kharchenkolab / dropest Goto Github PK

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

License: GNU General Public License v3.0

CMake 2.15% C++ 84.92% R 11.72% Shell 0.19% Python 0.11% Dockerfile 0.91%

pipeline scrna-seq single-cell-rna-seq preprocessing

dropest's Introduction

dropEst - Pipeline

Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements. If you use the pipeline in your research, please cite the corresponding paper. To reproduce results from the paper, please see this repository.

Documentation

For detailed explanations, please see the documentation

Particularly:

If you have problems with installation, please look at the Troubleshooting page and open an issue if there is nothing.

News

[0.8.6] - 2019-08-01

Added support for Drop-seq and CEL-Seq2

See Changelog for the full list.

General processing steps

dropTag: extraction of cell barcodes and UMIs from the library. Result: demultiplexed .fastq.gz files, which should be aligned to the reference.
Alignment of the demultiplexed files to reference genome. Result: .bam files with the alignment.
dropEst: building count matrix and estimation of some statistics, necessary for quality control. Result: .rds file with the count matrix and statistics. Optionally: count matrix in MatrixMarket format.
dropReport - Generating report on library quality.
dropEstR - R pacakge for UMI count corrections and cell quality classification

Examples

Complete examples of the pipeline can be found at EXAMPLES.md.

Here are results of processing of neurons_900 10x dataset.

Supported protocols

10x
CEL-Seq2
Drop-seq
iCLIP
inDrop (v1-3)
Seq-Well
SPLiT-seq

Citation

If you find this pipeline useful for your research, please consider citing the paper:

Petukhov, V., Guo, J., Baryawno, N., Severe, N., Scadden, D. T., Samsonova, M. G., & Kharchenko, P. V. (2018). dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. Genome biology, 19(1), 78. doi:10.1186/s13059-018-1449-6

dropest's People

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dropest's Issues

Code not building

I am on Centos
I've installed boost and bamtools with linuxbrew
I've installed RInside package to a specific directory as it is said here https://www.r-bloggers.com/installing-r-packages/
Then I tried to compile dropEst and got the massage:
"CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function TestTools::testR::test_method()': TestTools.cpp:(.text+0x4df): undefined reference to RInside::parseEval(std::string const&)'
TestTools.cpp:(.text+0x571): undefined reference to RInside::parseEval(std::string const&)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function boost::unit_test::make_test_case(boost::function<void ()> const&, boost::unit_test::basic_cstring, boost::unit_test::basic_cstring, unsigned long)':
TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x26): undefined reference to boost::unit_test::ut_detail::normalize_test_case_name(boost::unit_test::basic_cstring<char const>)' libDropTools.a(Logs.cpp.o): In function void boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits, std::allocator >::aligned_write<wchar_t>(wchar_t const*, long)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0xdc): undefined reference to boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const*, unsigned long, std::string&, unsigned long, std::locale const&)' Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0x139): undefined reference to boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const*, unsigned long, std::string&, unsigned long, std::locale const&)'
libDropTools.a(Logs.cpp.o): In function void 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<char>, std::allocator<char> > >&>, std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > >(void*, std::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEESbIwSB_IwESaIwEEEEvPvRKT0_[_ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEESbIwSB_IwESaIwEEEEvPvRKT0_]+0xf9): undefined reference to boost::log::v2_mt_posix::aux::code_convert_impl(wchar_t const*, unsigned long, std::string&, unsigned long, std::locale const&)'
libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE]+0xb8): undefined reference to boost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)'
libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::try_consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE]+0xde): undefined reference to boost::log::v2_mt_posix::sinks::basic_text_ostream_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)'
libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE]+0xb8): undefined reference to boost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)'
libDropTools.a(Logs.cpp.o): In function boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::try_consume(boost::log::v2_mt_posix::record_view const&)': Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE]+0xde): undefined reference to boost::log::v2_mt_posix::sinks::text_file_backend::consume(boost::log::v2_mt_posix::record_view const&, std::string const&)'
libDropTools.a(UtilFunctions.cpp.o): In function Tools::init_r()': UtilFunctions.cpp:(.text+0x5f0): undefined reference to RInside::parseEvalQ(std::string const&)'
/home/kalmykova/.linuxbrew/lib/libboost_log_setup-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::replace(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::ios_base::failure[abi:cxx11]::what() const@GLIBCXX_3.4.21'
//home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __pthread_barrier_init@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_mutate(unsigned long, unsigned long, wchar_t const*, unsigned long)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::find_first_not_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::ios_base::failure[abi:cxx11]::~failure()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_assign(std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/libquadmath.so.0: undefined reference to __signgam@GLIBC_2.23'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_erase(unsigned long, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::collate const& std::use_facet<std::__cxx11::collate >(std::locale const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::numpunct<wchar_t> const& std::use_facet<std::__cxx11::numpunct<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace_aux(unsigned long, unsigned long, unsigned long, char)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to typeinfo for std::ios_base::failure[abi:cxx11]@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::basic_istream<char, std::char_traits<char> >& std::operator>><char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::messages<wchar_t> const& std::use_facet<std::__cxx11::messages<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::append(char const*)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_stringstream()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::logic_error::logic_error(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log_setup-mt.so: undefined reference to std::basic_istream<wchar_t, std::char_traits<wchar_t> >& std::getline<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >(std::basic_istream<wchar_t, std::char_traits<wchar_t> >&, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::compare(char const*) const@GLIBCXX_3.4.21'
/home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::swap(std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&)@GLIBCXX_3.4.21'
/home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::ios_base::failure[abi:cxx11]::failure(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to typeinfo for std::__cxx11::basic_ostringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::ios_base::failure[abi:cxx11]::failure(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::rfind(char, unsigned long) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::numpunct<char> const& std::use_facet<std::__cxx11::numpunct<char> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct(unsigned long, char)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::resize(unsigned long, wchar_t)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_replace_aux(unsigned long, unsigned long, unsigned long, wchar_t)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::invalid_argument::invalid_argument(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __socket@GLIBC_PRIVATE'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::logic_error::logic_error(std::logic_error const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_replace(unsigned long, unsigned long, wchar_t const*, unsigned long)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::collate<wchar_t> const& std::use_facet<std::__cxx11::collate<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log_setup-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::compare(unsigned long, unsigned long, char const*) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to VTT for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::out_of_range::out_of_range(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_erase(unsigned long, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::resize(unsigned long, char)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::reserve(unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::push_back(char)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to bool std::has_facet<std::__cxx11::messages<wchar_t> >(std::locale const&)@GLIBCXX_3.4.21'
//home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __shm_directory@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_construct(unsigned long, wchar_t)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_istringstream()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::find_last_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to std::__cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::~basic_ostringstream()@GLIBCXX_3.4.21'
/home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::compare(wchar_t const*) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to bool std::has_facet<std::__cxx11::messages<char> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to std::ios_base::failure[abi:cxx11]::~failure()@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __libc_pread@GLIBC_PRIVATE'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::messages<char> const& std::use_facet<std::__cxx11::messages<char> >(std::locale const&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits, std::allocator >::compare(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_unit_test_framework-mt.so: undefined reference to vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::out_of_range::out_of_range(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::compare(std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > const&) const@GLIBCXX_3.4.21' //home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __pthread_barrier_wait@GLIBC_PRIVATE'
/home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >::_M_sync(char*, unsigned long, unsigned long)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_filesystem-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find_first_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to std::__cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::~basic_ostringstream()@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_append(wchar_t const*, unsigned long)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_iostreams-mt.so: undefined reference to vtable for std::ios_base::failure[abi:cxx11]@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::logic_error::logic_error(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::~basic_string()@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_regex-mt.so: undefined reference to std::overflow_error::overflow_error(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21'
//home/kalmykova/.linuxbrew/lib/librt.so.1: undefined reference to __recv@GLIBC_PRIVATE' /home/kalmykova/.linuxbrew/lib/libboost_thread-mt.so: undefined reference to std::basic_istream<char, std::char_traits >& std::getline<char, std::char_traits, std::allocator >(std::basic_istream<char, std::char_traits >&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >&, char)@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::swap(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)@GLIBCXX_3.4.21' /home/kalmykova/Rpackages/RInside/lib/libRInside.so: undefined reference to vtable for std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21'
/home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::basic_istream<wchar_t, std::char_traits<wchar_t> >& std::operator>><wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >(std::basic_istream<wchar_t, std::char_traits<wchar_t> >&, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >&)@GLIBCXX_3.4.21' /home/kalmykova/.linuxbrew/lib/libboost_log-mt.so: undefined reference to std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >::str() const@GLIBCXX_3.4.21'
collect2: error: ld returned 1 exit status
make[2]: *** [TestTools] Error 1
make[1]: *** [CMakeFiles/TestTools.dir/all] Error 2
make: *** [all] Error 2
"

Zero Cells in final dropEst output

After running dropEst the final output was empty. Can you help me ? This is the command I tried:

dropest -m -f -L eiEIBA -V -o run1 -g /home/trezende/cellranger/genes/genes.gtf -c /home/trezende/dropEst/c
onfigs/indrop_v3.xml IEL.bam LPL.bam MLN.bam 
Version: 0.8.3.
Run: 09/14/2018 00:12:21.
Real CBs merge selected.

Start parsing of bams: 00:12:21.
WARNING: Can't find chromosome 'JH584301.1'
WARNING: Can't find chromosome 'GL456379.1'
WARNING: Can't find chromosome 'GL456393.1'
WARNING: Can't find chromosome 'GL456366.1'
WARNING: Can't find chromosome 'GL456367.1'
WARNING: Can't find chromosome 'GL456239.1'
WARNING: Can't find chromosome 'GL456213.1'
WARNING: Can't find chromosome 'GL456383.1'
WARNING: Can't find chromosome 'GL456378.1'
WARNING: Can't find chromosome 'GL456372.1'
WARNING: Can't find chromosome 'GL456370.1'
WARNING: Can't find chromosome 'GL456390.1'
WARNING: Can't find chromosome 'GL456392.1'
WARNING: Can't find chromosome 'GL456382.1'
WARNING: Can't find chromosome 'GL456396.1'
WARNING: Can't find chromosome 'GL456368.1'
ERROR: can't find chromosome, id: -1
IEL.bam: 70488019 total reads; 8.1% intergenic; 57.8% touch exon; 16.7% touch intron; 0.682% touch not annotated regions; can't parse
 1.48036% reads; 183545 CBs read
WARNING: Can't find chromosome 'JH584301.1'
WARNING: Can't find chromosome 'JH584300.1'
WARNING: Can't find chromosome 'JH584302.1'
WARNING: Can't find chromosome 'GL456379.1'
WARNING: Can't find chromosome 'GL456366.1'
WARNING: Can't find chromosome 'GL456367.1'
WARNING: Can't find chromosome 'GL456239.1'
WARNING: Can't find chromosome 'GL456213.1'
WARNING: Can't find chromosome 'GL456383.1'
WARNING: Can't find chromosome 'GL456378.1'
WARNING: Can't find chromosome 'GL456372.1'
WARNING: Can't find chromosome 'GL456370.1'
WARNING: Can't find chromosome 'GL456390.1'
WARNING: Can't find chromosome 'GL456392.1'
WARNING: Can't find chromosome 'GL456382.1'
WARNING: Can't find chromosome 'GL456396.1'
ERROR: can't find chromosome, id: -1                                                                                       [123/9987]
LPL.bam: 113802132 total reads; 8.32% intergenic; 55.7% touch exon; 18.2% touch intron; 0.671% touch not annotated regions; can't par
se 1.51082% reads; 320152 CBs read
WARNING: Can't find chromosome 'JH584301.1'
WARNING: Can't find chromosome 'GL456379.1'
WARNING: Can't find chromosome 'GL456366.1'
WARNING: Can't find chromosome 'GL456367.1'
WARNING: Can't find chromosome 'GL456213.1'
WARNING: Can't find chromosome 'GL456383.1'
WARNING: Can't find chromosome 'GL456378.1'
WARNING: Can't find chromosome 'GL456372.1'
WARNING: Can't find chromosome 'GL456370.1'
WARNING: Can't find chromosome 'GL456390.1'
WARNING: Can't find chromosome 'GL456392.1'
WARNING: Can't find chromosome 'GL456382.1'
WARNING: Can't find chromosome 'GL456368.1'
ERROR: can't find chromosome, id: -1
MLN.bam: 140551180 total reads; 8.57% intergenic; 54.9% touch exon; 18.4% touch intron; 0.703% touch not annotated regions; can't par
se 1.51098% reads; 399448 CBs read
Bams parsed: 00:59:37.

