gatb / bcalm Goto Github PK

When bcalm has been statically linked with the -static flag at the link step it repeatably segfaults. This appears to happen during or just after the "Iterating DSK partitions" step. It should be reproducible with a very small test dataset.

implement that, someday

I just tried to compile bcalm today (as part of bwise) and I get this error message:
-- The C compiler identification is GNU 4.9.2
-- The CXX compiler identification is GNU 4.9.2
-- Check for working C compiler: /opt/rh/devtoolset-3/root/usr/bin/cc
-- Check for working C compiler: /opt/rh/devtoolset-3/root/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /opt/rh/devtoolset-3/root/usr/bin/c++
-- Check for working CXX compiler: /opt/rh/devtoolset-3/root/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- gatb-core is here '/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core'
-- CppUnit: found headers (in CPPUNIT_INCLUDE_DIR-NOTFOUND) but not the static library (CPPUNIT_INCLUDE_DIR-NOTFOUND/../lib/libcppunit.a)
-- CppUnit NOT FOUND
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of __uint128
-- Check size of __uint128 - failed
-- Check size of __uint128_t
-- Check size of __uint128_t - done
-- SSE 4.2 detected
-- Options: -std=c++11 -O3 -DNDEBUG -Wall -Wno-unused-function -Wno-format -Wno-unknown-pragmas -Wno-invalid-offsetof
-- OPTIMIZED KMER SIZES INTERVALS ARE 32 64 128 256 512 1024 <-- max supported kmer size without recompilation
-- SOVERSION: 10.2.1
-- SOVERSION_TOOLS: 10.0.4
-- SOVERSION_CXX: 13.0.0
-- SOVERSION_F: 10.0.4
-- SOVERSION_HL: 10.1.1
-- SOVERSION_HL_CXX: 11.1.0
-- SOVERSION_HL_F: 10.0.3
-- Check for STD namespace
-- Check for STD namespace - found
-- Looking for ceil in m;
-- Looking for ceil in m; - found
-- Looking for dlopen in dl;m
-- Looking for dlopen in dl;m - found
-- Looking for WSAStartup in ws2_32;m;dl
-- Looking for WSAStartup in ws2_32;m;dl - not found
-- Looking for gethostbyname in wsock32;m;dl
-- Looking for gethostbyname in wsock32;m;dl - not found
-- Looking for gethostname in ucb;m;dl
-- Looking for gethostname in ucb;m;dl - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Performing Other Test STDC_HEADERS - Success
-- Looking for include file sys/resource.h
-- Looking for include file sys/resource.h - found
-- Looking for include files sys/resource.h, sys/time.h
-- Looking for include files sys/resource.h, sys/time.h - found
-- Looking for 3 include files sys/resource.h, ..., unistd.h
-- Looking for 3 include files sys/resource.h, ..., unistd.h - found
-- Looking for 4 include files sys/resource.h, ..., sys/ioctl.h
-- Looking for 4 include files sys/resource.h, ..., sys/ioctl.h - found
-- Looking for 5 include files sys/resource.h, ..., sys/stat.h
-- Looking for 5 include files sys/resource.h, ..., sys/stat.h - found
-- Looking for 6 include files sys/resource.h, ..., sys/socket.h
-- Looking for 6 include files sys/resource.h, ..., sys/socket.h - found
-- Looking for 7 include files sys/resource.h, ..., sys/types.h
-- Looking for 7 include files sys/resource.h, ..., sys/types.h - found
-- Looking for 8 include files sys/resource.h, ..., stddef.h
-- Looking for 8 include files sys/resource.h, ..., stddef.h - found
-- Looking for 9 include files sys/resource.h, ..., setjmp.h
-- Looking for 9 include files sys/resource.h, ..., setjmp.h - found
-- Looking for 10 include files sys/resource.h, ..., features.h
-- Looking for 10 include files sys/resource.h, ..., features.h - found
-- Looking for 11 include files sys/resource.h, ..., dirent.h
-- Looking for 11 include files sys/resource.h, ..., dirent.h - found
-- Looking for 12 include files sys/resource.h, ..., stdint.h
-- Looking for 12 include files sys/resource.h, ..., stdint.h - found
-- Looking for C++ include stdint.h
-- Looking for C++ include stdint.h - found
-- Looking for 13 include files sys/resource.h, ..., mach/mach_time.h
-- Looking for 13 include files sys/resource.h, ..., mach/mach_time.h - not found
-- Looking for 13 include files sys/resource.h, ..., io.h
-- Looking for 13 include files sys/resource.h, ..., io.h - not found
-- Looking for 13 include files sys/resource.h, ..., winsock2.h
-- Looking for 13 include files sys/resource.h, ..., winsock2.h - not found
-- Looking for 13 include files sys/resource.h, ..., sys/timeb.h
-- Looking for 13 include files sys/resource.h, ..., sys/timeb.h - found
-- Looking for 14 include files sys/resource.h, ..., globus/common.h
-- Looking for 14 include files sys/resource.h, ..., globus/common.h - not found
-- Looking for 14 include files sys/resource.h, ..., pdb.h
-- Looking for 14 include files sys/resource.h, ..., pdb.h - not found
-- Looking for 14 include files sys/resource.h, ..., pthread.h
-- Looking for 14 include files sys/resource.h, ..., pthread.h - found
-- Looking for 15 include files sys/resource.h, ..., srbclient.h
-- Looking for 15 include files sys/resource.h, ..., srbclient.h - not found
-- Looking for 15 include files sys/resource.h, ..., string.h
-- Looking for 15 include files sys/resource.h, ..., string.h - found
-- Looking for 16 include files sys/resource.h, ..., strings.h
-- Looking for 16 include files sys/resource.h, ..., strings.h - found
-- Looking for 17 include files sys/resource.h, ..., stdlib.h
-- Looking for 17 include files sys/resource.h, ..., stdlib.h - found
-- Looking for 18 include files sys/resource.h, ..., memory.h
-- Looking for 18 include files sys/resource.h, ..., memory.h - found
-- Looking for 19 include files sys/resource.h, ..., dlfcn.h
-- Looking for 19 include files sys/resource.h, ..., dlfcn.h - found
-- Looking for 20 include files sys/resource.h, ..., inttypes.h
-- Looking for 20 include files sys/resource.h, ..., inttypes.h - found
-- Looking for 21 include files sys/resource.h, ..., netinet/in.h
-- Looking for 21 include files sys/resource.h, ..., netinet/in.h - found
-- Performing TEST_LFS_WORKS... yes
-- Performing Other Test HAVE_OFF64_T - Success
-- Looking for lseek64
-- Looking for lseek64 - found
-- Looking for fseeko64
-- Looking for fseeko64 - found
-- Looking for ftello64
-- Looking for ftello64 - found
-- Looking for ftruncate64
-- Looking for ftruncate64 - found
-- Looking for fseeko
-- Looking for fseeko - found
-- Looking for ftello
-- Looking for ftello - found
-- Performing Other Test HAVE_STAT64_STRUCT - Success
-- Looking for fstat64
-- Looking for fstat64 - found
-- Looking for stat64
-- Looking for stat64 - found
-- Check size of char
-- Check size of char - done
-- Check size of short
-- Check size of short - done
-- Check size of int
-- Check size of int - done
-- Check size of unsigned
-- Check size of unsigned - done
-- Check size of long
-- Check size of long - done
-- Check size of long long
-- Check size of long long - done
-- Check size of __int64
