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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
302 stars 38 forks source link

Illegal instruction (install issues) #131

Closed SemiQuant closed 4 years ago

SemiQuant commented 4 years ago

Hi,

I've tried installing from source, using conda and using a docker container docker but I get "Illegal instruction" when I run octopus. Not sure what I can try?

SemiQuant commented 4 years ago

version "octopus_0.5.2b" works. (The new version also looks like it's not using the correct gcc when I try to install)

dancooke commented 4 years ago

How did you try installation from source and which commit?

SemiQuant commented 4 years ago

Hi Dan I tried a bunch of things yesterday on osx and our cluster but I reran the below now on the cluster, all the requirements are installed. CentOS Linux release 7.8.2003 (Core) cmake version 3.12.2 Python 3.7.7 gcc (GCC) 7.3.1 20180712 (Red Hat 7.3.1-7)

Docker (singularity)

singularity pull docker://quay.io/biocontainers/octopus:0.6.3b--hbf2165f_2 Says "Illegal instruction" when running

singularity pull docker://quay.io/biocontainers/octopus:0.5.2b--hd4b4d59_2 Works

Quick installation with Python3

MAGICALLY, this got further than yesterday.

[100%] Linking CXX executable octopus CMakeFiles/octopus.dir/main.cpp.o: In function boost::system::error_category::std_category::equivalent(std::error_code const&, int) const': main.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei[_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei]+0x2d): undefined reference toboost::system::detail::generic_category_instance' main.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei[_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei]+0xac): undefined reference to boost::system::detail::generic_category_instance' main.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei[_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei]+0xca): undefined reference toboost::system::detail::generic_category_instance' main.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei[_ZNK5boost6system14error_category12std_category10equivalentERKSt10error_codei]+0xf3): undefined reference to boost::system::detail::generic_category_instance' CMakeFiles/octopus.dir/main.cpp.o: In functionboost::system::error_category::std_category::equivalent(int, std::error_condition const&) const': main.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition[_ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition]+0x30): undefined reference to boost::system::detail::generic_category_instance' CMakeFiles/octopus.dir/main.cpp.o:main.cpp:(.text._ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition[_ZNK5boost6system14error_category12std_category10equivalentEiRKSt15error_condition]+0xbd): more undefined references toboost::system::detail::generic_category_instance' follow CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function octopus::options::parse_config_file(boost::filesystem::path const&, boost::program_options::variables_map&, boost::program_options::options_description const&)': option_parser.cpp:(.text+0x12b0): undefined reference toboost::program_options::error_with_option_name::get_canonical_option_name[abi:cxx11]() const' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function octopus::options::option_dependency(boost::program_options::variables_map const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': option_parser.cpp:(.text+0x14b1): undefined reference toboost::program_options::abstract_variables_map::operator[](std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' option_parser.cpp:(.text+0x14e7): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function octopus::options::conflicting_options(boost::program_options::variables_map const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': option_parser.cpp:(.text+0x1611): undefined reference toboost::program_options::abstract_variables_map::operator[](std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' option_parser.cpp:(.text+0x1647): undefined reference to `boost::program_options::abstract_variables_map::operator[](std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function octopus::options::run(boost::program_options::basic_command_line_parser<char>&)': option_parser.cpp:(.text+0x283a): undefined reference toboost::program_options::error_with_option_name::get_canonical_option_name[abi:cxx11]() const' option_parser.cpp:(.text+0x28fb): undefined reference to boost::program_options::error_with_option_name::get_canonical_option_name[abi:cxx11]() const' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In functionoctopus::options::parse_options(int, char const*)': option_parser.cpp:(.text+0x4715): undefined reference to boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' option_parser.cpp:(.text+0x48df): undefined reference toboost::program_options::options_description::options_description(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, unsigned int, unsigned int)' option_parser.cpp:(.text+0x4d50): undefined reference to `boost::program_options::options_description::options_description(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, unsigned int, unsigned int)' option_parser.cpp:(.text+0x52ab): undefined reference to boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' option_parser.cpp:(.text+0x553b): undefined reference toboost::program_options::options_description::options_description(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, unsigned int, unsigned int)' CMakeFiles/octopus.dir/config/option_parser.cpp.o:option_parser.cpp:(.text+0x5be8): more undefined references to boost::program_options::options_description::options_description(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)' follow CMakeFiles/octopus.dir/config/option_parser.cpp.o: In functionboost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, int)': option_parser.