121907 CBs with more than 20 genes
top CBs:
4440    GTCTCGTGTATTCGTG-1
4303    TTTCCTCAGGCTAGCA-1
4195    TGAGAGGCAAACTGTC-1
4161    CCGTGGAGTCTCACCT-1
3866    CAGCTGGCACATTAGC-1
3843    ATCATCTAGAGACTTA-1
3839    GTCTTCGGTCGACTAT-1
3799    CACTCCATCCAGAAGG-1
3798    CTTCTCTCACATCCGG-1

Start merge: 00:59:53.
Merge initialized: 00:59:53.
Total 100000 tags processed
Total 0 cells merged
Total 121907 cells excluded
Merge finished: 01:01:00.
Merge UMIs with N's: 01:01:00.
0 cells processed. Merged 0 UMIs from 0 cells.
UMI merge finished: 01:01:00.
0 cells are considered as real.

0 CBs with more than 100 genes, which have UMIs of the requested type.
no valid CBs found

Done: 01:01:15.

Problems with Debyan docker image

Hi,
after built the docker image I was not able to run it since I got following error:

docker run -ti --name dropest dropest /bin/bash

/bin/bash: /bin/bash: cannot execute binary file

I fix it by commenting this part in the Docker file:

#ENTRYPOINT ["/bin/bash"]

Best,
Luca

--merge-umi is not recognised

Long version of u/--merge-umi parameter is not recognised, short one works fine

Splitting large bam file before processing - any associated issues?

I am processing a fairly large bam file for use in velocyto, using dropEst with the -V option.

My issue is that the file is too big for my computer to process, so half the way through everything hangs and I cannot finish the processing (after a while the system hangs, then aborts the process before any output is written)...

I have tried subsampling the file using sambamba and I can run the whole thing with the smaller bam file, suggesting the issue is not in the file itself or in the way I use dropEst. My idea is therefore to split the bam file in smaller chunks, for example by splitting it by chromosome, then run dropEst on each of them then merge the output matrices in R.

Could you advise on whether this is a sensible thing to do, or whether there could be issues in proceeding in this way?

10X genomics BAM with tags not working with dropest

Hello,

I have a BAM from cellranger 10x tool. I would like to use it for velocyto and therefore want to create input file using dropest.

Here is the command I use:
dropest -f -c 10x.xml 10x_001/001_possorted_genome_bam.bam
it runs successfully and created cell.counts.matrices.rds and cell.counts.rds files. The matrix only contains Exonic reads info and when I load the cell.counts.matrices.rds file for velocity it doesnt work as there is no data for intronic and intergenic.

Although I looked my BAM and found the reads for intronic and intergenic regions.

Any idea why dropest only selecting exonic reads?

Many thanks.

Error with dropReport.Rsc

Dear developers,
I got this error at the end of the procedure and I don't know how to solve it:

./dropReport.Rsc SRR1784313.est.rds -o $HOME/report.html

processing file: report.Rmd
|.. | 3%
inline R code fragments

|.... | 6%
label: unnamed-chunk-1 (with options)
List of 1
$ include: logi FALSE

Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> library
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
cannot open file 'report.knit.md': Permission denied

Execution halted

PS: I am using the docker image for debyan.

Can you help me, please?

Should UMI correction be done before or after QC ?

After going through vignette , I wonder that should the UMI correction phased be done before or after QC ?
The reads_per_umi_per_cell from dropEst is already filtered. If I perform some manual filter again and then rescued some cells not in the reads_per_umi_per_cell , how can I get reads_per_umi_per_cell for these rescued cells ?

Since the UMI count is the corrected count and the paper mention that

the proposed corrections can result in significantly higher expression profile correlation of cells belonging to the same cluster, compared to uncorrected molecular counts

I am wondering that do you have some specific gene examples in the specific known cell population ( CD4 in T cells for example) indicating that such correction is very important to accurate gene abundance quantification ?

Could NOT find BAMTOOLS

I got below issues when trying to install the pipeline:

~/dropEst$ cmake . && make
-- Boost version: 1.55.0
-- Found the following Boost libraries:
--   unit_test_framework
--   thread
--   system
--   log
--   iostreams
--   filesystem
--   chrono
--   date_time
--   atomic
--   log_setup
--   regex
-- Could NOT find BAMTOOLS (missing: BAMTOOLS_LIBRARY BAMTOOLS_INCLUDE_DIR) 
-- Found R: /usr/lib/R
-- Configuring done
CMake Error: Unable to open check cache file for write. /home/dz33/dropEst/CMakeFiles/cmake.check_cache

The bamtools have bee installed in:

:~/dropEst$ which bamtools
/usr/bin/bamtools

Any suggestions? Thanks

dropReport.Rsc issue with the v0.8.0

I used to get the right dropReport using the dropReport.Rsc, but once I upgraded to v0.8.0, it keeps failing:

~/dropEst/dropReport.Rsc dlib1.out/cell.counts.bcconfig.rds -o dlib1.filtered.bcconfig.report.html


processing file: report.Rmd
  |..                                                               |   3%
   inline R code fragments

  |....                                                             |   6%
label: unnamed-chunk-1 (with options) 
List of 1
 $ include: logi FALSE

  |......                                                           |   9%
  ordinary text without R code

  |.......                                                          |  11%
label: unnamed-chunk-2
  |.........                                                        |  14%
  ordinary text without R code

  |...........                                                      |  17%
label: unnamed-chunk-3 (with options) 
List of 3
 $ fig.width : num 5.5
 $ fig.height: num 3.5
 $ warning   : logi FALSE

  |.............                                                    |  20%
  ordinary text without R code

  |...............                                                  |  23%
label: unnamed-chunk-4 (with options) 
List of 2
 $ fig.width : num 3.5
 $ fig.height: num 3.5

Quitting from lines 55-56 (report.Rmd) 
Error in GetUmisDistributionNew(reads.per.umi.per.cb) : 
  Not compatible with STRSXP: [type=NULL].
Calls: <Anonymous> ... GetUmisDistribution -> GetUmisDistributionNew -> .Call
In addition: Warning messages:
1: In grDevices::png(f) : unable to open connection to X11 display ''
2: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
3: In bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
4: In bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
5: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
6: In bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
7: In bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
8: In bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
9: In bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector

Execution halted

The error in function appears to be coming from a Rcpp code so I couldn't get more useful information. I tried to install dropestr as well as dropest again without any improvement. (Compilation succeeds).

Problem with UMI Error Correction Using Bayesian Method

Hello,

I am trying to do UMI error correction using the Bayesian correction method (I also want to note that the other correction methods used here: https://vpetukhov.github.io/dropEstAnalysis/umi_correction__umi_bmmc1.html work with no issues). When I run something similar to:

CorrectUmiSequenceErrors(method='Bayesian', return='reads',
collisions.info=collisions_info, umi.probabilities=umi_probs,
verbosity.level=2, mc.cores=30)

from the DropEstAnalysis site (https://vpetukhov.github.io/dropEstAnalysis/umi_correction__umi_bmmc1.html) I get the following error:

Error in $<-.data.frame(*tmp*, "IsMerged", value = logical(0)) :
replacement has 0 rows, data has 2

The actual code that I run (using my own DropSeq data which has UMI and cell BC quality tags) is:
corrected_reads$Bayesian <- holder$reads_per_umi_per_cell %>%
CorrectUmiSequenceErrors(method='Bayesian', return='reads',
collisions.info=collisions_info, umi.probabilities=umi_probs,
verbosity.level=2, mc.cores=NULL)

Walking through the various functions, I am able to get to the CorrectUmiSequenceErrorsBayesian function, which is where the error occurs.

This step works ok:
clf <- try(TrainNBClassifier(reads.per.umi.per.cb, adj.umi.num=adj.umi.num, quality.quants.num=quality.quants.num, mc.cores=mc.cores))

The error occurs here:
filt.genes <- plapply(reads.per.umi.per.cb, FilterUmisInGene, clf, correction.info$dp.matrices,
correction.info$neighb.prob.index, collisions.info, mc.cores=mc.cores)

If I look inside the FilterUmisInGene function:
I see that the error occurs in the 10th entry in my reads.per.umi.per.cb object which looks as follows:

holder$reads_per_umi_per_cell$reads_per_umi[[10]]
$CCCCCGCT
$CCCCCGCT[[1]]
[1] 1

$CCCCCGCT[[2]]
[1] 41 41 41 41 41 41 41 41

$CCCCCGCG
$CCCCCGCG[[1]]
[1] 1

$CCCCCGCG[[2]]
[1] 41 41 41 41 41 41 41 41

Within FilterUmisInGene, the error occurs in:
predictions <- PredictBayesian(classifier, classifier.df, cur.gene[not.filtered.umis], dp.matrices,
neighbours.prob.index, size.adj)

my classifier.df looks as follows (when I look here, I am guessing maybe this is where the problems arise, they are both one edit distance away from the other with the same quality and sam quality and error probs):

Base   Target MinRpU MaxRpU Quality RealQualityProb ErrorQualityProb

1 CCCCCGCG CCCCCGCT 1 1 41 -0.6379865 -0.3912805
2 CCCCCGCT CCCCCGCG 1 1 41 -0.6379865 -0.3912805

classifier.dfs object is as follows:

$CCCCCGCG
MinRpUCS MaxRpU Target ErrorProb RealProb LargerNum
2 1 1 CCCCCGCG -0.3912805 -0.6379865 0

$CCCCCGCT
MinRpUCS MaxRpU Target ErrorProb RealProb LargerNum
1 1 1 CCCCCGCT -0.3912805 -0.6379865 0

err.prior.probs is as follows (where I assume the problems arise):

$CCCCCGCG
1 2
NA NA

$CCCCCGCT
1 2
NA NA

real.prior.probs is as follows:

$CCCCCGCG
[1] 0.999478247 0.000521753

$CCCCCGCT
[1] 0.9997391235 0.0002608765

When we put this into, there is a problem in the ErrorsNumMle function:

classifier.df$IsMerged <- mapply(function(e.p, r.p, df)
ErrorsNumMle(e.p, r.p, df$ErrorProb, df$RealProb, max.adj.num=classifier$MaxAdjacentUmisNum,
larger.num=df$LargerNum[1]) >= 1:nrow(df),
err.prior.probs, real.prior.probs, classifier.dfs, SIMPLIFY=F) %>% unlist()

The problem is at the end of the function:

return(which.max(log(prior.error.prob) + log(rev(prior.real.prob)) + error.part.prob + real.part.prob) - 1)

Because the prior.error.prob is NA NA this makes everything else inside NA NA and end up returning numeric(0)

Tldr: Do you have a suggested way to deal with UMIs which are a single edit distance away and have the same quality scores (which I assume results in the NA)? �Should I just return both (e.g. return(cur.gene[not.filtered.umis]) )?