-- Check size of __int64 - failed
-- Check size of float
-- Check size of float - done
-- Check size of double
-- Check size of double - done
-- Check size of long double
-- Check size of long double - done
-- Check size of int8_t
-- Check size of int8_t - done
-- Check size of uint8_t
-- Check size of uint8_t - done
-- Check size of int_least8_t
-- Check size of int_least8_t - done
-- Check size of uint_least8_t
-- Check size of uint_least8_t - done
-- Check size of int_fast8_t
-- Check size of int_fast8_t - done
-- Check size of uint_fast8_t
-- Check size of uint_fast8_t - done
-- Check size of int16_t
-- Check size of int16_t - done
-- Check size of uint16_t
-- Check size of uint16_t - done
-- Check size of int_least16_t
-- Check size of int_least16_t - done
-- Check size of uint_least16_t
-- Check size of uint_least16_t - done
-- Check size of int_fast16_t
-- Check size of int_fast16_t - done
-- Check size of uint_fast16_t
-- Check size of uint_fast16_t - done
-- Check size of int32_t
-- Check size of int32_t - done
-- Check size of uint32_t
-- Check size of uint32_t - done
-- Check size of int_least32_t
-- Check size of int_least32_t - done
-- Check size of uint_least32_t
-- Check size of uint_least32_t - done
-- Check size of int_fast32_t
-- Check size of int_fast32_t - done
-- Check size of uint_fast32_t
-- Check size of uint_fast32_t - done
-- Check size of int64_t
-- Check size of int64_t - done
-- Check size of uint64_t
-- Check size of uint64_t - done
-- Check size of int_least64_t
-- Check size of int_least64_t - done
-- Check size of uint_least64_t
-- Check size of uint_least64_t - done
-- Check size of int_fast64_t
-- Check size of int_fast64_t - done
-- Check size of uint_fast64_t
-- Check size of uint_fast64_t - done
-- Check size of size_t
-- Check size of size_t - done
-- Check size of ssize_t
-- Check size of ssize_t - done
-- Check size of ptrdiff_t
-- Check size of ptrdiff_t - done
-- Check size of off_t
-- Check size of off_t - done
-- Check size of off64_t
-- Check size of off64_t - done
-- Looking for 22 include files sys/resource.h, ..., stdbool.h
-- Looking for 22 include files sys/resource.h, ..., stdbool.h - found
-- Check size of _Bool
-- Check size of _Bool - done
-- Performing Other Test DEV_T_IS_SCALAR - Success
-- Looking for CLOCK_MONOTONIC
-- Looking for CLOCK_MONOTONIC - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Performing Other Test HAVE_TM_GMTOFF - Success
-- Performing Other Test HAVE___TM_GMTOFF - Failed
-- Performing Other Test HAVE_STRUCT_TIMEZONE - Success
-- Performing Other Test GETTIMEOFDAY_GIVES_TZ - Success
-- Performing Other Test TIME_WITH_SYS_TIME - Success
-- Performing Other Test HAVE_TM_ZONE - Failed
-- Performing Other Test HAVE_STRUCT_TM_TM_ZONE - Failed
-- Performing Other Test HAVE_TIMEZONE - Success
-- Performing Other Test HAVE_STAT_ST_BLOCKS - Success
-- Looking for ioctl
-- Looking for ioctl - found
-- Performing Other Test HAVE_STRUCT_VIDEOCONFIG - Failed
-- Performing Other Test HAVE_STRUCT_TEXT_INFO - Failed
-- Looking for _getvideoconfig
-- Looking for _getvideoconfig - not found
-- Looking for gettextinfo
-- Looking for gettextinfo - not found
-- Looking for scrsize
-- Looking for scrsize - not found
-- Looking for GetConsoleScreenBufferInfo
-- Looking for GetConsoleScreenBufferInfo - not found
-- Looking for TIOCGWINSZ
-- Looking for TIOCGWINSZ - found
-- Looking for TIOCGETD
-- Looking for TIOCGETD - found
-- Looking for getpwuid
-- Looking for getpwuid - found
-- Looking for alarm
-- Looking for alarm - found
-- Looking for fork
-- Looking for fork - found
-- Looking for frexpf
-- Looking for frexpf - found
-- Looking for frexpl
-- Looking for frexpl - found
-- Looking for gethostname
-- Looking for gethostname - found
-- Looking for getrusage
-- Looking for getrusage - found
-- Looking for lstat
-- Looking for lstat - found
-- Looking for rand_r
-- Looking for rand_r - found
-- Looking for random
-- Looking for random - found
-- Looking for setsysinfo
-- Looking for setsysinfo - not found
-- Looking for signal
-- Looking for signal - found
-- Looking for longjmp
-- Looking for longjmp - found
-- Looking for setjmp
-- Looking for setjmp - found
-- Looking for siglongjmp
-- Looking for siglongjmp - found
-- Looking for sigsetjmp
-- Looking for sigsetjmp - not found
-- Looking for sigprocmask
-- Looking for sigprocmask - found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for srandom
-- Looking for srandom - found
-- Looking for strdup
-- Looking for strdup - found
-- Looking for symlink
-- Looking for symlink - found
-- Looking for system
-- Looking for system - found
-- Looking for tmpfile
-- Looking for tmpfile - found
-- Looking for asprintf
-- Looking for asprintf - found
-- Looking for vasprintf
-- Looking for vasprintf - found
-- Looking for waitpid
-- Looking for waitpid - found
-- Looking for vsnprintf
-- Looking for vsnprintf - found
-- Performing Other Test VSNPRINTF_WORKS - Success
-- Looking for sigsetjmp
-- Looking for sigsetjmp - found
-- Performing Other Test HAVE_ATTRIBUTE - Success
-- Performing Other Test HAVE_C99_FUNC - Success
-- Performing Other Test HAVE_FUNCTION - Success
-- Performing Other Test HAVE_C99_DESIGNATED_INITIALIZER - Success
-- Performing Other Test SYSTEM_SCOPE_THREADS - Success
-- Performing Other Test HAVE_SOCKLEN_T - Success
-- Performing Other Test CXX_HAVE_OFFSETOF - Success
-- Performing CXX Test OLD_HEADER_FILENAME - Failed
-- Performing CXX Test H5_NO_NAMESPACE - Failed
-- Performing CXX Test H5_NO_STD - Failed
-- Performing CXX Test BOOL_NOTDEFINED - Failed
-- Performing CXX Test NO_STATIC_CAST - Failed
-- Performing Other Test HAVE_INLINE - Success
-- Performing Other Test HAVE___INLINE - Success
-- Performing Other Test HAVE___INLINE - Success
-- Checking for appropriate format for 64 bit long:
-- Checking for appropriate format for 64 bit long: found "l"
-- Looking for difftime
-- Looking for difftime - found
-- Looking for clock_gettime
-- Looking for clock_gettime - not found
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for clock_gettime in posix4
-- Looking for clock_gettime in posix4 - not found
-- Performing Other Test HAVE_DIRECT - Success
-- Checking IF your system converts long double to (unsigned) long values with special algorithm... no
-- Checking IF your system can convert (unsigned) long to long double values with special algorithm... no
-- Checking IF correctly converting long double to (unsigned) long long values... yes
-- Checking IF correctly converting (unsigned) long long to long double values... yes
-- Checking IF alignment restrictions are strictly enforced... yes
CMake Warning at gatb-core/gatb-core/thirdparty/hdf5/CMakeFilters.cmake:36 (find_package):
Could not find a package configuration file provided by "ZLIB" with any of
the following names:

ZLIBConfig.cmake
zlib-config.cmake

Add the installation prefix of "ZLIB" to CMAKE_PREFIX_PATH or set
"ZLIB_DIR" to a directory containing one of the above files. If "ZLIB"
provides a separate development package or SDK, be sure it has been
installed.
Call Stack (most recent call first):
gatb-core/gatb-core/thirdparty/hdf5/CMakeLists.txt:574 (include)

-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Filter ZLIB is ON
DYNAMIC BINARIES for gatb-h5dump
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Configuring done
-- Generating done
-- Build files have been written to: /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build
Scanning dependencies of target thirdparty_copy
Scanning dependencies of target hdf5_postbuild
Scanning dependencies of target H5make_libsettings
Scanning dependencies of target H5detect
[ 0%] Building C object ext/gatb-core/thirdparty/hdf5/src/CMakeFiles/H5make_libsettings.dir/H5make_libsettings.c.o
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[ 0%] Built target thirdparty_copy
[ 1%] Linking C executable ../../../bin/H5make_libsettings
[ 1%] Built target H5make_libsettings
[ 1%] Linking C executable ../../../bin/H5detect
[ 1%] Built target H5detect
[ 1%] Generating ../H5lib_settings.c
[ 1%] Generating ../H5Tinit.c
Scanning dependencies of target hdf5
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[ 74%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp.o
[ 74%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/BloomAlgorithm.cpp.o
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[ 75%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/DebloomAlgorithm.cpp.o
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[ 76%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/LinearCounter.cpp.o
[ 76%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/MPHFAlgorithm.cpp.o
[ 76%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/Model.cpp.o
[ 76%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/ModelData.cpp.o
[ 77%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartiInfo.cpp.o
[ 77%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/PartitionsCommand.cpp.o
[ 77%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/RepartitionAlgorithm.cpp.o
[ 78%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/kmer/impl/SortingCountAlgorithm.cpp.o
[ 78%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemCommon.cpp.o
[ 78%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemLinux.cpp.o
[ 78%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/FileSystemMacos.cpp.o
[ 79%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/System.cpp.o
[ 79%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/SystemInfoCommon.cpp.o
[ 79%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadLinux.cpp.o
[ 79%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/system/impl/ThreadMacos.cpp.o
[ 80%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/collections/impl/Bloom.cpp.o
[ 80%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/DnaCoder.cpp.o
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/system/impl/ThreadLinux.cpp: In constructor 'gatb::core::system::impl::ThreadLinux::ThreadLinux(void* ()(void), void*)':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:51:7: warning: variable 'ret' set but not used [-Wunused-but-set-variable]
int ret = pthread_attr_init ( &tattr ) ;
^
[ 80%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/HeaderCoder.cpp.o
[ 80%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/Leon.cpp.o
[ 81%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/compression/RangeCoder.cpp.o
[ 81%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Command.cpp.o
[ 81%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/designpattern/impl/Observer.cpp.o
[ 81%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Algorithm.cpp.o
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[ 82%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/OptionsParser.cpp.o
[ 82%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Progress.cpp.o
[ 82%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Property.cpp.o
[ 83%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/TimeInfo.cpp.o
[ 83%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tokenizer.cpp.o
[ 83%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/Tool.cpp.o
[ 83%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/misc/impl/XmlReader.cpp.o
[ 84%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/Storage.cpp.o
[ 84%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/tools/storage/impl/StorageTools.cpp.o
[ 84%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_1024.cpp.o
[ 84%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_128.cpp.o
[ 85%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_256.cpp.o
[ 85%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_32.cpp.o
[ 85%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_512.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_1024.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 1024ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_1024.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_128.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_256.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 256ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_256.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_32.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_512.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 512ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_512.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
[ 85%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization1.cpp.in_64.cpp.o
[ 86%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_1024.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.cpp:20:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization1.cpp.in_64.cpp:13:17: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
[ 86%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_128.cpp.o
[ 86%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_256.cpp.o
[ 86%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_32.cpp.o
[ 87%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_512.cpp.o
[ 87%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization10.cpp.in_64.cpp.o
[ 87%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 1024ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 1024ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 1024ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 1024ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 1024ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<1024ul>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_1024.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
[ 87%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_128.cpp.o
[ 88%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_256.cpp.o
[ 88%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_32.cpp.o
[ 88%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_512.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 128ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 128ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_256.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 256ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_256.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 128ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 128ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<128ul>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_128.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 256ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 256ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_256.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
[ 89%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization2.cpp.in_64.cpp.o
[ 89%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_1024.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 32ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 32ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_256.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 256ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 256ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<256ul>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_256.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_512.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 512ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_512.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 512ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 512ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_512.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
[ 89%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_128.cpp.o
[ 89%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_256.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 32ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 32ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_32.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_512.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 512ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 512ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<512ul>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_512.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:563:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:587:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:599:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:708:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:715:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountFileNames.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp: In instantiation of 'std::vector<std::basic_string > gatb::core::kmer::impl::TempCountFileMerger::mergeFiles(std::vector<std::basic_string >) [with long unsigned int span = 64ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:556:22: required from 'void gatb::core::kmer::impl::PartitionsByHashCommand::execute() [with long unsigned int span = 64ul]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:14:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:239:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(filenames.size() > _reduceTarget)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:257:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:335:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< _tmpCountIterators.size(); ii++)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:342:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int ii=0; ii< currentFiles.size(); ii++)
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:25:0,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp:33,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:24,
from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:5:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp: In instantiation of 'void gatb::core::kmer::impl::Kmer::SuperKmer::save(gatb::core::tools::storage::impl::CacheSuperKmerBinFiles&, int) [with long unsigned int span = 64ul]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:956:5: required from 'void gatb::core::kmer::impl::FillPartitions<span, true>::processSuperkmer(gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer&) [with long unsigned int span = 64ul; gatb::core::kmer::impl::FillPartitions<span, true>::SuperKmer = gatb::core::kmer::impl::Kmer<64ul>::SuperKmer]'
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization2.cpp.in_64.cpp:18:7: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1442:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while(uid<4 && skid < superKmerLen)
^
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/Model.hpp:1460:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(skid >= superKmerLen) break;
^
[ 90%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_32.cpp.o
[ 90%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_512.cpp.o
[ 90%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization3.cpp.in_64.cpp.o
[ 90%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_1024.cpp.o
[ 91%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_128.cpp.o
[ 91%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_256.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_1024.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 1024ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_1024.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 128ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_128.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
[ 91%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_32.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_256.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 256ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_256.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 32ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_32.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
[ 91%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_512.cpp.o
[ 92%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization4.cpp.in_64.cpp.o
[ 92%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_1024.cpp.o
[ 92%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_512.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 512ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_512.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
In file included from /cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:6:0:
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp: In instantiation of 'void gatb::core::kmer::impl::MPHFAlgorithm<span, Abundance_t, NodeState_t>::check() [with long unsigned int span = 64ul; Abundance_t = unsigned char; NodeState_t = unsigned char]':
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/build/ext/gatb-core/src/gatb/template/TemplateSpecialization4.cpp.in_64.cpp:13:16: required from here
/cluster/scratch4/ucbtlot/20171221BWISE/BWISE/src/bcalm/gatb-core/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:310:21: warning: unused variable 'abundance' [-Wunused-variable]
Abundance_t abundance = (_abundanceMap)[count.value];
^
[ 92%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_256.cpp.o
[ 93%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_32.cpp.o
[ 93%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_512.cpp.o
[ 93%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_64.cpp.o
[ 93%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_1024.cpp.o
[ 94%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_128.cpp.o
[ 94%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_256.cpp.o
[ 94%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_32.cpp.o
[ 95%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_512.cpp.o
[ 95%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization6.cpp.in_64.cpp.o
[ 95%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_1024.cpp.o
[ 95%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization7.cpp.in_128.cpp.o
c++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See http://bugzilla.redhat.com/bugzilla for instructions.
make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_1024.cpp.o] Error 4
make[2]: *** Waiting for unfinished jobs....
c++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See http://bugzilla.redhat.com/bugzilla for instructions.
make[2]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/template/TemplateSpecialization5.cpp.in_128.cpp.o] Error 4
make[1]: *** [ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/all] Error 2
make: *** [all] Error 2

