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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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spades-3.11.0 :: config.info included *.info files not found. #36

Open EricDeveaud opened 7 years ago

EricDeveaud commented 7 years ago

Hello

while running SPAdes-3.11.0 one of our users reported the following problem.

spades.py --meta -1 file1.fastq -2 file.fastq -o test/ -t 4

ends with the following error

== Running assembler: K21

Exception caught /scratch/eric/test/K21/configs/config.info(3): cannot open include file simplification.info

== Error ==  system call for: "['/mount/gensoft2/exe/SPAdes/3.11.0/bin/spades', '/scratch/eric/test/K21/configs/config.info', '/scratch/eric/test/K21/configs/mda_mode.info', '/scratch/eric/test/K21/configs/meta_mode.info']" finished abnormally, err code: 4

when checking the file config.info from test/configs/debruijn/config.info one ca notice the following. incudes are relative.

; input options:

#include "simplification.info"
#include "construction.info"
#include "distance_estimation.info"
#include "detail_info_printer.info"
#include "tsa.info"
#include "pe_params.info"

K               55

after some code reading I ended hacking spades_logic.py (plain old patch attached) to generate a config.info file that handles the full path for the included files regarding the running configuration directory.

eg it will have something like that.

#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/simplification.info"
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/construction.info"
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/distance_estimation.info"
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/detail_info_printer.info"
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/tsa.info"
#include "/mount/tests/SPAdes/3.11.0/test/K21/configs/debruijn/pe_params.info"

instead of just plain file name.

with this patch applied, spades hapilly runs to the normal end and provides expected results

let me know what you think about this patch.

NB as far as I understand the code config files are copied from share/spades/config files. maybee installer can set those path at install time.

regards

Eric

config_include_patch.txt

asl commented 7 years ago

How have you compiled SPAdes?

EricDeveaud commented 7 years ago

here are the relelvant part of the makefile used in our install framework

SRC= /local/gensoft2/src/SPAdes/SPAdes-3.11.0
EXE= /local/gensoft2/exe/SPAdes/3.11.0
BUILD= $(SRC)/build

build:
    cd $(BUILD)
    test -d $(BUILD) || $(MKDIR) -p $(BUILD)
    cd $(BUILD) && module load gcc/4.9.4 cmake/3.2.1 && cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=$(EXE)   $(SRC)/src
    cd $(BUILD) && module load gcc/4.9.4 && make -j `nproc`

install:
    cd $(BUILD) && make install
asl commented 7 years ago

Could you please post the build log as well? All the files are in the project configs directory and therefore no explicit path adjustment is necessary at all.

asl commented 6 years ago

Please reopen if there is still an issue here.

EricDeveaud commented 5 years ago

Hello

I installed SPADES-3.13.0 from source today and try to run some --test commands. and truspades failed with following error message

bigmess:SPAdes/3.13.0 > truspades.py --test
Generating truseq dataset from input directories:
        /mount/gensoft2/exe/SPAdes/3.13.0/share/spades/test_dataset_truspades
Printing dataset to /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/dataset.info
Dataset generated. See result in /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/dataset.info
Launching truSPAdes assembly in 8 threads
You can find logs for separate barcodes in /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/logs
Starting: BC_A
Starting: BC_B
Failed to finish: BC_B
Failed to finish: BC_A
2 barcodes failed to assemble
Warning: could not find assembly results for barcode BC_A
Warning: could not find assembly results for barcode BC_B
Assembled virtual long TruSeq reads can be found in /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/TSLR.fasta
TruSPAdes launch successfully finished
TruSPAdes test launch failed: incorrect output files

while lookig at logs 

bigmess:SPAdes/3.13.0 > tail   /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/logs/BC_A.log 
== Running assembler: K21

Exception caught /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_A/K21/configs/config.info(3): cannot open include file simplification.info

== Error ==  system call for: "['/mount/gensoft2/exe/SPAdes/3.13.0/bin/spades-core', '/mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_A/K21/configs/config.info', '/mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_A/K21/configs/moleculo_mode.info']" finished abnormally, err code: 4

In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.

same on other log file

bigmess:SPAdes/3.13.0 > tail   /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/logs/BC_B.log 
== Running assembler: K21

Exception caught /mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_B/K21/configs/config.info(3): cannot open include file simplification.info

== Error ==  system call for: "['/mount/gensoft2/exe/SPAdes/3.13.0/bin/spades-core', '/mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_B/K21/configs/config.info', '/mount/gensoft2/tests/SPAdes/3.13.0/spades_test_truspades/barcodes/BC_B/K21/configs/moleculo_mode.info']" finished abnormally, err code: 4

In case you have troubles running SPAdes, you can write to spades.support@cab.spbu.ru
or report an issue on our GitHub repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output directory.
asl commented 5 years ago

So, we still need to full build logs.

1dayac commented 5 years ago

Logs:

-- The C compiler identification is GNU 6.3.0 -- The CXX compiler identification is GNU 6.3.0 -- Check for working C compiler: /pbtech_mounts/softlib001/apps/EL7/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-6.3.0-4h22ps2wttqbknmpnjft4h5bd2uvzndl/bin/cc -- Check for working C compiler: /pbtech_mounts/softlib001/apps/EL7/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-6.3.0-4h22ps2wttqbknmpnjft4h5bd2uvzndl/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: /pbtech_mounts/softlib001/apps/EL7/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-6.3.0-4h22ps2wttqbknmpnjft4h5bd2uvzndl/bin/c++ -- Check for working CXX compiler: /pbtech_mounts/softlib001/apps/EL7/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/gcc-6.3.0-4h22ps2wttqbknmpnjft4h5bd2uvzndl/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done Setting default build configuration: RelWithAsserts CMake Warning (dev) at /pbtech_mounts/softlib001/apps/EL6/spack/opt/spack/linux-rhel6-x86_64/gcc-6.3.0/cmake-3.9.4-v3w54bykdxdf23psa6qe3yxyiwhchbob/share/cmake-3.9/Modules/FindOpenMP.cmake:200 (if): Policy CMP0054 is not set: Only interpret if() arguments as variables or keywords when unquoted. Run "cmake --help-policy CMP0054" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

Quoted variables like "c" will no longer be dereferenced when the policy is set to NEW. Since the policy is not set the OLD behavior will be used. Call Stack (most recent call first): /pbtech_mounts/softlib001/apps/EL6/spack/opt/spack/linux-rhel6-x86_64/gcc-6.3.0/cmake-3.9.4-v3w54bykdxdf23psa6qe3yxyiwhchbob/share/cmake-3.9/Modules/FindOpenMP.cmake:324 (_OPENMP_GET_FLAGS) cmake/deps.cmake:16 (find_package) CMakeLists.txt:52 (include) This warning is for project developers. Use -Wno-dev to suppress it.

-- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7") -- Found BZip2: /pbtech_mounts/softlib001/apps/EL7/spack/opt/spack/linux-centos7-x86_64/gcc-6.3.0/bzip2-1.0.6-ikn3syj2vtwcbna4lykyinhp6ydvs7lv/lib/libbz2.so (found version "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Could NOT find readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY) -- Boost version: 1.63.0 Making Release Configuration... Building SPAdes from N/A, sha: N/A -- Looking for include file features.h -- Looking for include file features.h - found -- Looking for include file sys/cdefs.h -- Looking for include file sys/cdefs.h - found -- Looking for atomic_fetchadd_long -- Looking for atomic_fetchadd_long - not found -- Looking for OSAtomicAdd64 -- Looking for OSAtomicAdd64 - not found -- Looking for OSSpinLockLock -- Looking for OSSpinLockLock - not found -- Looking for _malloc_thread_cleanup -- Looking for _malloc_thread_cleanup - not found -- Looking for _pthread_mutex_init_calloc_cb, -- Looking for _pthread_mutex_init_calloc_cb, - not found -- Looking for sbrk -- Looking for sbrk - found -- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED -- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED - Success -- 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 void -- Check size of void - done -- Performing Test JEMALLOC_TLS -- Performing Test JEMALLOC_TLS - Success -- Looking for memalign -- Looking for memalign - found -- Looking for valloc -- Looking for valloc - found -- Check size of int -- Check size of int - done -- Check size of long -- Check size of long - done -- Check size of intmax_t -- Check size of intmax_t - done -- Looking for open -- Looking for open - found -- Looking for include file execinfo.h -- Looking for include file execinfo.h - found -- Looking for include file signal.h -- Looking for include file signal.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file cxxabi.h -- Looking for include file cxxabi.h - not found -- Looking for include file dlfcn.h -- Looking for include file dlfcn.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - not found -- Looking for include file link.h -- Looking for include file link.h - found -- Looking for backtrace -- Looking for backtrace - found -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE
-- Looking for shm_open -- Looking for shm_open - not found -- Looking for shm_open in rt -- Looking for shm_open in rt - found -- Configuring done -- Generating done -- Build files have been written to: /home/dmm2017/cloudSPAdes-dev/build_spades Scanning dependencies of target cityhash Scanning dependencies of target getopt_pp Scanning dependencies of target ssw Scanning dependencies of target format [ 1%] Building CXX object ext/cityhash/CMakeFiles/cityhash.dir/city.cc.o [ 2%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o [ 3%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o [ 3%] Building C object ext/ssw/CMakeFiles/ssw.dir/ssw.c.o Scanning dependencies of target nlopt [ 4%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/api/general.c.o Scanning dependencies of target jemalloc Scanning dependencies of target BamTools [ 4%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o [ 5%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/arena.c.o [ 5%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/api/optimize.c.o [ 5%] Linking CXX static library libcityhash.a [ 5%] Building CXX object ext/ssw/CMakeFiles/ssw.dir/ssw_cpp.cpp.o [ 5%] Built target cityhash [ 5%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/api/options.c.o [ 5%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o [ 5%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/api/deprecated.c.o /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c: In function ‘nlopt_minimize_constrained’: /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c:149:6: warning: ‘nlopt_minimize_econstrained’ is deprecated [-Wdeprecated-declarations] return nlopt_minimize_econstrained( ^~ In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c:23:0: /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt.h:350:28: note: declared here NLOPT_EXTERN(nlopt_result) nlopt_minimize_econstrained( ^~~~~~~ /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c: In function ‘nlopt_minimize’: /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c:167:6: warning: ‘nlopt_minimize_constrained’ is deprecated [-Wdeprecated-declarations] return nlopt_minimize_constrained( ^~ In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/api/deprecated.c:23:0: /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt.h:339:28: note: declared here NLOPT_EXTERN(nlopt_result) nlopt_minimize_constrained( ^~~~~~ [ 6%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/auglag/auglag.c.o [ 6%] Linking CXX static library libgetopt_pp.a [ 6%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/bobyqa/bobyqa.c.o Scanning dependencies of target ConsensusCore [ 6%] Linking CXX static library libssw.a [ 6%] Built target getopt_pp [ 6%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o [ 6%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/base.c.o Scanning dependencies of target llvm-support [ 6%] Built target ssw [ 6%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/cdirect/cdirect.c.o [ 6%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o [ 7%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o [ 7%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o [ 7%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o [ 7%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o Scanning dependencies of target hattrie [ 7%] Building C object ext/htrie/CMakeFiles/hattrie.dir/ahtable.c.o [ 7%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamReader.cpp.o [ 8%] Building C object ext/htrie/CMakeFiles/hattrie.dir/hat-trie.c.o [ 9%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o [ 9%] Linking CXX static library libformat.a [ 9%] Building C object ext/htrie/CMakeFiles/hattrie.dir/misc.c.o [ 9%] Built target format [ 9%] Building C object ext/htrie/CMakeFiles/hattrie.dir/murmurhash3.c.o Scanning dependencies of target bwa [ 9%] Linking C static library libhattrie.a [ 10%] Building C object ext/bwa/CMakeFiles/bwa.dir/utils.c.o [ 10%] Built target hattrie [ 10%] Building C object ext/bwa/CMakeFiles/bwa.dir/kthread.c.o [ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o Scanning dependencies of target gqf [ 12%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o [ 12%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o [ 12%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o [ 12%] Linking C static library libgqf.a [ 12%] Built target gqf [ 12%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/cdirect/hybrid.c.o [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Mutex.cpp.o [ 12%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o [ 12%] Building C object ext/bwa/CMakeFiles/bwa.dir/ksw.c.o [ 12%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk.c.o [ 13%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o [ 13%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o [ 13%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwt.c.o [ 14%] Building C object ext/bwa/CMakeFiles/bwa.dir/bntseq.c.o [ 14%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o [ 15%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/cobyla/cobyla.c.o /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/cdirect/hybrid.c: In function ‘optimize_rect’: /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/cdirect/hybrid.c:91:6: warning: ‘nlopt_minimize’ is deprecated [-Wdeprecated-declarations] ret = nlopt_minimize(p->local_alg, n, fcount, p, ^~~ In file included from /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt-util.h:29:0, from /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/cdirect/hybrid.c:27: /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt.h:329:28: note: declared here NLOPT_EXTERN(nlopt_result) nlopt_minimize( ^~~~~~ [ 15%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/crs/crs.c.o [ 15%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwa.c.o [ 16%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o [ 16%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem.c.o [ 16%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/esch/esch.c.o [ 16%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o [ 17%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/isres/isres.c.o [ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o Scanning dependencies of target edlib [ 18%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o [ 18%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/mma/mma.c.o [ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o [ 18%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/mma/ccsa_quadratic.c.o [ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o [ 18%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/mlsl/mlsl.c.o [ 19%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/neldermead/nldrmd.c.o [ 20%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem_pair.c.o [ 20%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o [ 21%] Linking CXX static library libedlib.a [ 21%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o [ 21%] Built target edlib [ 21%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/neldermead/sbplx.c.o [ 21%] Building C object ext/bwa/CMakeFiles/bwa.dir/bwamem_extra.c.o [ 22%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o [ 22%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunkmmap.c.o [ 22%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/newuoa/newuoa.c.o /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c: In function ‘trsapp’: /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c:184:3: warning: ‘nlopt_minimize_constrained’ is deprecated [-Wdeprecated-declarations] ret = nlopt_minimize_constrained(NLOPT_LD_MMA, n, quad_model, &qmd, ^~~ In file included from /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt-util.h:29:0, from /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/newuoa.h:4, from /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c:33: /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt.h:339:28: note: declared here NLOPT_EXTERN(nlopt_result) nlopt_minimizeconstrained( ^~~~~~ /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c: In function ‘biglag’: /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c:1241:3: warning: ‘nlopt_minimize_constrained’ is deprecated [-Wdeprecated-declarations] return nlopt_minimize_constrained(NLOPT_LD_MMA, n, lag, &ld, ^~ In file included from /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt-util.h:29:0, from /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/newuoa.h:4, from /home/dmm2017/cloudSPAdes-dev/ext/src/nlopt/newuoa/newuoa.c:33: /home/dmm2017/cloudSPAdes-dev/src/../ext/include/nlopt/nlopt.h:339:28: note: declared here NLOPT_EXTERN(nlopt_result) nlopt_minimize_constrained( ^~~~~~ [ 22%] Building C object ext/bwa/CMakeFiles/bwa.dir/malloc_wrap.c.o [ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o [ 23%] Building C object ext/bwa/CMakeFiles/bwa.dir/is.c.o [ 23%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/ctl.c.o [ 23%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o [ 23%] Building CXX object 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dependencies of target gfa1 [ 27%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/hash.c.o [ 27%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o [ 27%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/jemalloc.c.o [ 28%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o [ 28%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o Scanning dependencies of target spades-bwa [ 28%] Linking C static library libgfa1.a [ 28%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bamlite.c.o [ 28%] Built target gfa1 