If I have missed the mark here and there is another underlying issue, I would greatly appreciate any help you can offer.

DropEst for 10x single cell sequence data for velocyto.R

Hi,

I'm trying DropEst in the 10X scRNAseq data (https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/neurons_900) for velocyto on Docker. But there is no result file after running.
My code is following:

dropest -V -f -g refdata-cellranger-mm10-1.2.0/genes/genes.gtf -c config_desc.xml neurons_900_possorted_genome_bam.bam

and standard output is following:
Version: 0.8.3.
Run: 07/13/2018 09:30:55.
config_desc.xml(43): expected =

Could you help me?

Error with dropEst

The following run (log):

cat est_main.log
/home/cl266/dropEst/dropest -m -V -r drop/dlib27.FC04320.L001.params.gz drop/dlib27.FC04320.L002.params.gz drop/dlib27.FC04320.L003.params.gz drop/dlib27.FC04320.L004.params.gz -g drop.reference.wo.pseudo/mm10.with.compact.transgenes.filtered.20180315.gtf -o drop/dlib27.out/cell.counts.bcconfig.rds -c /home/cl266/dropEst/configs/indrop_v3_with_barcodes.xml drop/dlib27.out/Aligned.out.sorted.bam 
Version: 0.8.3.

produces this immediate error:

Error in intToUtf8(8216) : 
  3 arguments passed to .Internal(intToUtf8) which requires 2
In addition: Warning message:
package "methods" in options("defaultPackages") was not found 
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 
  there is no .Internal function 'sorted_fpass'
Fatal error: unable to initialize the JIT

I am wondering whether it had to do with updating the R to 3.5.1. I tried to do all package updates but produces the same error. Would there by a workaround?

cmake error: Could not find the following Boost libraries

hi,
I had some errors with boost :

cmake  -DBAMTOOLS_ROOT=/BIGDATA1/cygene_sydu_1/local/usr/local  -DBOOST_ROOT=/BIGDATA1/cygene_sydu_1/local  ..
-- 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
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
CMake Error at /BIGDATA1/app/cmake/3.10.1-gcc-4.8.5/share/cmake-3.10/Modules/FindBoost.cmake:1928 (message):
  Unable to find the requested Boost libraries.

  Boost version: 1.60.0

  Boost include path: /BIGDATA1/cygene_sydu_1/local/include

  Could not find the following Boost libraries:

          boost_filesystem
          boost_log
          boost_system
          boost_thread
          boost_unit_test_framework

  Some (but not all) of the required Boost libraries were found.  You may
  need to install these additional Boost libraries.  Alternatively, set
  BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT
  to the location of Boost.
Call Stack (most recent call first):
  CMake/deps.cmake:19 (find_package)
  CMakeLists.txt:18 (include)


-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Found BAMTOOLS: /BIGDATA1/cygene_sydu_1/local/usr/local/bin/../lib64/libbamtools.a
-- Found R: /BIGDATA1/cygene_sydu_1/R/3.4/lib64/R/lib/libR.so
-- Found R: /BIGDATA1/cygene_sydu_1/R/3.4/lib64/R
-- Configuring incomplete, errors occurred!
See also "/BIGDATA1/cygene_sydu_1/software/dropEst-master/build/CMakeFiles/CMakeOutput.log".
See also "/BIGDATA1/cygene_sydu_1/software/dropEst-master/build/CMakeFiles/CMakeError.log".

I install boost followed by the user's guide like this :

./bootstrap.sh --with-libraries=filesystem,iostreams,log,system,thread,test
./b2 cxxflags="-std=c++11" include="$LOCAL_LIBS/include/" search="$LOCAL_LIBS/lib/" link=shared threading=multi install --prefix=$LOCAL_LIBS

anyone helps? Thanks!

Produce multiple files (each corresponding to a single cell) using dropTag

Hi,

Thank you for developing this excellent tool. I am trying to use dropTag to demultiplex fastq files generated by inDrop v1. The command line I am using is the following:

../dropEst/droptag -c ../dropEst/configs/indrop_v1_2.xml -l log.file.name -p 8 -S file_1.fastq.gz file_2.fastq.gz

Note that file_1.fastq.gz corresponds to the barcodes file and file_2.fatsq.gz corresponds to the gene reads file.

However, I am only getting a single tagged file called file_2.fastq.gz.tagged.1.fastq.gz instead of getting multiple demultiplexed files. Can I instead get two files for each cell, one corresponding to the demultiplexed barcode file, and the other to the demultiplexed gene reads file?

Thank you in advance!

Best,
Leon

When to use dropEst multiple bam input

I am confused about the usage of dropEst about how merging data from different samples when I found that it accepts multiple bams as input.
Assume I generated two 10X libraries from two samples , I ran the cellranger then I got two bams.
The question is that should I input these two bams for dropEst if I want to analysis them as one matrix ?
Or I should merge these two matrices after dropEst and dropEstR filtered ?

Issue with UMI correction

When I run the code from the vignette for UMI correction,

I get the following error:

> CorrectUmiSequenceErrors(d, umi_probabilities, collisions_info, 
+                          method = "Bayesian",
+                          mc.cores=NULL, verbosity.level=2)
Correcting UMI sequence errors.
Filling info about adjacent UMIs...0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
 Completed.
 Completed.


Estimating prior error probabilities...Error in reads.per.umi.per.cb[[1]][[1]][[2]] : subscript out of bounds

Another error with classic method:

CorrectUmiSequenceErrors(d, umi_probabilities, collisions_info, correction_info, adjust.collisions=TRUE, quality.quants.num=10, mc.cores=NULL, verbosity.level=3, return='matrix', distribution.smooth=10, method='Classic', mult=1)
Correcting UMI sequence errors.
Error in FUN(X[[i]], ...) : Not compatible with STRSXP: [type=NULL].

When I looked into the code, essentially the d$reads_per_umi does not have a training set. Maybe related to recent update of the code?

Also, this might be related, when I compare my UMI counts from a standard Indrops v3 run to that of from dropEst, roughly I see double the number for the dropEst (before UMI correction, which I cannot run). Is this a normal situation?

Thank you very much!

No reads_per_umi_per_cell saved in cell.counts.rds after dropEst

Hi,

I have updated from 0.8.0 version to 0.8.2, and ran dropEst and the cells.counts.rds does not seem to have a reads_per_umi_per_cell any more. (Note that the cell.counts.bcconfig.rds is just my way of naming convention of outputing the usual cell.counts.rds file).

> d <- readRDS("cell.counts.bcconfig.rds");
> names(d)
 [1] "cm"                      "cm_raw"                 
 [3] "reads_per_chr_per_cells" "mean_reads_per_umi"     
 [5] "saturation_info"         "merge_targets"          
 [7] "aligned_reads_per_cell"  "aligned_umis_per_cell"  
 [9] "requested_umis_per_cb"   "requested_reads_per_cb"

The following is the log after the dropEst run:

/home/cl266/dropEst/dropest -m -V -r drop/dlib7.FC03835.L001.params.gz drop/dlib7.FC03835.L002.params.gz drop/dlib7.FC03835.L003.params.gz drop/dlib7.FC03835.L004.params.gz -g drop.reference.wo.pseudo/mm10.with.compact.transgenes.filtered.20180315.gtf -o drop/dlib7.out/cell.counts.bcconfig.rds -c /home/cl266/dropEst/configs/indrop_v3_with_barcodes.xml drop/dlib7.out/Aligned.out.sorted.bam 
Version: 0.8.2.
Run: 05/11/2018 23:35:13.
Real CBs merge selected.

Start parsing of bams: 23:35:13.
Start loading read parameters
Start reading file: drop/dlib7.FC03835.L001.params.gz
Total 10000000 read records processed
Start reading file: drop/dlib7.FC03835.L002.params.gz
Total 20000000 read records processed
Total 30000000 read records processed
Start reading file: drop/dlib7.FC03835.L003.params.gz
Total 40000000 read records processed
Total 50000000 read records processed
Start reading file: drop/dlib7.FC03835.L004.params.gz
Total 60000000 read records processed
Total 70000000 read records processed
All read parameters were loaded
drop/dlib7.out/Aligned.out.sorted.bam: 10000000 total reads; 19.7% intergenic; 36.4% touch exon; 5.14% touch intron; 0.268% touch not annotated regions; 551120 CBs read
drop/dlib7.out/Aligned.out.sorted.bam: 20000000 total reads; 14.2% intergenic; 35.2% touch exon; 5.23% touch intron; 0.354% touch not annotated regions; 807385 CBs read
drop/dlib7.out/Aligned.out.sorted.bam: 30000000 total reads; 12.6% intergenic; 35.9% touch exon; 5.89% touch intron; 0.676% touch not annotated regions; 1054520 CBs read
drop/dlib7.out/Aligned.out.sorted.bam: 40000000 total reads; 13.3% intergenic; 37.7% touch exon; 5.84% touch intron; 0.555% touch not annotated regions; 1316740 CBs read
drop/dlib7.out/Aligned.out.sorted.bam: 50000000 total reads; 12.5% intergenic; 37.7% touch exon; 5.5% touch intron; 0.484% touch not annotated regions; 1523297 CBs read
WARNING: Can't find chromosome 'JH584301.1'
WARNING: Can't find chromosome 'GL456379.1'
WARNING: Can't find chromosome 'GL456393.1'
WARNING: Can't find chromosome 'GL456366.1'
WARNING: Can't find chromosome 'GL456367.1'
WARNING: Can't find chromosome 'GL456213.1'
WARNING: Can't find chromosome 'GL456383.1'
WARNING: Can't find chromosome 'GL456360.1'
WARNING: Can't find chromosome 'GL456378.1'
WARNING: Can't find chromosome 'GL456389.1'
WARNING: Can't find chromosome 'GL456370.1'
WARNING: Can't find chromosome 'GL456390.1'
WARNING: Can't find chromosome 'GL456392.1'
WARNING: Can't find chromosome 'GL456382.1'
WARNING: Can't find chromosome 'GL456396.1'
WARNING: Can't find chromosome 'GL456368.1'
drop/dlib7.out/Aligned.out.sorted.bam: 53226123 total reads; 12.2% intergenic; 37.9% touch exon; 5.35% touch intron; 0.476% touch not annotated regions; can't parse 0.00553863% reads; 1589231 CBs read
Bams parsed: 23:46:53.