Problem is in ographBin:

DSK created 32 partitions
[Iterating DSK partitions                ]  0    %   elapsed:   0 min 0  sec   remaining:   0 min 0  sec
Partition 0 has 1518 kmers
Iterated 1518 kmers, among them 350 has leftmin!=rightmin
==18709== Thread 5:
==18709== Conditional jump or move depends on uninitialised value(s)
==18709==    at 0xF7790C: graph4::debruijn() (ographBin.cpp:81)
==18709==    by 0xF7CFA9: bcalm_1::execute()::{lambda(int)#6}::operator()(int) const (bcalm_1.cpp:484)
==18709==    by 0xF84A88: void std::_Bind<bcalm_1::execute()::{lambda(int)#6} (std::_Placeholder<1>)>::__call<void, int&&, 0ul>(std::tuple<int&&>&&, std::_Index_tuple<0ul>) (functional:1264)
==18709==    by 0xF84A33: void std::_Bind<bcalm_1::execute()::{lambda(int)#6} (std::_Placeholder<1>)>::operator()<int, void>(int&&) (functional:1323)
==18709==    by 0xF849E4: std::enable_if<((!std::is_member_pointer<std::_Bind<bcalm_1::execute()::{lambda(int)#6} (std::_Placeholder<1>)> >::value)&&(!std::is_function<std::is_member_pointer>::value))&&(!std::is_member_pointer<std::_Bind<bcalm_1::execute()::{lambda(int)#6} (std::_Placeholder<1>)> ><std::remove_pointer<std::is_member_pointer>::type>::value), std::result_of<std::is_member_pointer& (int&&)>::type>::type std::__invoke<std::_Bind<bcalm_1::execute()::{lambda(int)#6} (std::_Placeholder<1>)>, int>(std::result_of, int&&) (functional:202)
==18709==    by 0xF8498F: std::result_of<bcalm_1::execute()::{lambda(int)#6} (&(int&&))(std::_Placeholder<1>)>::type std::reference_wrapper<std::_Bind<bcalm_1::execute()::{lambda(int)#6} (std::_Placeholder<1>)> >::operator()<int>(int&&) const (functional:435)
==18709==    by 0xF848BF: void std::_Bind_simple<std::reference_wrapper<std::_Bind<bcalm_1::execute()::{lambda(int)#6} (std::_Placeholder<1>)> > (int)>::_M_invoke<0ul>(std::_Index_tuple<0ul>) (functional:1700)
==18709==    by 0xF846C3: std::_Bind_simple<std::reference_wrapper<std::_Bind<bcalm_1::execute()::{lambda(int)#6} (std::_Placeholder<1>)> > (int)>::operator()() (functional:1688)
==18709==    by 0xF84548: std::_Function_handler<void (), std::reference_wrapper<std::_Bind_simple<std::reference_wrapper<std::_Bind<bcalm_1::execute()::{lambda(int)#6} (std::_Placeholder<1>)> > (int)> > >::_M_invoke(std::_Any_data const&) (functional:2069)
==18709==    by 0xFA6780: std::function<void ()>::operator()() const (functional:2439)
==18709==    by 0xFA5A07: std::__future_base::_Task_setter<std::unique_ptr<std::__future_base::_Result<void>, std::__future_base::_Result_base::_Deleter>, void>::operator()() (future:1264)
==18709==    by 0xFA4EAD: std::_Function_handler<std::unique_ptr<std::__future_base::_Result_base, std::__future_base::_Result_base::_Deleter> (), std::__future_base::_Task_setter<std::unique_ptr<std::__future_base::_Result<void>, std::__future_base::_Result_base::_Deleter>, void> >::_M_invoke(std::_Any_data const&) (functional:2025)

This is an enhancement request to add to the bcalm output a list of abundance counts for each kmer in the unitig. This should preserve the equivalent counts in DSK.

at Antoine's request

Hi guys,

As the title suggests, I think a really nice feature would be an -abundance-max parameter that would easily allow us to exclude kmers with counts above this threshold.

