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Illumina / strelka

Strelka2 germline and somatic small variant caller
GNU General Public License v3.0
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how to install strelka on linux? #238

Closed gabrielet closed 6 months ago

gabrielet commented 7 months ago

I know there are installing instructions, very clear and straightforward. What is not straightforward, however, is how to make them actually work.

It has been two days already but so far, i was unable to compile strelka and i am unsure what else needs to be done.

What i did:

STRELKA_VERSION="2.9.10"
wget https://github.com/Illumina/strelka/releases/download/v${STRELKA_VERSION}/strelka-${STRELKA_VERSION}.release_src.tar.bz2
tar -xjf strelka-${STRELKA_VERSION}.release_src.tar.bz2
mkdir build && cd build
../strelka-${STRELKA_VERSION}.release_src/configure --jobs=4 --prefix=/home/user/genomics/strelka-2.9.10/
make -j4 install

as outlined in the installation notes

This is what the configure script returns (all is finally fine here):

cmake version 3.22.1 (>= 2.8.12) is already installed Using existing cmake: cmake -- ==== Initializing project cmake configuration ==== -- BUILD_TYPE: Release -- CMAKE_PARALLEL: 4 -- The C compiler identification is GNU 11.4.0 -- The CXX compiler identification is GNU 11.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /bin/gcc-11 - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /bin/g++-11 - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- TARGET_ARCHITECTURE: x86_64 -- install prefix: /home/user/genomics/strelka-2.9.10 -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.58.0") -- Building external tools -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- zlib found -- Verifying target directories access -- Looking for floorf -- Looking for floorf - found -- Looking for round -- Looking for round - found -- Looking for roundf -- Looking for roundf - found -- Looking for powf -- Looking for powf - found -- Looking for pthread.h CMake Warning (dev) at /usr/share/cmake-3.22/Modules/CheckIncludeFile.cmake:82 (message): Policy CMP0075 is not set: Include file check macros honor CMAKE_REQUIRED_LIBRARIES. Run "cmake --help-policy CMP0075" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

CMAKE_REQUIRED_LIBRARIES is set to:

m

For compatibility with CMake 3.11 and below this check is ignoring it. Call Stack (most recent call first): /usr/share/cmake-3.22/Modules/FindThreads.cmake:146 (CHECK_INCLUDE_FILE) src/cmake/cxxConfigure.cmake:79 (find_package) src/c++/CMakeLists.txt:38 (include) This warning is for project developers. Use -Wno-dev to suppress it.

-- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found ccache: /usr/bin/ccache -- Using compiler: g++ version 11.4.0 -- Adding c++ library subdirectory: test -- Adding c++ library subdirectory: strelka_common -- Adding c++ library subdirectory: starling_common -- Adding c++ test subdirectory: starling_common/test -- Adding c++ library subdirectory: alignment -- Adding c++ test subdirectory: alignment/test -- Adding c++ library subdirectory: assembly -- Adding c++ test subdirectory: assembly/test -- Adding c++ library subdirectory: blt_common -- Adding c++ test subdirectory: blt_common/test -- Adding c++ library subdirectory: calibration -- Adding c++ library subdirectory: errorAnalysis -- Adding c++ library subdirectory: options -- Adding c++ library subdirectory: appstats -- Adding c++ library subdirectory: htsapi -- Adding c++ test subdirectory: htsapi/test -- Adding c++ library subdirectory: common -- Adding c++ library subdirectory: blt_util -- Adding c++ test subdirectory: blt_util/test -- Adding c++ library subdirectory: DumpSequenceAlleleCounts -- Adding c++ library subdirectory: EstimateParametersFromAlleleCounts -- Adding c++ library subdirectory: EstimateVariantErrorRates -- Adding c++ library subdirectory: GetChromDepth -- Adding c++ library subdirectory: GetRegionDepth -- Adding c++ library subdirectory: GetSequenceAlleleCounts -- Adding c++ library subdirectory: MergeRunStats -- Adding c++ library subdirectory: MergeSequenceAlleleCounts -- Adding c++ library subdirectory: starling -- Adding c++ test subdirectory: starling/test -- 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 "1.9.1") found components: doxygen dot -- Doxygen: /usr/bin/doxygen. Dot: /usr/bin/dot. -- Creating Doxygen config file: /home/user/genomics/build/src/c++/Doxyfile -- Configuring done -- Generating done -- Build files have been written to: /home/user/genomics/build

The build directory /home/user/genomics/build was configured successfully

Type "make -C /home/user/genomics/build" to build

At this point, i am on the fence because the line just above this one says:

Type "make -C /home/user/genomics/build" to build

while the instructions report:

make -j4 install

So, i did both and none worked. Here is the output of the "official" approach, i.e. make -j4 install:

[ 1%] Building bgzf_extras [ 1%] Unpacking htslib library [ 1%] Updating buildtime config info [ 1%] Built target strelka_buildtime_config [ 1%] Unpacking rapidjson package [ 1%] Building htslib library [ 1%] Built target strelka_rapidjson [ 1%] Unpacking CodeMin [ 1%] Built target strelka_codemin [ 1%] Unpacking pyflow [ 1%] Building pyflow [ 1%] Built target strelka_pyflow [ 1%] Built target strelka_python_buildtime_config [ 1%] Built target strelka_cxx_buildtime_config [ 2%] Compiling python library source [ 2%] Built target strelka_bgzfx [ 2%] Built target strelka_pythonlib_compile [ 2%] Built target strelka_source_check [ 3%] Unpacking samtools package [ 3%] Building samtools package [ 3%] Built target strelka_samtools [ 3%] Built target strelka_opt [ 3%] Building CXX object src/c++/lib/strelka_common/CMakeFiles/strelka_strelka_common.dir/position_snp_call_grid_lhood_cached.cpp.o [ 3%] Building CXX object src/c++/lib/test/CMakeFiles/strelka_test.dir/testIndelBuffer.cpp.o [ 3%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/SiteNoise.cpp.o [ 3%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/ActiveRegionDetector.cpp.o [ 4%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/SomaticIndelVcfWriter.cpp.o [ 4%] Linking CXX static library libstrelka_test.a [ 5%] Linking CXX static library libstrelka_strelka_common.a [ 5%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/ActiveRegionProcessor.cpp.o [ 5%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/position_somatic_snv_strand_grid.cpp.o [ 5%] Built target strelka_strelka_common In file included from /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/blt_util/algo_util.hh:35, from /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/starling_common/ActiveRegionProcessor.cpp:27: /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/blt_util/algo_util_impl.hh: In instantiation of 'std::set<typename std::iterator_traits< >::value_type> getDuplicatesInSortedInput(Iter, Iter, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator<const unsigned int*, std::vector >; typename std::iterator_traits< >::value_type = unsigned int]': /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/starling_common/ActiveRegionProcessor.cpp:360:35: required from here /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/blt_util/algo_util_impl.hh:49:26: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 49 | return std::move(dups); | ^ /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/blt_util/algo_util_impl.hh:49:26: note: remove 'std::move' call [ 5%] Built target strelka_test [ 6%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/ActiveRegionReadBuffer.cpp.o [ 6%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/position_somatic_snv_strand_grid_lhood_cached.cpp.o [ 6%] Building CXX object src/c++/lib/alignment/CMakeFiles/strelka_alignment.dir/Alignment.cpp.o [ 7%] Building CXX object src/c++/lib/assembly/CMakeFiles/strelka_assembly.dir/AssembledContig.cpp.o [ 7%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/AlleleGroupGenotype.cpp.o [ 8%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/position_somatic_snv_strand_grid_vcf.cpp.o [ 8%] Linking CXX static library libstrelka_alignment.a [ 8%] Building CXX object src/c++/lib/assembly/CMakeFiles/strelka_assembly.dir/IterativeAssembler.cpp.o [ 8%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/AlleleReportInfo.cpp.o [ 8%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/qscore_calculator.cpp.o [ 8%] Building CXX object src/c++/lib/assembly/CMakeFiles/strelka_assembly.dir/SmallAssembler.cpp.o [ 8%] Built target strelka_alignment [ 8%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/AlleleReportInfoUtil.cpp.o [ 8%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/somatic_indel_grid.cpp.o [ 8%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/somaticAlleleUtil.cpp.o [ 8%] Linking CXX static library libstrelka_assembly.a [ 9%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/CandidateAlignment.cpp.o [ 10%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/somatic_indel_scoring_features.cpp.o [ 10%] Built target strelka_assembly [ 10%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/CandidateSnvBuffer.cpp.o [ 10%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/MapqTracker.cpp.o [ 10%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/adjust_joint_eprob.cpp.o [ 10%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/somatic_result_set.cpp.o [ 10%] Building CXX object src/c++/lib/calibration/CMakeFiles/strelka_calibration.dir/IndelErrorModel.cpp.o [ 10%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/HtsMergeStreamer.cpp.o [ 10%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/blt_arg_validate.cpp.o [ 