差分

このページの2つのバージョン間の差分を表示します。

--- bowtie [2017/05/02 22:17] – 作成 118.240.79.26
+++ bowtie [Unknown date] (現在) – 削除 - 外部編集 (Unknown date) 127.0.0.1
@@ 行 1: / 行 1: @@
-```
-[yoshitake.kazutoshi@m24 ~]$ cd /suikou/download/
-[yoshitake.kazutoshi@m24 download]$ git clone https://github.com/BenLangmead/bowtie.git
-Cloning into 'bowtie'...
-remote: Counting objects: 10215, done.
-remote: Total 10215 (delta 0), reused 0 (delta 0), pack-reused 10215
-Receiving objects: 100% (10215/10215), 22.54 MiB | 7.66 MiB/s, done.
-Resolving deltas: 100% (7280/7280), done.
-[yoshitake.kazutoshi@m24 download]$ mv bowtie bowtie
-bowtie/                         bowtie2-2.3.1-linux-x86_64.zip
-[yoshitake.kazutoshi@m24 download]$ mv bowtie bowtie_v2017-05-03
-[yoshitake.kazutoshi@m24 download]$ cd bowtie_v2017-05-03/
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ ls
-AUTHORS            alphabet.h             chaincat.cpp             edit.cpp          pat.h                refmap.cpp              sequence_io.h
-LICENSE            annot.cpp              color.cpp                edit.h            pool.h               refmap.h                shmem.cpp
-MANUAL             annot.h                color.h                  endian_swap.h     processor_support.h  row_chaser.h            shmem.h
-MANUAL.markdown    assert_helpers.h       color_dec.cpp            fast_mutex.h      qual.cpp             sam.cpp                 str_util.h
-Makefile           auto_array.h           color_dec.h              filebuf.h         qual.h               sam.h                   third_party
-NEWS               binary_sa_search.h     cpu_numa_info.cpp        formats.h         random_source.h      scripts                 threading.h
-README             bitpack.h              cpu_numa_info.h          genomes           random_test.cpp      search_1mm_phase1.c     timer.h
-SeqAn-1.1          bitset.h               diff_sample.h            hit.cpp           range.h              search_1mm_phase2.c     tinythread.cpp
-TUTORIAL           blockwise_sa.h         doc                      hit.h             range_cache.h        search_23mm_phase1.c    tinythread.h
-VERSION            bowtie                 ebwt.cpp                 hit_set.cpp       range_chaser.h       search_23mm_phase2.c    tokenize.h
-aligner.h          bowtie-build           ebwt.h                   hit_set.h         range_source.h       search_23mm_phase3.c    word_io.h
-aligner_0mm.h      bowtie-inspect         ebwt_build.cpp           indexes           reads                search_exact.c          zbox.h
-aligner_1mm.h      bowtie_build_main.cpp  ebwt_search.cpp          log.cpp           ref_aligner.cpp      search_globals.h
-aligner_23mm.h     bowtie_inspect.cpp     ebwt_search.h            log.h             ref_aligner.h        search_seeded_phase1.c
-aligner_metrics.h  bowtie_main.cpp        ebwt_search_backtrack.h  mm.h              ref_read.cpp         search_seeded_phase2.c
-aligner_seed_mm.h  btypes.h               ebwt_search_util.cpp     multikey_qsort.h  ref_read.h           search_seeded_phase3.c
-alphabet.cpp       ccnt_lut.cpp           ebwt_search_util.h       pat.cpp           reference.h          search_seeded_phase4.c
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ make
-g++ -w -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include  \""  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include    \
-        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -w -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
-        -I SeqAn-1.1 -I third_party -I third_party \
-        -o bowtie-build-s ebwt_build.cpp \
-        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp  bowtie_build_main.cpp \
-        -lpthread -ltbb -ltbbmalloc_proxy
-In file included from pat.h:17:0,
-                 from sequence_io.h:12,
-                 from multikey_qsort.h:8,
-                 from diff_sample.h:8,
-                 from blockwise_sa.h:13,
-                 from ebwt.h:27,
-                 from ebwt_build.cpp:11:
-threading.h:10:24: 致命的エラー: tbb/mutex.h: そのようなファイルやディレクトリはありません
- # include <tbb/mutex.h>
-                        ^
-コンパイルを停止しました。
-make: *** [bowtie-build-s] エラー 1
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ ./bowtie
-Traceback (most recent call last):
-  File "./bowtie", line 107, in <module>
-    main()
-  File "./bowtie", line 104, in main
-    os.execv(bin_spec, bowtie_args)
-OSError: [Errno 2] No such file or directory
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ cd ..
-[yoshitake.kazutoshi@m24 download]$ git clone https://github.com/wjakob/tbb.git
-Cloning into 'tbb'...
-remote: Counting objects: 6385, done.
