Hi,
I am interested in trying strelka because I have been trying GATK but it takes a ridiculously large time for variant calling.
I downloaded and unzipped the binary distribution (CENTOS-6) and I got the following error: "ERROR: Strelka must be installed prior to running demo." - In addition, the HPC uses SLURM so I had to modify the bash and it failed nonetheless.
I loaded in the system both boost and cmake to build
Then I tried building it,
I created the build directory ----@pitzer-login01 strelka-2.9.10.centos6_x86_64]$ mkdir build && cd build
and then tried installing it: {../configure --jobs=24 }
It kind worked well with a few errors:
cmake version 3.17.2 (>= 2.8.12) is already installed
Using existing cmake: cmake
-- ==== Initializing project cmake configuration ====
-- BUILD_TYPE: Release
-- CMAKE_PARALLEL: 24
-- The C compiler identification is GNU 4.8.5
-- The CXX 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
...
...
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- 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 ccache found
and the final lines - without errors:
...
-- Adding c++ library subdirectory: strelka
-- Adding c++ test subdirectory: strelka/test
-- Adding c++ library subdirectory: strelkaNoiseExtractor
-- Adding c++ program subdirectory: bin
-- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components: doxygen dot
-- Doxygen: /usr/bin/doxygen. Dot: /usr/bin/dot.
-- Creating Doxygen config file: /fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build/src/c++/Doxyfile
-- Configuring done
-- Generating done
-- Build files have been written to: /fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build
The build directory /fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build was configured successfully
Type "make -C /fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build" to build
So I did {make -j24 -C /fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build install}
Hi, I am interested in trying strelka because I have been trying GATK but it takes a ridiculously large time for variant calling. I downloaded and unzipped the binary distribution (CENTOS-6) and I got the following error: "ERROR: Strelka must be installed prior to running demo." - In addition, the HPC uses SLURM so I had to modify the bash and it failed nonetheless. I loaded in the system both boost and cmake to build
Then I tried building it, I created the build directory ----@pitzer-login01 strelka-2.9.10.centos6_x86_64]$ mkdir build && cd build and then tried installing it: {../configure --jobs=24 } It kind worked well with a few errors: cmake version 3.17.2 (>= 2.8.12) is already installed Using existing cmake: cmake -- ==== Initializing project cmake configuration ==== -- BUILD_TYPE: Release -- CMAKE_PARALLEL: 24 -- The C compiler identification is GNU 4.8.5 -- The CXX 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 ... ...
-- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- 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 ccache found
and the final lines - without errors: ... -- Adding c++ library subdirectory: strelka -- Adding c++ test subdirectory: strelka/test -- Adding c++ library subdirectory: strelkaNoiseExtractor -- Adding c++ program subdirectory: bin -- Found Doxygen: /usr/bin/doxygen (found version "1.8.5") found components: doxygen dot -- Doxygen: /usr/bin/doxygen. Dot: /usr/bin/dot. -- Creating Doxygen config file: /fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build/src/c++/Doxyfile -- Configuring done -- Generating done -- Build files have been written to: /fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build The build directory /fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build was configured successfully Type "make -C /fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build" to build
So I did {make -j24 -C /fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build install}
But I got some error messages: [ 77%] Linking CXX executable GetChromDepth [ 78%] Linking CXX executable GetRegionDepth [ 78%] Linking CXX executable strelka2 [ 78%] Linking CXX executable MergeRunStats [ 78%] Linking CXX executable DumpSequenceAlleleCounts [ 78%] Linking CXX executable GetSequenceAlleleCounts [ 78%] Linking CXX executable EstimateVariantErrorRates [ 78%] Linking CXX executable MergeSequenceAlleleCounts [ 78%] Linking CXX executable starlingSiteSimulator [ 78%] Linking CXX executable starling2 make[2]: Leaving directory
/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[2]: Leaving directory/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: [src/c++/bin/GetChromDepth] Error 1 make[2]: Leaving directory `/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: [src/c++/bin/CMakeFiles/GetChromDepth.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... make[2]: Leaving directory `/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: [src/c++/bin/GetRegionDepth] Error 1 make[2]: Leaving directory/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: *** [src/c++/bin/CMakeFiles/GetRegionDepth.dir/all] Error 2 /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: *** [src/c++/bin/MergeRunStats] Error 1 make[2]: Leaving directory/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: [src/c++/bin/CMakeFiles/MergeRunStats.dir/all] Error 2 make[2]: Entering directory `/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: [src/c++/bin/strelkaSiteSimulator] Error 1 make[2]: Leaving directory/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: *** [src/c++/bin/CMakeFiles/strelkaSiteSimulator.dir/all] Error 2 make[2]: Entering directory/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: [src/c++/bin/starlingSiteSimulator] Error 1 make[2]: Leaving directory `/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: [src/c++/bin/CMakeFiles/starlingSiteSimulator.dir/all] Error 2 make[2]: [src/c++/bin/MergeSequenceAlleleCounts] Error 1 make[2]: Leaving directory `/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: [src/c++/bin/CMakeFiles/MergeSequenceAlleleCounts.dir/all] Error 2 /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: [src/c++/bin/DumpSequenceAlleleCounts] Error 1 make[2]: Leaving directory `/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: [src/c++/bin/CMakeFiles/DumpSequenceAlleleCounts.dir/all] Error 2 [ 78%] Building CXX object src/c++/lib/blt_common/test/CMakeFiles/strelka_unit_test_blt_common.dir/ref_context_test.cpp.o [ 79%] Building CXX object src/c++/lib/blt_common/test/CMakeFiles/strelka_unit_test_blt_common.dir/test_main.cpp.o /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: Entering directory/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' [ 80%] Building CXX object src/c++/lib/alignment/test/CMakeFiles/strelka_unit_test_alignment.dir/GlobalAlignerTest.cpp.o /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: *** [src/c++/bin/EstimateVariantErrorRates] Error 1 make[2]: Leaving directory/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: *** [src/c++/bin/CMakeFiles/EstimateVariantErrorRates.dir/all] Error 2 ... ...make[1]: [src/c++/bin/CMakeFiles/strelkaNoiseExtractor.dir/all] Error 2 [ 81%] Building CXX object src/c++/lib/assembly/test/CMakeFiles/strelka_unit_test_assembly.dir/test_main.cpp.o /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: [src/c++/bin/strelka2] Error 1 make[2]: Leaving directory
/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: *** [src/c++/bin/CMakeFiles/strelka2.dir/all] Error 2 /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: *** [src/c++/bin/GetSequenceAlleleCounts] Error 1 make[2]: Leaving directory/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: [src/c++/bin/CMakeFiles/GetSequenceAlleleCounts.dir/all] Error 2 make[2]: Leaving directory `/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make[2]: [src/c++/bin/starling2] Error 1 make[2]: Leaving directory/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[1]: *** [src/c++/bin/CMakeFiles/starling2.dir/all] Error 2 make[2]: Entering directory/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build' make[2]: Leaving directory `/fs/scratch/PHS0338/appz/strelka-2.9.10.release_src/build'Is there a way to fix this error to finally test strelka?
Thank you very much;