Biostar Beta. Not for public use.
bam-readcount installation problem: Linking CXX executable
0
Entering edit mode
14 months ago
user31888 • 60
United States

I am trying to filter false positives from a VarScan2 somatic variant call using the fpfilter program.

For that I need to install bam-headcount, but get the following error when invoking make (cmake seems to work fine):

$ cmake
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- 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
-- 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
-- Looking for include file pthread.h
-- Looking for include file 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  
No CMAKE_BUILD_TYPE specified, defaulting to release
Extracting boost from /home/user/lib/bam-readcount_master/bam-readcount/vendor/boost-1.55-bamrc.tar.gz
Boost build log can be found at /home/user/lib/bam-readcount_master/vendor/boost-src/build.log
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3") 
-- Configuring done
-- Generating done
-- Build files have been written to: /home/user/lib/bam-readcount_master

$ make
...
Scanning dependencies of target bam-readcount
[ 87%] Building CXX object build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/bamreadcount.cpp.o
Linking CXX executable ../../../../bin/bam-readcount
../../../../vendor/boost/lib/libboost_program_options.a(cmdline.o): In function `boost::program_options::detail::cmdline::parse_long_option(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
cmdline.cpp:(.text+0x1c8a): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
cmdline.cpp:(.text+0x1cb4): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
cmdline.cpp:(.text+0x1cdf): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
../../../../vendor/boost/lib/libboost_program_options.a(cmdline.o): In function `boost::program_options::detail::cmdline::parse_dos_option(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
cmdline.cpp:(.text+0x23ef): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
../../../../vendor/boost/lib/libboost_program_options.a(cmdline.o): In function `boost::program_options::detail::cmdline::parse_short_option(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
cmdline.cpp:(.text+0x2ff6): undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)'
../../../../vendor/boost/lib/libboost_program_options.a(cmdline.o):cmdline.cpp:(.text+0x544d): more undefined references to `std::__throw_out_of_range_fmt(char const*, ...)' follow
collect2: ld returned 1 exit status
make[2]: *** [bin/bam-readcount] Error 1
make[1]: *** [build/src/exe/bam-readcount/CMakeFiles/bam-readcount.dir/all] Error 2
make: *** [all] Error 2

Any idea?

Is there another way to filter false positives without read-bamcount (except processSomatic that I already used)? Or even another Somatic SNP + indeed caller than VarScan2 (except GATK MuTect2 that takes ages)?

Thanks for your help !

Note:

Linux version 2.6.32

EDIT:

It seemed that the program did not like my gcc compiler. Switching to g++ solved the issue.

export CXX=/path/to/g++
git clone https://github.com/genome/bam-readcount.git
cmake /path/to/bam-readcount/repo
make
bam-readcount • 1.6k views
ADD COMMENTlink
1
Entering edit mode
13 months ago
natasha.sernova ♦ 3.5k

Have you seen this post?

A: Installing Bam-Readcount

It requires a lot. An old version may be a problem.

https://github.com/genome/bam-readcount

ADD COMMENTlink
0
Entering edit mode

Thanks Natasha. The gcc compiler was the problem (see EDIT above).

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1