40620 CBs with more than 20 genes
top CBs:
12988	GGGGGGGGGGGGGGGG
4082	AGGAGTCGTTCACATA
4042	CCACGTTGCAACAAAT
3537	CGTGTACAGGTTTCTC
3474	CCGAGATCGATGTATT
3422	GTTCTGCTCCACATTA
3405	ATGGGCTCATGCATGG
3348	TGCTTGGGAGACACCA
3335	CATTCGGGATGACCGA

Start merge: 23:46:56.
Merge initialized: 23:46:56.
Total 2471 cells merged
Total 5847 cells excluded
Merge finished: 23:47:20.
Merge UMIs with N's: 23:47:20.
32302 cells processed. Merged 9571 UMIs from 9534 cells.
UMI merge finished: 23:47:25.
32302 cells are considered as real.

4897 CBs with more than 100 genes, which have UMIs of the requested type.
top CBs:
4105	AGGAGTCGTTCACATA
4063	CCACGTTGCAACAAAT
3567	CGTGTACAGGTTTCTC
3515	CCGAGATCGATGTATT
3439	GTTCTGCTCCACATTA
3436	ATGGGCTCATGCATGG
3367	CATTCGGGATGACCGA
3360	TGCTTGGGAGACACCA
3353	CCGAGATCCGCTAGTC

Done: 23:47:28.

22997 genes
top genes:
mt-Nd4	113333
Myo3a	106538
mt-Cytb	99032
S100a6	90587
mt-Nd1	90403
H19	81416
Saa3	72838
Col1a2	62978
Gm10076	62151
Rpl23	62003

Compiling diagnostic stats: 
Reads per chromosome per cell;
Fill exon results
Fill intron results
Fill intergenic results
Saturation info;
Mean reads per UMI;
Merge targets;
Completed.

Compiling raw count matrix: 23:48:01.
23326 genes, 32302 cells.
Done: 23:48:05.
Compiling filtered count matrix: 23:48:05.
19283 genes, 4897 cells.
Done: 23:48:14.
Reads per UMI per gene;

Writing R data to drop/dlib7.out/cell.counts.bcconfig.rds ...: 23:49:20.
Completed: 23:49:55.

Compiling intron/exon matrices: 23:49:55.
Exon
18964 genes, 4897 cells.
Intron
16313 genes, 4897 cells.
Intron/exon spanning
4748 genes, 4897 cells.
Done: 23:50:10.

Writing R data to drop/dlib7.out/cell.counts.bcconfig.matrices.rds ...: 23:50:10.
Completed: 23:50:15.
All done: 23:50:48.

Specify bam output file name

There is no way to to specify the output file name for the --bam-output parameter

dropest "wrong quality length"

I am trying to run dropest on my .bam file generated from DropSeq and get the following error:
Start parsing of bams: 22:06:27.
Wrong quality length: 0, expected: 5

I am not sure what this is in reference to, is it something to do with my bam file? Any help would be much appreciated.

error at the step Linking CXX executable TestEstimation

Dear dropEst developer, I confronted an error to install dropEst at the step of
Linking CXX executable TestEstimation .
It seems that the error may relate to the following error. But I am not sure how to fix this, any suggestions?

/usr/bin/ld: warning: liblzma.so.5, needed by /net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so, not found (try using -rpath or -rpath-link)```


[ 11%] Built target DropTools
[ 65%] Built target Estimation
[ 88%] Built target TagsSearch
Linking CXX executable TestEstimation
/usr/bin/ld: warning: libpcre.so.1, needed by /net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: warning: liblzma.so.5, needed by /net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so, not found (try using -rpath or -rpath-link)
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_fullinfo'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_lzma_preset@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_alone_decoder@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_crc64@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_raw_encoder@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_config'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_code@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_stream_decoder@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_free'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_raw_decoder@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_free_study'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_assign_jit_stack'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_exec'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_version_string@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_maketables'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_stream_encoder@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_compile'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_study'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_version'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `lzma_end@XZ_5.0'
/net/gs/vol3/software/modules-sw/R/3.4.0/Linux/RHEL6/x86_64/lib64/R/lib/libR.so: undefined reference to `pcre_jit_stack_alloc'
collect2: error: ld returned 1 exit status
make[2]: *** [TestEstimation] Error 1
make[1]: *** [CMakeFiles/TestEstimation.dir/all] Error 2
make: *** [all] Error 2

Support for ddSEQ?

Hello,

We have some ddSEQ data, and were interested in applying an open-source tool to generate counts from our reads. I'm assuming we would need a list of barcodes, but in theory could dropEST work for this type of droplet-based data? The library preps are organized like in the following link:

https://teichlab.github.io/scg_lib_structs/SureCell.html

Config file for 10X single-cell V1 chemistry

Hello--I'm testing dropEst on a dataset generated with the 10X V1 chemistry (https://support.10xgenomics.com/single-cell-gene-expression/sequencing/doc/specifications-sequencing-requirements-for-single-cell-3). It seems that the V2 chemistry is the one that's specified in the 10x.xml file, and the necessary changes for V1 data aren't obvious to me.

Naively trying

barcode1_length: 0
barcode2_length: 14
umi_length: 10
r1_rc_length: 0

in the config.xml seems to stall at the reads per UMI per gene estimation step. I'd appreciate any advice you might have!

Make return error with Boost

The error occurs at 62%. GCC 7.1.0, boost 1.61.0. Any suggestions would be appreciated.

[ 60%] Building CXX object CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o
[ 62%] Linking CXX executable TestTools
/usr/bin/ld: warning: libboost_date_time.so.1.61.0, needed by /home/zhuqin/.local/lib/gcc/x86_64-pc-linux-gnu/7.1.0/../../../libboost_log.so, may conflict with libboost_date_time.so.5
/usr/bin/ld: warning: libboost_filesystem.so.1.61.0, needed by /home/zhuqin/.local/lib/gcc/x86_64-pc-linux-gnu/7.1.0/../../../libboost_log.so, may conflict with libboost_filesystem.so.5
/usr/bin/ld: warning: libboost_system.so.1.61.0, needed by /home/zhuqin/.local/lib/gcc/x86_64-pc-linux-gnu/7.1.0/../../../libboost_log.so, may conflict with libboost_system.so.5
/usr/bin/ld: warning: libboost_regex.so.1.61.0, needed by /home/zhuqin/.local/lib/gcc/x86_64-pc-linux-gnu/7.1.0/../../../libboost_log.so, may conflict with libboost_regex.so.5
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function _ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEmiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_.constprop.442': TestTools.cpp:(.text+0x27c): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function _ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEmiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_.constprop.441': TestTools.cpp:(.text+0x4ed): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function TestTools::testReadParams::test_method()': TestTools.cpp:(.text+0x29a7): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
TestTools.cpp:(.text+0x3105): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function TestTools::testGeneMerge::test_method()':
TestTools.cpp:(.text+0x3ae9): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text+0x3d50): more undefined references to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' follow
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function boost::unit_test::make_test_case(boost::function<void ()()> const&, boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long)': TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x22): undefined reference to _ZN5boost9unit_test9ut_detail24normalize_test_case_nameB5cxx11ENS0_13basic_cstringIKcEE'
TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x61): undefined reference to boost::unit_test::test_case::test_case(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::function<void ()()> const&)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function _Z41__static_initialization_and_destruction_0ii.constprop.437':
TestTools.cpp:(.text.startup+0x2b4): undefined reference to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::unit_test::decorator::collector&)' TestTools.cpp:(.text.startup+0x325): undefined reference to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x3ac): undefined reference to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)' TestTools.cpp:(.text.startup+0x43c): undefined reference to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x4cc): undefined reference to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)' TestTools.cpp:(.text.startup+0x55c): undefined reference to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text.startup+0x5ec): more undefined references to boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)' follow CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, char [5]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char const*, char const (&) [5], char const*)':
TestTools.cpp:(.text.ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA5_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO[ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA5_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO]+0xdb): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, char [7]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char const*, char const (&) [7], char const*)':
TestTools.cpp:(.text.ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA7_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO[ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA7_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO]+0xdb): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, unsigned int, int>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned int const&, char const*, int const&, char const*)':
TestTools.cpp:(.text.ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEjiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH[ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEjiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH]+0xfa): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, char [6]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char const*, char const (&) [6], char const*)':
TestTools.cpp:(.text.ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA6_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO[ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA6_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO]+0xdb): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, char [3]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char const*, char const (&) [3], char const*)':
TestTools.cpp:(.text.ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA3_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO[ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA3_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO]+0xdb): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EEbT_RKNS_9unit_test12lazy_ostreamENSB_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSG_RKT1_SN_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EEbT_RKNS_9unit_test12lazy_ostreamENSB_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSG_RKT1_SN_]+0x11c): more undefined references to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' follow
collect2: error: ld returned 1 exit status
make[2]: *** [TestTools] Error 1
make[1]: *** [CMakeFiles/TestTools.dir/all] Error 2
make: *** [all] Error 2

dropest error

my command is
/dropest -w -m -r sample8.params.gz sample7.params.gz sample6.params.gz sample5.params.gz sample4.params.gz sample3.params.gz sample2.params.gz sample1.params.gz -g /home/dushiyi/database/refdata-cellranger-GRCh38-1.2.0/genes/genes.gtf -c /cygene/work/02.dropEst/10x.test.xml ../02_alignment/Aligned.out.bam
while the output is :

../02_alignment/Aligned.out.bam: 400000000 total reads; 14.9% intergenic; 65.1% touch exon; 12.4% touch intron; 0.489% touch not annotated regions; can't parse 0.0792053% reads; 7678441 CBs read
../02_alignment/Aligned.out.bam: 410000000 total reads; 14.9% intergenic; 65.1% touch exon; 12.4% touch intron; 0.487% touch not annotated regions; can't parse 0.078822% reads; 7874334 CBs read
WARNING: Can't find chromosome 'KI270510.1'
../02_alignment/Aligned.out.bam: 420000000 total reads; 14.9% intergenic; 65.1% touch exon; 12.4% touch intron; 0.485% touch not annotated regions; can't parse 0.0784669% reads; 8050887 CBs read
../02_alignment/Aligned.out.bam: 430000000 total reads; 14.9% intergenic; 65.1% touch exon; 12.4% touch intron; 0.483% touch not annotated regions; can't parse 0.078086% reads; 8214251 CBs read
../02_alignment/Aligned.out.bam: 440000000 total reads; 14.9% intergenic; 65.1% touch exon; 12.4% touch intron; 0.481% touch not annotated regions; can't parse 0.0777873% reads; 8365859 CBs read
std::bad_alloc

and the result is

$ cat cell.counts.mtx
%%MatrixMarket matrix coordinate pattern symmetric
0 0 0

what's wrong with me? The step1 dropTag and step 2 alignment are all correct.