Scanning dependencies of target sequence [ 28%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwa.c.o [ 28%] Building CXX object common/sequence/CMakeFiles/sequence.dir/sequence_tools.cpp.o [ 29%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/mutex.c.o [ 29%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/quarantine.c.o [ 29%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwamem.c.o [ 30%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o [ 30%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/stats.c.o [ 30%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o [ 30%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/tsd.c.o [ 31%] Linking CXX static library libsequence.a [ 31%] Built target sequence [ 31%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/util/rescale.c.o [ 31%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o [ 31%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/util/stop.c.o [ 31%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o [ 32%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/util/timer.c.o [ 32%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/util/qsort_r.c.o [ 32%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/util/sobolseq.c.o [ 32%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o Scanning dependencies of target modules [ 32%] Building C object ext/nlopt/CMakeFiles/nlopt.dir/util/mt19937ar.c.o [ 32%] Building CXX object common/modules/CMakeFiles/modules.dir/genome_consistance_checker.cpp.o [ 32%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConsensus.cpp.o [ 33%] Linking C static library libnlopt.a [ 33%] Built target nlopt Scanning dependencies of target assembly_graph [ 33%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/components/connected_component.cpp.o Scanning dependencies of target paired_info [ 33%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/distance_estimation.cpp.o [ 33%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o [ 34%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o [ 34%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o [ 35%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwase.c.o [ 35%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwashm.c.o [ 35%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwtaln.c.o [ 36%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwtgap.c.o [ 36%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o [ 36%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwtindex.c.o [ 36%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwt_lite.c.o [ 36%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwtsw2_aux.c.o [ 36%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o [ 37%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o [ 38%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwtsw2_core.c.o [ 38%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path.cpp.o [ 39%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o [ 39%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o [ 39%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwtsw2_pair.c.o [ 39%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o [ 39%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o [ 40%] Linking CXX static library libllvm-support.a [ 40%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/fastmap.c.o [ 40%] Built target llvm-support [ 40%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/kstring.c.o [ 40%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o [ 41%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/main.c.o [ 42%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/io_support.cpp.o [ 42%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/utils.c.o [ 42%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o [ 42%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bntseq.c.o [ 42%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o [ 43%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwape.c.o [ 44%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o [ 44%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwaseqio.c.o [ 44%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o [ 44%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwt.c.o Scanning dependencies of target stages [ 44%] Building CXX object common/stages/CMakeFiles/stages.dir/construction.cpp.o [ 44%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o [ 44%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwt_gen.c.o [ 44%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o [ 45%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwtsw2_chain.c.o [ 45%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwtsw2_main.c.o [ 45%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/is.c.o [ 45%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/ksw.c.o [ 46%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o [ 47%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/pemerge.c.o [ 47%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/QSufSort.c.o [ 47%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/kopen.c.o [ 47%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwamem_extra.c.o [ 47%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o [ 48%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/bwamem_pair.c.o [ 48%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o [ 49%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/block.c:5:0: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined safe_mutex_unlock(pthread_mutex_t mutex); ^~~~~ /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined safe_mutex_lock(pthread_mutex_t mutex); ^~~~~~~ In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/block.c:4:0: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function ‘unpackInt16’ declared but never defined unpackInt16(const uint8_t buffer); ^~~ [ 49%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12:0: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined safe_mutex_unlock(pthread_mutex_t mutex); ^~~~~ /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined safe_mutex_lock(pthread_mutex_t mutex); ^~~~~~~ In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11:0: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function ‘unpackInt16’ declared but never defined unpackInt16(const uint8_t buffer); ^~~ [ 49%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/kthread.c.o [ 49%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14:0: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined safe_mutex_unlock(pthread_mutex_t mutex); ^~~~~ /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined safe_mutex_lock(pthread_mutex_t mutex); ^~~~~~~ In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13:0: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function ‘unpackInt16’ declared but never defined unpackInt16(const uint8_t buffer); ^~~ [ 49%] Building C object ext_tools/bwa-0.7.12/CMakeFiles/spades-bwa.dir/malloc_wrap.c.o [ 50%] Linking C executable ../../bin/spades-bwa [ 50%] Built target spades-bwa [ 51%] Building CXX object common/stages/CMakeFiles/stages.dir/simplification.cpp.o [ 51%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6:0: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined safe_mutex_unlock(pthread_mutex_t mutex); ^~~~~ /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined safe_mutex_lock(pthread_mutex_t mutex); ^~~~~~~ [ 52%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8:0: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined safe_mutex_unlock(pthread_mutex_t mutex); ^~~~~ /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined safe_mutex_lock(pthread_mutex_t mutex); ^~~~~~~ In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7:0: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function ‘unpackInt16’ declared but never defined unpackInt16(const uint8_t buffer); ^~~ [ 52%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o [ 52%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11:0, from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function ‘safe_mutex_unlock’ declared but never defined safe_mutex_unlock(pthread_mutex_t mutex); ^~~~~ /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function ‘safe_mutex_lock’ declared but never defined safe_mutex_lock(pthread_mutex_t mutex); ^~~~~~~ In file included from /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7:0: /home/dmm2017/cloudSPAdes-dev/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function ‘unpackInt16’ declared but never defined unpackInt16(const uint8_t buffer); ^~~ [ 52%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o [ 53%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o [ 53%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o [ 53%] Linking CXX static library libConsensusCore.a [ 53%] Built target ConsensusCore [ 54%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o [ 54%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/atomic.c.o [ 54%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/paths/bidirectional_path_io/bidirectional_path_output.cpp.o [ 54%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/bitmap.c.o [ 54%] Linking CXX static library libBamTools.a [ 54%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk_dss.c.o [ 54%] Built target BamTools [ 54%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/weighted_distance_estimation.cpp.o [ 54%] Building CXX object common/assembly_graph/CMakeFiles/assembly_graph.dir/graph_support/scaff_supplementary.cpp.o [ 54%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/gap_info.cpp.o [ 55%] Building CXX object common/modules/CMakeFiles/modules.dir/alignment/bwa_index.cpp.o [ 55%] Building CXX object common/paired_info/CMakeFiles/paired_info.dir/smoothing_distance_estimation.cpp.o [ 55%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/ckh.c.o Scanning dependencies of target utils [ 55%] Building CXX object common/utils/CMakeFiles/utils.dir/memory_limit.cpp.o [ 55%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/copy_file.cpp.o [ 55%] Linking CXX static library libmodules.a [ 55%] Built target modules [ 56%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/path_helper.cpp.o /home/dmm2017/cloudSPAdes-dev/src/common/assembly_graph/graph_support/scaff_supplementary.cpp: In member function ‘bool path_extend::ScaffoldingUniqueEdgeAnalyzer::ConservativeByPaths(path_extend::EdgeId, const path_extend::GraphCoverageMap&, const path_extend::pe_config::LongReads&, int) const’: /home/dmm2017/cloudSPAdes-dev/src/common/assembly_graph/graph_support/scaff_supplementary.cpp:130:63: warning: conversion to ‘double’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion] if (maxx < lr_config.unique_edge_priority double(alt)) { ^ [ 56%] Building CXX object common/utils/CMakeFiles/utils.dir/filesystem/temporary.cpp.o [ 56%] Building CXX object 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common/assembly_graph/CMakeFiles/assembly_graph.dir/contracted_graph/contracted_statistics.cpp.o [ 64%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/fastg_writer.cpp.o [ 64%] Building CXX object common/io/graph/CMakeFiles/graphio.dir/gfa_writer.cpp.o Scanning dependencies of target samtools [ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o [ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o [ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o [ 65%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o [ 66%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o [ 66%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o [ 66%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o [ 66%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o [ 67%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o [ 67%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o [ 67%] Linking CXX static library libgraphio.a [ 67%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o [ 67%] Built target graphio [ 68%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o Scanning dependencies of target coverage_model [ 68%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o [ 68%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o [ 69%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o [ 69%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o [ 70%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o [ 70%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o [ 70%] Linking CXX static library libsamtools.a [ 70%] Built target samtools Scanning dependencies of target input [ 71%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o [ 71%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o [ 71%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o /home/dmm2017/cloudSPAdes-dev/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function ‘void coverage_model::KMerCoverageModel::Fit()’: /home/dmm2017/cloudSPAdes-dev/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion to ‘gnu_cxx::alloc_traits<std::allocator >::value_type {aka double}’ from ‘sizet {aka long unsigned int}’ may alter its value [-Wconversion] if (converged && Valley_ > x[2] && x[2] > 2) { ^~~ /home/dmm2017/cloudSPAdes-dev/src/common/modules/coverage_model/kmer_coverage_model.cpp:359:28: warning: conversion to ‘double’ from ‘sizet {aka long unsigned int}’ may alter its value [-Wconversion] ErrorThreshold = (Valley_ < meancoverage ? ^~~ [ 71%] Linking CXX static library libassembly_graph.a [ 71%] Linking CXX static library libinput.a [ 71%] Built target assembly_graph [ 71%] Built target input Scanning dependencies of target pipeline [ 71%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o [ 72%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/genomic_info_filler.cpp.o [ 72%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/library.cpp.o [ 72%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/config_struct.cpp.o Scanning dependencies of target path_extend [ 72%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pe_config_struct.cpp.o [ 72%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launch_support.cpp.o [ 72%] Linking CXX static library libcoverage_model.a [ 72%] Built target coverage_model [ 72%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/launcher.cpp.o [ 73%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/pipeline/extenders_logic.cpp.o In file included from /home/dmm2017/cloudSPAdes-dev/src/common/pipeline/stage.cpp:9:0: /home/dmm2017/cloudSPAdes-dev/src/common/pipeline/graphio.hpp: In instantiation of ‘void debruijn_graph::graphio::ScanReadCloudDistributions(const string&, path_extend::cluster_model::DistributionPack&, const Graph&, bool) [with Graph = debruijn_graph::DeBruijnGraph; std::cxx11::string = std::cxx11::basic_string]’: /home/dmm2017/cloudSPAdes-dev/src/common/pipeline/graphio.hpp:1143:31: required from ‘void debruijn_graph::graphio::ScanAll(const string&, graph_pack&, bool) [with graph_pack = debruijn_graph::graph_pack; std::cxx11::string = std::__cxx11::basic_string]’ /home/dmm2017/cloudSPAdes-dev/src/common/pipeline/stage.cpp:24:50: required from here /home/dmm2017/cloudSPAdes-dev/src/common/pipeline/graphio.hpp:1026:46: warning: unused parameter ‘g’ [-Wunused-parameter] const Graph& g, bool force_exists = true) { ^ [ 73%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/extension_chooser2015.cpp.o [ 73%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph.cpp.o [ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_constructor.cpp.o [ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_graph_visualizer.cpp.o /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp: In member function ‘path_extend::ExtensionChooser::EdgeContainer path_extend::ExtensionChooser2015::FindNextUniqueEdge(path_extend::EdgeId) const’: /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp:29:19: warning: conversion to ‘double’ from ‘long unsigned int’ may alter its value [-Wconversion] if (sum < absolute_weightthreshold) { ^~~~~~ [ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/connection_condition2015.cpp.o [ 74%] Linking CXX static library libstages.a [ 74%] Built target stages [ 74%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/path_polisher.cpp.o [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/scaffolder2015/scaffold_vertex.cpp.o [ 75%] Linking CXX static library libpipeline.a [ 75%] Built target pipeline [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/scaffold_graph_construction/read_cloud_connection_conditions.cpp.o [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_construction_pipeline.cpp.o /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp: In member function ‘virtual std::map<restricted::pure_pointer<omnigraph::PairedEdge >, double> path_extend::LongReadsLibConnectionCondition::ConnectedWith(path_extend::EdgeId, const path_extend::ScaffoldingUniqueEdgeStorage&) const’: /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp:105:28: warning: conversion to ‘double’ from ‘long unsigned int’ may alter its value [-Wconversion] if (iter->second < min_readcount){ ^~~~~~~ [ 75%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_storage.cpp.o [ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/validation/scaffold_graph_validation.cpp.o /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_construction_pipeline.cpp: In member function ‘path_extend::LongEdgePairGapCloserParams path_extend::ScaffolderParamsConstructor::ConstructGapCloserParamsFromMainParams(const path_extend::ScaffolderParams&, const Graph&, std::shared_ptr, size_t, size_t) const’: /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_construction_pipeline.cpp:43:33: warning: unused parameter ‘params’ [-Wunused-parameter] const ScaffolderParams &params, ^~ /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_construction_pipeline.cpp:44:22: warning: unused parameter ‘g’ [-Wunused-parameter] const Graph &g, ^ /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_construction_pipeline.cpp:45:67: warning: unused parameter ‘barcode_extractor’ [-Wunused-parameter] shared_ptr barcode_extractor, ^~~~~ /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_construction_pipeline.cpp:46:16: warning: unused parameter ‘unique_edge_length’ [-Wunused-parameter] size_t unique_edge_length, ^~~~~~ /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_construction_pipeline.cpp:47:16: warning: unused parameter ‘max_threads’ [-Wunused-parameter] size_t max_threads) const { ^~~ /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_construction_pipeline.cpp: In member function ‘path_extend::ScaffolderParams::ScoreEstimationParams path_extend::ScaffolderParamsConstructor::GetScoreEstimationParams(const Graph&, path_extend::cluster_model::ClusterStatisticsExtractor, double, double, size_t) const’: /home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_construction_pipeline.cpp:75:22: warning: unused parameter ‘g’ [-Wunused-parameter] const Graph &g, cluster_model::ClusterStatisticsExtractor cluster_statistics_extractor, ^ [ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/validation/transition_extractor.cpp.o [ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/scaffold_graph_extractor.cpp.o [ 76%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/intermediate_scaffolding/scaffold_graph_polisher.cpp.o [ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/transitions/transitions.cpp.o [ 77%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/intermediate_scaffolding/scaffold_vertex_predicates.cpp.o Scanning dependencies of target spades-hammer [ 78%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/main.cpp.o [ 78%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hammer_tools.cpp.o [ 78%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/hamcluster.cpp.o [ 78%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_cluster.cpp.o In file included from /home/dmm2017/miniconda2/include/boost/numeric/ublas/io.hpp:19:0, from /home/dmm2017/cloudSPAdes-dev/src/projects/hammer/kmer_cluster.cpp:16: /home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix_expression.hpp: In member function ‘void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)’: /home/dmm2017/miniconda2/include/boost/numeric/ublas/matrixexpression.hpp:2224:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (it2 != it2end) ^~ /home/dmm2017/miniconda2/include/boost/numeric/ublas/matrixexpression.hpp:2227:21: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if (it2 != it2end) { ^~ /home/dmm2017/cloudSPAdes-dev/src/projects/hammer/kmer_cluster.cpp: In member function ‘size_t KMerClustering::SubClusterSingle(const std::vector&, std::vector<std::vector >&)’: /home/dmm2017/cloudSPAdes-dev/src/projects/hammer/kmer_cluster.cpp:356:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (uint32_t j=0; j<K; ++j) std::cout << std::setw(3) << (unsigned)getQual(kms, j) << " "; std::cout << "\n"; ^~~ /home/dmm2017/cloudSPAdes-dev/src/projects/hammer/kmer_cluster.cpp:356:101: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘for’ for (uint32_t j=0; j<K; ++j) std::cout << std::setw(3) << (unsigned)getQual(kms, j) << " "; std::cout << "\n"; ^~~ In file included from /home/dmm2017/miniconda2/include/boost/numeric/ublas/expression_types.hpp:16:0, from /home/dmm2017/miniconda2/include/boost/numeric/ublas/vector_expression.hpp:16, from /home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix_expression.hpp:16, from /home/dmm2017/miniconda2/include/boost/numeric/ublas/io.hpp:19, from /home/dmm2017/cloudSPAdes-dev/src/projects/hammer/kmer_cluster.cpp:16: /home/dmm2017/miniconda2/include/boost/numeric/ublas/functional.hpp: In instantiation of ‘static void boost::numeric::ublas::scalar_assign<T1, T2>::apply(boost::numeric::ublas::scalar_assign<T1, T2>::argument1_type, boost::numeric::ublas::scalar_assign<T1, T2>::argument2_type) [with T1 = long unsigned int&; T2 = double; boost::numeric::ublas::scalar_assign<T1, T2>::argument1_type = long unsigned int&; boost::numeric::ublas::scalar_assign<T1, T2>::argument2_type = const double&]’: /home/dmm2017/miniconda2/include/boost/numeric/ublas/detail/matrix_assign.hpp:589:37: required from ‘void boost::numeric::ublas::indexing_matrix_assign(M&, const boost::numeric::ublas::matrix_expression&, boost::numeric::ublas::row_major_tag) [with F = boost::numeric::ublas::scalar_assign; M = boost::numeric::ublas::matrix; E = boost::numeric::ublas::matrix]’ /home/dmm2017/miniconda2/include/boost/numeric/ublas/detail/matrix_assign.hpp:622:35: required from ‘void boost::numeric::ublas::matrix_assign(M&, const boost::numeric::ublas::matrix_expression&, boost::numeric::ublas::dense_proxy_tag, C) [with F = boost::numeric::ublas::scalar_assign; R = boost::numeric::ublas::basic_full<>; M = boost::numeric::ublas::matrix; E = boost::numeric::ublas::matrix; C = boost::numeric::ublas::row_major_tag]’ /home/dmm2017/miniconda2/include/boost/numeric/ublas/detail/matrix_assign.hpp:1224:40: required from ‘void boost::numeric::ublas::matrix_assign(M&, const boost::numeric::ublas::matrix_expression&) [with F = boost::numeric::ublas::scalar_assign; M = boost::numeric::ublas::matrix; E = boost::numeric::ublas::matrix]’ /home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix.hpp:172:42: required from ‘boost::numeric::ublas::matrix<T, L, A>::matrix(const boost::numeric::ublas::matrix_expression&) [with AE = boost::numeric::ublas::matrix; T = long unsigned int; L = boost::numeric::ublas::basic_row_major<>; A = boost::numeric::ublas::unbounded_array]’ /home/dmm2017/cloudSPAdes-dev/src/projects/hammer/kmer_cluster.cpp:602:93: required from here /home/dmm2017/miniconda2/include/boost/numeric/ublas/functional.hpp:201:16: warning: conversion to ‘long unsigned int’ from ‘boost::numeric::ublas::type_traits::value_type {aka double}’ may alter its value [-Wfloat-conversion] t1 = t2;