-remote: Total 6385 (delta 0), reused 0 (delta 0), pack-reused 6385
-Receiving objects: 100% (6385/6385), 5.88 MiB | 2.84 MiB/s, done.
-Resolving deltas: 100% (4698/4698), done.
-[yoshitake.kazutoshi@m24 download]$ mv tbb tbb_v2017-05-03
-[yoshitake.kazutoshi@m24 download]$ cd tbb_v2017-05-03/
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ ls
-CHANGES  CMakeLists.txt  LICENSE  Makefile  README  README.md  build  doc  examples  include  index.html  jni  python  src
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ cmake .
--- The CXX compiler identification is GNU 4.8.5
--- Check for working CXX compiler: /usr/bin/c++
--- Check for working CXX compiler: /usr/bin/c++ -- works
--- Detecting CXX compiler ABI info
--- Detecting CXX compiler ABI info - done
--- Detecting CXX compile features
--- Detecting CXX compile features - done
--- Setting build type to 'Release' as none was specified.
--- Performing Test SUPPORTS_STDCXX11
--- Performing Test SUPPORTS_STDCXX11 - Success
--- Performing Test SUPPORTS_MRTM
--- Performing Test SUPPORTS_MRTM - Success
--- Performing Test SUPPORTS_FLIFETIME
--- Performing Test SUPPORTS_FLIFETIME - Failed
--- The C compiler identification is GNU 4.8.5
--- Check for working C compiler: /usr/bin/cc
--- Check for working C compiler: /usr/bin/cc -- works
--- Detecting C compiler ABI info
--- Detecting C compiler ABI info - done
--- Detecting C compile features
--- Detecting C compile features - done
--- Looking for pthread.h
--- Looking for pthread.h - found
--- Looking for pthread_create
--- Looking for pthread_create - not found
--- Looking for pthread_create in pthreads
--- Looking for pthread_create in pthreads - not found
--- Looking for pthread_create in pthread
--- Looking for pthread_create in pthread - found
--- Found Threads: TRUE
--- Try OpenMP C flag = [-fopenmp]
--- Performing Test OpenMP_FLAG_DETECTED
--- Performing Test OpenMP_FLAG_DETECTED - Success
--- Try OpenMP CXX flag = [-fopenmp]
--- Performing Test OpenMP_FLAG_DETECTED
--- Performing Test OpenMP_FLAG_DETECTED - Success
--- Found OpenMP: -fopenmp
--- Configuring done
--- Generating done
--- Build files have been written to: /suikou/download/tbb_v2017-05-03
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ ls
-CHANGES         CMakeFiles      CTestTestfile.cmake  Makefile  README.md  cmake_install.cmake  examples  index.html  python  version_string.ver
-CMakeCache.txt  CMakeLists.txt  LICENSE              README    build      doc                  include   jni         src
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ cmake -DCMAKE_INSTALL_PREFIX=/suikou/tool/tbb_v2017-05-03 .
--- Configuring done
--- Generating done
--- Build files have been written to: /suikou/download/tbb_v2017-05-03
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ ls
-CHANGES         CMakeFiles      CTestTestfile.cmake  Makefile  README.md  cmake_install.cmake  examples  index.html  python  version_string.ver
-CMakeCache.txt  CMakeLists.txt  LICENSE              README    build      doc                  include   jni         src
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ make -j 4
-Scanning dependencies of target tbb_def_files
-Scanning dependencies of target tbbmalloc_proxy_static
-Scanning dependencies of target tbbmalloc_static
-Scanning dependencies of target tbb_static
-[  1%] Preprocessing tbb.def
-[  1%] Preprocessing tbbmalloc.def
-[  1%] Building CXX object CMakeFiles/tbbmalloc_proxy_static.dir/src/tbbmalloc/proxy.cpp.o
-[  1%] Built target tbb_def_files
-[  1%] Building CXX object CMakeFiles/tbbmalloc_proxy_static.dir/src/tbbmalloc/tbb_function_replacement.cpp.o
-[  1%] Building CXX object CMakeFiles/tbbmalloc_static.dir/src/tbbmalloc/backend.cpp.o
-[  2%] Building CXX object CMakeFiles/tbbmalloc_static.dir/src/tbbmalloc/large_objects.cpp.o
-[  3%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/arena.cpp.o
-[  4%] Linking CXX static library libtbbmalloc_proxy_static.a
-[  4%] Built target tbbmalloc_proxy_static
-[  4%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/cache_aligned_allocator.cpp.o
-[  4%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/concurrent_hash_map.cpp.o
-Scanning dependencies of target tbbmalloc
-[  4%] Building CXX object CMakeFiles/tbbmalloc.dir/src/tbbmalloc/backend.cpp.o
-Scanning dependencies of target tbb
-[  4%] Building CXX object CMakeFiles/tbb.dir/src/tbb/arena.cpp.o
-[  5%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/concurrent_monitor.cpp.o
-[  5%] Building CXX object CMakeFiles/tbbmalloc_static.dir/src/tbbmalloc/backref.cpp.o
-[  5%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/concurrent_queue.cpp.o
-[  5%] Building CXX object CMakeFiles/tbbmalloc_static.dir/src/tbbmalloc/tbbmalloc.cpp.o
-[  5%] Building CXX object CMakeFiles/tbbmalloc.dir/src/tbbmalloc/large_objects.cpp.o
-[  6%] Building CXX object CMakeFiles/tbbmalloc_static.dir/src/tbbmalloc/frontend.cpp.o
-[  6%] Building CXX object CMakeFiles/tbb.dir/src/tbb/cache_aligned_allocator.cpp.o
-[  7%] Building CXX object CMakeFiles/tbb.dir/src/tbb/concurrent_hash_map.cpp.o