[Question] How cell names are determined?

Here is an example of cell names present in the generated count matrix: TGACAATACTTGATTAGAC.

I would assume it isTGACAATACTT|GATTAGAC where the last 8 letters come from barcode-2 with fixed length and the rest comes from barcode-1 with variable length. Is it correct?
Do you reverse transcribe barcode-1/barcode-2 to determine cell names?

I am using indrop_v2 with two cell barcodes list. One for BC-1 and the other for BC-2.

Thanks.

Statistics about mapping

Hi,
In my lab, we sequenced for the first time some libraries by using the SeqWell protocol.
Then I ran the Dropseq pipeline to get my count matrix. But, I would like to have some statistics about the mapping, for example number of exonic, intronic and intergenic reads.
After the alignment step I got a unique bam file for all barcodes. Is there a way to run dropEst with this bam file to get these statistics per CB?

Thank you,

Elisabetta

Issue in filtration and QC/ making figures (e.g. fig 4 in paper)

I have now these following files after running dropest pipeline..

cell.count.rds
cell.counts.matrices.rds
cell.count.cells.tsv
cell.counts.genes.tsv
cell.count.mtx files
I am interested in having a comparison between dropEst and cellRanger. I am trying to make figures but I am not getting how to make it. I also want to do filtration and QC. I am following this links but still unable to do. Which file should I use?

https://github.com/VPetukhov/dropEstAnalysis
https://github.com/hms-dbmi/dropEst/tree/master/dropestr/vignettes

I am looking forward to.

Code not building

Linker error on compilation of current code:

libEstimation.a(BamController.cpp.o): In function `Estimation::BamProcessing::BamController::parse_bam_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<c
har> > const&, std::shared_ptr<Estimation::BamProcessing::BamProcessorAbstract>&, std::shared_ptr<Estimation::BamProcessing::ReadParamsParser>&, bool) const':
BamController.cpp:(.text+0xb85): undefined reference to `BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
libEstimation.a(BamProcessorAbstract.cpp.o): In function `Estimation::BamProcessing::BamProcessorAbstract::save_alignment(BamTools::BamAlignment, std::__cxx11::basic_string<char, st
d::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::ch
ar_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
BamProcessorAbstract.cpp:(.text+0x474): undefined reference to `BamTools::BamAlignment::IsValidSize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > c
onst&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
BamProcessorAbstract.cpp:(.text+0x4cf): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const
&, char*&, unsigned int const&, unsigned int&) const'
BamProcessorAbstract.cpp:(.text+0x526): undefined reference to `BamTools::BamAlignment::IsValidSize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > c
onst&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
BamProcessorAbstract.cpp:(.text+0x57f): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const
&, char*&, unsigned int const&, unsigned int&) const'
BamProcessorAbstract.cpp:(.text+0x5d6): undefined reference to `BamTools::BamAlignment::IsValidSize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > c
onst&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
BamProcessorAbstract.cpp:(.text+0x62f): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const
&, char*&, unsigned int const&, unsigned int&) const'
libEstimation.a(BamProcessorAbstract.cpp.o): In function `Estimation::BamProcessing::BamProcessorAbstract::update_bam(std::__cxx11::basic_string<char, std::char_traits<char>, std::a
llocator<char> > const&, BamTools::BamReader const&)':
BamProcessorAbstract.cpp:(.text+0xccb): undefined reference to `BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Bam
Tools::SamHeader const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)'
libEstimation.a(FilledBamParamsParser.cpp.o): In function `Estimation::BamProcessing::FilledBamParamsParser::get_read_params(BamTools::BamAlignment const&, Tools::ReadParameters&)':
FilledBamParamsParser.cpp:(.text+0xd2): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const
&, char*&, unsigned int const&, unsigned int&) const'
FilledBamParamsParser.cpp:(.text+0x1b2): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > cons
t&, char*&, unsigned int const&, unsigned int&) const'
libEstimation.a(ReadParamsParser.cpp.o): In function `Estimation::BamProcessing::ReadParamsParser::get_gene(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<c
har> > const&, BamTools::BamAlignment, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&) const':
ReadParamsParser.cpp:(.text+0xb70): undefined reference to `BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, c
har*&, unsigned int const&, unsigned int&) const'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/dropest.dir/build.make:112: dropest] Error 1
make[1]: *** [CMakeFiles/Makefile2:218: CMakeFiles/dropest.dir/all] Error 2
make: *** [Makefile:95: all] Error 2

FillCollisionsAdjustmentInfo is taking too long to complete

Hi @VPetukhov ,
I am trying to use DropEst with one of the 10x datasets from here.
I downloaded the BAM from the above link and used dropest -f mode to generate the count matrix and the rds file for the downstream UMI correction. Unfortunately I am noob in R and just copy pasting code from this tutorial. I have got a couple of question regarding the working of dropEst pipeline:

When we provide an external BAM (like from 10x website in my case) what type of UMI correction does dropest command do before generating the count matrix? I am guessing it simply count the tags from the BAM if I don't give either -m or -M?
When I try to use dropestr R package following the above tutorial it seems to give good umi distribution till here. But once I try to use the function

collisions_info <- FillCollisionsAdjustmentInfo(umi_probabilities, max_umi_per_gene, step=20, mc.cores=5, verbose=T)

the program give following error

> FillCollisionsAdjustmentInfo(umi_probabilities, max_umi_per_gene, step=20, mc.cores=5, verbose=T)
Error in FillCollisionsAdjustmentInfo(umi_probabilities, max_umi_per_gene,  :
  unused arguments (step = 20, mc.cores = 5, verbose = T)

So I removed step = 20, mc.cores = 5, verbose = T but it has been 3 days now and the program won't finish.

What am I doing wrong? Thanks again for your help.

my config.xml

<config>
    <!-- droptag -->
    <TagsSearch>
        <protocol>10x</protocol>
        <BarcodesSearch>
            <barcode1_length>8</barcode1_length>
            <barcode2_length>16</barcode2_length>
            <umi_length>10</umi_length>
            <r1_rc_length>0</r1_rc_length>
        </BarcodesSearch>

        <Processing>
            <min_align_length>10</min_align_length>
            <reads_per_out_file>10000000</reads_per_out_file>
            <poly_a_tail>AAAAAAAA</poly_a_tail>
        </Processing>
    </TagsSearch>

    <!-- dropest -->
    <Estimation>
        <Merge>
	    <barcodes_file>/mnt/scratch5/avi/dropest_data/barcodes.tsv</barcodes_file>
            <barcodes_type>const</barcodes_type>
            <min_merge_fraction>0.2</min_merge_fraction>
            <max_cb_merge_edit_distance>2</max_cb_merge_edit_distance>
            <max_umi_merge_edit_distance>1</max_umi_merge_edit_distance>
            <min_genes_after_merge>100</min_genes_after_merge>
            <min_genes_before_merge>20</min_genes_before_merge>
        </Merge>

        <PreciseMerge>
            <max_merge_prob>1e-5</max_merge_prob>
            <max_real_merge_prob>1e-7</max_real_merge_prob>
        </PreciseMerge>
    </Estimation>

    <BamTags> <!-- Optional. Tags, which are used to parse .bam file (-f option) or to print tagged .bam file (-b or -F options). Default values correspond to 10x protocol. -->
        <cb>CB</cb> <!-- Cell barcode. Default: CB. -->
        <cb_raw>CR</cb_raw> <!-- Cell barcode raw. Used only for bam output. Default: CR. -->
        <umi>UB</umi> <!-- UMI. Default: UB. -->
        <umi_raw>UR</umi_raw> <!-- UMI raw. Used only for bam output. Default: UR. -->
        <gene>GX</gene> <!-- Gene id. Default: GX. -->
        <cb_quality>CQ</cb_quality> <!-- Cell barcode quality. Default: CQ. -->
        <umi_quality>UQ</umi_quality> <!-- UMI quality. Default: UQ. -->
    </BamTags>
</config>

barcode config

I am afraid people will keep missing the barcode configs. It's commented out in the standard configs, so most will probably leave it that way (and the program will run, but the output will be worse).
Also, specifying "~/dropEst/data/barcodes/indrop_v3" doesnt' work for me .. I have to specify full path (i.e. /home/pkharchenko/dropEst/...).

Perhaps we should just have another tag and paste the whole barcode list there? Will make for an ugly xml file though.

Ld error when compiling with Cmake

Hi I am trying to compile dropEst but I am getting a strange ld error with 62%. By looking the code I can't tell any clue about what is going on. Can you help me ? Thanks!


cmake ..
-- The C compiler identification is GNU 5.5.0
-- The CXX compiler identification is GNU 5.5.0
-- Check for working C compiler: /ru-auth/local/home/linuxbrew/.linuxbrew/bin/cc
-- Check for working C compiler: /ru-auth/local/home/linuxbrew/.linuxbrew/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: /ru-auth/local/home/linuxbrew/.linuxbrew/bin/c++
-- Check for working CXX compiler: /ru-auth/local/home/linuxbrew/.linuxbrew/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Boost version: 1.67.0
-- Found the following Boost libraries:
--   filesystem
--   iostreams
--   log
--   system
--   thread
--   unit_test_framework
--   regex
--   date_time
--   log_setup
--   chrono
--   atomic
-- ** Boost Include: /ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/include
-- ** Boost Libraries: /ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib
-- ** Boost Link-Libs: /ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_filesystem-mt.so;/ru-auth/local/home/linuxbrew/.linuxb
rew/Cellar/boost/1.67.0_1/lib/libboost_iostreams-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_log-mt.so;/ru-auth/loc
al/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_system-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_
thread-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_unit_test_framework-mt.so;/ru-auth/local/home/linuxbrew/.linuxbr
ew/Cellar/boost/1.67.0_1/lib/libboost_regex-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_date_time-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_log_setup-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/[6$
ost_chrono-mt.so;/ru-auth/local/home/linuxbrew/.linuxbrew/Cellar/boost/1.67.0_1/lib/libboost_atomic-mt.so
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3") 
-- Found BAMTOOLS: /data_alpha/local/bioinformatic_tools/bamtools/bin/../lib/libbamtools.so  
-- Found R: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so  
-- Found R: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R
-- Configuring done
-- Generating done
-- Build files have been written to: /ru-auth/local/home/trezende/localPrograms/dropEst/build

