illumina / isaac2 Goto Github PK
View Code? Open in Web Editor NEWAligner for sequencing data
License: Other
isaac2's People
Contributors
Stargazers
Watchers
isaac2's Issues
Error occurs when isaac-unpack-reference
Hi Come,
I was doing some testing trying to move around isaac reference files.
First I ran isaac-pack-reference -r /path/to/sorted-reference.xml and then I got packed-reference.tar.gz and a Temp directory which contains .16bpb.gz, a copy of original fasta, sorted-reference.xml and a .sentinel file.
Then how can I unpack the .tar.gz file to the target directory? I tried to run ./isaac-unpack-reference -i packed-reference.tar.gz but I got "../share/iSAAC-02.15.07.16/makefiles/reference/UnpackReferenceSubmake.mk:67: *** "Expected 1 annotation path, got: ". Stop.". Am I missing something here?
I didn't see an example in the manual or an input option to specify the output directory.
Thank you,
Ivan
make error
I am getting the similar error as (#1)
I am using Red Hat 4.4.5-6 version (Linux version 2.6.32-220.el6.x86_64)
I have already included #include <fcntl.h> in between lines 154 and 155 and still getting the error.
How could I fix the same
ERROR MESSAGE
[root@master ISAAC2]# make
-- install prefix: ../ISAAC2/
-- install exec prefix: ../ISAAC2/
-- install bin dir: bin
-- install lib dir: lib/iSAAC-02.15.10.21
-- install libexec dir: libexec/iSAAC-02.15.10.21
-- install data dir: share/iSAAC-02.15.10.21
-- Could NOT find Boost
-- Boost 1.59.0 not found. Boost will be built from the distribution...
Decompressing /illumina/Softwares/isaac2-master/src/../redist/boost_1_59_0.tar.bz2
Building Boost.Build engine with toolset gcc... tools/build/src/engine/bin.linuxx86_64/b2
Unicode/ICU support for Boost.Regex?... not found.
Backing up existing Boost.Build configuration in project-config.jam.4
Generating Boost.Build configuration in project-config.jam...
Bootstrapping is done. To build, run:
./b2
To adjust configuration, edit 'project-config.jam'.
Further information:
- Command line help:
./b2 --help - Getting started guide:
http://www.boost.org/more/getting_started/unix-variants.html - Boost.Build documentation:
http://www.boost.org/build/doc/html/index.html
Performing configuration checks
- 32-bit : no (cached)
- 64-bit : yes (cached)
- arm : no (cached)
- mips1 : no (cached)
- power : no (cached)
- sparc : no (cached)
- x86 : yes (cached)
- symlinks supported : yes (cached)
- zlib : yes (cached)
- has_icu builds : no (cached)
- lockfree boost::atomic_flag : yes (cached)
Component configuration:
- atomic : not building
- chrono : not building
- container : not building
- context : not building
- coroutine : not building
- coroutine2 : not building
- date_time : building
- exception : not building
- filesystem : building
- graph : not building
- graph_parallel : not building
- iostreams : building
- locale : not building
- log : not building
- math : not building
- mpi : not building
- program_options : building
- python : not building
- random : not building
- regex : building
- serialization : building
- signals : not building
- system : building
- test : not building
- thread : building
- timer : not building
- wave : not building
...patience...
...patience...
...found 24581 targets...
boost-1_59_0 installed successfully
-- Successfuly built boost 1.59.0 from the distribution package...