-[  8%] Building CXX object CMakeFiles/tbbmalloc.dir/src/tbbmalloc/backref.cpp.o
-[  8%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/concurrent_vector.cpp.o
-[  8%] Building CXX object CMakeFiles/tbb.dir/src/tbb/concurrent_monitor.cpp.o
-[  8%] Building CXX object CMakeFiles/tbbmalloc.dir/src/tbbmalloc/tbbmalloc.cpp.o
-[  8%] Building CXX object CMakeFiles/tbb.dir/src/tbb/concurrent_queue.cpp.o
-[  9%] Building CXX object CMakeFiles/tbbmalloc.dir/src/tbbmalloc/frontend.cpp.o
-[  9%] Building CXX object CMakeFiles/tbbmalloc_static.dir/src/tbb/itt_notify.cpp.o
-[ 10%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/condition_variable.cpp.o
-[ 10%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/critical_section.cpp.o
-[ 11%] Building CXX object CMakeFiles/tbb.dir/src/tbb/concurrent_vector.cpp.o
-[ 12%] Linking CXX static library libtbbmalloc_static.a
-[ 12%] Built target tbbmalloc_static
-[ 12%] Building CXX object CMakeFiles/tbb.dir/src/tbb/condition_variable.cpp.o
-[ 13%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/dynamic_link.cpp.o
-[ 13%] Building CXX object CMakeFiles/tbbmalloc.dir/src/tbb/itt_notify.cpp.o
-[ 13%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/governor.cpp.o
-[ 13%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/itt_notify.cpp.o
-[ 14%] Building CXX object CMakeFiles/tbb.dir/src/tbb/critical_section.cpp.o
-[ 15%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/market.cpp.o
-[ 15%] Linking CXX shared library libtbbmalloc.so
-[ 15%] Built target tbbmalloc
-[ 15%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/mutex.cpp.o
-[ 15%] Building CXX object CMakeFiles/tbb.dir/src/tbb/dynamic_link.cpp.o
-Scanning dependencies of target tbbmalloc_proxy
-[ 16%] Building CXX object CMakeFiles/tbbmalloc_proxy.dir/src/tbbmalloc/proxy.cpp.o
-[ 16%] Building CXX object CMakeFiles/tbbmalloc_proxy.dir/src/tbbmalloc/tbb_function_replacement.cpp.o
-[ 17%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/observer_proxy.cpp.o
-[ 17%] Building CXX object CMakeFiles/tbb.dir/src/tbb/governor.cpp.o
-[ 18%] Linking CXX shared library libtbbmalloc_proxy.so
-[ 18%] Built target tbbmalloc_proxy
-[ 19%] Building CXX object CMakeFiles/tbb.dir/src/tbb/itt_notify.cpp.o
-[ 19%] Building CXX object CMakeFiles/tbb.dir/src/tbb/market.cpp.o
-[ 19%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/pipeline.cpp.o
-[ 19%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/private_server.cpp.o
-[ 20%] Building CXX object CMakeFiles/tbb.dir/src/tbb/mutex.cpp.o
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-[ 22%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/reader_writer_lock.cpp.o
-[ 22%] Building CXX object CMakeFiles/tbb.dir/src/tbb/pipeline.cpp.o
-[ 22%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/recursive_mutex.cpp.o
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-[ 26%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/task.cpp.o
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-[ 30%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/tbb_main.cpp.o
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-[ 32%] Building CXX object CMakeFiles/tbb.dir/src/tbb/tbb_thread.cpp.o
-[ 33%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/tbb_statistics.cpp.o
-[ 33%] Building CXX object CMakeFiles/tbb.dir/src/tbb/x86_rtm_rw_mutex.cpp.o
-[ 33%] Building CXX object CMakeFiles/tbb.dir/src/old/concurrent_queue_v2.cpp.o
-[ 33%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/tbb_thread.cpp.o
-[ 34%] Building CXX object CMakeFiles/tbb_static.dir/src/tbb/x86_rtm_rw_mutex.cpp.o
-[ 35%] Building CXX object CMakeFiles/tbb.dir/src/old/concurrent_vector_v2.cpp.o
-[ 35%] Building CXX object CMakeFiles/tbb_static.dir/src/old/concurrent_queue_v2.cpp.o
-[ 35%] Building CXX object CMakeFiles/tbb_static.dir/src/old/concurrent_vector_v2.cpp.o
-[ 35%] Building CXX object CMakeFiles/tbb.dir/src/old/spin_rw_mutex_v2.cpp.o
-[ 36%] Building CXX object CMakeFiles/tbb_static.dir/src/old/spin_rw_mutex_v2.cpp.o
-[ 37%] Building CXX object CMakeFiles/tbb.dir/src/old/task_v2.cpp.o
-[ 37%] Building CXX object CMakeFiles/tbb_static.dir/src/old/task_v2.cpp.o
-[ 37%] Building CXX object CMakeFiles/tbb.dir/src/rml/client/rml_tbb.cpp.o
-[ 38%] Building CXX object CMakeFiles/tbb_static.dir/src/rml/client/rml_tbb.cpp.o
-[ 38%] Linking CXX shared library libtbb.so
-[ 38%] Built target tbb
-Scanning dependencies of target tbb_test_tbb_condition_variable
-Scanning dependencies of target tbb_test_task_scheduler_observer
-Scanning dependencies of target tbb_test_tick_count
-[ 38%] Linking CXX static library libtbb_static.a
-[ 38%] Building CXX object CMakeFiles/tbb_test_tick_count.dir/src/test/test_tick_count.cpp.o
-[ 39%] Building CXX object CMakeFiles/tbb_test_tbb_condition_variable.dir/src/test/test_tbb_condition_variable.cpp.o
-[ 39%] Building CXX object CMakeFiles/tbb_test_task_scheduler_observer.dir/src/test/test_task_scheduler_observer.cpp.o
-[ 39%] Built target tbb_static
-Scanning dependencies of target tbb_test_std_thread