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x25): undefined reference to boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)' option_parser.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_i]+0x3d): undefined reference toboost::program_options::error_with_option_name::error_with_option_name(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, int)' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function `boost::program_options::typed_value<std::cxx11::basic_string<char, std::char_traits, std::allocator >, char>::xparse(boost::any&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&) const': option_parser.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x17): undefined reference to `boost::program_options::validate(boost::any&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int)' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) const': option_parser.cpp:(.text._ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE[_ZNK5boost15program_options11typed_valueIbcE6xparseERNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE]+0x17): undefined reference toboost::program_options::validate(boost::any&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, bool, int)' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function boost::program_options::typed_value<octopus::MemoryFootprint, char>::name[abi:cxx11]() const': option_parser.cpp:(.text._ZNK5boost15program_options11typed_valueIN7octopus15MemoryFootprintEcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueIN7octopus15MemoryFootprintEcE4nameB5cxx11Ev]+0x1a): undefined reference toboost::program_options::arg[abi:cxx11]' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function boost::program_options::typed_value<octopus::options::ContigOutputOrder, char>::name[abi:cxx11]() const': option_parser.cpp:(.text._ZNK5boost15program_options11typed_valueIN7octopus7options17ContigOutputOrderEcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueIN7octopus7options17ContigOutputOrderEcE4nameB5cxx11Ev]+0x1a): undefined reference toboost::program_options::arg[abi:cxx11]' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function boost::program_options::typed_value<std::vector<boost::filesystem::path, std::allocator<boost::filesystem::path> >, char>::name[abi:cxx11]() const': option_parser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINS_10filesystem4pathESaIS4_EEcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueISt6vectorINS_10filesystem4pathESaIS4_EEcE4nameB5cxx11Ev]+0x1a): undefined reference toboost::program_options::arg[abi:cxx11]' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function boost::program_options::typed_value<std::vector<int, std::allocator<int> >, char>::name[abi:cxx11]() const': option_parser.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorIiSaIiEEcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueISt6vectorIiSaIiEEcE4nameB5cxx11Ev]+0x1a): undefined reference toboost::program_options::arg[abi:cxx11]' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function boost::program_options::typed_value<double, char>::name[abi:cxx11]() const': option_parser.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueIdcE4nameB5cxx11Ev]+0x1a): undefined reference toboost::program_options::arg[abi:cxx11]' CMakeFiles/octopus.dir/config/option_parser.cpp.o:option_parser.cpp:(.text._ZNK5boost15program_options11typed_valueIN7octopus7options14ExtensionLevelEcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueIN7octopus7options14ExtensionLevelEcE4nameB5cxx11Ev]+0x1a): more undefined references to boost::program_options::arg[abi:cxx11]' follow CMakeFiles/octopus.dir/config/option_parser.cpp.o: In functionboost::program_options::basic_command_line_parser::basic_command_line_parser(int, char const const)': option_parser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x2ad): undefined reference to boost::program_options::to_internal(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' option_parser.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x2f6): undefined reference toboost::program_options::detail::cmdline::cmdline(std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&)' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function `void boost::program_options::validate<std::cxx11::basic_string<char, std::char_traits, std::allocator >, char>(boost::any&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > >, int)': option_parser.cpp:(.text._ZN5boost15program_options8validateINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x90): undefined reference to boost::program_options::validate(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)' option_parser.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x3c1): undefined reference toboost::program_options::invalid_option_value::invalid_option_value(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function `void boost::program_options::validate<int, char>(boost::any&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, int*, long)': option_parser.