-- inttypes.h found as 1
-- malloc.h found as 1
-- memory.h found as 1
-- signal.h found as 1
-- stdint.h found as 1
-- stdlib.h found as 1
-- string.h found as 1
-- strings.h found as 1
-- time.h found as 1
-- sys/stat.h found as 1
-- unistd.h found as 1
-- No support for NUMA
-- Found ZLIB header: 1/zlib.h
-- Found ZLIB library: /usr/lib64/libz.so
-- gzip compression supported
-- Found RT header: 1/time.h
-- Found RT library: /usr/lib64/librt.so
-- adding librt dependency to support clock_gettime linking on legacy platforms
-- Found PTHREAD header: 1/pthread.h
-- Found PTHREAD library: /usr/lib64/libpthread.so
-- pthread supported
-- Boost version: 1.59.0
-- Found the following Boost libraries:
-- date_time
-- filesystem
-- iostreams
-- program_options
-- regex
-- serialization
-- system
-- thread
-- using compiler: gcc version 4.4.6
-- No ccache found
-- Adding the c++ library subdirectory: bgzf
-- Adding the c++ library subdirectory: common
-- Adding the c++ library subdirectory: oligo
-- Adding the c++ library subdirectory: io
-- Adding the c++ library subdirectory: rta
-- Adding the c++ library subdirectory: flowcell
-- Adding the c++ library subdirectory: demultiplexing
-- Adding the c++ library subdirectory: xml
-- Adding the c++ library subdirectory: reference
-- Adding the c++ library subdirectory: bam
-- Adding the c++ library subdirectory: options
-- Adding the c++ library subdirectory: statistics
-- Adding the c++ library subdirectory: alignment
-- Adding the c++ library subdirectory: build
-- Adding the c++ library subdirectory: package
-- Adding the c++ library subdirectory: reports
-- Adding the c++ library subdirectory: workflow
-- Adding the c++ program subdirectory: bin
-- Adding the c++ program subdirectory: libexec
-- Doxygen: /usr/bin/doxygen. Dot: DOXYGEN_DOT_EXECUTABLE-NOTFOUND.
-- Creating Doxygen config file: /illumina/Softwares/ISAAC2/c++/Doxyfile
-- Markdown: /usr/bin/markdown.
-- Configuring done
-- Generating done
-- Build files have been written to: /illumina/Softwares/ISAAC2
[ 0%] Built target iSAAC_OPT
Scanning dependencies of target isaac_bgzf
make[2]: Warning: File `/illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp' has modification time 2.3e+04 s in the future
[ 1%] Building CXX object c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/BgzfReader.cpp.o
In file included from /illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp:26,
from /illumina/Softwares/isaac2-master/src/c++/include/bgzf/BgzfReader.hh:29,
from /illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:25:
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:23:18: error: atomic: No such file or directory
In file included from /illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp:26,
from /illumina/Softwares/isaac2-master/src/c++/include/bgzf/BgzfReader.hh:29,
from /illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:25:
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:145: error: ‘atomic_int’ in namespace ‘std’ does not name a type
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh: In constructor ‘isaac::common::detail::CerrBlocker::CerrBlocker()’:
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:149: error: ‘cerrBlocked_’ was not declared in this scope
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh: In static member function ‘static bool isaac::common::detail::CerrBlocker::blocked()’:
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:158: error: ‘cerrBlocked_’ was not declared in this scope
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh: In destructor ‘isaac::common::detail::CerrBlocker::~CerrBlocker()’:
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:188: error: ‘cerrBlocked_’ was not declared in this scope
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:189: error: ‘cerrBlocked_’ was not declared in this scope
/illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp: In member function ‘void isaac::bgzf::ParallelBgzfReader::open(const boost::filesystem::path&)’:
/illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:153: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker_)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public_>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink_)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public_>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::basic_streambuf<CharT, Traits>) [with CharT = char, Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
/illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp: In member function ‘void isaac::bgzf::ParallelBgzfReader::readMoreDataParallel(unsigned int, std::istream&, char, size_t, size_t&)’:
/illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:217: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<CharT, Traits>) [with CharT = char, Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
/illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:238: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<CharT, Traits>) [with CharT = char, Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
/illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:243: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<_CharT, Traits>) [with _CharT = char, _Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
In file included from /illumina/Softwares/isaac2-master/src/c++/include/bgzf/BgzfReader.hh:30,
from /illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:25:
/illumina/Softwares/isaac2-master/src/c++/include/io/FileBufWithReopen.hh: In member function ‘typename std::basic_filebuf<T0, T1>::__filebuf_type* isaac::io::basic_FileBufWithReopen<_CharT, Traits>::reopen(const char, size_t, isaac::io::basic_FileBufWithReopen<_CharT, _Traits>::FadviseFlags) [with _CharT = char, _Traits = std::char_traits]’:
/illumina/Softwares/isaac2-master/src/c++/include/io/FileBufWithReopen.hh:77: instantiated from ‘typename std::basic_filebuf<T0, T1>::_filebuf_type isaac::io::basic_FileBufWithReopen<_CharT, Traits>::reopen(const char, isaac::io::basic_FileBufWithReopen<CharT, Traits>::FadviseFlags) [with CharT = char, Traits = std::char_traits]’
/illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:146: instantiated from here