 make
Scanning dependencies of target DropTools
[  1%] Building CXX object CMakeFiles/DropTools.dir/Tools/CollisionsAdjuster.cpp.o
[  2%] Building CXX object CMakeFiles/DropTools.dir/Tools/GeneAnnotation/GtfRecord.cpp.o
[  4%] Building CXX object CMakeFiles/DropTools.dir/Tools/GeneAnnotation/Interval.cpp.o
[  5%] Building CXX object CMakeFiles/DropTools.dir/Tools/GeneAnnotation/RefGenesContainer.cpp.o
[  7%] Building CXX object CMakeFiles/DropTools.dir/Tools/Logs.cpp.o
[  8%] Building CXX object CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o
[ 10%] Building CXX object CMakeFiles/DropTools.dir/Tools/UtilFunctions.cpp.o
[ 11%] Linking CXX static library libDropTools.a
[ 11%] Built target DropTools
Scanning dependencies of target Estimation
[ 13%] Building CXX object CMakeFiles/Estimation.dir/Estimation/BamProcessing/BamController.cpp.o
[ 14%] Building CXX object CMakeFiles/Estimation.dir/Estimation/BamProcessing/BamProcessor.cpp.o
[ 15%] Building CXX object CMakeFiles/Estimation.dir/Estimation/BamProcessing/BamProcessorAbstract.cpp.o
[ 17%] Building CXX object CMakeFiles/Estimation.dir/Estimation/BamProcessing/BamTags.cpp.o
[ 18%] Building CXX object CMakeFiles/Estimation.dir/Estimation/BamProcessing/FilledBamParamsParser.cpp.o
[ 20%] Building CXX object CMakeFiles/Estimation.dir/Estimation/BamProcessing/FilteringBamProcessor.cpp.o
[ 21%] Building CXX object CMakeFiles/Estimation.dir/Estimation/BamProcessing/ReadMapParamsParser.cpp.o
[ 23%] Building CXX object CMakeFiles/Estimation.dir/Estimation/BamProcessing/ReadParamsParser.cpp.o
[ 24%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Cell.cpp.o
[ 26%] Building CXX object CMakeFiles/Estimation.dir/Estimation/CellsDataContainer.cpp.o
[ 27%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Gene.cpp.o
[ 28%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/BarcodesParsing/BarcodesParser.cpp.o
[ 30%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/BarcodesParsing/ConstLengthBarcodesParser.cpp.o
[ 31%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/BarcodesParsing/InDropBarcodesParser.cpp.o
[ 33%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/BrokenRealBarcodesMergeStrategy.cpp.o
[ 34%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/MergeProbabilityValidator.cpp.o
[ 36%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/MergeStrategyAbstract.cpp.o
[ 37%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/MergeStrategyBase.cpp.o
[ 39%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/MergeStrategyFactory.cpp.o
[ 40%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/PoissonRealBarcodesMergeStrategy.cpp.o
[ 42%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/PoissonSimpleMergeStrategy.cpp.o
[ 43%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/PoissonTargetEstimator.cpp.o
[ 44%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/RealBarcodesMergeStrategy.cpp.o
[ 46%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/SimpleMergeStrategy.cpp.o
[ 47%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/UMIs/MergeUMIsStrategyAbstract.cpp.o
[ 49%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/UMIs/MergeUMIsStrategyDirectional.cpp.o
[ 50%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Merge/UMIs/MergeUMIsStrategySimple.cpp.o
[ 52%] Building CXX object CMakeFiles/Estimation.dir/Estimation/ReadParametersEfficient.cpp.o
[ 53%] Building CXX object CMakeFiles/Estimation.dir/Estimation/ResultsPrinter.cpp.o
[ 55%] Building CXX object CMakeFiles/Estimation.dir/Estimation/Stats.cpp.o
[ 56%] Building CXX object CMakeFiles/Estimation.dir/Estimation/StringIndexer.cpp.o
[ 57%] Building CXX object CMakeFiles/Estimation.dir/Estimation/UMI.cpp.o
[ 59%] Linking CXX static library libEstimation.a
[ 59%] Built target Estimation
Scanning dependencies of target TestTools
[ 60%] Building CXX object CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o
[ 62%] Linking CXX executable TestTools
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: warning: libreadline.so.6, needed by /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so, 
not found (try using -rpath or -rpath-link)
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: warning: libicuuc.so.42, needed by /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so, no
t found (try using -rpath or -rpath-link)
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: warning: libicui18n.so.42, needed by /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so, 
not found (try using -rpath or -rpath-link)
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_mark'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `read_history'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_attempted_
completion_over'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_completio$_append_character'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_getLocal
eByType_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_library_ve
rsion'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_open_4_2
'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_close_4_
2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_strcollI
ter_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_setStren
gth_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_attempted_
completion_function'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_completion
_matches'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_callback_h
andler_remove'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_point'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `u_getVersion_
4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_basic_word
_break_characters'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_line_buffe
r'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `uiter_setUTF8
_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `tilde_expand'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_end'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_readline_n
ame'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_free_line_
state'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_completer_
word_break_characters'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_callback_r
ead_char'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `clear_history
'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_callback_h
andler_install'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `ucol_setAttri
bute_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_sort_compl
etion_matches'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_cleanup_af
ter_signal'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `add_history'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `u_versionToSt
ring_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `history_trunc
ate_file'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_readline_s
tate'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `write_history
'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `uloc_setDefau
lt_4_2'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `rl_done'
/ru-auth/local/home/linuxbrew/.linuxbrew/bin/ld: /ru-auth/local/home/trezende/compiled/R-3.4.4/lib64/R/lib/libR.so: undefined reference to `stifle_histor
y'
collect2: error: ld returned 1 exit status
make[2]: *** [TestTools] Error 1
make[1]: *** [CMakeFiles/TestTools.dir/all] Error 2
make: *** [all] Error 2

bzip website down

It looks like the bzip website is currently down. Not sure if it's permanent, but for anyone else that is having the same issue I was able to install 1.0.6 with wget https://web.archive.org/web/20180624184835/http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz.

build fails at 36% (boost)

Hi,

I've been trying to build dropEst, but I keep running against these errors:

Scanning dependencies of target droptag
[ 34%] Building CXX object CMakeFiles/droptag.dir/droptag.cpp.o
[ 36%] Linking CXX executable droptag
libDropTools.a(Logs.cpp.o): In function `boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::consume(boost::log::v2_mt_posix::record_view const&)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE7consumeERKNS1_11record_viewE]+0x2ba): undefined reference to `boost::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<char>, std::allocator<char> > const&)'
libDropTools.a(Logs.cpp.o): In function `boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::consume(boost::log::v2_mt_posix::record_view const&)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE7consumeERKNS1_11record_viewE]+0x2ba): undefined reference to `boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char>::consume(boost::log::v2_mt_posix::record_view const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
libDropTools.a(Logs.cpp.o): In function `void boost::log::v2_mt_posix::basic_formatting_ostream<char, std::char_traits<char>, std::allocator<char> >::aligned_write<wchar_t>(wchar_t const*, long)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0x77): undefined reference to `boost::log::v2_mt_posix::aux::code_convert(wchar_t const*, unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::locale const&)'
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l[_ZN5boost3log11v2_mt_posix24basic_formatting_ostreamIcSt11char_traitsIcESaIcEE13aligned_writeIwEEvPKT_l]+0xf1): undefined reference to `boost::log::v2_mt_posix::aux::code_convert(wchar_t const*, unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::locale const&)'
libDropTools.a(Logs.cpp.o): In function `void 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<char>, std::allocator<char> > >&>, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > >(void*, std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> > const&)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEENSt7__cxx1112basic_stringIwSB_IwESaIwEEEEEvPvRKT0_[_ZN5boost3log11v2_mt_posix15type_dispatcher13callback_base10trampolineINS1_9binder1stINS1_10output_funERNS1_11expressions3aux10stream_refINS1_24basic_formatting_ostreamIcSt11char_traitsIcESaIcEEEEEEENSt7__cxx1112basic_stringIwSB_IwESaIwEEEEEvPvRKT0_]+0x5e): undefined reference to `boost::log::v2_mt_posix::aux::code_convert(wchar_t const*, unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::locale const&)'
libDropTools.a(Logs.cpp.o): In function `boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::text_file_backend>::try_consume(boost::log::v2_mt_posix::record_view const&)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_17text_file_backendEE11try_consumeERKNS1_11record_viewE]+0x2d8): undefined reference to `boost::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<char>, std::allocator<char> > const&)'
libDropTools.a(Logs.cpp.o): In function `boost::log::v2_mt_posix::sinks::synchronous_sink<boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char> >::try_consume(boost::log::v2_mt_posix::record_view const&)':
Logs.cpp:(.text._ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE[_ZN5boost3log11v2_mt_posix5sinks16synchronous_sinkINS2_26basic_text_ostream_backendIcEEE11try_consumeERKNS1_11record_viewE]+0x2d8): undefined reference to `boost::log::v2_mt_posix::sinks::basic_text_ostream_backend<char>::consume(boost::log::v2_mt_posix::record_view const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
collect2: error: ld returned 1 exit status
make[2]: *** [droptag] Error 1
make[1]: *** [CMakeFiles/droptag.dir/all] Error 2
make: *** [all] Error 2

This was my configuration output:

/share/pkg/cmake/3.10.0/install/bin/cmake \
>  -DCMAKE_C_COMPILER=/share/pkg/gcc/7.2.0/install/bin/gcc \
>  -DCMAKE_CXX_COMPILER=/share/pkg/gcc/7.2.0/install/bin/g++ \
>  -D R_ROOT="/share/pkg/r/3.4.2/install/lib64/R" \
>  -D BOOST_ROOT="/share/pkg/boost/1.57.0/install" \
>  .
-- The C compiler identification is GNU 7.2.0
-- The CXX compiler identification is GNU 7.2.0
-- Check for working C compiler: /share/pkg/gcc/7.2.0/install/bin/gcc
-- Check for working C compiler: /share/pkg/gcc/7.2.0/install/bin/gcc -- 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: /share/pkg/gcc/7.2.0/install/bin/g++
-- Check for working CXX compiler: /share/pkg/gcc/7.2.0/install/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.57.0
-- Found the following Boost libraries:
--   filesystem
--   iostreams
--   log
--   system
--   thread
--   unit_test_framework
--   regex
--   log_setup
--   date_time
--   chrono
--   atomic
-- ** Boost Include: /share/pkg/boost/1.57.0/install/include
-- ** Boost Libraries: /share/pkg/boost/1.57.0/install/lib
-- ** Boost Link-Libs: /share/pkg/boost/1.57.0/install/lib/libboost_filesystem.so;/share/pkg/boost/1.57.0/install/lib/libboost_iostreams.so;/share/pkg/boost/1.57.0/install/lib/libboost_log.so;/share/pkg/boost/1.57.0/install/lib/libboost_system.so;/share/pkg/boost/1.57.0/install/lib/libboost_thread.so;/share/pkg/boost/1.57.0/install/lib/libboost_unit_test_framework.so;/share/pkg/boost/1.57.0/install/lib/libboost_regex.so;/share/pkg/boost/1.57.0/install/lib/libboost_log_setup.so;/share/pkg/boost/1.57.0/install/lib/libboost_date_time.so;/share/pkg/boost/1.57.0/install/lib/libboost_chrono.so;/share/pkg/boost/1.57.0/install/lib/libboost_atomic.so
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Found BAMTOOLS: /share/pkg/bamtools/2.4.0/install/bin/../lib/libbamtools.so
-- Found R: /share/pkg/r/3.4.2/install/lib64/R/lib/libR.so
-- Found R: /share/pkg/r/3.4.2/install/lib64/R
-- Configuring done
-- Generating done
-- Build files have been written to: /my/path/dropEst/dropEst

Any advice?