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0x1c8): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function void boost::program_options::validate<int, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::vector<int, std::allocator<int> >*, int)': option_parser.cpp:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x47e): undefined reference toboost::program_options::invalid_option_value::invalid_option_value(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function `void boost::program_options::validate<octopus::options::PhasingLevel, char>(boost::any&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, octopus::options::PhasingLevel*, long)': option_parser.cpp:(.text._ZN5boost15program_options8validateIN7octopus7options12PhasingLevelEcEEvRNS_3anyERKSt6vectorINSt7cxx1112basic_stringIT0_St11char_traitsISA_ESaISA_EEESaISE_EEPT_l[_ZN5boost15program_options8validateIN7octopus7options12PhasingLevelEcEEvRNS_3anyERKSt6vectorINSt7cxx1112basic_stringIT0_St11char_traitsISA_ESaISA_EEESaISE_EEPT_l]+0x2f7): undefined reference to `boost::program_options::invalid_option_value::invalid_option_value(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/octopus.dir/config/option_parser.cpp.o: In function void boost::program_options::validate<octopus::options::NormalContaminationRisk, char>(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, octopus::options::NormalContaminationRisk*, long)': option_parser.cpp:(.text._ZN5boost15program_options8validateIN7octopus7options23NormalContaminationRiskEcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsISA_ESaISA_EEESaISE_EEPT_l[_ZN5boost15program_options8validateIN7octopus7options23NormalContaminationRiskEcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsISA_ESaISA_EEESaISE_EEPT_l]+0x2f7): undefined reference toboost::program_options::invalid_option_value::invalid_option_value(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/octopus.dir/config/option_parser.cpp.o:option_parser.cpp:(.text._ZN5boost15program_options8validateIN7octopus7options11RefCallTypeEcEEvRNS_3anyERKSt6vectorINSt7cxx1112basic_stringIT0_St11char_traitsISA_ESaISA_EEESaISE_EEPT_l[_ZN5boost15program_options8validateIN7octopus7options11RefCallTypeEcEEvRNS_3anyERKSt6vectorINSt7cxx1112basic_stringIT0_St11char_traitsISA_ESaISA_EEESaISE_EEPT_l]+0x2f7): more undefined references to boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' follow CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30): undefined reference toboost::program_options::error_with_option_name::substitute_placeholders(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30): undefined reference to boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38): undefined reference toboost::program_options::error_with_option_name::substitute_placeholders(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30): more undefined references to boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' follow CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueINS_10filesystem4pathEcEE[_ZTVN5boost15program_options11typed_valueINS_10filesystem4pathEcEE]+0x38): undefined reference toboost::program_options::value_semantic_codecvt_helper::parse(boost::any&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, bool) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIbcEE[_ZTVN5boost15program_options11typed_valueIbcEE]+0x38): undefined reference to boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[_ZTVN5boost15program_options11typed_valueIicEE]+0x38): undefined reference toboost::program_options::value_semantic_codecvt_helper::parse(boost::any&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, bool) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIN7octopus15MemoryFootprintEcEE[_ZTVN5boost15program_options11typed_valueIN7octopus15MemoryFootprintEcEE]+0x38): undefined reference to boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINS_10filesystem4pathESaIS4_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINS_10filesystem4pathESaIS4_EEcEE]+0x38): undefined reference toboost::program_options::value_semantic_codecvt_helper::parse(boost::any&, std::vector<std::cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::cxx11::basic_string<char, std::char_traits, std::allocator > > > const&, bool) const' CMakeFiles/octopus.dir/config/option_parser.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x38): more undefined references to boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const' follow CMakeFiles/octopus.dir/logging/logging.cpp.o: In functionboost::recursive_mutex::recursive_mutex()': logging.cpp:(.text._ZN5boost15recursive_mutexC2Ev[_ZN5boost15recursive_mutexC5Ev]+0x7a): undefined reference to boost::system::detail::generic_category_instance' logging.cpp:(.text._ZN5boost15recursive_mutexC2Ev[_ZN5boost15recursive_mutexC5Ev]+0xeb): undefined reference toboost::system::detail::generic_category_instance' logging.cpp:(.text._ZN5boost15recursive_mutexC2Ev[_ZN5boost15recursive_mutexC5Ev]+0x13e): undefined reference to boost::system::detail::generic_category_instance' CMakeFiles/octopus.dir/logging/logging.cpp.o: In functionvoid boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits, std::allocator >::aligned_write(wchar_t const, long)': logging.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0xb9): undefined reference to `boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const, unsigned long, std::cxx11::basic_string<char, std::char_traits, std::allocator >&, unsigned long, std::locale const&)' logging.