/illumina/Softwares/isaac2-master/src/c++/include/io/FileBufWithReopen.hh:102: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<CharT, Traits>) [with CharT = char, Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
/illumina/Softwares/isaac2-master/src/c++/include/io/FileBufWithReopen.hh:109: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<CharT, Traits>) [with CharT = char, Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
/illumina/Softwares/isaac2-master/src/c++/include/io/FileBufWithReopen.hh:116: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<_CharT, Traits>) [with _CharT = char, Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
In file included from /illumina/Softwares/isaac2-master/src/c++/include/bgzf/BgzfReader.hh:29,
from /illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:25:
/illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp: In member function ‘void isaac::common::BasicThreadVector::cycle(isaac::common::BasicThreadVector::Executor, unsigned int) [with bool crashOnExceptions = false]’:
/illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp:214: instantiated from ‘void isaac::common::BasicThreadVector::execute(F, unsigned int) [with F = boost::_bi::bind_t<void, boost::mfi::mf5<void, isaac::bgzf::ParallelBgzfReader, unsigned int, std::istream&, char, long unsigned int, size_t&>, boost::_bi::list6boost::bi::value<isaac::bgzf::ParallelBgzfReader*, boost::arg<1>, boost::reference_wrapper<std::basic_istream<char, std::char_traits > >, boost::bi::value<char*>, boost::bi::value, boost::reference_wrapper > >, bool crashOnExceptions = false]’
/illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:304: instantiated from here
/illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp:252: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<CharT, Traits>) [with CharT = char, Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
/illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp: In member function ‘void isaac::common::BasicThreadVector::safeExecute(size_t, boost::unique_lockboost::mutex&) [with bool crashOnExceptions = false]’:
/illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp:336: instantiated from ‘void isaac::common::BasicThreadVector::threadFunc(size_t) [with bool crashOnExceptions = false]’
/illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp:168: instantiated from ‘isaac::common::BasicThreadVector::BasicThreadVector(size_t) [with bool crashOnExceptions = false]’
/illumina/Softwares/isaac2-master/src/c++/include/bgzf/BgzfReader.hh:148: instantiated from here
/illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp:285: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<CharT, Traits>) [with CharT = char, Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
In file included from /illumina/Softwares/isaac2-master/src/c++/include/bgzf/BgzfReader.hh:29,
from /illumina/Softwares/isaac2-master/src/c++/lib/bgzf/BgzfReader.cpp:25:
/illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp:289: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<CharT, Traits>) [with CharT = char, Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
/illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp:297: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<CharT, Traits>) [with CharT = char, Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
/illumina/Softwares/isaac2-master/src/c++/include/common/Threads.hpp:301: error: no match for ‘operator<<’ in ‘(((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((const boost::iostreams::null_sink&)((const boost::iostreams::null_sink)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stream<boost::iostreams::output, char, std::char_traits, std::allocator, boost::iostreams::public>(((std::basic_ostream<char, std::char_traits >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()’
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, Traits>& ()(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:117: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_ios<_CharT, Traits>& ()(std::basic_ios<_CharT, _Traits>&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:127: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(std::ios_base& ()(std::ios_base&)) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:165: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:169: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:173: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(bool) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:91: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:180: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(short unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:105: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:191: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:200: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:204: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long long unsigned int) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:209: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:213: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(float) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:221: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(long double) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/ostream:225: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, Traits>::operator<<(const void) [with _CharT = char, _Traits = std::char_traits]
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/ostream.tcc:119: note: std::basic_ostream<_CharT, _Traits>& std::basic_ostream<_CharT, _Traits>::operator<<(std::basic_streambuf<_CharT, Traits>) [with _CharT = char, _Traits = std::char_traits]
/illumina/Softwares/isaac2-master/src/c++/include/common/Debug.hh:121: note: std::ostream& isaac::common::detail::operator<<(std::ostream&, const isaac::common::detail::ThreadTimestamp&)
make[2]: *** [c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/BgzfReader.cpp.o] Error 1
make[1]: *** [c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/all] Error 2
make: *** [all] Error 2
Thanks
Shams
isaac-sort-reference: --jobs 1 results in 2400% CPU load?