Right now in order to do this I have to run Jellyfish count and then dump specifying -U [int] and then running BCALM with the same kmer size on the dumped fasta. It works but it's a pain in the ass and would be nice if BCALM could directly filter out high-abundance kmers.

Cheers!

Hello,

BCalm is a great program and we use it in several projects. However, its major limitation in practice is that it can't be installed from Bioconda.

Would it be possible to create a BCalm Bioconda recipe, please? I strongly believe that this single thing could bring many additional citations to your paper.

Thanks.

Hi,

I am trying to compile bcalm on my Surface Pro. I am using cygwin64 and gcc 5.4. I got a bunch of warnings while running cmake and running the Make command resulted in errors. All the errors were about some functions (stderror_r(..) and fseeko(..)) not being declared in scope. I am also attaching the outputs of cmake and make. Could you please help me out?

Thanks in advance,
Nithin

output-of-cmake.txt
output-of-make.txt

I'd like to optimize the -abundance parameter, and to that end it would be nice to separate the dsk stage from the bcalm stage so that the -abundance parameter can be optimized without having to rerun the k-mer counting stage.

Hi, I have a set of k-mers (with k=20) from which I want the compacted unitigs. I was going to make a fasta file out of them, with one k-mer per sequence, as I am okay with the abundance information being lost. But the problem is that, bcalm2 does not work with k-mer size of multiples of 4. Do you know any workaround in this case?

I saw in the discussion in issue #30 that bcalm2 can take as input a custom HDF5 file that contains counted k-mers. Can I use the hdf5 file generated by DSK as an input to bcalm2? I get error when I try that.

I am trying to install bcalm2 on my Macbook. I am facing issues while compiling the code. More specifically while running the make command. I am using gcc 5.4. These are the steps that I took to build bcalm2 -

1. Cloning the repo
2. mkdir build
3. cd build
4. cmake -D CMAKE_C_COMPILER=/usr/local/bin/gcc-5 -D CMAKE_CXX_COMPILER=/usr/local/bin/g++-5 ..
5. make -j 8

I have attached the error that pops up during the make command and then stops the script.
I tried to pass the compiler version during the make command as well (make -j 8 CC=/usr/local/bin/gcc-5 CXX=/usr/local/bin/g++-5) but it gave the same error.

Can you guide me if I am doing something wrong or missing something? Also if you need any other information, let me know.

When ZLIB is not installed on your system, CMake promises it will compile without ZLIB support:

-- Could NOT find ZLIB (missing: ZLIB_DIR)
-- Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR)
-- zlib not found, compiling without zlib support

yet...

[ 70%] Building CXX object ext/gatb-core/src/CMakeFiles/gatbcore-static.dir/gatb/bank/impl/Bank.cpp.o
In file included from bcalm/gatb-core/gatb-core/src/gatb/bank/impl/Bank.cpp:22:0:
bcalm/gatb-core/gatb-core/src/gatb/bank/impl/BankFasta.hpp:30:10: fatal error: zlib.h: No such file or directory
#include <zlib.h>

Probably some missing #ifndef?

Thanks,

Jan.

I was trying to run BCALM on the (zipped)
test_genome.zip
file attached. My command was

bcalm -in "filename" -kmer-size 21 -abundance-min 1

BCALM threw an exception. After a while, I decided to insert a dummy line starting with > at the beginning of the file and again ran BCALM on it and it worked fine.

Is it mandatory for the input files to BCALM to start with '>'?

Hi,
as stated in the object of this issue, bcalm outputs some wrong links in the FASTA headers when running with multiple threads.
For example, when running with 4 threads bcalm outputs the following 3 unitigs (this is a subset of the whole FASTA file):

>17218 LN:i:39 KC:i:855 KM:f:95.0 L:-:2543:+ L:-:28347:+ L:+:23183:- L:+:31763:- 
AGGAGCGAGCGATTGTAACTTGGTGTTATCCAGACTGGC
>2543 LN:i:31 KC:i:5 KM:f:5.0 L:+:37145:+ 
AGGCATACTTCCAAATGCCCCCGTCTCGAAG
>2544 LN:i:33 KC:i:281 KM:f:93.7 L:-:17218:+ L:+:2542:- L:+:29893:+ 
GATAACACCAAGTTACAATCGCTCGCTCCTCTA

As you can see, unitig 17218 reports an incorrect link with unitig 2543 with orientation -+ and the dual link is not in the header of unitig 2543.

The link should be 17218(-) -> 2544(+) and you can find it in the header of unitig 2544.

If I run the tool with only one thread, the unitigs change IDs and the links are correct (the ID mapping are 17218 -> 17435, 2543 -> 13814, 2544 -> 1213)

>17435 LN:i:39 KC:i:855 KM:f:95.0 L:-:1213:+ L:-:28181:+ L:+:19629:- L:+:28584:+ 
AGGAGCGAGCGATTGTAACTTGGTGTTATCCAGACTGGC
>13814 LN:i:31 KC:i:5 KM:f:5.0 L:+:37228:- 
AGGCATACTTCCAAATGCCCCCGTCTCGAAG
>1213 LN:i:33 KC:i:281 KM:f:93.7 L:-:17435:+ L:+:1212:- L:+:29855:+ 
GATAACACCAAGTTACAATCGCTCGCTCCTCTA

In this case both links are correctly reported as 17345(-) -> 1213(+) and 1213(-) -> 17345(+).

I found this behavior only when running with multiple threads but I'm not sure this never happens with a single thread.

I obtained the previous results with -kmer-size 31 -min-abundance 5 , I can share the input and output files if you want to take a look at them or reproduce this behavior.

Hello everyone,

I used BCALM recently to build the compacted de Bruijn graph of a set of reads (k=31) and I think some unitigs in the output are not compacted correctly (maybe you can correct me on this):

>49858 LN:i:122 KC:i:3673 KM:f:34.0  L:-:28131:- L:-:103021:-  L:+:110899:- 
CTGCACCAGGCAAGCGGCGGCGACGGCGAACAGCACCAGCAGTGCGGCGACCAGCAGCCGGCGCCAGGGCGGCGCGGCCTGTGCGCCATGGCCGTGATCGTGATCGTGATCGTGATCGTGAT

>21262 LN:i:36 KC:i:603 KM:f:100.5  L:-:21262:-  L:+:21262:+ 
TCGTGATCGTGATCGTGATCGTGATCGTGATCGTGA

>110899 LN:i:99 KC:i:2130 KM:f:27.0  L:-:53854:+ L:-:69039:+  L:+:49858:- 
CAATCCGCACCATGAGGAGAGCGCTCTTGAGCCTCGGTCACTCCCACTCGCACAGCCACCACGAGCATCATCACGATCACGATCACGATCACGATCACG

Here, unitig 21262 is reported as an isolated self-loop. However, the 31-mer at the end of unitig 49858 (forward strand) overlaps (as stated) the 31-mer starting at position 0 of unitig 110899 (reverse strand) BUT it also overlaps the 31-mer starting at position 1 of unitig 21262 (forward strand). Therefore, unitig 21262 should not be an isolated self-loop, right?