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0x154): undefined reference to boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const*, unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long, std::locale const&)' CMakeFiles/octopus.dir/logging/logging.cpp.o: In functionvoid boost::log::v2_mt_posix::type_dispatcher::callback_base::trampoline<boost::log::v2_mt_posix::binder1st<boost::log::v2_mt_posix::output_fun, boost::log::v2_mt_posix::expressions::aux::stream_ref<boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits, std::allocator > >&>, std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator > >(void*, std::__cxx11::basic_string<wchar_t, std::char_traits, std::allocator > const&)': logging.cpp:(.text._ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEENSt7cxx1112basic_stringIwSBIwESaIwEEEEEvPvRKT0[_ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEENSt7cxx1112basic_stringIwSBIwESaIwEEEEEvPvRKT0]+0xa5): undefined reference to `boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const*, unsigned long, std::cxx11::basic_string<char, std::char_traits, std::allocator >&, unsigned long, std::locale const&)' CMakeFiles/octopus.dir/logging/logging.cpp.o: In function void boost::log::v2_mt_posix::sinks::basic_formatting_sink_frontend<char>::feed_record<boost::recursive_mutex, boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >(boost::log::v2_mt_posix::record_view const&, boost::recursive_mutex&, boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char>&)': logging.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks30basic_formatting_sink_frontendIcE11feed_recordINS_15recursive_mutexENS2_26basic_text_ostream_backendIcEEEEvRKNS1_11record_viewERT_RT0_[_ZN5boost3log11v2_mt_posix5sinks30basic_formatting_sink_frontendIcE11feed_recordINS_15recursive_mutexENS2_26basic_text_ostream_backendIcEEEEvRKNS1_11record_viewERT_RT0_]+0xb5): undefined reference toboost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/octopus.dir/logging/logging.cpp.o: In function void boost::log::v2_mt_posix::sinks::basic_formatting_sink_frontend<char>::feed_record<boost::recursive_mutex, boost::log::v2_mt_posix::sinks::text_file_backend>(boost::log::v2_mt_posix::record_view const&, boost::recursive_mutex&, boost::log::v2_mt_posix::sinks::text_file_backend&)': logging.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks30basic_formatting_sink_frontendIcE11feed_recordINS_15recursive_mutexENS2_17text_file_backendEEEvRKNS1_11record_viewERT_RT0_[_ZN5boost3log11v2_mt_posix5sinks30basic_formatting_sink_frontendIcE11feed_recordINS_15recursive_mutexENS2_17text_file_backendEEEvRKNS1_11record_viewERT_RT0_]+0xb5): undefined reference toboost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/octopus.dir/logging/logging.cpp.o: In function void boost::log::v2_mt_posix::sinks::basic_formatting_sink_frontend<char>::feed_record<boost::log::v2_mt_posix::aux::fake_mutex, boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >(boost::log::v2_mt_posix::record_view const&, boost::log::v2_mt_posix::aux::fake_mutex&, boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char>&)': logging.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks30basic_formatting_sink_frontendIcE11feed_recordINS1_3aux10fake_mutexENS2_26basic_text_ostream_backendIcEEEEvRKNS1_11record_viewERT_RT0_[_ZN5boost3log11v2_mt_posix5sinks30basic_formatting_sink_frontendIcE11feed_recordINS1_3aux10fake_mutexENS2_26basic_text_ostream_backendIcEEEEvRKNS1_11record_viewERT_RT0_]+0xa8): undefined reference toboost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/octopus.dir/logging/logging.cpp.o: In function void boost::log::v2_mt_posix::sinks::basic_formatting_sink_frontend<char>::feed_record<boost::log::v2_mt_posix::aux::fake_mutex, boost::log::v2_mt_posix::sinks::text_file_backend>(boost::log::v2_mt_posix::record_view const&, boost::log::v2_mt_posix::aux::fake_mutex&, boost::log::v2_mt_posix::sinks::text_file_backend&)': logging.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks30basic_formatting_sink_frontendIcE11feed_recordINS1_3aux10fake_mutexENS2_17text_file_backendEEEvRKNS1_11record_viewERT_RT0_[_ZN5boost3log11v2_mt_posix5sinks30basic_formatting_sink_frontendIcE11feed_recordINS1_3aux10fake_mutexENS2_17text_file_backendEEEvRKNS1_11record_viewERT_RT0_]+0xa8): undefined reference toboost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/octopus.dir/timers.cpp.o: In function print_all_timers()': timers.cpp:(.text+0xe2): undefined reference toboost::timer::format[abi:cxx11](boost::timer::cpu_times const&, short)' timers.cpp:(.text+0x193): undefined reference to boost::timer::format[abi:cxx11](boost::timer::cpu_times const&, short)' timers.cpp:(.text+0x244): undefined reference toboost::timer::format[abi:cxx11](boost::timer::cpu_times const&, short)' timers.cpp:(.text+0x2f5): undefined reference to boost::timer::format[abi:cxx11](boost::timer::cpu_times const&, short)' timers.cpp:(.text+0x3a6): undefined reference toboost::timer::format[abi:cxx11](boost::timer::cpu_times const&, short)' CMakeFiles/octopus.dir/timers.cpp.o:timers.cpp:(.text+0x46d): more undefined references to `boost::timer::format[abi:cxx11](boost::timer::cpu_times const&, short)' follow collect2: error: ld returned 1 exit status make[2]: [src/octopus] Error 1 make[1]: [src/CMakeFiles/octopus.dir/all] Error 2 make: *** [all] Error 2