-[ 39%] Building CXX object CMakeFiles/tbb_test_std_thread.dir/src/test/test_std_thread.cpp.o
-[ 39%] Linking CXX executable tbb_test_tick_count
-[ 39%] Built target tbb_test_tick_count
-Scanning dependencies of target tbb_test_split_node
-[ 40%] Building CXX object CMakeFiles/tbb_test_split_node.dir/src/test/test_split_node.cpp.o
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-[ 41%] Built target tbb_test_std_thread
-Scanning dependencies of target tbb_test_source_node
-[ 42%] Building CXX object CMakeFiles/tbb_test_source_node.dir/src/test/test_source_node.cpp.o
-[ 42%] Linking CXX executable tbb_test_tbb_condition_variable
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-[ 42%] Built target tbb_test_tbb_condition_variable
-Scanning dependencies of target tbb_test_ScalableAllocator_STL
-[ 42%] Building CXX object CMakeFiles/tbb_test_ScalableAllocator_STL.dir/src/test/test_ScalableAllocator_STL.cpp.o
-[ 42%] Built target tbb_test_task_scheduler_observer
-Scanning dependencies of target tbb_test_tagged_msg
-[ 42%] Building CXX object CMakeFiles/tbb_test_tagged_msg.dir/src/test/test_tagged_msg.cpp.o
-[ 42%] Linking CXX executable tbb_test_tagged_msg
-[ 42%] Built target tbb_test_tagged_msg
-Scanning dependencies of target tbb_test_rwm_upgrade_downgrade
-[ 42%] Building CXX object CMakeFiles/tbb_test_rwm_upgrade_downgrade.dir/src/test/test_rwm_upgrade_downgrade.cpp.o
-[ 43%] Linking CXX executable tbb_test_rwm_upgrade_downgrade
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-[ 44%] Built target tbb_test_rwm_upgrade_downgrade
-Scanning dependencies of target tbb_test_reader_writer_lock
-[ 44%] Building CXX object CMakeFiles/tbb_test_reader_writer_lock.dir/src/test/test_reader_writer_lock.cpp.o
-[ 44%] Built target tbb_test_ScalableAllocator_STL
-Scanning dependencies of target tbb_test_queue_node
-[ 45%] Building CXX object CMakeFiles/tbb_test_queue_node.dir/src/test/test_queue_node.cpp.o
-[ 46%] Linking CXX executable tbb_test_reader_writer_lock
-[ 46%] Built target tbb_test_reader_writer_lock
-Scanning dependencies of target tbb_test_priority_queue_node
-[ 46%] Building CXX object CMakeFiles/tbb_test_priority_queue_node.dir/src/test/test_priority_queue_node.cpp.o
-[ 46%] Linking CXX executable tbb_test_source_node
-[ 46%] Built target tbb_test_source_node
-Scanning dependencies of target tbb_test_parallel_scan
-[ 47%] Building CXX object CMakeFiles/tbb_test_parallel_scan.dir/src/test/test_parallel_scan.cpp.o
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-[ 47%] Built target tbb_test_parallel_scan
-Scanning dependencies of target tbb_test_parallel_reduce
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-Scanning dependencies of target tbb_test_parallel_invoke
-[ 47%] Building CXX object CMakeFiles/tbb_test_parallel_invoke.dir/src/test/test_parallel_invoke.cpp.o
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-Scanning dependencies of target tbb_test_parallel_for
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-Scanning dependencies of target tbb_test_tbb_fork
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-Scanning dependencies of target tbb_test_mutex
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-Scanning dependencies of target tbb_test_malloc_pools
-[ 54%] Building CXX object CMakeFiles/tbb_test_malloc_pools.dir/src/test/test_malloc_pools.cpp.o
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-Scanning dependencies of target tbb_test_cache_aligned_allocator_STL
-[ 56%] Building CXX object CMakeFiles/tbb_test_cache_aligned_allocator_STL.dir/src/test/test_cache_aligned_allocator_STL.cpp.o
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-[ 61%] Building CXX object CMakeFiles/tbb_test_flow_graph.dir/src/test/test_flow_graph.cpp.o
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-Scanning dependencies of target tbb_test_parallel_sort
-[ 62%] Building CXX object CMakeFiles/tbb_test_parallel_sort.dir/src/test/test_parallel_sort.cpp.o
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-Scanning dependencies of target tbb_test_eh_flow_graph
-[ 63%] Building CXX object CMakeFiles/tbb_test_eh_flow_graph.dir/src/test/test_eh_flow_graph.cpp.o
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-Scanning dependencies of target tbb_test_yield
-[ 64%] Building CXX object CMakeFiles/tbb_test_yield.dir/src/test/test_yield.cpp.o
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-Scanning dependencies of target tbb_test_task_steal_limit
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-Scanning dependencies of target tbb_test_parallel_while
-[ 68%] Building CXX object CMakeFiles/tbb_test_parallel_while.dir/src/test/test_parallel_while.cpp.o
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-Scanning dependencies of target tbb_test_async_msg
-[ 70%] Building CXX object CMakeFiles/tbb_test_async_msg.dir/src/test/test_async_msg.cpp.o
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-Scanning dependencies of target tbb_test_assembly
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-Scanning dependencies of target tbb_test_concurrent_unordered_map
