacbios' failed
  693. make[2]: *** [bin/findGapsInCoverageOfPacbios] Error 1
  694. /usr/bin/ld: cannot find -ljellyfish-2.0
  695. collect2: error: ld returned 1 exit status
  696. Makefile:1094: recipe for target 'bin/get_super_read_sizes' failed
  697. make[2]: *** [bin/get_super_read_sizes] Error 1
  698. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/PacBio' から出ます
  699. Makefile:1613: recipe for target 'install' failed
  700. make[1]: *** [install] Error 2
  701. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/PacBio' から出ます
  702. Making install in MUMmer pwd /home/nakajima/biotools/MaSuRCA-3.3.3/global-1
  703. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/MUMmer' に入ります
  704. make  install-am
  705. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/MUMmer' に入ります
  706.   CXX      swig/perl5/swig_perl5_mummer_la-swig_wrap.lo
  707. swig/perl5/swig_wrap.cpp:322:10: fatal error: string.h: No such file or directory
  708.  #include <string.h>
  709.           ^~~~~~~~~~
  710. compilation terminated.
  711. Makefile:1830: recipe for target 'swig/perl5/swig_perl5_mummer_la-swig_wrap.lo' failed
  712. make[2]: *** [swig/perl5/swig_perl5_mummer_la-swig_wrap.lo] Error 1
  713. make[2]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/MUMmer' から出ます
  714. Makefile:2418: recipe for target 'install' failed
  715. make[1]: *** [install] Error 2
  716. make[1]: ディレクトリ '/home/nakajima/biotools/MaSuRCA-3.3.3/global-1/MUMmer' から出ます
  717. Makefile:847: recipe for target 'install-special' failed
  718. make: *** [install-special] Error 2
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