Installing with CMake

[ 75%] Building CXX object src/CMakeFiles/octopus.dir/core/models/haplotype_likelihood_model.cpp.o .../octopus/src/core/models/haplotype_likelihood_model.cpp: In function ‘octopus::HaplotypeLikelihoodModel octopus::make_haplotype_likelihood_model(std::__cxx11::string, bool)’: .../octopus/src/core/models/haplotype_likelihood_model.cpp:87:18: error: ‘config.octopus::HaplotypeLikelihoodModel::Config::mapping_quality_cap_trigger.boost::optional::.boost::optional_detail::tc_optional_base::mstorage’ is used uninitialized in this function [-Werror=uninitialized] , config {config} ^ .../octopus/src/core/models/haplotype_likelihood_model.cpp:391:38: note: ‘config.octopus::HaplotypeLikelihoodModel::Config::mapping_quality_cap_trigger.boost::optional::.boost::optional_detail::tc_optional_base::m_storage’ was declared here HaplotypeLikelihoodModel::Config config {}; ^~ cc1plus: all warnings being treated as errors make[2]: [src/CMakeFiles/octopus.dir/core/models/haplotype_likelihood_model.cpp.o] Error 1 make[1]: [src/CMakeFiles/octopus.dir/all] Error 2

Conda

installs fine but "Illegal instruction" error

I was hoping you could point me to a description of how your polyclone algorithm reconstructs (phases) the global haplotypes. I didn't see it in your paper.

dancooke commented 4 years ago

Have you tried installing with automatic dependency installation (the recommended way to install Octopus)? i.e.:

$ ./install.py --dependencies --clean

Please also use the HEAD develop branch version - v0.6.3b is quite old now.

Regarding the polyclone phasing. All phasing in Octopus is done using the same algorithm independent of the calling model - as described in the paper. The latest version has changed slightly from the paper version to allow discontiguous phase blocks, but the basic principle is the same; the algorithm examines the entropy of the genotype posterior distribution computed by the calling model.

SemiQuant commented 4 years ago

Thanks, I tried install.py --dependencies --forests before and I hung, install.py --dependencies --clean gave me errors.

==> make check Last 15 lines from ....cache/Homebrew/Logs/xz/02.make: /bin/sh: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8) /bin/sh: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8) /bin/sh: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8) /bin/sh: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8) unexpected output from xzgrep FAIL: test_scripts.sh

1 of 9 tests failed Please report to lasse.collin@tukaani.org

make[2]: [check-TESTS] Error 1 make[2]: Leaving directory `/tmp/xz-20200729-11144-1q1reqz/xz-5.2.5/tests' make[1]: [check-am] Error 2 make[1]: Leaving directory `/tmp/xz-20200729-11144-1q1reqz/xz-5.2.5/tests' make: *** [check-recursive] Error 1 sh: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8)

READ THIS: https://docs.brew.sh/Troubleshooting

-- The C compiler identification is GNU 5.5.0 -- The CXX compiler identification is GNU 5.5.0 -- Check for working C compiler: ...bin/octopus/build/brew/bin/cc -- Check for working C compiler: ...bin/octopus/build/brew/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: ...bin/octopus/build/brew/bin/c++ -- Check for working CXX compiler: ...bin/octopus/build/brew/bin/c++ - works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Error at CMakeLists.txt:54 (message): GCC version must be at least 6.3!

-- Configuring incomplete, errors occurred!

I'll try it again in a singularity container and see if it works.

dancooke commented 4 years ago

Ah, this is due to a current issue with Homebrew. A workaround is just to call the installation script twice like this:

$ ./install.py --dependencies --clean
$ ./install.py --dependencies

You shouldn't need any containers.

SemiQuant commented 4 years ago

That appears to have done the trick! Thanks.

dancooke commented 4 years ago

For future reference: the issue with Homebrew is now resolved - the workout should no longer be necessary.