No ".reads.gz" file generated

I updated to the most recent version of dropEst package (0.8.0) and had successfully compiled it. When I am running the droptag with -s option, I get an extra ".params.gz" file, but not ".reads.gz" file. The documentation specifies I should use ".reads.gz" file for the -r option. Am I missing something?

Error: unable to parse out UMI

Can anyone tell me why I get this error when I run Dropest on a 10x aligned bam file? I have configured everything correctly, I assume.

problem with dropReport.Rsc

Dear developers,
once installed dropReport.Rsc I manged to have the report in html but I cannot when I use -t option and providing the tagged rds file.
I got the following error:
label: unnamed-chunk-9 (with options)
List of 2
$ fig.width : num 5
$ fig.height: num 3

|................................... | 54%
ordinary text without R code

|..................................... | 57%
label: unnamed-chunk-10
Quitting from lines 95-97 (report.Rmd)
Error in total.reads.per.cell[merge.targets] :
invalid subscript type 'list'
Calls: ... eval -> ScorePipelineCells -> PrepareLqCellsDataPipeline
In addition: Warning messages:
1: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
2: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
3: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
4: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
5: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
6: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
7: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
8: In bind_rows_(x, .id) :
binding character and factor vector, coercing into character vector
9: Removed 1 rows containing missing values (geom_bar).

Execution halted

Two compile errors - FIXED

Not really sure these are issues but might be useful for future reference.

[ 61%] Linking CXX executable TestTools
/usr/lib/R/lib/libR.so: undefined reference to `GOMP_parallel@GOMP_4.0'

Fixed this by editing line 7 of CMakeLists.txt to include '-fopenmp':

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -m64 -DBOOST_LOG_DYN_LINK -std=c++11 -Wno-attributes -Wno-deprecated -Wno-deprecated-declarations")

Also, when having previously installed the software GMAP/GSNAP it seems to add two files in /usr/local/include/ - except.h and assert.h which causes the below errors, until they are removed .

                 from /home/transcriptomics/software/dropEst/Tools/ReadParameters.cpp:1:
/usr/local/include/except.h:15:32: error: conflicting declaration ‘typedef struct Except_Frame_T* Except_Frame_T’
 typedef struct Except_Frame_T *Except_Frame_T;
                                ^
/usr/local/include/except.h:15:16: note: previous declaration as ‘struct Except_Frame_T’
 typedef struct Except_Frame_T *Except_Frame_T;
                ^
/usr/local/include/except.h:17:18: error: field ‘prev’ has incomplete type ‘Except_Frame_T’
   Except_Frame_T prev;
                  ^
/usr/local/include/except.h:16:8: note: definition of ‘struct Except_Frame_T’ is not complete until the closing brace
 struct Except_Frame_T {
        ^
CMakeFiles/DropTools.dir/build.make:62: recipe for target 'CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o' failed
make[2]: *** [CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o] Error 1
CMakeFiles/Makefile2:179: recipe for target 'CMakeFiles/DropTools.dir/all' failed
make[1]: *** [CMakeFiles/DropTools.dir/all] Error 2
Makefile:94: recipe for target 'all' failed
make: *** [all] Error 2
master@transcriptomics:/ho

and

/usr/local/include/assert.h:5:20: fatal error: except.h: No such file or directory
compilation terminated.
CMakeFiles/DropTools.dir/build.make:62: recipe for target 'CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o' failed
make[2]: *** [CMakeFiles/DropTools.dir/Tools/ReadParameters.cpp.o] Error 1
CMakeFiles/Makefile2:179: recipe for target 'CMakeFiles/DropTools.dir/all' failed
make[1]: *** [CMakeFiles/DropTools.dir/all] Error 2
Makefile:94: recipe for target 'all' failed
make: *** [all] Error 2

Cannot link to

When I try to install, I get the following errors that prevent installation in following steps. I want to know which libraries these packages are trying to link to so that I might specify the paths, but can't seem to figure out what the targets need. Any help would be appreciated.

WARNING: Target "DropTools" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "Estimation" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TestEstimation" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TestEstimationMergeProbs" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TestTagsSearch" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "TestTools" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "dropest" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "droptag" requests linking to directory "/home/abhaduri/packages/lib". Targets may link only to libraries. CMake is dropping the item.

cmake .. && make error

when I type “cmake .. && make” ,errors show below, help....

-- Boost version: 1.60.0
-- Found the following Boost libraries:
-- filesystem
-- iostreams
-- log
-- system
-- thread
-- unit_test_framework
-- regex
-- date_time
-- log_setup
-- chrono
-- atomic
-- ** Boost Include: /usr/local/include
-- ** Boost Libraries: /usr/local/lib
-- ** Boost Link-Libs: /usr/local/lib/libboost_filesystem.so;/usr/local/lib/libboost_iostreams.a;/usr/local/lib/libboost_log.so;/usr/local/lib/libboost_system.so;/usr/local/lib/libboost_thread.so;/usr/local/lib/libboost_unit_test_framework.so;/usr/local/lib/libboost_regex.so;/usr/local/lib/libboost_date_time.so;/usr/local/lib/libboost_log_setup.so;/usr/local/lib/libboost_chrono.so;/usr/local/lib/libboost_atomic.so
-- Could not find libR shared library.
CMake Error at /usr/local/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
Could NOT find R (missing: R_LIBRARIES)
Call Stack (most recent call first):
/usr/local/share/cmake-3.10/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
CMake/FindR.cmake:136 (find_package_handle_standard_args)
CMake/deps.cmake:34 (find_package)
CMakeLists.txt:18 (include)

-- Configuring incomplete, errors occurred!

No reads_per_umi_per_cell in cell.counts.rds after dropEst

I have successfully run dropEst (v0.8.3) on my .bam file generated by 10X cellranger (2.1.1)
the command is
dropest -f -w -u -V -G 20 -c /home/reprod/bin/dropEst/configs/10x.xml ./possorted_genome_bam.bam
Log file looks good with no serious problem.

dropest -f -w -u -V -G 20 -c /home/reprod/bin/dropEst/configs/10x.xml ./possorted_genome_bam.bam 
Version: 0.8.3.
Run: 07/18/2018 21:19:30.
No merge selected.

Start parsing of bams: 21:19:30.
ERROR: can't find chromosome, id: -1
./possorted_genome_bam.bam: 4673842 total reads; 26.6% intergenic; 68.2% touch exon; 0% touch intron; 0% touch not annotated regions; can't parse 0.0305316% reads; 348073 CBs read
Bams parsed: 21:20:23.

13075 CBs with more than 20 genes
top CBs:
1531	CAGCGACCATGTCCTC
1504	ACAGCTAGTAAATGTG
1494	GACGTTAAGCCAGGAT
1448	GTTCGGGAGGGTTTCT
1422	CACACCTCAGCATGAG
1417	GAGGTGAGTTTGGGCC
1376	ACACCAATCTCTTATG
1357	CTAATGGAGAAGGACA
1353	TCAGGTATCTGTCTCG

Start merge: 21:20:23.
Merge initialized: 21:20:23.
Merge finished: 21:20:23.
Start UMI merge: 21:20:23.
13075 cells processed. Merged 58 UMIs from 58 cells.
UMI merge finished: 21:20:24.
13075 cells are considered as real.

13075 CBs with more than 20 genes, which have UMIs of the requested type.
top CBs:
1531	CAGCGACCATGTCCTC
1504	ACAGCTAGTAAATGTG
1494	GACGTTAAGCCAGGAT
1448	GTTCGGGAGGGTTTCT
1422	CACACCTCAGCATGAG
1417	GAGGTGAGTTTGGGCC
1376	ACACCAATCTCTTATG
1357	CTAATGGAGAAGGACA
1353	TCAGGTATCTGTCTCG

Done: 21:20:25.

20783 genes
top genes:
ENSG00000122304	42526
ENSG00000175646	21533
ENSG00000065978	9621
ENSG00000106013	7076
ENSG00000167468	7074
ENSG00000010318	6500
ENSG00000163467	6138
ENSG00000167526	6100
ENSG00000170315	5772
ENSG00000198804	5054

Compiling diagnostic stats: 
Reads per chromosome per cell;
Fill exon results
Fill intron results
Fill intergenic results
Saturation info;
Mean reads per UMI;
Merge targets;
Completed.

Compiling raw count matrix: 21:20:29.
20783 genes, 13075 cells.
Done: 21:20:29.
Compiling filtered count matrix: 21:20:29.
20783 genes, 13075 cells.
Done: 21:20:30.

Writing R data to cell.counts.rds ...: 21:20:30.
Completed: 21:20:39.
Writing cell.counts.mtx ...
Completed.

Compiling intron/exon matrices: 21:20:40.
Exon
20783 genes, 13075 cells.
Intron
0 genes, 13075 cells.
Intron/exon spanning
0 genes, 13075 cells.
Done: 21:20:42.

Writing R data to cell.counts.matrices.rds ...: 21:20:42.
Completed: 21:20:43.
All done: 21:20:45.

However, command dropReport.Rsc ./cell.counts.rds ran with error:

Quitting from lines 118-122 (report.Rmd)
Error: 'ds.mincount' is not an exported object from 'namespace:preseqR'
In addition: Warning messages:
1: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
2: In bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
3: In bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
4: In bind_rows_(x, .id) : Unequal factor levels: coercing to character
5: In bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
6: In bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
7: In GetUmisDistributionOld(reads.per.umi.per.cb, smooth = smooth) :
  UMIs distribution is empty
8: Removed 2 rows containing missing values (geom_bar).
9: In PredictKDE(clf, bc.df.pca, bandwidth.mult = kde.bandwidth.mult) :
  Found 2 points with 0 density. Either it's outliers or you should increase bandwidth. Setting score for these points to 0.5.

Execution halted

Some results have been generated. One of them appears wrong.

So I guess it may be caused by the cell.counts.rds. It does not have reads_per_umi_per_cell.
This problem appeared in the older version #29 . And I tried to re-run dropEst but the cell.counts.rds but it had no change
Here is the fields in cell.counts.rds

d <- readRDS("./cell.counts.rds")
names(d)
 [1] "cm"                      "cm_raw"                  "reads_per_chr_per_cells" "mean_reads_per_umi"     
 [5] "saturation_info"         "merge_targets"           "aligned_reads_per_cell"  "aligned_umis_per_cell"  
 [9] "requested_umis_per_cb"   "requested_reads_per_cb"

DropEst does not accept cellbarcodes from 10x.

I have got cellbarcode whitelist from 10X Genomics. I tried to link it via configuration xml file and tried running dropEst, but it did not accept the input. Cell barcodes look like following.

AAACCTGAGAAACCAT
AAACCTGAGAAACCGC
AAACCTGAGAAACCTA
AAACCTGAGAAACGAG
AAACCTGAGAAACGCC
.
.
.