10%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelka.cpp.o [ 10%] Building CXX object src/c++/lib/calibration/CMakeFiles/strelka_calibration.dir/IndelErrorModelJson.cpp.o [ 11%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/blt_shared.cpp.o [ 12%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/HtsMergeStreamerUtil.cpp.o [ 12%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelkaSiteSimulator.cpp.o [ 12%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/hapscore.cpp.o [ 12%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/IndelBuffer.cpp.o [ 13%] Building CXX object src/c++/lib/calibration/CMakeFiles/strelka_calibration.dir/RandomForestModel.cpp.o [ 14%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelka_digt_states.cpp.o [ 14%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/position_loghood_minfunc.cpp.o [ 14%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/IndelData.cpp.o [ 14%] Building CXX object src/c++/lib/calibration/CMakeFiles/strelka_calibration.dir/ThetaJson.cpp.o [ 14%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelka_info.cpp.o [ 15%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/position_nonref_2allele_test.cpp.o [ 15%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/IndelKey.cpp.o [ 15%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelka_option_parser.cpp.o [ 15%] Building CXX object src/c++/lib/calibration/CMakeFiles/strelka_calibration.dir/VariantScoringModelMetadata.cpp.o [ 15%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/position_nonref_test.cpp.o [ 16%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/LocusSupportingReadStats.cpp.o [ 16%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/OrthogonalVariantAlleleCandidateGroup.cpp.o [ 17%] Building CXX object src/c++/lib/calibration/CMakeFiles/strelka_calibration.dir/VariantScoringModelServer.cpp.o [ 18%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelka_pile_test_run.cpp.o [ 18%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/position_snp_call_lrt.cpp.o [ 18%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelka_pos_processor.cpp.o [ 18%] Building CXX object src/c++/lib/calibration/CMakeFiles/strelka_calibration.dir/featuresetUtil.cpp.o [ 18%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/OrthogonalVariantAlleleCandidateGroupUtil.cpp.o [ 18%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/position_snp_call_pprob_digt.cpp.o [ 18%] Linking CXX static library libstrelka_calibration.a [ 18%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/PileupCleaner.cpp.o [ 18%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelka_run.cpp.o [ 20%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/ReferenceRepeatFinder.cpp.o [ 20%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/position_snp_call_pprob_monogt.cpp.o [ 20%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/Tier2OptionsParser.cpp.o [ 20%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelka_shared.cpp.o [ 20%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/position_snp_call_pprob_nploid.cpp.o [ 20%] Built target strelka_calibration [ 20%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/position_strand_coverage_anomaly.cpp.o [ 20%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/alignment.cpp.o [ 21%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelka_sim_test.cpp.o [ 21%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/position_strand_distro_anomaly.cpp.o [ 21%] Building CXX object src/c++/lib/errorAnalysis/CMakeFiles/strelka_errorAnalysis.dir/BasecallCounts.cpp.o /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp: In function 'unsigned int get_binom(unsigned int, float)': /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:79:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::nr' may be used uninitialized [-Wmaybe-uninitialized] 79 | bdist_t bdist(n,p); | ^~~~~ /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:79:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::npq' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:79:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::b' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:79:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::a' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:79:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::c' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:79:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::alpha' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:79:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::v_r' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp: In function 'void strelka_site_sim(strelka_options&, strelka_site_sim_options&)': /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:272:12: warning: 'tdist.boost::random::poisson_distribution<>::_u.boost::random::poisson_distribution<>::::_ptrd.boost::random::poisson_distribution<>::::::inv_alpha' may be used uninitialized in this function [-Wmaybe-uninitialized] 272 | dist_t tdist(sim_opt.tcov); | ^~~~~ /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:272:12: warning: 'tdist.boost::random::poisson_distribution<>::_u.boost::random::poisson_distribution<>::::_ptrd.boost::random::poisson_distribution<>::::::smu' may be used uninitialized in this function [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:272:12: warning: 'tdist.boost::random::poisson_distribution<>::_u.boost::random::poisson_distribution<>::::_ptrd.boost::random::poisson_distribution<>::::::b' may be used uninitialized in this function [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:272:12: warning: 'tdist.boost::random::poisson_distribution<>::_u.boost::random::poisson_distribution<>::::_ptrd.boost::random::poisson_distribution<>::::::a' may be used uninitialized in this function [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:271:12: warning: 'ndist.boost::random::poisson_distribution<>::_u.boost::random::poisson_distribution<>::::_ptrd.boost::random::poisson_distribution<>::::::inv_alpha' may be used uninitialized in this function [-Wmaybe-uninitialized] 271 | dist_t ndist(sim_opt.ncov); | ^~~~~ /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:271:12: warning: 'ndist.boost::random::poisson_distribution<>::_u.boost::random::poisson_distribution<>::::_ptrd.boost::random::poisson_distribution<>::::::smu' may be used uninitialized in this function [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:271:12: warning: 'ndist.boost::random::poisson_distribution<>::_u.boost::random::poisson_distribution<>::::_ptrd.boost::random::poisson_distribution<>::::::b' may be used uninitialized in this function [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/strelka/strelka_sim_test.cpp:271:12: warning: 'ndist.boost::random::poisson_distribution<>::_u.boost::random::poisson_distribution<>::::_ptrd.boost::random::poisson_distribution<>::::::a' may be used uninitialized in this function [-Wmaybe-uninitialized] [ 22%] Building CXX object src/c++/lib/applications/strelka/CMakeFiles/strelka_strelka.dir/strelka_streams.cpp.o [ 22%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/alignment_util.cpp.o [ 23%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/position_strand_distro_anomaly_lrt.cpp.o [ 24%] Building CXX object src/c++/lib/errorAnalysis/CMakeFiles/strelka_errorAnalysis.dir/IndelCounts.cpp.o [ 24%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/indel.cpp.o [ 24%] Linking CXX static library libstrelka_strelka.a [ 24%] Building CXX object src/c++/lib/errorAnalysis/CMakeFiles/strelka_errorAnalysis.dir/SequenceAlleleCounts.cpp.o [ 24%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/ref_context.cpp.o [ 24%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/indel_set.cpp.o [ 24%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/snp_pos_info.cpp.o [ 25%] Building CXX object src/c++/lib/blt_common/CMakeFiles/strelka_blt_common.dir/sparse_function_1d.cpp.o [ 25%] Linking CXX static library libstrelka_errorAnalysis.a [ 25%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/indel_util.cpp.o [ 25%] Linking CXX static library libstrelka_blt_common.a [ 25%] Built target strelka_strelka [ 26%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/min_count_binom_gte_cache.cpp.o [ 26%] Building CXX object src/c++/lib/options/CMakeFiles/strelka_options.dir/AlignmentFileOptionsParser.cpp.o [ 26%] Building CXX object src/c++/lib/starling_common/CMakeFiles/strelka_starling_common.dir/normalizeAlignment.cpp.o [ 26%] Built target strelka_errorAnalysis [ 26%] Built target strelka_blt_common [ 26%] Building CXX object 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src/c++/lib/blt_util/CMakeFiles/strelka_blt_util.dir/table_test.cpp.o [ 52%] Linking CXX static library libstrelka_starling_common.a [ 52%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/gvcf_options.cpp.o [ 52%] Building CXX object src/c++/lib/blt_util/CMakeFiles/strelka_blt_util.dir/time_util.cpp.o [ 52%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/gvcf_writer.cpp.o [ 53%] Linking CXX static library libstrelka_blt_util.a [ 53%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/ploidyUtil.cpp.o [ 53%] Built target strelka_starling_common [ 54%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/starling.cpp.o [ 54%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/starlingSiteSimulator.cpp.o [ 54%] Built target strelka_blt_util [ 54%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/starling_continuous_variant_caller.cpp.o [ 55%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/starling_info.cpp.o [ 55%] Building CXX object src/c++/lib/applications/DumpSequenceAlleleCounts/CMakeFiles/strelka_DumpSequenceAlleleCounts.dir/DSACOptions.cpp.o [ 55%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/starling_option_parser.cpp.o [ 55%] Building CXX object src/c++/lib/applications/DumpSequenceAlleleCounts/CMakeFiles/strelka_DumpSequenceAlleleCounts.dir/DumpSequenceAlleleCounts.cpp.o [ 55%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/starling_pile_test_run.cpp.o [ 55%] Linking CXX static library libstrelka_DumpSequenceAlleleCounts.a [ 55%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/starling_pos_processor.cpp.o [ 55%] Built target strelka_DumpSequenceAlleleCounts [ 56%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/starling_run.cpp.o [ 57%] Building CXX object src/c++/lib/applications/EstimateParametersFromAlleleCounts/CMakeFiles/strelka_EstimateParametersFromAlleleCounts.dir/EPACOptions.cpp.o [ 57%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/starling_sim_test.cpp.o [ 57%] Building CXX object src/c++/lib/applications/EstimateParametersFromAlleleCounts/CMakeFiles/strelka_EstimateParametersFromAlleleCounts.dir/EstimateParametersFromAlleleCounts.cpp.o /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/starling/starling_sim_test.cpp: In function 'unsigned int get_binom(unsigned int, float)': /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/starling/starling_sim_test.cpp:80:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::nr' may be used uninitialized [-Wmaybe-uninitialized] 80 | bdist_t bdist(n,p); | ^~~~~ /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/starling/starling_sim_test.cpp:80:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::npq' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/starling/starling_sim_test.cpp:80:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::b' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/starling/starling_sim_test.cpp:80:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::a' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/starling/starling_sim_test.cpp:80:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::c' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/starling/starling_sim_test.cpp:80:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::alpha' may be used uninitialized [-Wmaybe-uninitialized] /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/applications/starling/starling_sim_test.cpp:80:13: warning: 'bdist.boost::random::binomial_distribution<int, float>::_u.boost::random::binomial_distribution<int, float>::::btrd.boost::random::binomial_distribution<int, float>::::::v_r' may be used uninitialized [-Wmaybe-uninitialized] [ 57%] Building CXX object src/c++/lib/applications/EstimateParametersFromAlleleCounts/CMakeFiles/strelka_EstimateParametersFromAlleleCounts.dir/indelModel1.cpp.o [ 57%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/starling_streams.cpp.o [ 57%] Building CXX object src/c++/lib/applications/starling/CMakeFiles/strelka_starling.dir/variant_prefilter_stage.cpp.o [ 58%] Building CXX object src/c++/lib/applications/EstimateParametersFromAlleleCounts/CMakeFiles/strelka_EstimateParametersFromAlleleCounts.dir/indelModelVariantAndBetaBinomialError.cpp.o [ 58%] Building CXX object 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src/c++/lib/applications/EstimateVariantErrorRates/CMakeFiles/strelka_EstimateVariantErrorRates.dir/IndelModelProduction.cpp.o [ 60%] Building CXX object src/c++/lib/applications/EstimateParametersFromAlleleCounts/CMakeFiles/strelka_EstimateParametersFromAlleleCounts.dir/indelModelVariantAndIndyErrorNoOverlap.cpp.o [ 60%] Linking CXX static library libstrelka_EstimateVariantErrorRates.a [ 60%] Building CXX object src/c++/lib/applications/EstimateParametersFromAlleleCounts/CMakeFiles/strelka_EstimateParametersFromAlleleCounts.dir/snvModel1.cpp.o [ 60%] Built target strelka_EstimateVariantErrorRates [ 60%] Building CXX object src/c++/lib/applications/EstimateParametersFromAlleleCounts/CMakeFiles/strelka_EstimateParametersFromAlleleCounts.dir/snvModelVariantAndBinomialMixtureError.cpp.o [ 60%] Building CXX object src/c++/lib/applications/GetChromDepth/CMakeFiles/strelka_GetChromDepth.dir/ChromDepthOptions.cpp.o [ 60%] Building CXX object src/c++/lib/applications/GetChromDepth/CMakeFiles/strelka_GetChromDepth.dir/GetChromDepth.cpp.o [ 60%] Building CXX object src/c++/lib/applications/EstimateParametersFromAlleleCounts/CMakeFiles/strelka_EstimateParametersFromAlleleCounts.dir/snvModelVariantAndIndyError.cpp.o [ 61%] Building CXX object