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icthrm / cwSDTWnano

Here we proposed two novel algorithms, the Direct Subsequence Dynamic Time Warping for nanopore raw signal search (DSDTWnano) and the continuous wavelet Subsequence DTW for nanopore raw signal search (cwSDTWnano), to enable the direct subsequence inquiry and exact mapping in the nanopore raw signal datasets. The proposed algorithms are based on the idea of Subsequence-extended Dynamic Time Warping (SDTW) and directly operates on the raw signals, without any loss of information. DSDTWnano could ensure an output of highly accurate query result and cwSDTWnano is the accelerated version of DSDTWnano, with the help of seeding and multi-scale coarsening of signals that based on continuous wavelet transform (CWT).
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Empty bin folder after compiling #1

Open cwbcm opened 4 years ago

cwbcm commented 4 years ago

Hi,

I have some problem installing the package from SATnano folder. I used cmake, but I got nothing in the bin folder after compiling. I also tried to use the sat-query_ubuntu14 on a Linux machine, but it won't recognize the -f argument in the example 2. Could you help me out with installing the package? Thanks, Chen

This is the output I got when building the package. I got the same empty bin folder when building on a Linux machine. (base) Chens-MacBook-Air:~ chen$ git clone https://github.com/icthrm/cwSDTWnano Cloning into 'cwSDTWnano'... remote: Enumerating objects: 376, done. remote: Total 376 (delta 0), reused 0 (delta 0), pack-reused 376 Receiving objects: 100% (376/376), 6.95 MiB | 9.11 MiB/s, done. Resolving deltas: 100% (108/108), done. (base) Chens-MacBook-Air:~ chen$ cd cwSDTWnano/ (base) Chens-MacBook-Air:cwSDTWnano chen$ cd SATnano/ (base) Chens-MacBook-Air:SATnano chen$ cmake ./ -- The C compiler identification is AppleClang 10.0.1.10010046 -- The CXX compiler identification is AppleClang 10.0.1.10010046 -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test COMPILER_SUPPORTS_CXX11 -- Performing Test COMPILER_SUPPORTS_CXX11 - Success -- Performing Test COMPILER_SUPPORTS_CXX0X -- Performing Test COMPILER_SUPPORTS_CXX0X - Success -- building main -- building main -- building util -- building 6mer -- building mer2seq -- building proc -- Configuring done -- Generating done -- Build files have been written to: /Users/chen/cwSDTWnano/SATnano

icthrm commented 4 years ago

Dear Sir,

Thank you for using our code. Here I have a small question, can you delete the build directory. Then:

mkdir build cd build cmake .. make -j 6

try this operation and see if the exe built in build/bin

Jenny-dan commented 4 years ago

Hi,

I meet the same problem with Ubuntu and after doing what you said, it returned dzha@DESKTOP-4U9JHDU:/mnt/d/ape/cwSDTWnano/SATnano/build$ make -j 6 Scanning dependencies of target 6mer Scanning dependencies of target wavelib Scanning dependencies of target util [ 3%] Building CXX object src/6mer/CMakeFiles/6mer.dir/6mer_index.cpp.o [ 7%] Building CXX object src/util/CMakeFiles/util.dir/exception.cpp.o [ 11%] Building CXX object src/util/CMakeFiles/util.dir/qsort.cpp.o [ 19%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/conv.c.o [ 19%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/cwt.c.o [ 23%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/cwtmath.c.o [ 26%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/hsfft.c.o [ 30%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/real.c.o [ 34%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wavefilt.c.o [ 38%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wavefunc.c.o [ 42%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wavelib.c.o [ 46%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wtmath.c.o [ 50%] Linking CXX static library ../../lib/libutil.a [ 53%] Linking CXX static library ../../lib/lib6mer.a [ 53%] Built target util [ 57%] Linking C static library ../../libwavelib.a [ 57%] Built target 6mer [ 57%] Built target wavelib Scanning dependencies of target proc [ 61%] Building CXX object src/proc/CMakeFiles/proc.dir/base_fun.cpp.o [ 65%] Building CXX object src/proc/CMakeFiles/proc.dir/proc.cpp.o [ 69%] Building CXX object src/proc/CMakeFiles/proc.dir/io.cpp.o [ 73%] Building CXX object src/proc/CMakeFiles/proc.dir/resample.cpp.o /mnt/d/ape/cwSDTWnano/SATnano/src/proc/resample.cpp:1:10: fatal error: boost/math/special_functions/bessel.hpp: No such file or directory

