gmarcais / quorum Goto Github PK

In file included from src/error_correct_reads.cc:31:
./include/gzip_stream.hpp:6:10: fatal error: 'ext/stdio_filebuf.h' file not found
#include <ext/stdio_filebuf.h>
         ^
1 error generated.

/bin/bash ./libtool  --tag=CXX   --mode=link g++ -Wall -g -O2 -std=c++0x -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/quorum-1.1.1-7 -DHAVE_NUMERIC_LIMITS128  -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o quorum_error_correct_reads src/error_correct_reads.o src/err_log.o -ljellyfish-2.0 -lpthread  -lrt -lpthread 
libtool: link: g++ -Wall -g -O2 -std=c++0x -Werror -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/quorum-1.1.1-7 -DHAVE_NUMERIC_LIMITS128 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o quorum_error_correct_reads src/error_correct_reads.o src/err_log.o  /usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so -lrt -lpthread
In member function '__ct ',
    inlined from '__ct_base .constprop' at ./include/jflib/multiplexed_io.hpp:82:18:
./include/jflib/pool.hpp:36:26: error: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Werror=alloc-size-larger-than=]
   36 |       size_(size), elts_(new T[size]), B2A(size, elts_), A2B(size, elts_)
      |                          ^
/usr/include/c++/12/new: In member function '__ct_base .constprop':
/usr/include/c++/12/new:128:26: note: in a call to allocation function 'operator new []' declared here
  128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
lto1: all warnings being treated as errors
make[3]: *** [/tmp/ccDYJbhe.mk:5: /tmp/cclUyevp.ltrans1.ltrans.o] Error 1
make[3]: *** Waiting for unfinished jobs....
lto-wrapper: fatal error: make returned 2 exit status
compilation terminated.
/usr/bin/ld: error: lto-wrapper failed
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:897: quorum_error_correct_reads] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:707: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 returned exit code 2
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

$ quorum -t 104 -s 2.5T -k 31 myfile.fastq
Invalid size '2.5T'. It must be a number, maybe followed by a suffix (like k, M, G for thousand, million and billion).
$

$ quorum -t 104 -s 2500G -k 31 myfile.fastq
terminate called after throwing an instance of 'jellyfish::large_hash::array_base<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, jellyfish::large_hash::array<jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>, unsigned long, atomic::gcc, allocators::mmap> >::ErrorAllocation'
  what():  Failed to allocate 9000000000000 bytes of memory
Creating the mer database failed. Most likely the size passed to the -s switch is too small. at /apps/gentoo/usr/bin/quorum line 143.
$

(gdb) bt full
#0  0x00002aaaab776124 in raise () from /apps/gentoo/lib64/libc.so.6
No symbol table info available.
#1  0x00002aaaab77758a in abort () from /apps/gentoo/lib64/libc.so.6
No symbol table info available.
#2  0x00002aaaab1e2ecd in __gnu_cxx::__verbose_terminate_handler() () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-5.4.0-r3/work/gcc-5.4.0/libstdc++-v3/libsupc++/vterminate.cc:95
No locals.
#3  0x00002aaaab1e0d06 in __cxxabiv1::__terminate(void (*)()) () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-5.4.0-r3/work/gcc-5.4.0/libstdc++-v3/libsupc++/eh_terminate.cc:47
No locals.
#4  0x00002aaaab1e0d51 in std::terminate() () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-5.4.0-r3/work/gcc-5.4.0/libstdc++-v3/libsupc++/eh_terminate.cc:57
No locals.
#5  0x00002aaaab1e0f68 in __cxa_throw () at /apps/gentoo/var/tmp/portage/sys-devel/gcc-5.4.0-r3/work/gcc-5.4.0/libstdc++-v3/libsupc++/eh_throw.cc:87
No locals.
#6  0x0000000000406a7b in main () at /apps/gentoo/usr/include/jellyfish/large_hash_array.hpp:180
        args = {size_arg = 2500000000000, size_given = true, mer_arg = 31, mer_given = true, bits_arg = 7, bits_given = true, min_qual_value_arg = 38, min_qual_value_given = true, min_qual_char_arg = {<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >> = {static npos = 
    18446744073709551615, _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, _M_p = 0x616c98 ""}, _M_string_length = 0, {_M_local_buf = '\000' <repeats 15 times>, _M_allocated_capacity = 0}}, <No data fields>}, min_qual_char_given = false, 
          threads_arg = 104, threads_given = true, output_arg = 0x7fffffffd6ec "quorum_corrected_mer_database.jf", output_given = true, reprobe_arg = 126, reprobe_given = false, reads_arg = {<std::_Vector_base<char const*, std::allocator<char const*> >> = {
              _M_impl = {<std::allocator<char const*>> = {<__gnu_cxx::new_allocator<char const*>> = {<No data fields>}, <No data fields>}, _M_start = 0x628fa0, _M_finish = 0x628fa8, _M_end_of_storage = 0x628fa8}}, <No data fields>}}
        std::__ioinit = {static _S_refcount = 10, static _S_synced_with_stdio = true}
        jellyfish::mer_dna_ns::mer_base_static<unsigned long, 0>::k_ = 31
(gdb)