>119880 LN:i:33 KC:i:343 KM:f:49.0  L:-:45472:+ L:-:125102:+  
ATGCACAAGGGCGCCCGCGGGCGCCCTTGTGCC

Here, I think that unitig 119880 contains one character too much at the end (forward strand) and should be decomposed into two unitigs: [1] ATGCACAAGGGCGCCCGCGGGCGCCCTTGTGC and [2] GCACAAGGGCGCCCGCGGGCGCCCTTGTGCC. The reason is that [2] (forward strand) has one incoming edge from [1] (forward strand) AND one incoming edge from its own reverse-complement [2] (reverse strand). Similarly, [1] (forward strand) has one out-going edge to [2] (forward strand) and one out-going edge to its own reverse-complement [1] (reverse strand).

For these examples, I used BCALM 2, git commit 1d179b9 (is the -version argument supposed to output something?) with the arguments -nb-cores 1 -kmer-size 31. I have let the minimum abundance to its default (2). The read file used has the accession number ERX397266 (https://www.ncbi.nlm.nih.gov/sra/ERR430991/).

Thank you for your help.

Best, Guillaume

Dear authors,
I tried to build bcalm on CentOS 5 in order to package it for Bioconda. Unfortunately, I get an error that I can't easily solve (see here). Please apologize for the logging around the true build output. This comes from our CI system.

Best,
Johannes

The latest release is now a little over a year old. Are you planning on a new release soon?

In the description of how bi-directed graphs are implemented in bcalm2, it would be nice to add another example to the "Bi-directed de Bruijn graph section." Currently, the example there is a tricky one with self loops, and it would help to add a simpler more straightforward one as well. This example would carry through also to the Walk section

bcalm 2>&1 | grep version
       -version  (0 arg) :    version

% bcalm -version

I assume it is because

bcalm | head -n1
BCALM 2, git commit c8ac602 

in spacegraphcats, we are consuming the output of your excellent tool and doing (or attempting to do) Clever Graph Things with it. (thank you for bcalm!) however, we are running into a problem that in some cases there are nodes u, v where node u has an edge to v but node v does not have an edge to u.

more specifically, we see a number of examples like the following two headers in the unitigs output:

>206849 LN:i:41 KC:i:96 km:f:8.7  L:-:55026:- L:-:69342:-  L:+:103808:- L:+:203510:-
...
>69342 LN:i:134 KC:i:2260 km:f:21.7  L:+:69614:- L:+:155497:-  L:-:61581:+ L:-:167785:+
...

which show that 69342 is in the edge list of 206849, but 206849 is not in the edge list of 69342.

We have code to detect this here,

spacegraphcats/spacegraphcats@dc9a9cc

and I am happy to provide full execution instructions should you wish (should be: checkout that branch; pip install -r requirements.txt; make twofoo.fq.gz; conf/run twofoo build)

your thoughts appreciated!

output from latest bcalm master is here: https://osf.io/zgx3r/ (generated with bcalm built from commit c41f70f on my mac os x laptop)

input files are generated from the rules here,

briefly

curl -o akker-reads.abundtrim.gz -L https://osf.io/dk7nb/download
curl -L 'https://osf.io/7az9p/?action=download' > shew-reads.abundtrim.gz
gunzip -c shew-reads.abundtrim.gz akker-reads.abundtrim.gz | gzip -9c > twofoo.fq.gz

and then the command line execution is:

bcalm -in bcalm.twofoo.k31.inputlist.txt -out twofoo/bcalm.twofoo.k31 -kmer-size 31 -abundance-min 1

bug noted by Antoine. Apparently a significant number of compactions aren't made by bcalm since the new version 2.1.
(the result is correct but not complete in terms of compacting all possible paths in the graph, some remain splitted)

bcalm -version
BCALM 2, git commit 8137cc2
Using gatb-core version 1.4.1

was hoping for 2.2.1 as i git git clone recursive --tag 2.2.1 etc

• faster glue by writing minimizers and canonical kmers in the FASTA header of seqs to glue
• a separate thread is responsible for all disk writes (by continuously checking buffers)

on only one cluster (Paris-Sud), that error occurs right at the beginning of k-mer counting. Then it crashes with
EXCEPTION: Unable to load Repartitor (minimRepart), possibly due to bad format.

A temporary fix is to use -storage-type file, but a more robust fix should be sought some day.

I am running the tool with two pair-end fastq.gz files (High Coverage Human Genome from the 1000Genome project -- SRR1291070_1 (26G) and SRR1291070_2 (24G)).
Every run is producing a resulting unitig file with different size.

The output-log ends with a series of "Couldn't flush" (log file attached).

The available disk space after .h5 file (64G) is produced is about 42G. Is it sufficient or could low disk space be the root of this problem?
bcalm_result.txt

In #34, I reported that in not-very-reproducible circumstances on my HPC, when I compiled bcalm from source, it produced bad cDBG files. I ended up automating the heck out of the check and being unable to reproduce it so I gave up. But I cleverly never removed the validation code from the spacegraphcats application :)

Fast forward to today, and I found the same problem as in #34 when I installed bcalm using bioconda! Hopefully this time it will be more reproducible. I reproduce the bug on both my HPC and Amazon's Linux box, which kind of makes sense because bioconda provides a binary install so I would hope that it would fail the same way on both :).