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-Scanning dependencies of target tbb_test_parallel_for_each
-[ 74%] Building CXX object CMakeFiles/tbb_test_parallel_for_each.dir/src/test/test_parallel_for_each.cpp.o
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-[ 91%] Building CXX object CMakeFiles/tbb_test_continue_node.dir/src/test/test_continue_node.cpp.o
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-[ 94%] Building CXX object CMakeFiles/tbb_test_task_group.dir/src/test/test_task_group.cpp.o
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-[100%] Built target tbb_test_enumerable_thread_specific
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ make install
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-[ 37%] Built target tbbmalloc_proxy
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-Install the project...
--- Install configuration: "Release"
--- Installing: /suikou/tool/tbb_v2017-05-03/lib/libtbb_static.a
--- Installing: /suikou/tool/tbb_v2017-05-03/lib/libtbb.so
--- Installing: /suikou/tool/tbb_v2017-05-03/lib/libtbbmalloc_static.a
--- Installing: /suikou/tool/tbb_v2017-05-03/lib/libtbbmalloc.so
--- Installing: /suikou/tool/tbb_v2017-05-03/lib/libtbbmalloc_proxy_static.a
--- Installing: /suikou/tool/tbb_v2017-05-03/lib/libtbbmalloc_proxy.so
--- Set runtime path of "/suikou/tool/tbb_v2017-05-03/lib/libtbbmalloc_proxy.so" to ""
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/tbb_profiling.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_flow_graph_streaming_node.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_template_helpers.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_x86_rtm_rw_mutex_impl.h
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--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/flow_graph.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/reader_writer_lock.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/tbb_allocator.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/queuing_mutex.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/memory_pool.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/blocked_range3d.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/flow_graph_abstractions.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/task_arena.h
--- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/parallel_scan.h
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ ls /suikou/tool/t
-tbb_v2017-05-03/              texinfo-6.3/                  tophat-2.1.1.Linux_x86_64/    trinityrnaseq-Trinity-v2.4.0/
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ ls /suikou/tool/tbb_v2017-05-03/
-include  lib
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ link2 /suikou/tool/tbb_v2017-05-03
-rm: `/suikou/tool-all/include/*' を削除できません: そのようなファイルやディレクトリはありません
-[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ cd ../bowtie_v2017-05-03/
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ make
-g++ -w -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include  \""  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include    \
-        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -w -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
-        -I SeqAn-1.1 -I third_party -I third_party \
-        -o bowtie-build-s ebwt_build.cpp \
-        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp  bowtie_build_main.cpp \
-        -lpthread -ltbb -ltbbmalloc_proxy
-/usr/bin/ld: -ltbb が見つかりません
-/usr/bin/ld: -ltbbmalloc_proxy が見つかりません
-collect2: エラー: ld はステータス 1 で終了しました
-make: *** [bowtie-build-s] エラー 1
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ ls /suikou/tool/tbb_v2017-05-03/lib/libtbb
-libtbb.so                    libtbbmalloc.so              libtbbmalloc_proxy_static.a
-libtbb_static.a              libtbbmalloc_proxy.so        libtbbmalloc_static.a
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ ls /suikou/tool-all/lib/libtbb
-libtbb.so                    libtbbmalloc.so              libtbbmalloc_proxy_static.a
-libtbb_static.a              libtbbmalloc_proxy.so        libtbbmalloc_static.a
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ nano Makefile
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ make
-g++ -w -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include  \""  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include    \
-        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -w -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
-        -I SeqAn-1.1 -I third_party -I third_party \
-        -o bowtie-build-s ebwt_build.cpp \
-        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp  bowtie_build_main.cpp \
-        -lpthread -ltbb -ltbbmalloc_proxy -L/suikou/tool-all/lib
-g++ -w -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include  \""  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include    \
-        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -w -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-        -I SeqAn-1.1 -I third_party -I third_party \