include <boost/math/special_functions/bessel.hpp>

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

compilation terminated. src/proc/CMakeFiles/proc.dir/build.make:134: recipe for target 'src/proc/CMakeFiles/proc.dir/resample.cpp.o' failed make[2]: [src/proc/CMakeFiles/proc.dir/resample.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... In file included from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/proc.h:4:0, from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/base_fun.cpp:4: /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.h:10:10: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

      ^~~~~~~~

compilation terminated. In file included from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/proc.h:4:0, from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/proc.cpp:1: /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.h:10:10: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

      ^~~~~~~~

src/proc/CMakeFiles/proc.dir/build.make:62: recipe for target 'src/proc/CMakeFiles/proc.dir/base_fun.cpp.o' failed compilation terminated. make[2]: *** [src/proc/CMakeFiles/proc.dir/base_fun.cpp.o] Error 1 In file included from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.cpp:1:0: /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.h:10:10: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

      ^~~~~~~~

src/proc/CMakeFiles/proc.dir/build.make:110: recipe for target 'src/proc/CMakeFiles/proc.dir/proc.cpp.o' failed compilation terminated. make[2]: [src/proc/CMakeFiles/proc.dir/proc.cpp.o] Error 1 src/proc/CMakeFiles/proc.dir/build.make:86: recipe for target 'src/proc/CMakeFiles/proc.dir/io.cpp.o' failed make[2]: [src/proc/CMakeFiles/proc.dir/io.cpp.o] Error 1 CMakeFiles/Makefile2:495: recipe for target 'src/proc/CMakeFiles/proc.dir/all' failed make[1]: [src/proc/CMakeFiles/proc.dir/all] Error 2 Makefile:83: recipe for target 'all' failed make: [all] Error 2

I have installed libhdf5-serial-dev.

Thanks.

icthrm commented 4 years ago

Hi, what operation system you have used?

cwbcm notifications@github.com 于2019年11月19日周二 上午7:00写道：

Hi,

I have some problem installing the package from SATnano folder. I used cmake, but I got nothing in the bin folder after compiling. I also tried to use the sat-query_ubuntu14 on a Linux machine, but it won't recognize the -f argument in the example 2. Could you help me out with installing the package? Thanks, Chen

This is the output I got when building the package. I got the same empty bin folder when building on a Linux machine. (base) Chens-MacBook-Air:~ chen$ git clone https://github.com/icthrm/cwSDTWnano Cloning into 'cwSDTWnano'... remote: Enumerating objects: 376, done. remote: Total 376 (delta 0), reused 0 (delta 0), pack-reused 376 Receiving objects: 100% (376/376), 6.95 MiB | 9.11 MiB/s, done. Resolving deltas: 100% (108/108), done. (base) Chens-MacBook-Air:~ chen$ cd cwSDTWnano/ (base) Chens-MacBook-Air:cwSDTWnano chen$ cd SATnano/ (base) Chens-MacBook-Air:SATnano chen$ cmake ./ -- The C compiler identification is AppleClang 10.0.1.10010046 -- The CXX compiler identification is AppleClang 10.0.1.10010046 -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test COMPILER_SUPPORTS_CXX11 -- Performing Test COMPILER_SUPPORTS_CXX11 - Success -- Performing Test COMPILER_SUPPORTS_CXX0X -- Performing Test COMPILER_SUPPORTS_CXX0X - Success -- building main -- building main -- building util -- building 6mer -- building mer2seq -- building proc -- Configuring done -- Generating done -- Build files have been written to: /Users/chen/cwSDTWnano/SATnano

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/icthrm/cwSDTWnano/issues/1?email_source=notifications&email_token=AB2IPE6CII2VVC3O6XK7UE3QUMNABA5CNFSM4JO3J65KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4H2F2XUQ, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB2IPEZFNF5DNMDE644735LQUMNABANCNFSM4JO3J65A .

icthrm commented 4 years ago

Can you find bessel.hpp in your system?