/home/dmm2017/miniconda2/include/boost/numeric/ublas/functional.hpp: In instantiation of ‘static boost::numeric::ublas::matrix_matrix_prod<M1, M2, TV>::result_type boost::numeric::ublas::matrix_matrix_prod<M1, M2, TV>::apply(const boost::numeric::ublas::matrix_expression<E1>&, const boost::numeric::ublas::matrix_expression<E2>&, boost::numeric::ublas::matrix_matrix_prod<M1, M2, TV>::size_type, boost::numeric::ublas::matrix_matrix_prod<M1, M2, TV>::size_type) [with E1 = boost::numeric::ublas::matrix_reference<const boost::numeric::ublas::matrix<long unsigned int> >; E2 = boost::numeric::ublas::matrix_reference<const boost::numeric::ublas::scalar_matrix<double> >; M1 = boost::numeric::ublas::matrix<long unsigned int>; M2 = boost::numeric::ublas::scalar_matrix<double>; TV = double; boost::numeric::ublas::matrix_matrix_prod<M1, M2, TV>::result_type = double; boost::numeric::ublas::matrix_matrix_prod<M1, M2, TV>::size_type = long unsigned int]’:
/home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix_expression.hpp:4832:40:   required from ‘boost::numeric::ublas::matrix_matrix_binary<E1, E2, F>::const_reference boost::numeric::ublas::matrix_matrix_binary<E1, E2, F>::operator()(boost::numeric::ublas::matrix_matrix_binary<E1, E2, F>::size_type, boost::numeric::ublas::matrix_matrix_binary<E1, E2, F>::size_type) const [with E1 = boost::numeric::ublas::matrix<long unsigned int>; E2 = boost::numeric::ublas::scalar_matrix<double>; F = boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<long unsigned int>, boost::numeric::ublas::scalar_matrix<double>, double>; boost::numeric::ublas::matrix_matrix_binary<E1, E2, F>::const_reference = double; boost::numeric::ublas::matrix_matrix_binary<E1, E2, F>::size_type = long unsigned int]’
/home/dmm2017/miniconda2/include/boost/numeric/ublas/detail/matrix_assign.hpp:589:53:   required from ‘void boost::numeric::ublas::indexing_matrix_assign(M&, const boost::numeric::ublas::matrix_expression<E2>&, boost::numeric::ublas::row_major_tag) [with F = boost::numeric::ublas::scalar_assign; M = boost::numeric::ublas::matrix<long unsigned int>; E = boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<long unsigned int>, boost::numeric::ublas::scalar_matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<long unsigned int>, boost::numeric::ublas::scalar_matrix<double>, double> >]’
/home/dmm2017/miniconda2/include/boost/numeric/ublas/detail/matrix_assign.hpp:622:35:   required from ‘void boost::numeric::ublas::matrix_assign(M&, const boost::numeric::ublas::matrix_expression<E>&, boost::numeric::ublas::dense_proxy_tag, C) [with F = boost::numeric::ublas::scalar_assign; R = boost::numeric::ublas::basic_full<>; M = boost::numeric::ublas::matrix<long unsigned int>; E = boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<long unsigned int>, boost::numeric::ublas::scalar_matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<long unsigned int>, boost::numeric::ublas::scalar_matrix<double>, double> >; C = boost::numeric::ublas::row_major_tag]’
/home/dmm2017/miniconda2/include/boost/numeric/ublas/detail/matrix_assign.hpp:1224:40:   required from ‘void boost::numeric::ublas::matrix_assign(M&, const boost::numeric::ublas::matrix_expression<E2>&) [with F = boost::numeric::ublas::scalar_assign; M = boost::numeric::ublas::matrix<long unsigned int>; E = boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<long unsigned int>, boost::numeric::ublas::scalar_matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<long unsigned int>, boost::numeric::ublas::scalar_matrix<double>, double> >]’
/home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix.hpp:172:42:   required from ‘boost::numeric::ublas::matrix<T, L, A>::matrix(const boost::numeric::ublas::matrix_expression<E1>&) [with AE = boost::numeric::ublas::matrix_matrix_binary<boost::numeric::ublas::matrix<long unsigned int>, boost::numeric::ublas::scalar_matrix<double>, boost::numeric::ublas::matrix_matrix_prod<boost::numeric::ublas::matrix<long unsigned int>, boost::numeric::ublas::scalar_matrix<double>, double> >; T = long unsigned int; L = boost::numeric::ublas::basic_row_major<>; A = boost::numeric::ublas::unbounded_array<long unsigned int>]’
/home/dmm2017/cloudSPAdes-dev/src/projects/hammer/kmer_cluster.cpp:643:92:   required from here
/home/dmm2017/miniconda2/include/boost/numeric/ublas/functional.hpp:1179:35: warning: conversion to ‘double’ from ‘long unsigned int’ may alter its value [-Wconversion]
                 t += e1 () (i, k) * e2 () (k, j);
                      ~~~~~~~~~~~~~^~~~~~~~~~~~~~
[ 79%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/kmer_data.cpp.o
[ 79%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/config_struct_hammer.cpp.o
[ 79%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/read_corrector.cpp.o
[ 79%] Building CXX object projects/hammer/CMakeFiles/spades-hammer.dir/expander.cpp.o
[ 80%] Linking CXX executable ../../bin/spades-hammer
[ 80%] Built target spades-hammer
Scanning dependencies of target spades-ionhammer
[ 80%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_data.cpp.o
[ 80%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/subcluster.cpp.o
In file included from /home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix.hpp:19:0,
                 from /home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/consensus.hpp:13,
                 from /home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/subcluster.cpp:10:
/home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix_expression.hpp: In member function ‘void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)’:
/home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                     if (it2_ != it2_end_) {
                     ^~
[ 80%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/err_helper_table.cpp.o
[ 81%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/config_struct.cpp.o
[ 81%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/kmer_helpers.cpp.o
[ 81%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/BaseHypothesisEvaluator.cpp.o
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function ‘void BaseHypothesisEvaluator(BamTools::BamAlignment&, const string&, const string&, float&, float&, int)’:
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:26:56: warning: conversion to ‘int’ from ‘std::__cxx11::basic_string<char>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
     if (not GetBamTags(alignment, flow_order_str.length(), measurements, phase_params, start_flow))
                                   ~~~~~~~~~~~~~~~~~~~~~^~
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:28:34: warning: conversion to ‘int’ from ‘std::vector<float>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
     num_flows = measurements.size();
                 ~~~~~~~~~~~~~~~~~^~
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:46:57: warning: conversion to ‘unsigned int’ from ‘std::vector<char>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
     unsigned int prefix_size = master_read.sequence.size();
                                ~~~~~~~~~~~~~~~~~~~~~~~~~^~
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp: In function ‘void RevComplementInPlace(std::__cxx11::string&)’:
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/BaseHypothesisEvaluator.cpp:292:32: warning: conversion to ‘int’ from ‘std::__cxx11::basic_string<char>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
   int backward_idx = seq.size()-1;
                      ~~~~~~~~~~^~
[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/seqeval/TreephaserLite.cpp.o
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function ‘void TreephaserLite::SetModelParameters(double, double, double)’:
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp:85:76: warning: conversion to ‘__gnu_cxx::__alloc_traits<std::allocator<float> >::value_type {aka float}’ from ‘double’ may alter its value [-Wfloat-conversion]
       transition_base_[nuc][flow] = nuc_avaliability[nuc] * (1-droop_rate) * (1-incomplete_extension_rate);
                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp:86:63: warning: conversion to ‘__gnu_cxx::__alloc_traits<std::allocator<float> >::value_type {aka float}’ from ‘double’ may alter its value [-Wfloat-conversion]
       transition_flow_[nuc][flow] = (1-nuc_avaliability[nuc]) + nuc_avaliability[nuc] * (1-droop_rate) * incomplete_extension_rate;
                                     ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function ‘void TreephaserLite::WindowedNormalize(BasecallerRead&, int, int) const’:
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp:97:45: warning: conversion to ‘int’ from ‘std::vector<float>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
   int num_flows = read.raw_measurements.size();
                   ~~~~~~~~~~~~~~~~~~~~~~~~~~^~
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp:127:52: warning: conversion to ‘float’ from ‘int’ may alter its value [-Wconversion]
     float delta = (next_normalizer - normalizer) / window_size;
                                                    ^~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp:166:52: warning: conversion to ‘float’ from ‘int’ may alter its value [-Wconversion]
     float delta = (next_normalizer - normalizer) / window_size;
                                                    ^~~~~~~~~~~
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp: In member function ‘void TreephaserLite::Solve(BasecallerRead&, int, int)’:
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp:350:38: warning: conversion to ‘float’ alters ‘double’ constant value [-Wfloat-conversion]
   float sum_of_squares_upper_bound = 1e20;  //max_flows; // Squared distance of solution to measurements
                                      ^~~~
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp:409:36: warning: conversion to ‘float’ alters ‘double’ constant value [-Wfloat-conversion]
       float max_per_flow_metric = -0.1;
                                    ^~~
/home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/seqeval/TreephaserLite.cpp:514:72: warning: conversion to ‘float’ from ‘double’ may alter its value [-Wfloat-conversion]
         child->per_flow_metric = (child->path_metric + 0.5 * penalty1) / child->flow;
                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/main.cpp.o
In file included from /home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix.hpp:19:0,
                 from /home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/consensus.hpp:13,
                 from /home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/io_read_corrector.hpp:13,
                 from /home/dmm2017/cloudSPAdes-dev/src/projects/ionhammer/main.cpp:24:
/home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix_expression.hpp: In member function ‘void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)’:
/home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/home/dmm2017/miniconda2/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’
                     if (it2_ != it2_end_) {
                     ^~
[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/reference.cpp.o
[ 82%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_metrics.cpp.o
[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/quality_thresholds_estimator.cpp.o
[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/hamcluster_1.cpp.o
[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/gamma_poisson_model.cpp.o
[ 83%] Building CXX object projects/ionhammer/CMakeFiles/spades-ionhammer.dir/normal_quality_model.cpp.o
[ 84%] Linking CXX executable ../../bin/spades-ionhammer
[ 84%] Built target spades-ionhammer
[ 84%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/intermediate_scaffolding/path_cluster_helper.cpp.o
[ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/intermediate_scaffolding/predicate_builders.cpp.o
[ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/intermediate_scaffolding/pe_extraction.cpp.o
[ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/path_scaffolder.cpp.o
[ 85%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/scaffold_graph_construction/containment_index_threshold_finder.cpp.o
[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/read_cloud_polisher_support.cpp.o
[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/scaffold_graph_construction/construction_callers.cpp.o
[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/scaffold_graph_construction/scaffold_graph_storage_constructor.cpp.o
/home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/path_scaffolder.cpp: In member function ‘void path_extend::PathScaffolder::MergePaths(const path_extend::PathContainer&) const’:
/home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/path_scaffolder.cpp:48:33: warning: unused variable ‘scaffold_graph_serializer’ [-Wunused-variable]
         ScaffoldGraphSerializer scaffold_graph_serializer;
                                 ^~~~~~~~~~~~~~~~~~~~~~~~~
[ 86%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/scaffold_graph_gap_closer/cloud_scaffold_graph_gap_closer.cpp.o
[ 87%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/scaffold_graph_gap_closer/scaffold_graph_gap_closer.cpp.o
[ 87%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/fragment_model/secondary_stats_estimators.cpp.o
[ 87%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/extender_support/candidate_selectors.cpp.o
[ 87%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/extender_support/entry_collectors.cpp.o
[ 88%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/validation/transition_subgraph_validation.cpp.o
[ 88%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/statistics/path_cluster_statistics.cpp.o
[ 88%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/intermediate_scaffolding/scaffold_graph_path_cleaner.cpp.o
[ 89%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/validation/reference_path_index.cpp.o
[ 89%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/validation/path_cluster_validation.cpp.o
/home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/statistics/path_cluster_statistics.cpp: In member function ‘path_extend::PathClusterStatisticsExtractor::IdMap path_extend::PathClusterStatisticsExtractor::GetIdMap(const SimpleTransitionGraph&, const std::vector<path_extend::scaffold_graph::ScaffoldVertex>&) const’:
/home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/statistics/path_cluster_statistics.cpp:187:71: warning: unused parameter ‘correct_path’ [-Wunused-parameter]
         const vector<PathClusterStatisticsExtractor::ScaffoldVertex> &correct_path) const {
                                                                       ^~~~~~~~~~~~
[ 89%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/statistics/cloud_check_statistics.cpp.o
[ 89%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/statistics/component_validation.cpp.o
[ 90%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/statistics/long_edge_dataset.cpp.o
[ 90%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/statistics/perfect_transitions.cpp.o
[ 90%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/statistics/perfect_clouds.cpp.o
[ 90%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/statistics/coverage_break_analysis.cpp.o
/home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/statistics/component_validation.cpp: In member function ‘std::vector<path_extend::SimpleGraph<path_extend::scaffold_graph::ScaffoldVertex> > path_extend::ScaffoldGraphComponentExtractor::GetConnectedComponents(const ScaffoldGraph&) const’:
/home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/statistics/component_validation.cpp:38:12: warning: unused variable ‘trivial_components’ [-Wunused-variable]
     size_t trivial_components = 0;
            ^~~~~~~~~~~~~~~~~~
[ 91%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/statistics/path_scaffolder_analyzer.cpp.o
[ 91%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/contracted_graph_scaffolding/contracted_graph_scaffolder.cpp.o
/home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/statistics/perfect_transitions.cpp: In member function ‘path_extend::scaffold_graph::ScaffoldGraph path_extend::PerfectScaffoldGraphConstructor::ConstuctPerfectGraph(const std::vector<std::vector<path_extend::validation::EdgeWithMapping> >&, size_t) const’:
/home/dmm2017/cloudSPAdes-dev/src/common/modules/path_extend/read_cloud_path_extend/statistics/perfect_transitions.cpp:32:77: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (auto it2 = std::next(it1); it2 != path.end() and it2 - it1 <= next_edges; ++it2) {
                                                                   ~~~~~~~~~~^~~~~~~~~~~~~
[ 91%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/contracted_graph_scaffolding/contracted_gfa_writer.cpp.o
[ 91%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/statistics/short_edge_dataset.cpp.o
[ 92%] Building CXX object common/modules/path_extend/CMakeFiles/path_extend.dir/read_cloud_path_extend/statistics/split_index_statistics.cpp.o
[ 92%] Linking CXX static library libpath_extend.a
[ 92%] Built target path_extend
Scanning dependencies of target common_modules
[ 92%] Building CXX object common/CMakeFiles/common_modules.dir/empty.cpp.o
[ 92%] Linking CXX static library libcommon_modules.a
[ 92%] Built target common_modules
Scanning dependencies of target spades-kmercount
[ 92%] Building CXX object projects/kmercount/CMakeFiles/spades-kmercount.dir/main.cpp.o
Scanning dependencies of target spades-read-filter
Scanning dependencies of target spades-gbuilder
[ 92%] Building CXX object projects/kmercount/CMakeFiles/spades-read-filter.dir/read_filter.cpp.o
[ 92%] Building CXX object projects/gbuilder/CMakeFiles/spades-gbuilder.dir/main.cpp.o
Scanning dependencies of target spades-corrector-core
Scanning dependencies of target spades-truseq-scfcorrection
[ 92%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/positional_read.cpp.o
[ 92%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/interesting_pos_processor.cpp.o
[ 92%] Building CXX object projects/scaffold_correction/CMakeFiles/spades-truseq-scfcorrection.dir/main.cpp.o
Scanning dependencies of target spades-dipspades-core
[ 92%] Building CXX object projects/dipspades/CMakeFiles/spades-dipspades-core.dir/dipspades_config.cpp.o
Scanning dependencies of target spades-core
[ 92%] Building CXX object projects/dipspades/CMakeFiles/spades-dipspades-core.dir/utils/files_utils.cpp.o
[ 92%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o
[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/contig_processor.cpp.o
[ 93%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/gap_closer.cpp.o
/home/dmm2017/cloudSPAdes-dev/src/projects/corrector/contig_processor.cpp: In member function ‘bool corrector::ContigProcessor::CountPositions(const sam_reader::SingleSamRead&, std::unordered_map<long unsigned int, corrector::position_description>&) const’:
/home/dmm2017/cloudSPAdes-dev/src/projects/corrector/contig_processor.cpp:165:94: warning: conversion to ‘double’ from ‘size_t {aka long unsigned int}’ may alter its value [-Wconversion]
     if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) {
                                                                                              ^
/home/dmm2017/cloudSPAdes-dev/src/projects/corrector/contig_processor.cpp:165:115: warning: conversion to ‘double’ from ‘std::__cxx11::basic_string<char>::size_type {aka long unsigned int}’ may alter its value [-Wconversion]
     if ((aligned_length < min(read_len_double * 0.4, 40.0)) && (position > read_len_double / 2) && (contig_.length() > read_len_double / 2 + (double) position)) {
                                                                                                     ~~~~~~~~~~~~~~^~
[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/dataset_processor.cpp.o
[ 93%] Linking CXX executable ../../bin/spades-kmercount
[ 93%] Built target spades-kmercount
[ 93%] Building CXX object projects/dipspades/CMakeFiles/spades-dipspades-core.dir/main.cpp.o
[ 93%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/mismatch_correction.cpp.o
[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/config_struct.cpp.o
[ 93%] Building CXX object projects/corrector/CMakeFiles/spades-corrector-core.dir/main.cpp.o
[ 94%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/pair_info_count.cpp.o
[ 95%] Linking CXX executable ../../bin/spades-read-filter
[ 95%] Linking CXX executable ../../bin/spades-truseq-scfcorrection
[ 95%] Built target spades-read-filter
[ 95%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/second_phase_setup.cpp.o
[ 95%] Built target spades-truseq-scfcorrection
[ 95%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/distance_estimation.cpp.o
[ 96%] Linking CXX executable ../../bin/spades-corrector-core
[ 96%] Built target spades-corrector-core
[ 96%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/repeat_resolving.cpp.o
/home/dmm2017/cloudSPAdes-dev/src/projects/spades/pair_info_count.cpp: In function ‘bool debruijn_graph::CollectLibInformation(const conj_graph_pack&, size_t&, size_t, size_t)’:
/home/dmm2017/cloudSPAdes-dev/src/projects/spades/pair_info_count.cpp:224:46: warning: conversion to ‘double’ from ‘long unsigned int’ may alter its value [-Wconversion]
     if (data.median_insert_size < gp.k_value + 2)
                                   ~~~~~~~~~~~^~~
In file included from /home/dmm2017/cloudSPAdes-dev/src/projects/dipspades/polymorphic_bulge_remover/complex_bulge_remover.hpp:11:0,
                 from /home/dmm2017/cloudSPAdes-dev/src/projects/dipspades/polymorphic_bulge_remover/polymorphic_bulge_remover.hpp:11,
                 from /home/dmm2017/cloudSPAdes-dev/src/projects/dipspades/dipspades.hpp:16,
                 from /home/dmm2017/cloudSPAdes-dev/src/projects/dipspades/main.cpp:22:
/home/dmm2017/cloudSPAdes-dev/src/common/pipeline/graphio.hpp: In instantiation of ‘void debruijn_graph::graphio::ScanReadCloudDistributions(const string&, path_extend::cluster_model::DistributionPack&, const Graph&, bool) [with Graph = debruijn_graph::DeBruijnGraph; std::__cxx11::string = std::__cxx11::basic_string<char>]’:
/home/dmm2017/cloudSPAdes-dev/src/common/pipeline/graphio.hpp:1143:31:   required from ‘void debruijn_graph::graphio::ScanAll(const string&, graph_pack&, bool) [with graph_pack = debruijn_graph::graph_pack<debruijn_graph::DeBruijnGraph>; std::__cxx11::string = std::__cxx11::basic_string<char>]’
/home/dmm2017/cloudSPAdes-dev/src/projects/dipspades/dipspades.hpp:92:54:   required from here
/home/dmm2017/cloudSPAdes-dev/src/common/pipeline/graphio.hpp:1026:46: warning: unused parameter ‘g’ [-Wunused-parameter]
                                 const Graph& g, bool force_exists = true) {
                                              ^
In file included from /home/dmm2017/cloudSPAdes-dev/src/common/paired_info/insert_size_refiner.hpp:12:0,
                 from /home/dmm2017/cloudSPAdes-dev/src/common/paired_info/is_counter.hpp:12,
                 from /home/dmm2017/cloudSPAdes-dev/src/projects/spades/pair_info_count.cpp:8:
/home/dmm2017/cloudSPAdes-dev/src/common/assembly_graph/stats/picture_dump.hpp: In instantiation of ‘size_t debruijn_graph::stats::Nx(Graph&, double) [with Graph = debruijn_graph::DeBruijnGraph; size_t = long unsigned int]’:
/home/dmm2017/cloudSPAdes-dev/src/projects/spades/pair_info_count.cpp:319:109:   required from here
/home/dmm2017/cloudSPAdes-dev/src/common/assembly_graph/stats/picture_dump.hpp:457:24: warning: conversion to ‘double’ from ‘__gnu_cxx::__alloc_traits<std::allocator<long unsigned int> >::value_type {aka long unsigned int}’ may alter its value [-Wconversion]
         if (lengths[i] >= len_perc)