-        -o bowtie-build-l ebwt_build.cpp \
-        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp  bowtie_build_main.cpp \
-        -lpthread -ltbb -ltbbmalloc_proxy -L/suikou/tool-all/lib
-g++ -w -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include  \""  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include   \
-        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -w -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
-        -I SeqAn-1.1 -I third_party -I third_party \
-        -o bowtie-align-s ebwt_search.cpp \
-        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
-        -lpthread -ltbb -ltbbmalloc_proxy -L/suikou/tool-all/lib
-g++ -w -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include  \""  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include   \
-        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -w -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -DBOWTIE_64BIT_INDEX -Wall \
-        -I SeqAn-1.1 -I third_party -I third_party \
-        -o bowtie-align-l ebwt_search.cpp \
-        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
-        -lpthread -ltbb -ltbbmalloc_proxy -L/suikou/tool-all/lib
-g++ -w -O3 -m64 \
-        -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include  \""  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include   \
-        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -w -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \
-        -I SeqAn-1.1 -I third_party -I third_party -I . \
-        -o bowtie-inspect-s bowtie_inspect.cpp \
-        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp \
-        -lpthread -ltbb -ltbbmalloc_proxy -L/suikou/tool-all/lib
-g++ -w -O3 -m64 \
-        -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include  \""  -Wl,--hash-style=both -DWITH_TBB -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -I/suikou/tool-all//include -I/suikou/tool-all//include   -I/suikou/tool-all//include -I/suikou/tool-all//include   \
-        -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -w -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall \
-        -I SeqAn-1.1 -I third_party -I third_party -I . \
-        -o bowtie-inspect-l bowtie_inspect.cpp \
-        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp \
-        -lpthread -ltbb -ltbbmalloc_proxy -L/suikou/tool-all/lib
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ ls
-AUTHORS            annot.cpp              bowtie_inspect.cpp  ebwt_search_backtrack.h  multikey_qsort.h     reference.h             sequence_io.h
-LICENSE            annot.h                bowtie_main.cpp     ebwt_search_util.cpp     pat.cpp              refmap.cpp              shmem.cpp
-MANUAL             assert_helpers.h       btypes.h            ebwt_search_util.h       pat.h                refmap.h                shmem.h
-MANUAL.markdown    auto_array.h           ccnt_lut.cpp        edit.cpp                 pool.h               row_chaser.h            str_util.h
-Makefile           binary_sa_search.h     chaincat.cpp        edit.h                   processor_support.h  sam.cpp                 third_party
-NEWS               bitpack.h              color.cpp           endian_swap.h            qual.cpp             sam.h                   threading.h
-README             bitset.h               color.h             fast_mutex.h             qual.h               scripts                 timer.h
-SeqAn-1.1          blockwise_sa.h         color_dec.cpp       filebuf.h                random_source.h      search_1mm_phase1.c     tinythread.cpp
-TUTORIAL           bowtie                 color_dec.h         formats.h                random_test.cpp      search_1mm_phase2.c     tinythread.h
-VERSION            bowtie-align-l         cpu_numa_info.cpp   genomes                  range.h              search_23mm_phase1.c    tokenize.h
-aligner.h          bowtie-align-s         cpu_numa_info.h     hit.cpp                  range_cache.h        search_23mm_phase2.c    word_io.h
-aligner_0mm.h      bowtie-build           diff_sample.h       hit.h                    range_chaser.h       search_23mm_phase3.c    zbox.h
-aligner_1mm.h      bowtie-build-l         doc                 hit_set.cpp              range_source.h       search_exact.c
-aligner_23mm.h     bowtie-build-s         ebwt.cpp            hit_set.h                reads                search_globals.h
-aligner_metrics.h  bowtie-inspect         ebwt.h              indexes                  ref_aligner.cpp      search_seeded_phase1.c
-aligner_seed_mm.h  bowtie-inspect-l       ebwt_build.cpp      log.cpp                  ref_aligner.h        search_seeded_phase2.c
-alphabet.cpp       bowtie-inspect-s       ebwt_search.cpp     log.h                    ref_read.cpp         search_seeded_phase3.c
-alphabet.h         bowtie_build_main.cpp  ebwt_search.h       mm.h                     ref_read.h           search_seeded_phase4.c
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ ./bowtie
-No index, query, or output file specified!