src/c++/lib/applications/GetChromDepth/CMakeFiles/strelka_GetChromDepth.dir/ReadChromDepthUtil.cpp.o [ 62%] Linking CXX static library libstrelka_EstimateParametersFromAlleleCounts.a [ 62%] Linking CXX static library libstrelka_GetChromDepth.a [ 62%] Built target strelka_EstimateParametersFromAlleleCounts [ 62%] Built target strelka_GetChromDepth [ 62%] Building CXX object src/c++/lib/applications/GetRegionDepth/CMakeFiles/strelka_GetRegionDepth.dir/GetRegionDepth.cpp.o [ 62%] Building CXX object src/c++/lib/applications/GetSequenceAlleleCounts/CMakeFiles/strelka_GetSequenceAlleleCounts.dir/GetSequenceAlleleCounts.cpp.o [ 62%] Building CXX object src/c++/lib/applications/GetRegionDepth/CMakeFiles/strelka_GetRegionDepth.dir/ReadRegionDepthUtil.cpp.o [ 64%] Building CXX object src/c++/lib/applications/GetSequenceAlleleCounts/CMakeFiles/strelka_GetSequenceAlleleCounts.dir/GetSequenceAlleleCountsInfo.cpp.o [ 64%] Building CXX object src/c++/lib/applications/GetRegionDepth/CMakeFiles/strelka_GetRegionDepth.dir/RegionDepthOptions.cpp.o [ 65%] Linking CXX static library libstrelka_starling.a [ 65%] Building CXX object src/c++/lib/applications/GetSequenceAlleleCounts/CMakeFiles/strelka_GetSequenceAlleleCounts.dir/GetSequenceAlleleCountsRun.cpp.o [ 65%] Linking CXX static library libstrelka_GetRegionDepth.a [ 65%] Building CXX object src/c++/lib/applications/GetSequenceAlleleCounts/CMakeFiles/strelka_GetSequenceAlleleCounts.dir/SequenceAlleleCountsOptions.cpp.o [ 65%] Built target strelka_GetRegionDepth [ 65%] Built target strelka_starling [ 65%] Building CXX object src/c++/lib/applications/GetSequenceAlleleCounts/CMakeFiles/strelka_GetSequenceAlleleCounts.dir/SequenceAlleleCountsOptionsParser.cpp.o [ 66%] Building CXX object src/c++/lib/applications/GetSequenceAlleleCounts/CMakeFiles/strelka_GetSequenceAlleleCounts.dir/SequenceAlleleCountsPosProcessor.cpp.o [ 67%] Building CXX object src/c++/lib/common/CMakeFiles/strelka_common.dir/ProgramUtil.cpp.o [ 67%] Building CXX object src/c++/lib/applications/GetSequenceAlleleCounts/CMakeFiles/strelka_GetSequenceAlleleCounts.dir/SequenceAlleleCountsStreams.cpp.o [ 67%] Building CXX object src/c++/lib/common/CMakeFiles/strelka_common.dir/SegmentTimeTracker.cpp.o [ 67%] Building CXX object src/c++/lib/applications/MergeRunStats/CMakeFiles/strelka_MergeRunStats.dir/MRSOptions.cpp.o [ 67%] Linking CXX static library libstrelka_GetSequenceAlleleCounts.a [ 68%] Building CXX object src/c++/lib/applications/MergeRunStats/CMakeFiles/strelka_MergeRunStats.dir/MergeRunStats.cpp.o [ 68%] Building CXX object src/c++/lib/applications/MergeSequenceAlleleCounts/CMakeFiles/strelka_MergeSequenceAlleleCounts.dir/MSACOptions.cpp.o [ 68%] Linking CXX static library libstrelka_MergeRunStats.a [ 68%] Built target strelka_GetSequenceAlleleCounts [ 69%] Building CXX object src/c++/lib/applications/MergeSequenceAlleleCounts/CMakeFiles/strelka_MergeSequenceAlleleCounts.dir/MergeSequenceAlleleCounts.cpp.o [ 69%] Building CXX object src/c++/lib/applications/strelkaNoiseExtractor/CMakeFiles/strelka_strelkaNoiseExtractor.dir/snoise_info.cpp.o [ 69%] Linking CXX static library libstrelka_MergeSequenceAlleleCounts.a [ 69%] Built target strelka_MergeRunStats [ 70%] Building CXX object src/c++/lib/applications/strelkaNoiseExtractor/CMakeFiles/strelka_strelkaNoiseExtractor.dir/snoise_option_parser.cpp.o [ 70%] Building CXX object src/c++/lib/applications/strelkaNoiseExtractor/CMakeFiles/strelka_strelkaNoiseExtractor.dir/snoise_pos_processor.cpp.o [ 70%] Built target strelka_MergeSequenceAlleleCounts [ 70%] Building CXX object src/c++/lib/applications/strelkaNoiseExtractor/CMakeFiles/strelka_strelkaNoiseExtractor.dir/snoise_run.cpp.o [ 71%] Building CXX object src/c++/lib/applications/strelkaNoiseExtractor/CMakeFiles/strelka_strelkaNoiseExtractor.dir/snoise_streams.cpp.o [ 71%] Building CXX object src/c++/lib/applications/strelkaNoiseExtractor/CMakeFiles/strelka_strelkaNoiseExtractor.dir/strelkaNoiseExtractor.cpp.o [ 71%] Linking CXX static library libstrelka_common.a [ 71%] Built target strelka_common [ 71%] Linking CXX static library libstrelka_strelkaNoiseExtractor.a [ 72%] Building CXX object src/c++/lib/alignment/test/CMakeFiles/strelka_unit_test_alignment.dir/GlobalAlignerTest.cpp.o [ 72%] Building CXX object src/c++/lib/starling_common/test/CMakeFiles/strelka_unit_test_starling_common.dir/ActiveRegionPloidyTest.cpp.o [ 73%] Building CXX object src/c++/lib/applications/strelka/test/CMakeFiles/strelka_unit_test_strelka.dir/SiteNoise_test.cpp.o [ 73%] Building CXX object src/c++/lib/applications/strelka/test/CMakeFiles/strelka_unit_test_strelka.dir/somatic_indel_scoring_features_test.cpp.o [ 73%] Building CXX object src/c++/lib/alignment/test/CMakeFiles/strelka_unit_test_alignment.dir/test_main.cpp.o [ 73%] Built target strelka_strelkaNoiseExtractor [ 73%] Building CXX object src/c++/lib/starling_common/test/CMakeFiles/strelka_unit_test_starling_common.dir/ActiveRegionTest.cpp.o [ 73%] Building CXX object src/c++/lib/applications/strelka/test/CMakeFiles/strelka_unit_test_strelka.dir/test_main.cpp.o [ 73%] Linking CXX executable strelka_unit_test_alignment [ 74%] Building CXX object src/c++/lib/starling_common/test/CMakeFiles/strelka_unit_test_starling_common.dir/IndelErrorModelTest.cpp.o [ 75%] Linking CXX executable strelka_unit_test_strelka [ 75%] Building CXX object src/c++/lib/starling_common/test/CMakeFiles/strelka_unit_test_starling_common.dir/ReferenceRepeatFinderTest.cpp.o [ 75%] Built target strelka_unit_test_alignment [ 75%] Building CXX object src/c++/lib/assembly/test/CMakeFiles/strelka_unit_test_assembly.dir/IterativeAssemblerTest.cpp.o [ 75%] Built target strelka_unit_test_strelka [ 75%] Building CXX object src/c++/lib/blt_common/test/CMakeFiles/strelka_unit_test_blt_common.dir/ref_context_test.cpp.o [ 76%] Building CXX object src/c++/lib/assembly/test/CMakeFiles/strelka_unit_test_assembly.dir/SmallAssemblerTest.cpp.o [ 77%] Building CXX object src/c++/lib/blt_common/test/CMakeFiles/strelka_unit_test_blt_common.dir/test_main.cpp.o [ 77%] Building CXX object src/c++/lib/assembly/test/CMakeFiles/strelka_unit_test_assembly.dir/test_main.cpp.o [ 77%] Linking CXX executable strelka_unit_test_assembly [ 77%] Linking CXX executable strelka_unit_test_blt_common [ 77%] Built target strelka_unit_test_assembly [ 77%] Built target strelka_unit_test_blt_common [ 77%] Building CXX object src/c++/lib/htsapi/test/CMakeFiles/strelka_unit_test_htsapi.dir/align_path_bam_util_test.cpp.o [ 77%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/CircularCounter_test.cpp.o [ 77%] Building CXX object src/c++/lib/htsapi/test/CMakeFiles/strelka_unit_test_htsapi.dir/bam_streamer_test.cpp.o [ 78%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/IntegerLogCompressor_test.cpp.o [ 79%] Building CXX object src/c++/lib/htsapi/test/CMakeFiles/strelka_unit_test_htsapi.dir/bed_streamer_test.cpp.o [ 79%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/MedianDepthTracker_test.cpp.o [ 79%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/RangeMap_test.cpp.o [ 79%] Building CXX object src/c++/lib/htsapi/test/CMakeFiles/strelka_unit_test_htsapi.dir/test_main.cpp.o [ 79%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/RegionTracker_test.cpp.o [ 79%] Building CXX object src/c++/lib/htsapi/test/CMakeFiles/strelka_unit_test_htsapi.dir/vcf_record_test.cpp.o [ 80%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/algo_util_test.cpp.o [ 80%] Building CXX object src/c++/lib/htsapi/test/CMakeFiles/strelka_unit_test_htsapi.dir/vcf_record_util_test.cpp.o In file included from /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/blt_util/algo_util.hh:35, from /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/blt_util/test/algo_util_test.cpp:22: /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/blt_util/algo_util_impl.hh: In instantiation of 'std::set<typename std::iterator_traits< >::value_type> getDuplicatesInSortedInput(Iter, Iter, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator<int*, std::vector >; typename std::iterator_traits< >::value_type = int]': /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/blt_util/test/algo_util_test.cpp:32:47: required from here /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/blt_util/algo_util_impl.hh:49:26: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 49 | return std::move(dups); | ^ /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/blt_util/algo_util_impl.hh:49:26: note: remove 'std::move' call [ 80%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/align_path_test.cpp.o [ 81%] Building CXX object src/c++/lib/htsapi/test/CMakeFiles/strelka_unit_test_htsapi.dir/vcf_streamer_test.cpp.o [ 81%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/binomial_test_test.cpp.o [ 81%] Building CXX object src/c++/lib/htsapi/test/CMakeFiles/strelka_unit_test_htsapi.dir/vcf_util_test.cpp.o [ 81%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/compat_util_test.cpp.o [ 81%] Linking CXX executable strelka_unit_test_htsapi [ 82%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/depth_buffer_test.cpp.o [ 82%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/fastRanksum_test.cpp.o [ 82%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/fisher_exact_test_test.cpp.o [ 83%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/id_map_test.cpp.o [ 83%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/io_util_test.cpp.o [ 83%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/istream_line_splitter_test.cpp.o [ 83%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/known_pos_range2_test.cpp.o [ 84%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/logSumUtilTest.cpp.o [ 84%] Built target strelka_unit_test_htsapi [ 84%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/math_util_test.cpp.o [ 84%] Building CXX object src/c++/lib/applications/starling/test/CMakeFiles/strelka_unit_test_starling.dir/VariantOverlapResolver_test.cpp.o [ 84%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/observer_test.cpp.o [ 84%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/parse_util_test.cpp.o In file included from /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/starling_common/test/IndelErrorModelTest.cpp:24: /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/calibration/IndelErrorModel.hh:100:33: error: 'numeric_limits' is not a member of 'st ' 100 | double logErrorRate = -std::numeric_limits::infinity(); | ^~~~~~ /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/calibration/IndelErrorModel.hh:100:48: error: expected primary-expression before 'double' 100 | double logErrorRate = -std::numeric_limits::infinity(); | ^~ /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/calibration/IndelErrorModel.hh:101:38: error: 'numeric_limits' is not a member of 'st ' 101 | double logNoisyLocusRate = -std::numeric_limits::infinity(); | ^~~~~~ /home/user/genomics/strelka-2.9.10.release_src/src/c++/lib/calibration/IndelErrorModel.hh:101:53: error: expected primary-expression before 'double' 101 | double logNoisyLocusRate = -std::numeric_limits::infinity(); | ^~ make[2]: [src/c++/lib/starling_common/test/CMakeFiles/strelka_unit_test_starling_common.dir/build.make:104: src/c++/lib/starling_common/test/CMakeFiles/strelka_unit_test_starling_common.dir/IndelErrorModelTest.cpp.o] Error 1 [ 85%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/pos_range_test.cpp.o make[2]: Waiting for unfinished jobs.... [ 85%] Building CXX object src/c++/bin/CMakeFiles/DumpSequenceAlleleCounts.dir/DumpSequenceAlleleCounts.cpp.o [ 85%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/prob_util_test.cpp.o [ 85%] Linking CXX executable DumpSequenceAlleleCounts [ 85%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/qscore_test.cpp.o [ 86%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/ranksum_test.cpp.o [ 86%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/seq_util_test.cpp.o [ 86%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/set_util_test.cpp.o [ 86%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/stage_manager_test.cpp.o [ 87%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/stream_stat_test.cpp.o [ 87%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/string_util_test.cpp.o make[1]: [CMakeFiles/Makefile2:1646: src/c++/lib/starling_common/test/CMakeFiles/strelka_unit_test_starling_common.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... [ 88%] Building CXX object src/c++/lib/applications/starling/test/CMakeFiles/strelka_unit_test_starling.dir/VariantPhaserTest.cpp.o [ 88%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/test_main.cpp.o [ 88%] Building CXX object src/c++/lib/blt_util/test/CMakeFiles/strelka_unit_test_blt_util.dir/window_util_test.cpp.o [ 88%] Built target DumpSequenceAlleleCounts [ 88%] Building CXX object src/c++/lib/applications/starling/test/CMakeFiles/strelka_unit_test_starling.dir/continuous_variant_caller_test.cpp.o [ 89%] Linking CXX executable strelka_unit_test_blt_util [ 89%] Built target strelka_unit_test_blt_util [ 89%] Building CXX object src/c++/lib/applications/starling/test/CMakeFiles/strelka_unit_test_starling.dir/gvcf_writer_test.cpp.o [ 90%] Building CXX object src/c++/lib/applications/starling/test/CMakeFiles/strelka_unit_test_starling.dir/test_main.cpp.o [ 90%] Linking CXX executable strelka_unit_test_starling [ 90%] Built target strelka_unit_test_starling make: *** [Makefile:146: all] Error 2

At this point, i really have no clue what to do. Is there anyone with the same/similar problem? Some suggestions? I installed a tons of libraries, but probably some are still missing? Maybe a path?

thanks for any hint!

jessie4fun commented 6 months ago

I met same question

Stikus commented 6 months ago

Looks like you have similar problem as described here: https://github.com/Illumina/ExpansionHunter/issues/165#issuecomment-1846870366 (and here https://github.com/Illumina/ExpansionHunter/issues/168).

I've posted fix for build - add limits. For strelka my fix is:

sed -i '/^#include "IndelErrorRateSet.hh"/a #include <limits>' "$SOFT/strelka-${STRELKA_VERSION}.release_src/src/c++/lib/calibration/IndelErrorModel.hh"
gabrielet commented 6 months ago

@Stikus yes, that definitely worked, thank you a ton!