To reproduce using spacegraphcats

this is running on Amazon Linux 2 AMI (HVM), SSD Volume Type - ami-01bbe152bf19d0289, region us-west-2. I created a t2-large with 20 GB of disk space, logged in as ec2-user, and then ran the following commands (some require answering interactive prompts, sorry):

# install C compiler
sudo yum groupinstall "Development Tools"

# install conda
curl -L -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh 
source ~/.bashrc
. /home/ec2-user/miniconda3/etc/profile.d/conda.sh

# add bioconda
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

# create a conda environment called 'sgc' with python 3.6 and baclm installed.
conda create -n sgc python==3.6 bcalm

Now, activate and try running the spacegraphcats example:

conda activate sgc

# install prereqs for spacegraphcats
pip install Cython
pip install https://github.com/dib-lab/pybbhash/archive/spacegraphcats.zip
pip install https://github.com/dib-lab/khmer/archive/master.zip
pip install git+https://github.com/dib-lab/sourmash@master#egg=sourmash

# install spacegraphcats
pip install spacegraphcats

# grab example repo
git clone https://github.com/spacegraphcats/spacegraphcats-twofoo-example.git
cd spacegraphcats-twofoo-example/

# run example workflow
snakemake

this fails for me after a few minutes of running with:

/home/ec2-user/miniconda3/envs/sgc/bin/python -m spacegraphcats.cdbg.bcalm_to_gxt  -k 31 twofoo/bcalm.twofoo.k31.unitigs.fa twofoo_k31_r1/cdbg.gxt twofoo_k31_r1/contigs.fa.gz
reading unitigs from twofoo/bcalm.twofoo.k31.unitigs.fa
...read 206855 unitigs
577 -> 181159, but not 181159 -> 577
576 -> 81582, but not 81582 -> 576
4675 -> 101520, but not 101520 -> 4675
4675 -> 104265, but not 104265 -> 4675
...
204785 -> 12508, but not 12508 -> 204785
Traceback (most recent call last):
  File "/home/ec2-user/miniconda3/envs/sgc/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/ec2-user/miniconda3/envs/sgc/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/ec2-user/miniconda3/envs/sgc/lib/python3.6/site-packages/spacegraphcats/cdbg/bcalm_to_gxt.py", line 375, in <module>
    main(sys.argv[1:])
  File "/home/ec2-user/miniconda3/envs/sgc/lib/python3.6/site-packages/spacegraphcats/cdbg/bcalm_to_gxt.py", line 257, in main
    neighbors, sequences, mean_abunds, sizes = read_bcalm(unitigs, debug, k)
  File "/home/ec2-user/miniconda3/envs/sgc/lib/python3.6/site-packages/spacegraphcats/cdbg/bcalm_to_gxt.py", line 214, in read_bcalm
    assert not fail
AssertionError
[Sun Dec 23 20:23:27 2018]
Error in rule bcalm_catlas_input:
...

Here's what I have installed for bcalm:

% conda list | grep bcalm
bcalm                     2.2.0                hd28b015_3    bioconda

cc @natir viz #32.

Hello,

I am running bcalm as part of the spacegraph cats pipeline in collaboration with @taylorreiter. The command I am running is: bcalm -in INFILES -out OUTFILE -kmer-size 31 -abundance-min 1

I got an interesting error today that ended with:

UF MPHF constructed (4803 MB)                   01:52:39     memory [current, maxRSS]: [19184, 88111] MB 
cannot create a union-find data structure, too many elements. This should in fact not even happen. Please contact a BCALM developer

So, I am contacting you.

You can see the full error here: bcalm.MS-all-SRF-5-20.00.k31.unitigs.fa.log.txt

Any insight into what this error might indicate?

Thank you!

Hello,

I tried to use BCalm on this small_example.zip with k=41 and it did not work (for k=31, it works perfectly though). The BCalm step, itself, worked correctly and it was invoked as ./bcalm -in rf -k 41 -abundance 2 . The BGlue step, however, gave an error message and it was invoked as ./bglue -in unitigs.h5 -k 41:

Gluing partition 127 (size: 0 MB)               18:50:33     memory [current, maxRSS]: [   7,    0] MB
bglue(78546,0x700000081000) malloc: *** mach_vm_map(size=6072894397144846336) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Gluing partition 128 (size: 0 MB)               18:50:33     memory [current, maxRSS]: [   7,    0] MB

Several other similar malloc errors succeeded this one. Weirdly enough, for k=31, it works perfectly. Am I doing something wrong or is this indeed a bug?

Here some segfault when using bcalm on a reference genome with small k

[Iterating DSK partitions ] 25 % elapsed: 0 min 6 sec remaining: 0 min 17 secwtf? traveller kmer = AAGGGCATACTAGGTTA, min_minimizer=64801 max_minimizer=1048575, repart(min_minimizer)=3, repart(max_minimizer)=2
Segmentation fault (core dumped)

Hi,
I tried to run the example run-tiny.sh and it rises a segmentation fault.
I tried with a bigger input fasta file but with no better result.
It works only if I use -kmer-size 17, and no other size is working.

Thank you.

Some initial kmer are not present in the unitigs

The tool aborted with a segmentation fault. Ran on the high coverage dataset "SRR1298980_1.fastq.gz" (paired end with SRR1298980_2.fastq.gz) from 1000genomes project. Following are the details -

Command:
./bcalm -in SRR1298980 -kmer-size 41 -abundance-min 4

Back trace (using gdb):
#0 0x0000000000881db5 in gatb::core::tools::dp::IDispatcher::IteratorCommand<gatb::core::bank::Sequence, void gatb::core::debruijn::impl::bglue<64ul>(gatb::core::tools::storage::impl::Storage*, std::__cxx11::basic_string<char, std::char_traits, std::allocator >, int, int, bool)::{lambda(gatb::core::bank::Sequence const&)#1}>::execute() ()
#1 0x0000000000792d35 in gatb::core::tools::dp::impl::Dispatcher::mainloop(void*) ()
#2 0x00007ffff7bc16ba in start_thread (arg=0x7fffd2639700) at pthread_create.c:333
#3 0x00007ffff6c3841d in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:109

Output (from a previous run on the same file with the same parameters using nohup):
output.txt
attached

Many thanks & best wishes,
Ritu

For packaging.

output copy.txt
I get the above exception when running BCALM on the set of all 50-mers of the ecoli genome (given in FASTQ format).

Bcalm 2.2.1 fails to build with clang on macOS 10.15.

In file included from /tmp/bcalm-20200120-5545-zrb02j/build/ext/gatb-core/src/gatb/template/TemplateSpecialization5.cpp.in_128.cpp:5:
1373
/tmp/bcalm-20200120-5545-zrb02j/gatb-core/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:155:58: error: 'predecessors' following the 'template' keyword does not refer to a template
1374
        GraphVector<Node> predecessors = graph->template predecessors (node);
1375
                                                         ^
1376

See https://github.com/brewsci/homebrew-bio/pull/870/checks?check_run_id=399734948#step:3:1373
and brewsci/homebrew-bio#870

When we use bcalm on multiple read files like this:

../bcalm/build/bcalm -in file1,file2

we get
...
Nb bglue threads: 8
unitigs graph destructor called
EXCEPTION: Unable to open bank 'file2.unitigs.fa.glue'

But the files file1,file2.unitigs.fa.glue etc .. exist

This is not an issue but just a question: what would be the optimal settings for fast generation of unitigs? I expect running on a SSD or even better a ram drive should help. What about any of the options? Increasing -max-memory to reduce disk use seems to be a no-brainer, what else could help?

Given that minia uses bcalm I guess it makes sense to use use bcalm directly for this purpose or could there be any advantage in using minia for fast generation of unitigs?