-Usage:
-bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | <s>} [<hit>]
-  <m1>    Comma-separated list of files containing upstream mates (or the
-          sequences themselves, if -c is set) paired with mates in <m2>
-  <m2>    Comma-separated list of files containing downstream mates (or the
-          sequences themselves if -c is set) paired with mates in <m1>
-  <r>     Comma-separated list of files containing Crossbow-style reads.  Can be
-          a mixture of paired and unpaired.  Specify "-" for stdin.
-  <s>     Comma-separated list of files containing unpaired reads, or the
-          sequences themselves, if -c is set.  Specify "-" for stdin.
-  <hit>   File to write hits to (default: stdout)
-Input:
-  -q                 query input files are FASTQ .fq/.fastq (default)
-  -f                 query input files are (multi-)FASTA .fa/.mfa
-  -r                 query input files are raw one-sequence-per-line
-  -c                 query sequences given on cmd line (as <mates>, <singles>)
-  -C                 reads and index are in colorspace
-  -Q/--quals <file>  QV file(s) corresponding to CSFASTA inputs; use with -f -C
-  --Q1/--Q2 <file>   same as -Q, but for mate files 1 and 2 respectively
-  -s/--skip <int>    skip the first <int> reads/pairs in the input
-  -u/--qupto <int>   stop after first <int> reads/pairs (excl. skipped reads)
-  -5/--trim5 <int>   trim <int> bases from 5' (left) end of reads
-  -3/--trim3 <int>   trim <int> bases from 3' (right) end of reads
-  --phred33-quals    input quals are Phred+33 (default)
-  --phred64-quals    input quals are Phred+64 (same as --solexa1.3-quals)
-  --solexa-quals     input quals are from GA Pipeline ver. < 1.3
-  --solexa1.3-quals  input quals are from GA Pipeline ver. >= 1.3
-  --integer-quals    qualities are given as space-separated integers (not ASCII)
-  --large-index      force usage of a 'large' index, even if a small one is present
-Alignment:
-  -v <int>           report end-to-end hits w/ <=v mismatches; ignore qualities
-    or
-  -n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2)
-  -e/--maqerr <int>  max sum of mismatch quals across alignment for -n (def: 70)
-  -l/--seedlen <int> seed length for -n (default: 28)
-  --nomaqround       disable Maq-like quality rounding for -n (nearest 10 <= 30)
-  -I/--minins <int>  minimum insert size for paired-end alignment (default: 0)
-  -X/--maxins <int>  maximum insert size for paired-end alignment (default: 250)
-  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)
-  --nofw/--norc      do not align to forward/reverse-complement reference strand
-  --maxbts <int>     max # backtracks for -n 2/3 (default: 125, 800 for --best)
-  --pairtries <int>  max # attempts to find mate for anchor hit (default: 100)
-  -y/--tryhard       try hard to find valid alignments, at the expense of speed
-  --chunkmbs <int>   max megabytes of RAM for best-first search frames (def: 64)
- --reads-per-batch   # of reads to read from input file at once (default: 16)
-Reporting:
-  -k <int>           report up to <int> good alignments per read (default: 1)
-  -a/--all           report all alignments per read (much slower than low -k)
-  -m <int>           suppress all alignments if > <int> exist (def: no limit)
-  -M <int>           like -m, but reports 1 random hit (MAPQ=0); requires --best
-  --best             hits guaranteed best stratum; ties broken by quality
-  --strata           hits in sub-optimal strata aren't reported (requires --best)
-Output:
-  -t/--time          print wall-clock time taken by search phases
-  -B/--offbase <int> leftmost ref offset = <int> in bowtie output (default: 0)
-  --quiet            print nothing but the alignments
-  --refout           write alignments to files refXXXXX.map, 1 map per reference
-  --refidx           refer to ref. seqs by 0-based index rather than name
-  --al <fname>       write aligned reads/pairs to file(s) <fname>
-  --un <fname>       write unaligned reads/pairs to file(s) <fname>
-  --max <fname>      write reads/pairs over -m limit to file(s) <fname>
-  --suppress <cols>  suppresses given columns (comma-delim'ed) in default output