I got following warning.
WARNING: barcodes line has wrong format: 'AAACCTGAGAAACCAT'
WARNING: barcodes line has wrong format: 'AAACCTGAGAAACCGC'
WARNING: barcodes line has wrong format: 'AAACCTGAGAAACCTA'
WARNING: barcodes line has wrong format: 'AAACCTGAGAAACGAG'
WARNING: barcodes line has wrong format: 'AAACCTGAGAAACGCC'

I used configs/10x.xml file and changed my_fiile.txt>myfile</barcodes_file>.

Error during Scanning dependencies of target TestEstimation

I used cmake/2.8.10.2 (cmake3 had a bug), boost 1.6.0 during compilation.
However, compiling fails at 90% (TestEstimation step) with the error below. Any ideas what might be going on?

CMakeFiles/TestEstimation.dir/Tests/TestEstimation.cpp.o:

In function _ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEliEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_.constprop.507': TestEstimation.cpp:(.text+0x448): undefined reference to boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
...
collect2: error: ld returned 1 exit status
make[2]: *** [TestEstimation] Error 1
make[1]: *** [CMakeFiles/TestEstimation.dir/all] Error 2
make: *** [all] Error 2

Cannot run UMI errors correction using reads_per_umi_per_cell from dropEst

When running CorrectUmiSequenceErrors function, it occurs error

Estimating prior error probabilities...
Error in CorrectUmiSequenceErrorsBayesian(reads.per.umi.per.cb, adj.umi.num = adj.umi.num,  : 
  Information about quality is required for UMI correction

It seems that format of reads_per_umi_per_cell is different from the example data "reads_per_umi_per_cell" in umi-correction vignette.
I tried to modify the format but failed to make the function work.
What can i do excluding run dropEst with "-u" ?

can not install

I loaded all the modules and install R packeges.
module load boost/1.54.0
module load bamtools/2.4.1
module load cmake/3.9.6
module load gcc/6.3.0
module load zlib/1.2.5

Firstly:
$ cmake . && make
......
CMake Error at CMake/deps.cmake:3 (message):
DropEst requires gcc version 4.8 or later

However, my gcc version is gcc/6.3.0. So I removed CMake/deps.cmake line "message(FATAL_ERROR "DropEst requires gcc version 4.8 or later")"

Then:
$ cmake . && make
......
[ 1%] Building CXX object CMakeFiles/DropTools.dir/Tools/CollisionsAdjuster.cpp.o
cc1plus: error: unrecognized command line option "-std=c++11"
make[2]: *** [CMakeFiles/DropTools.dir/Tools/CollisionsAdjuster.cpp.o] Error 1
make[1]: *** [CMakeFiles/DropTools.dir/all] Error 2
make: *** [all] Error 2

Does anyone meet the same problem? Thanks.

Extract High Quality Cells

Hi,

I have run the pipeline and have gotten great data. However, I am a little but stuck trying to extract high quality cells from the filtered count matrix in R. I can see the cells qualified as high quality in dropreport, but cant seem to find cell rank in any of the rds files. Any advice on how to better extract high quality cells?

Best,
Dylan

Confusing error message

If you accidentally provide a ill-formatted configuration file (such as forgetting to specify the config and resulting in the first file being considered the config), you get a confusing error message:

input/sample.fq.tagged.1.tophat/accepted_hits.bam(1): expected <

An message like 'Error processing configuration file', would be must more useful.

make error

hi,
I had errors with running make command:

Firstly, cmake was ran as below.

$ cmake  -DCMAKE_INSTALL_PREFIX=~/local 
                -DCMAKE_C_COMPILER=~/local/bin/gcc 
                -DCMAKE_CXX_COMPILER=~/local/bin/g++
                -DBOOST_ROOT=~/local/include
                -DBOOST_LIBRARYDIR:PATH=~/src/boost_1_68_0/libs 
                -DR_EXECUTABLE=~/local/bin/R
                -DR_ROOT=~/local/bin/R
                -DR_LIB_DIRS=~/local/lib64/R/lib
                -DR_LIBRARIES=~/local/lib64/R/lib/libR.so
                -DBAMTOOLS_ROOT=~/local/include
                -DRINSIDE_INCLUDE_DIR=~/local/lib64/R/library/RInside/include
                -DRINSIDE_LIBRARY=~/local/lib64/R/library/RInside/lib/libRInside.a
                -DR_CORE_LIBRARY=~/local/lib64/R/library
                -DLIBR_CORE_LIBRARY=~/local/lib64/R/library
                -DR_INCLUDE_DIRS=~/local/lib64/R/include
                -DRCPP_INCLUDE_DIR=~/local/lib64/R/library/Rcpp/include
                -DRCPP_EIGEN_INCLUDE_DIR=~/local/lib64/R/library/RcppEigen/include
                -DR_MATRIX_PKG=~/local/lib64/R/library/Matrix ..

It completed without errors.

Then, I ran make command, and got below error.

[ 84%] Linking CXX executable TestTools
/usr/bin/ld: warning: libboost_date_time.so.1.68.0, needed by /lustre4/home/akimitsu-lab/local/bin/../lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../libboost_log.so, may conflict with libboost_date_time.so.5
/usr/bin/ld: warning: libboost_filesystem.so.1.68.0, needed by /lustre4/home/akimitsu-lab/local/bin/../lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../libboost_log.so, may conflict with libboost_filesystem.so.5
/usr/bin/ld: warning: libboost_system.so.1.68.0, needed by /lustre4/home/akimitsu-lab/local/bin/../lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../libboost_log.so, may conflict with libboost_system.so.5
/usr/bin/ld: warning: libboost_regex.so.1.68.0, needed by /lustre4/home/akimitsu-lab/local/bin/../lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../libboost_log.so, may conflict with libboost_regex.so.5
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEmiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_.constprop.548':
TestTools.cpp:(.text+0x1fe): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `TestTools::testEditDistance::test_method()':
TestTools.cpp:(.text+0xde6): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `TestTools::testReadParams::test_method()':
TestTools.cpp:(.text+0x2f40): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `TestTools::testRelativePaths::test_method()':
TestTools.cpp:(.text+0x3ce9): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
TestTools.cpp:(.text+0x3eb7): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text+0x46d0): more undefined references to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' follow
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `boost::unit_test::lazy_ostream_impl<boost::unit_test::lazy_ostream, boost::test_tools::tt_detail::print_helper_t<bool>, boost::test_tools::tt_detail::print_helper_t<bool> const&>::operator()(std::ostream&) const':
TestTools.cpp:(.text._ZNK5boost9unit_test17lazy_ostream_implINS0_12lazy_ostreamENS_10test_tools9tt_detail14print_helper_tIbEERKS6_EclERSo[_ZNK5boost9unit_test17lazy_ostream_implINS0_12lazy_ostreamENS_10test_tools9tt_detail14print_helper_tIbEERKS6_EclERSo]+0x29): undefined reference to `boost::test_tools::tt_detail::print_log_value<bool>::operator()(std::ostream&, bool)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `_ZN9TestTools14testReadParams11test_methodEv.cold.559':
TestTools.cpp:(.text.unlikely+0x63b): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `boost::unit_test::make_test_case(boost::function<void ()()> const&, boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long)':
TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x25): undefined reference to `_ZN5boost9unit_test9ut_detail24normalize_test_case_nameB5cxx11ENS0_13basic_cstringIKcEE'
TestTools.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x72): undefined reference to `boost::unit_test::test_case::test_case(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::function<void ()()> const&)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `_Z41__static_initialization_and_destruction_0ii.constprop.538':
TestTools.cpp:(.text.startup+0x233): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long, boost::unit_test::decorator::collector&)'
TestTools.cpp:(.text.startup+0x2ba): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x361): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x409): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x4b1): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
TestTools.cpp:(.text.startup+0x559): undefined reference to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text.startup+0x601): more undefined references to `boost::unit_test::ut_detail::auto_test_unit_registrar::auto_test_unit_registrar(boost::unit_test::test_case*, boost::unit_test::decorator::collector&, unsigned long)' follow
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char [5]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char const*, char const (&) [5], char const*)':
TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA5_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA5_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_]+0x120): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char [7]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char const*, char const (&) [7], char const*)':
TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA7_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA7_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_]+0x120): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, unsigned int, int>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned int const&, char const*, int const&, char const*)':
TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEjiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdEjiEEbT_RKNS_9unit_test12lazy_ostreamENS5_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSA_RKT1_SH_]+0x11a): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char [6]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char const*, char const (&) [6], char const*)':
TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA6_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA6_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_]+0x120): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o: In function `bool boost::test_tools::tt_detail::check_frwd<boost::test_tools::tt_detail::equal_impl_frwd, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, char [3]>(boost::test_tools::tt_detail::equal_impl_frwd, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char const*, char const (&) [3], char const*)':
TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA3_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEA3_cEEbT_RKNS_9unit_test12lazy_ostreamENSC_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSH_RKT1_SO_]+0x120): undefined reference to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)'
CMakeFiles/TestTools.dir/Tests/TestTools.cpp.o:TestTools.cpp:(.text._ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EEbT_RKNS_9unit_test12lazy_ostreamENSB_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSG_RKT1_SN_[_ZN5boost10test_tools9tt_detail10check_frwdINS1_15equal_impl_frwdENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_EEbT_RKNS_9unit_test12lazy_ostreamENSB_13basic_cstringIKcEEmNS1_10tool_levelENS1_10check_typeERKT0_PSG_RKT1_SN_]+0x121): more undefined references to `boost::test_tools::tt_detail::report_assertion(boost::test_tools::assertion_result const&, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring<char const>, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, unsigned long, ...)' follow
collect2: error: ld returned 1 exit status
make[2]: *** [TestTools] error 1
make[1]: *** [CMakeFiles/TestTools.dir/all] error 2
make: *** [all] error 2

anyone helps?
Thanks!

undefined reference error when installing dropEst

Hello, I keep gettting this error when I'm compiling dropEst. Has anyone seen this error before, thank you!
libDropTools.a(UtilFunctions.cpp.o): In function Tools::init_r()':
UtilFunctions.cpp:(.text+0x747): undefined reference toRInside::instancePtr()'
UtilFunctions.cpp:(.text+0x797): undefined reference to RInside::parseEvalQ(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
UtilFunctions.cpp:(.text+0x7e0): undefined reference toRInside::RInside(int, char const* const*, bool, bool, bool)'
collect2: error: ld returned 1 exit status
make[2]: *** [droptag] Error 1
make[1]: *** [CMakeFiles/droptag.dir/all] Error 2
make: *** [all] Error 2

Use two fastq files for 10x in dropTag

Hi, I am trying to apply your pipeline on my 10X Genomics data. When I run command for dropTaq. It didn't work for me. I don't have separate 3 files in my data as you explained in your pipeline. I am also attaching the files that I received from 10X.

I also tried to get help from dropTag but I received this error.
[sikh@login-0 dropEst]$ droptag -h
-bash: droptag: command not found

How I can fix this issue. Thanks in advance.

kharchenkolab / dropest Goto Github PK

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