Hi,
I just wanted to create a GRCh38 index for iSAAC (iSAAC-02.16.03.29).
isaac-sort-reference \
--genome-file genome.main_chr.fa \
--jobs 1 \
--output-directory iSAACIndex.k32.main_chr \
--seed-lengths 32
This produces a heavy cpu load. I ran two jobs on a 80-core machine with 1TB RAM. The CPU load was constantly raising over 80, up to insane 128 ... I killed my jobs as I don't want to overload the machine and to avoid that my sysadmin will kill me :-)
--jobs 1 should use just one CPU, shouldn't it? If not, how can I direct isaac-sort-reference to just use a specified number of cpu cores?
Did I miss something?
best,
Sven
Improper CIGARs
Hi there,
We've come across several improper CIGAR strings produced by isaac and have as a temporary measure addressed them in our variant caller. Could you take a look when you have the time please. Ticket with example data available here:
AstraZeneca-NGS/VarDictJava#37 (comment)
mm10 reference
Hi Come,
just for the sake of completeness I'd like to request mm10 as pre-built index in basespace.
In case I use mouse, I usually use mm10 as reference ..
thanks,
Sven
Can Isaac2 align fasta files?
Hi Come,
Can Isaac2 align not only fastq files but also fasta files? If it can, do I need to set the -f parameter?
Thanks,
Ivan
error building isaac2
Hi illumina,
I've started installing isaac2.
./configure is OK but when i type make i receive the following error:
In file included from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Threads.hpp:26,
from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/bgzf/BgzfReader.hh:29,
from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/lib/bgzf/BgzfReader.cpp:25:
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:23:18: error: atomic: No such file or direc
tory
In file included from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Threads.hpp:26,
from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/bgzf/BgzfReader.hh:29,
from /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/lib/bgzf/BgzfReader.cpp:25:
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:145: error: 'atomic_int' in namespace 'std'
does not name a type
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh: In constructor 'isaac::common::detail::Cer
rBlocker::CerrBlocker()':
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:149: error: 'cerrBlocked_' was not declared
in this scope
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh: In static member function 'static bool isa
ac::common::detail::CerrBlocker::blocked()':
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:158: error: 'cerrBlocked_' was not declared
in this scope
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh: In destructor 'isaac::common::detail::Cerr
Blocker::~CerrBlocker()':
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:188: error: 'cerrBlocked_' was not declared
in this scope
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/include/common/Debug.hh:189: error: 'cerrBlocked_' was not declared
in this scope
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/lib/bgzf/BgzfReader.cpp: In member function 'void isaac::bgzf::Para
llelBgzfReader::open(const boost::filesystem::path&)':
/ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/lib/bgzf/BgzfReader.cpp:145: error: no match for 'operator<<' in '(
((const isaac::common::detail::CerrLocker*)isaac_cerr_lock)->isaac::common::detail::CerrLocker::cerrBlocked() ? boost::iostreams::filtering_stream<bo
ost::iostreams::output, char, std::char_traits<char>, std::allocator<char>, boost::iostreams::public_>(((const boost::iostreams::null_sink&)((const b
oost::iostreams::null_sink*)(& boost::iostreams::null_sink()))), -0x00000000000000001l, -0x00000000000000001l, 0u) : boost::iostreams::filtering_stre
am<boost::iostreams::output, char, std::char_traits<char>, std::allocator<char>, boost::iostreams::public_>(((std::basic_ostream<char, std::char_trai
ts<char> >&)(& std::cerr)), -0x00000000000000001l, -0x00000000000000001l)) << isaac::common::detail::ThreadTimestamp()'
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream:108: note: candidates are: std::basic_ostream<_CharT, _Traits>& std::bas
ic_ostream<_CharT, _Traits>::operator<<(std::basic_ostream<_CharT, _Traits>& (*)(std::basic_ostream<_CharT, _Traits>&)) [with _CharT = char, _Traits
= std::char_traits<char>]
(...)