-  --fullref          write entire ref name (default: only up to 1st space)
-Colorspace:
-  --snpphred <int>   Phred penalty for SNP when decoding colorspace (def: 30)
-     or
-  --snpfrac <dec>    approx. fraction of SNP bases (e.g. 0.001); sets --snpphred
-  --col-cseq         print aligned colorspace seqs as colors, not decoded bases
-  --col-cqual        print original colorspace quals, not decoded quals
-  --col-keepends     keep nucleotides at extreme ends of decoded alignment
-SAM:
-  -S/--sam           write hits in SAM format
-  --mapq <int>       default mapping quality (MAPQ) to print for SAM alignments
-  --sam-nohead       supppress header lines (starting with @) for SAM output
-  --sam-nosq         supppress @SQ header lines for SAM output
-  --sam-RG <text>    add <text> (usually "lab=value") to @RG line of SAM header
-Performance:
-  -o/--offrate <int> override offrate of index; must be >= index's offrate
-  -p/--threads <int> number of alignment threads to launch (default: 1)
-  --mm               use memory-mapped I/O for index; many 'bowtie's can share
-  --shmem            use shared mem for index; many 'bowtie's can share
-Other:
-  --seed <int>       seed for random number generator
-  --verbose          verbose output (for debugging)
-  --version          print version information and quit
-  -h/--help          print this usage message
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ ls
-AUTHORS            annot.cpp              bowtie_inspect.cpp  ebwt_search_backtrack.h  multikey_qsort.h     reference.h             sequence_io.h
-LICENSE            annot.h                bowtie_main.cpp     ebwt_search_util.cpp     pat.cpp              refmap.cpp              shmem.cpp
-MANUAL             assert_helpers.h       btypes.h            ebwt_search_util.h       pat.h                refmap.h                shmem.h
-MANUAL.markdown    auto_array.h           ccnt_lut.cpp        edit.cpp                 pool.h               row_chaser.h            str_util.h
-Makefile           binary_sa_search.h     chaincat.cpp        edit.h                   processor_support.h  sam.cpp                 third_party
-NEWS               bitpack.h              color.cpp           endian_swap.h            qual.cpp             sam.h                   threading.h
-README             bitset.h               color.h             fast_mutex.h             qual.h               scripts                 timer.h
-SeqAn-1.1          blockwise_sa.h         color_dec.cpp       filebuf.h                random_source.h      search_1mm_phase1.c     tinythread.cpp
-TUTORIAL           bowtie                 color_dec.h         formats.h                random_test.cpp      search_1mm_phase2.c     tinythread.h
-VERSION            bowtie-align-l         cpu_numa_info.cpp   genomes                  range.h              search_23mm_phase1.c    tokenize.h
-aligner.h          bowtie-align-s         cpu_numa_info.h     hit.cpp                  range_cache.h        search_23mm_phase2.c    word_io.h
-aligner_0mm.h      bowtie-build           diff_sample.h       hit.h                    range_chaser.h       search_23mm_phase3.c    zbox.h
-aligner_1mm.h      bowtie-build-l         doc                 hit_set.cpp              range_source.h       search_exact.c
-aligner_23mm.h     bowtie-build-s         ebwt.cpp            hit_set.h                reads                search_globals.h
-aligner_metrics.h  bowtie-inspect         ebwt.h              indexes                  ref_aligner.cpp      search_seeded_phase1.c
-aligner_seed_mm.h  bowtie-inspect-l       ebwt_build.cpp      log.cpp                  ref_aligner.h        search_seeded_phase2.c
-alphabet.cpp       bowtie-inspect-s       ebwt_search.cpp     log.h                    ref_read.cpp         search_seeded_phase3.c
-alphabet.h         bowtie_build_main.cpp  ebwt_search.h       mm.h                     ref_read.h           search_seeded_phase4.c
-[yoshitake.kazutoshi@m24 bowtie_v2017-05-03]$ cd ..
-[yoshitake.kazutoshi@m24 download]$ mv bowtie
-bowtie2-2.3.1-linux-x86_64.zip  bowtie_v2017-05-03/
-[yoshitake.kazutoshi@m24 download]$ mv bowtie_v2017-05-03 /suikou/tool/
-[yoshitake.kazutoshi@m24 download]$ link1 /suikou/tool/bowtie_v2017-05-03
-```