[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
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[ 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
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[yoshitake.kazutoshi@m24 tbb_v2017-05-03]$ make install
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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
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_aggregator_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_flow_graph_indexer_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_flow_graph_async_msg_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_x86_eliding_mutex_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_flow_graph_node_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_flow_graph_tagged_buffer_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_flow_graph_item_buffer_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_mutex_padding.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_tbb_windef.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_tbb_hash_compare_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_flow_graph_join_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_concurrent_queue_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_concurrent_unordered_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_range_iterator.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_flow_graph_types_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_flow_graph_trace_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_flow_graph_impl.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/internal/_tbb_strings.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/critical_section.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/flow_graph_opencl_node.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/parallel_do.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/spin_rw_mutex.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/parallel_for_each.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/enumerable_thread_specific.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/tbb_machine.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/blocked_range.h
-- Installing: /suikou/tool/tbb_v2017-05-03/include/tbb/machine
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[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