gcc version
]$ g++ -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.7 20120313 (Red Hat 4.4.7-16) (GCC)
$ uname -a
Linux airain71 2.6.32-573.1.1.el6.Bull.80.x86_64 #1 SMP Fri Jul 31 01:43:22 CEST 2015 x86_64 x86_64 x86_64 GNU/Linux
contigs.xml does not support seed length 32
Hi all,
I've indexed GRCh38
isaac-sort-reference -g GRCh38.fa -o path/GRCh38 -j 15
Then, when I try to align a pair of fastqs, I get the following error
isaac-align -r path/GRCh38/Temp/contigs.xml -b my/path/FASTQ -f fastq-gz -o OUT -m 15 -j 15 --seed-length 32
2016-05-24 12:05:50 [2b2ba31566a0] Discovered data read: ReadMetadata(1, 100 [1, 100], 0id, 0off,1frc)
2016-05-24 12:05:50 [2b2ba31566a0] Discovered data read: ReadMetadata(2, 100 [102, 201], 1id, 100off,102frc)
2016-05-24 12:05:50 [2b2ba31566a0] constructed extremity seed SeedMetadata(0, 32, 0, 0)
2016-05-24 12:05:50 [2b2ba31566a0] constructed extremity seed SeedMetadata(68, 32, 0, 1)
2016-05-24 12:05:50 [2b2ba31566a0] constructed SeedMetadata(32, 32, 0, 2)
2016-05-24 12:05:50 [2b2ba31566a0] constructed overlapping SeedMetadata(16, 32, 0, 3)
2016-05-24 12:05:50 [2b2ba31566a0] constructed extremity seed SeedMetadata(0, 32, 1, 4)
2016-05-24 12:05:50 [2b2ba31566a0] constructed extremity seed SeedMetadata(68, 32, 1, 5)
2016-05-24 12:05:50 [2b2ba31566a0] constructed SeedMetadata(32, 32, 1, 6)
2016-05-24 12:05:50 [2b2ba31566a0] constructed overlapping SeedMetadata(16, 32, 1, 7)
2016-05-24 12:05:50 [2b2ba31566a0] Generated 'none' barcode: BarcodeMetadata(7,1,default,none,(0), 4294967295)
2016-05-24 12:05:50 [2b2ba31566a0] align: Setting memory limit to 16106127360 bytes.
Error: 2016-May-24 12:05:51: Invalid argument: /ccc/work/cont007/fg0019/lindenbp/packages/isaac/isaac2-iSAAC-02.16.03.09/src/c++/lib/workflow/AlignWorkflow.cpp(232): Throw in function static isaac::reference::SortedReferenceMetadataList isaac::workflow::AlignWorkflow::loadSortedReferenceXml(unsigned int, const ReferenceMetadataList&)
Dynamic exception type: boost::exception_detail::clone_impl<isaac::common::PreConditionException>
std::exception::what: Sorted reference /ccc/work/cont007/fg0019/lindenbp/packages/GRCh38/Temp/contigs.xml does not support seed length 32
: Sorted reference /ccc/work/cont007/fg0019/lindenbp/packages/GRCh38/Temp/contigs.xml does not support seed length 32
Makefile:6: recipe for target '/ccc/scratch/cont007/fg0019/lindenbp/20160524.ISAAC2/B00GG8X/BAM/B00GG8X.bam' failed
make: *** [/ccc/scratch/cont007/fg0019/lindenbp/20160524.ISAAC2/B00GG8X/BAM/B00GG8X.bam] Error 1
I tried to remove '--seed-length 32', to change the seed to 16, 32,64, I'm always getting the same kind of error.
$ head /ccc/work/cont007/fg0019/lindenbp/packages/GRCh38/Temp/contigs.xml
<?xml version="1.0"?>
<SortedReference>
<FormatVersion>6</FormatVersion>
<SoftwareVersion>iSAAC-02.16.03.09</SoftwareVersion>
<Contigs>
<Contig Position="0">
<Index>0</Index>
<KaryotypeIndex>0</KaryotypeIndex>
<Name>chr1</Name>
<Sequence>
(...)