In file included from /home/dmm2017/cloudSPAdes-dev/src/common/utils/standard_base.hpp:135:0,
                 from /home/dmm2017/cloudSPAdes-dev/src/common/paired_info/insert_size_refiner.hpp:10,
                 from /home/dmm2017/cloudSPAdes-dev/src/common/paired_info/is_counter.hpp:12,
                 from /home/dmm2017/cloudSPAdes-dev/src/projects/spades/pair_info_count.cpp:8:
/home/dmm2017/cloudSPAdes-dev/src/common/math/xmath.h: In instantiation of ‘bool math::ls(T, U) [with T = int; U = omnigraph::de::DEWeight]’:
/home/dmm2017/cloudSPAdes-dev/src/common/math/xmath.h:314:34:   required from ‘bool math::gr(T, U) [with T = omnigraph::de::DEWeight; U = int]’
/home/dmm2017/cloudSPAdes-dev/src/common/paired_info/pair_info_filler.hpp:75:39:   required from here
/home/dmm2017/cloudSPAdes-dev/src/common/math/xmath.h:303:21: warning: conversion to ‘float’ from ‘int’ may alter its value [-Wconversion]
         return (lhs < rhs);
                ~~~~~^~~~~~
[ 96%] Linking CXX executable ../../bin/spades-gbuilder
[ 96%] Built target spades-gbuilder
[ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/contig_output_stage.cpp.o
[ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/hybrid_aligning.cpp.o
[ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/chromosome_removal.cpp.o
[ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/barcode_index_construction.cpp.o
[ 98%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/scaffold_graph_construction_stage.cpp.o
[ 98%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/scaffolder_analysis_stage.cpp.o
[ 98%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o
[ 99%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o
[ 99%] Linking CXX executable ../../bin/spades-core
[ 99%] Built target spades-core
[100%] Linking CXX executable ../../bin/spades-dipspades-core
[100%] Built target spades-dipspades-core
[  7%] Built target jemalloc
[ 15%] Built target nlopt
[ 19%] Built target ConsensusCore
[ 29%] Built target BamTools
[ 34%] Built target samtools
[ 34%] Built target format
[ 35%] Built target ssw
[ 36%] Built target cityhash
[ 37%] Built target getopt_pp
[ 43%] Built target llvm-support
[ 44%] Built target hattrie
[ 48%] Built target bwa
[ 49%] Built target gqf
[ 50%] Built target edlib
[ 50%] Built target gfa1
[ 59%] Built target spades-bwa
[ 60%] Built target coverage_model
[ 61%] Built target input
[ 62%] Built target pipeline
[ 63%] Built target sequence
[ 66%] Built target assembly_graph
[ 79%] Built target path_extend
[ 80%] Built target modules
[ 81%] Built target paired_info
[ 82%] Built target stages
[ 84%] Built target utils
[ 84%] Built target mph_index
[ 84%] Built target common_modules
[ 85%] Built target graphio
[ 89%] Built target spades-core
[ 92%] Built target spades-hammer
[ 96%] Built target spades-ionhammer
[ 97%] Built target spades-dipspades-core
[ 99%] Built target spades-corrector-core
[ 99%] Built target spades-truseq-scfcorrection
[100%] Built target spades-read-filter
[100%] Built target spades-kmercount
[100%] Built target spades-gbuilder
Install the project...
-- Install configuration: "RelWithAsserts"
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/bin/spades.py
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/bin/dipspades.py
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/bin/metaspades.py
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/bin/plasmidspades.py
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/bin/rnaspades.py
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/bin/truspades.py
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/bin/spades_init.py
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/VERSION
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset/ecoli_1K_1.fq.gz
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset/ecoli_1K_2.fq.gz
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset/genes_1K.gff
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset/genes_1K.txt
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset/operons_1K.gff
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset/operons_1K.txt
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset/reference_1K.fa.gz
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset_truspades
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset_truspades/A_R1.fastq.gz
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset_truspades/A_R2.fastq.gz
-- Up-to-date: /home/dmm2017/cloudSPAdes-dev/share/spades/test_dataset_truspades/B_R1.fastq.gz
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pgonzale60 commented 5 years ago