Per #37, I (and others in my group) are finding that bcalm 2.2.1 in bioconda continues to produce an incorrect cDBG. To reproduce, use the same procedure and you should see the same complaint in the output.

Here is what conda reports as far as what is installed.

(sgc) ctbrown@farm:~/spacegraphcats-twofoo-example$ conda list | grep -i bcalm
bcalm                     2.2.1                hdbcaa40_1    bioconda

cc @natir @rchikhi

Let me know if there's anything I can do!

When using very large k value like 1000 or 10,000.
A segfault occur during the DSK pass
...
[DSK: Pass 1/1, Step 1: partitioning ] 49.5 % elapsed: 3 min 53 sec remaining: 3 min 57 sec cpu: 100.7 % mem: [DSK: Pass 1/1, Step 1: partitioning ] 49.5 % elapsed: 3 min 53 sec remaining: 3 min 57 sec cpu: 100.7 % mem: [DSK: Pass 1/1, Step 1: partitioning ] 49.5 % elapsed: 3 min 53 sec remaining: 3 min 57 sec cpu: 100.7 % mem: [DSK: Pass 1/1, Step 2: counting kmers ] 49.5 % elapsed: 3 min 57 sec remaining: 4 min 2 sec cpu: 100.7 % mem: [58640, 66692, 66726] MB zsh: segmentation fault bcalm -in contigs1.fa -kmer-size 1000 -abundance-min 1

Hello,

I have issues with installing bcalm. I managed to get it to work (with some warnings) for the most part, but at the 'make -j 8' step it only loads up to 98% before throwing an error:
c++: internal compiler error: Killed (program cc1plus)

I have no idea how to deal with c++. Help would be much appreciated!

Hi,

I am puzzled by the result of BCALM in one of my experiments.
With the main purpose of removing duplicate k-mers from the human genome reference, I ran the following command:

bcalm -in GRCh38_latest_genomic.fna -kmer-size 31 -nb-cores 20 -abundance-min 1 -max-memory 30000

Apart from another know issue (#15) which highly affected the results (557 contigs and 3.1GB for the reference VS 39253840 unitigs and 6.7GB with k=31, 56968323 unitigs and 8.4GB with k=25), I noticed that the k-mer count of BCALM's output is slightly greater than the one of the reference.
To be precise, the 31-mer count of GRCh38_latest_genomic.fna is 2504380308 while BCALM's is 2504381531 (1223 more), and the 25-mer count is respectively 2386251821 and 2386252760 (939 more).

Here is the link to the reference version I used:
ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz
The k-mer count was obtained using jellyfish.

I suppose this is due to a bug in the program, have you observed this already?
I thank you in advance for your time, and I hope this will be useful. Please tell me if you need any other detail.

Simone

For some cases, the output edge representation of Bcalm2 is hard to work with. I will describe another natural representation below, and this "issue" is a feature request to add a flag to support this type of output.

Per this description here, there are four types of connections between a node x and y. Each connection corresponds to two directed edges, with a +/- sign at each node. Instead, lets have a representation where the connection type corresponds to an undirected edge with a 0/1 bit at each vertex. So,

Type 1: (u,v) with the bit at u = 1 and the bit at v = 0
Type 2: (u,v) with the bit at u = 0 and the bit at v = 1
Type 4: (u,v) with the bit at u = 1 and the bit at v = 1
Type 4: (u,v) with the bit at u = 0 and the bit at v = 0

This representation is consistent with the bidirected graph representation introduced by Kececioglu & Myers.

In terms of the fasta file header in bcalm output, that means converting
L:<e.fromSign>:<e.to>:<e.toSign> in the header to
J:<e.fromBit>:<e.to>:<e.toBit>, where the mapping is

(I suggest using J instead of L as the tag, to avoid confusing downstream parsers? The J is arbitrary, could be something else)

>1 a self-overlapping sequence (k=31) 
TATATATAAATATACATATAGATATATATAAATATACATATAGATATATATA
>2 a kmer that overlaps with the last kmer of sequence 1, to the left of it
TATATATATAAATATACATATAGATATATAT

it seems that bcalm incorrectly performs a compaction in this small example (sequence 1 should be splitted, but it is not)

I'm seeing a few duplicate kmers in my output, which would seem to be unintended according to this statement in the github README:

... a k-mer and its reverse complement are considered to be the same object,
appearing only once in the output, either in forward or reverse orientation.

My bcalm reports version as "BCALM 2, git commit 8137cc2, gatb-core version 1.4.1". I built from source fetched from --branch v2.2.1 a couple days ago.

The rate of duplicates is so low it makes me wonder if I have done something wrong. Exactly 100 duplicate 21-mers out of 140 million.

I had no luck creating a small example. But this is reproducible starting with SRR957915.sra from the short read archive. Here's what I did:

(1) Get abundance 2 21-mers and strip the non-names from the fasta headers.

fastq-dump --fasta SRR957915.sra --stdout > SRR957915.fa
bcalm -kmer-size 21 -abundance-min 2 \
  -in SRR957915.fa \
  -out scrap.SRR957915.bcalm
cat scrap.SRR957915.bcalm.unitigs.fa \
  | sed "s/ .*//" \
  | gzip \
  > SRR957915.unitigs_21.abun_2.fa.gz
rm scrap.SRR957915.bcalm.*

(2) I was expecting the results of step 1 to contain no duplicated 21-mers. So asking bcalm for abundance 2 21-mers from that result should produce an empty file. But instead I end up with 100 length 21 unitigs.

bcalm -kmer-size 21 -abundance-min 2 \
  -in SRR957915.unitigs_21.abun_2.fa.gz \
  -out scrap.SRR957915.bcalm_twice
cat scrap.SRR957915.bcalm_twice.unitigs.fa \
  | sed "s/ .*//" \
  | gzip \
  > SRR957915.unitigs_twice_21.abun_2.fa.gz
rm scrap.SRR957915.bcalm_twice.*

Hi Rayan,
I hope everything is going well.

Considering that KMC is faster than dsk, is it possible to use KMC's kmer count results for running bcalm/minia and skip the dsk step?

Hello Rayan et al,

I want the unitigs induced by a subset of the kmers from a read set. Is there any way to create a file of kmers that you can read into bcalm2, and then compact into unitigs?

In fact I want to pick out kmers that I think are single copy in a diploid, based on depth. So a simple way to do that would be for you to allow me to give a maximum as well as a minimum copy number for each kmer. I would then set those by looking at a histogram. But ultimately I would like the freedom to correct the kmer counts by GC content (of their parent read pairs), so it would be more general to allow me to pass you a set of kmers.

I guess I could make a fasta file out of them, with one kmer per sequence...

Thanks, Richard