In the simple example I've found, there is no 'seed'. where am i wrong ? thanks
Compile error
I am getting the following error when running the make command after running configure:
$ make
Scanning dependencies of target iSAAC_OPT
[ 0%] Built target iSAAC_OPT
Scanning dependencies of target isaac_bgzf
[ 1%] Building CXX object c++/lib/bgzf/CMakeFiles/isaac_bgzf.dir/BgzfReader.cpp.o
Linking CXX static library libisaac_bgzf.a
[ 1%] Built target isaac_bgzf
Scanning dependencies of target isaac_common
[ 2%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/Debug.cpp.o
[ 3%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/Exceptions.cpp.o
[ 4%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/FileSystem.cpp.o
[ 4%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/MD5Sum.cpp.o
[ 5%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/Process.cpp.o
[ 6%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/Program.cpp.o
[ 7%] Building CXX object c++/lib/common/CMakeFiles/isaac_common.dir/SystemCompatibility.cpp.o
/nas02/apps/isaac2-15.07.14/src/isaac2/src/c++/lib/common/SystemCompatibility.cpp: In function 'int isaac::common::linuxFallocate(int, std::size_t, std::size_t)':
/nas02/apps/isaac2-15.07.14/src/isaac2/src/c++/lib/common/SystemCompatibility.cpp:162:58: error: 'fallocate' was not declared in this scope
return fallocate(fd, FALLOC_FL_KEEP_SIZE, offset, len);
^
/nas02/apps/isaac2-15.07.14/src/isaac2/src/c++/lib/common/SystemCompatibility.cpp:163:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
make[2]: *** [c++/lib/common/CMakeFiles/isaac_common.dir/SystemCompatibility.cpp.o] Error 1
make[1]: *** [c++/lib/common/CMakeFiles/isaac_common.dir/all] Error 2
make: *** [all] Error 2
isaac-sort-reference: --jobs N is ignored
Hi,
isaac-sort-reference --genome-file $(pwd)/genome.fa --jobs 1 --seed-lengths 32 --output-directory isaac2_hg19 uses all cpu cores on the machine running.
On our 48 core server the load is constantly beyond 52, in the very beginning it raises to >128!
My sysadmin is going to kill me :-)
It also seems that the seed length is ignored, as the terminal output reports things like ./../libexec/iSAAC-02.15.07.16/sortReference -r Temp/contigs.xml --mask-width 0 --mask 0 --seed-length 16 [...]
best,
Sven
Aligned reads only have 25 bases.
Hi Come,
Sorry to bother you so often. Without changing any default parameter values, aligned reads in output bam always only have 25 bases. Is it because the parameter --base-quality-cutoff? I changed it to different value but the number of bases in aligned reads still didn't change.
Please advise how I can keep the original read bases without trimming them in bam file.
Thank you so much!
Ivan
isaac-sort-preferenc: space in file path
Dear Isaac2 developers:
When I use isaac-sort-preference to create a preference to a fasta file, if the file path following -g has a space in it, isaac-sort-preference will throw an error saying "./isaac-sort-reference: line 104: /file/path/before/space/: No such file or directory ERROR: File not found: '/file/path/after/space'".
Error still occurs even though I add "" before space or quote the whole path.
I am not sure if the same problem happens to other isaac binaries which I haven't tested yet.
Really appreciate your help!
Ivan
Compile on Mac
Hi,
Does isaac2 compile on MAC or Windows? It compiles perfect on my Linux machine.
I noticed it uses some Linux lib files and I tried to comment them and then compile on MAC with specifying gcc-4.9, but some linking issues occurred. Any manuals or suggestions on compiling on MAC and Windows?
Thank you so much,
Ivan
Base quality scores [0-63] supported only.
Hi,
I was aligning a fastq file and I got the error "Invalid quality 72 found in ....... Base quality scores [0-63] supported only."
Just realized that the fastq file quality score is Phred+64 encoded. Does Isaac only support Phred+33?
Can I set some parameters to make it work with Phred+64?
Thanks in advance.
Ivan
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.