Hi @asl and @1dayac,

I'm using SPAdes 3.11.1 which was available in the cluster. However, I get err -11. Several of my assemblies stopped at the counting kmer step reporting only using 132 Mb of memory which makes me think that the problem is unrelated to memory.

I expected to solve this issue by compiling the source code (v3.13.1.tar.gz), but the compilation fails with a puzzling error 2.

params.txt spades.log compilation_spades_assembler.log

Any ideas on how to solve this?

Best wishes

Pablo

asl commented 5 years ago

I expected to solve this issue by compiling the source code (v3.13.1.tar.gz), but the compilation fails with a puzzling error 2.

The error is:

/ceph/users/pgonzales/.conda/envs/testForNext/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status

You need to have zlib installed. The configure seems to be picking the library from the conda env, but this won't work outside the environment.

I'm using SPAdes 3.11.1 which was available in the cluster. However, I get err -11. Several of my assemblies stopped at the counting kmer step reporting only using 132 Mb of memory which makes me think that the problem is unrelated to memory.

Yes. Most probably the problem is due to some I/O issues on your cluster.

pgonzale60 commented 5 years ago

I used a conda environment to try to compile SPAdes because cmake is not installed in the cluster and cmake failed to compile ("The C++ compiler does not support C++11 (e.g. std::unique_ptr)"). I'm planning to load the environment every time I launch SPAdes. I used conda install -c anaconda zlib in this environment and returned that all requested packages already installed. I'm now trying the SPAdes available through conda. So far it has gone beyond the kmer counting step and keeps going. If this doesn't work, I'll ask the cluster admins to help me compile it. Thanks for the quick response pointing what was the compilation error and clarifying that compiling from source would be my the best bet.