Jenny-dan notifications@github.com 于2020年7月1日周三 上午2:30写道：

Hi,

I meet the same problem with Ubuntu and after doing what you said, it returned dzha@DESKTOP-4U9JHDU:/mnt/d/ape/cwSDTWnano/SATnano/build$ make -j 6 Scanning dependencies of target 6mer Scanning dependencies of target wavelib Scanning dependencies of target util [ 3%] Building CXX object src/6mer/CMakeFiles/6mer.dir/6mer_index.cpp.o [ 7%] Building CXX object src/util/CMakeFiles/util.dir/exception.cpp.o [ 11%] Building CXX object src/util/CMakeFiles/util.dir/qsort.cpp.o [ 19%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/conv.c.o [ 19%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/cwt.c.o [ 23%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/cwtmath.c.o [ 26%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/hsfft.c.o [ 30%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/real.c.o [ 34%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wavefilt.c.o [ 38%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wavefunc.c.o [ 42%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wavelib.c.o [ 46%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wtmath.c.o [ 50%] Linking CXX static library ../../lib/libutil.a [ 53%] Linking CXX static library ../../lib/lib6mer.a [ 53%] Built target util [ 57%] Linking C static library ../../libwavelib.a [ 57%] Built target 6mer [ 57%] Built target wavelib Scanning dependencies of target proc [ 61%] Building CXX object src/proc/CMakeFiles/proc.dir/base_fun.cpp.o [ 65%] Building CXX object src/proc/CMakeFiles/proc.dir/proc.cpp.o [ 69%] Building CXX object src/proc/CMakeFiles/proc.dir/io.cpp.o [ 73%] Building CXX object src/proc/CMakeFiles/proc.dir/resample.cpp.o /mnt/d/ape/cwSDTWnano/SATnano/src/proc/resample.cpp:1:10: fatal error: boost/math/special_functions/bessel.hpp: No such file or directory

include <boost/math/special_functions/bessel.hpp>

^~~~~~~~~ compilation terminated. src/proc/CMakeFiles/proc.dir/build.make:134: recipe for target 'src/proc/CMakeFiles/proc.dir/resample.cpp.o' failed make[2]: [src/proc/CMakeFiles/proc.dir/resample.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... In file included from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/proc.h:4:0, from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/base_fun.cpp:4: /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.h:10:10: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

^~~~ compilation terminated. In file included from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/proc.h:4:0, from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/proc.cpp:1: /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.h:10:10: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

^~~~ src/proc/CMakeFiles/proc.dir/build.make:62: recipe for target 'src/proc/CMakeFiles/proc.dir/base_fun.cpp.o' failed compilation terminated. make[2]: *** [src/proc/CMakeFiles/proc.dir/base_fun.cpp.o] Error 1 In file included from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.cpp:1:0: /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.h:10:10: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

^~~~ src/proc/CMakeFiles/proc.dir/build.make:110: recipe for target 'src/proc/CMakeFiles/proc.dir/proc.cpp.o' failed compilation terminated. make[2]: [src/proc/CMakeFiles/proc.dir/proc.cpp.o] Error 1 src/proc/CMakeFiles/proc.dir/build.make:86: recipe for target 'src/proc/CMakeFiles/proc.dir/io.cpp.o' failed make[2]: [src/proc/CMakeFiles/proc.dir/io.cpp.o] Error 1 CMakeFiles/Makefile2:495: recipe for target 'src/proc/CMakeFiles/proc.dir/all' failed make[1]: [src/proc/CMakeFiles/proc.dir/all] Error 2 Makefile:83: recipe for target 'all' failed make: [all] Error 2

I have installed libhdf5-serial-dev.

Thanks.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/icthrm/cwSDTWnano/issues/1#issuecomment-651967973, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB2IPE336SZT7GCY3YRBI3DRZIVNDANCNFSM4JO3J65A .

Jenny-dan commented 4 years ago

I use Ubuntu as a subsystem under windows 10. I can not find bessel.hpp.

icthrm commented 4 years ago

Sorry for late replay. I have some problems with my computer these days. I guess you should install a boost lib in your system.

Jenny-dan notifications@github.com 于2020年7月1日周三 上午11:08写道：

I use Ubuntu as a subsystem under windows 10. I can not find bessel.hpp.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/icthrm/cwSDTWnano/issues/1#issuecomment-652160497, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB2IPE2TWNR27EW3YDZUPS3RZKSBXANCNFSM4JO3J65A .

Jenny-dan commented 4 years ago

I installed a boost lib but the bin folder is still empty. dzha@DESKTOP-4U9JHDU:/mnt/d/ape/cwSDTWnano/SATnano/build$ make -j 6 Scanning dependencies of target util Scanning dependencies of target wavelib Scanning dependencies of target 6mer [ 3%] Building CXX object src/6mer/CMakeFiles/6mer.dir/6mer_index.cpp.o [ 7%] Building CXX object src/util/CMakeFiles/util.dir/exception.cpp.o [ 11%] Building CXX object src/util/CMakeFiles/util.dir/qsort.cpp.o [ 15%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/conv.c.o [ 19%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/cwt.c.o [ 23%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/cwtmath.c.o [ 26%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/hsfft.c.o [ 30%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/real.c.o [ 34%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wavefilt.c.o [ 38%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wavefunc.c.o [ 42%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wavelib.c.o [ 46%] Building C object lib/wavelib/src/CMakeFiles/wavelib.dir/wtmath.c.o [ 50%] Linking CXX static library ../../lib/libutil.a [ 53%] Linking CXX static library ../../lib/lib6mer.a [ 53%] Built target util [ 57%] Linking C static library ../../libwavelib.a [ 57%] Built target 6mer [ 57%] Built target wavelib Scanning dependencies of target proc [ 61%] Building CXX object src/proc/CMakeFiles/proc.dir/base_fun.cpp.o [ 69%] Building CXX object src/proc/CMakeFiles/proc.dir/io.cpp.o [ 69%] Building CXX object src/proc/CMakeFiles/proc.dir/proc.cpp.o [ 73%] Building CXX object src/proc/CMakeFiles/proc.dir/resample.cpp.o In file included from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/proc.h:4:0, from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/base_fun.cpp:4: /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.h:10:10: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

      ^~~~~~~~

In file included from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.cpp:1:0: /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.h:10:10: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

      ^~~~~~~~

In file included from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/proc.h:4:0, from /mnt/d/ape/cwSDTWnano/SATnano/src/proc/proc.cpp:1: /mnt/d/ape/cwSDTWnano/SATnano/src/proc/io.h:10:10: fatal error: hdf5.h: No such file or directory

include "hdf5.h"

      ^~~~~~~~

compilation terminated. compilation terminated. compilation terminated. src/proc/CMakeFiles/proc.dir/build.make:62: recipe for target 'src/proc/CMakeFiles/proc.dir/base_fun.cpp.o' failed make[2]: [src/proc/CMakeFiles/proc.dir/base_fun.cpp.o] Error 1 make[2]: Waiting for unfinished jobs.... src/proc/CMakeFiles/proc.dir/build.make:86: recipe for target 'src/proc/CMakeFiles/proc.dir/io.cpp.o' failed make[2]: [src/proc/CMakeFiles/proc.dir/io.cpp.o] Error 1 src/proc/CMakeFiles/proc.dir/build.make:110: recipe for target 'src/proc/CMakeFiles/proc.dir/proc.cpp.o' failed make[2]: [src/proc/CMakeFiles/proc.dir/proc.cpp.o] Error 1 CMakeFiles/Makefile2:495: recipe for target 'src/proc/CMakeFiles/proc.dir/all' failed make[1]: [src/proc/CMakeFiles/proc.dir/all] Error 2 Makefile:83: recipe for target 'all' failed make: [all] Error 2