https://bioinformaticsonline.com/snippets/view/37500/installing-nextsv-on-ubuntu? https://bioinformaticsonline.com/snippets/view/37500/installing-nextsv-on-ubuntu Mon, 06 Aug 2018 17:35:56 -0500 https://bioinformaticsonline.com/snippets/view/37500/installing-nextsv-on-ubuntu ➜ Tools git:(master) ✗ git clone https://github.com/Nextomics/nextsv.git Cloning into 'nextsv'... remote: Counting objects: 369, done. remote: Total 369 (delta 0), reused 0 (delta 0), pack-reused 369 Receiving objects: 100% (369/369), 51.81 MiB | 21.72 MiB/s, done. Resolving deltas: 100% (223/223), done. Checking connectivity... done. ➜ Tools git:(master) ✗ cd nextsv ➜ nextsv git:(master) pip install argparse Collecting argparse Downloading https://files.pythonhosted.org/packages/f2/94/3af39d34be01a24a6e65433d19e107099374224905f1e0cc6bbe1fd22a2f/argparse-1.4.0-py2.py3-none-any.whl Installing collected packages: argparse Successfully installed argparse-1.4.0 ➜ nextsv git:(master) pip install pysam Requirement already satisfied: pysam in /home/urbe/anaconda3/lib/python3.6/site-packages (0.14.1) ➜ nextsv git:(master) pip install networkx Requirement already satisfied: networkx in /home/urbe/anaconda3/lib/python3.6/site-packages (2.1) Requirement already satisfied: decorator>=4.1.0 in /home/urbe/anaconda3/lib/python3.6/site-packages (from networkx) (4.3.0) ➜ nextsv git:(master) pip install h5py Requirement already satisfied: h5py in /home/urbe/anaconda3/lib/python3.6/site-packages (2.7.1) Requirement already satisfied: numpy>=1.7 in /home/urbe/anaconda3/lib/python3.6/site-packages (from h5py) (1.14.3) Requirement already satisfied: six in /home/urbe/anaconda3/lib/python3.6/site-packages (from h5py) (1.11.0) ➜ nextsv git:(master) pip install PyIntervalTree Collecting PyIntervalTree Downloading https://files.pythonhosted.org/packages/aa/53/dbdb521c8e36301108114878ff1620255c559c12ba8fe0ce2eaf9b65cbef/PyIntervalTree-0.5.zip Requirement already satisfied: sortedcontainers in /home/urbe/anaconda3/lib/python3.6/site-packages (from PyIntervalTree) (1.5.10) Building wheels for collected packages: PyIntervalTree Running setup.py bdist_wheel for PyIntervalTree ... done Stored in directory: /home/urbe/.cache/pip/wheels/23/26/eb/83ac050fa1d31ed660d26a2508a47799728b29a9a0048a6b17 Successfully built PyIntervalTree Installing collected packages: PyIntervalTree Successfully installed PyIntervalTree-0.5 ➜ nextsv git:(master) sh install_pbhoney.sh #### installation of PBHoney #### ######################################################################## Please add the following environmental variables to your ~/.bashrc file: export SWEETPATH=/home/urbe/Tools/nextsv/aligners_and_callers/PBSuite_15.8.24 export PYTHONPATH=$PYTHONPATH:$SWEETPATH export PATH=$PATH:$SWEETPATH/bin ######################################################################## ➜ nextsv git:(master) ✗ sh install_sniffles.sh #### installation of Sniffles #### building Sniffles -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- No build type specified. Using 'release' -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- 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 off64_t -- Check size of off64_t - done -- Looking for fseeko -- Looking for fseeko - found -- Looking for unistd.h -- Looking for unistd.h - found -- Configuring done -- Generating done -- Build files have been written to: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/build Scanning dependencies of target zlibstatic [ 1%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/adler32.o [ 2%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/compress.o [ 3%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/crc32.o [ 4%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/deflate.o [ 5%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzclose.o [ 6%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzlib.o [ 7%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzread.o [ 8%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/gzwrite.o [ 9%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inflate.o [ 10%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/infback.o [ 11%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inftrees.o [ 12%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/inffast.o [ 13%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/trees.o [ 14%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/uncompr.o [ 15%] Building C object lib/zlib-1.2.7/CMakeFiles/zlibstatic.dir/zutil.o [ 16%] Linking C static library libz.a [ 16%] Built target zlibstatic Scanning dependencies of target BamTools-static [ 17%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o [ 18%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o [ 19%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o [ 20%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o [ 21%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o [ 22%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o [ 23%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o [ 24%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o [ 25%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o [ 26%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o [ 27%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o [ 28%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o [ 29%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamMultiReader_p.cpp.o [ 30%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamRandomAccessController_p.cpp.o [ 31%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamReader_p.cpp.o [ 32%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamWriter_p.cpp.o [ 34%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/index/BamIndexFactory_p.cpp.o [ 35%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/index/BamStandardIndex_p.cpp.o /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp: In member function ‘void BamTools::Internal::BamStandardIndex::WriteLinearOffsets(const int&, BamTools::Internal::BaiLinearOffsetVector&)’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/index/BamStandardIndex_p.cpp:958:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( numBytesWritten != (sizeof(offsetCount) + linearOffsets.size()*sizeof( ^ [ 36%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/index/BamToolsIndex_p.cpp.o [ 37%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BamDeviceFactory_p.cpp.o [ 38%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFile_p.cpp.o [ 39%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BamFtp_p.cpp.o [ 40%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp:409:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) { ^ /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/lib/bamtools-2.3.0/src/api/internal/io/BamHttp_p.cpp:501:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( WriteToSocket(requestHeader.c_str(), headerSize) != headerSize ) { ^ [ 41%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o [ 42%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o [ 43%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o [ 44%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o [ 45%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o [ 46%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o [ 47%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o [ 48%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o [ 49%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o [ 50%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o [ 51%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o [ 52%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o [ 53%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o [ 54%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o [ 55%] Building CXX object lib/bamtools-2.3.0/src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o [ 56%] Linking CXX static library libbamtools.a [ 56%] Built target BamTools-static Scanning dependencies of target sniffles [ 57%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o [ 58%] Building CXX object src/CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/Genotyper/Genotyper.cpp: In member function ‘void Genotyper::update_file(Breakpoint_Tree&, breakpoint_node*&)’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/Genotyper/Genotyper.cpp:219:22: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(move.c_str()); ^ /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/Genotyper/Genotyper.cpp: In member function ‘void Genotyper::update_SVs()’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/Genotyper/Genotyper.cpp:293:21: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(del.c_str()); ^ [ 59%] Building CXX object src/CMakeFiles/sniffles.dir/Alignment.cpp.o [ 60%] Building CXX object src/CMakeFiles/sniffles.dir/BamParser.cpp.o [ 61%] Building CXX object src/CMakeFiles/sniffles.dir/Sniffles.cpp.o [ 62%] Building CXX object src/CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o [ 63%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o [ 64%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o [ 65%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o [ 67%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o [ 68%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o [ 69%] Building CXX object src/CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/realign/SWCPU.cpp: In constructor ‘SWCPUCor::SWCPUCor(int)’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/realign/SWCPU.cpp:30:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] fprintf(stderr, "Allocationg: %llu\n", maxLen * sizeof(MatrixElement)); ^ [ 70%] Building CXX object src/CMakeFiles/sniffles.dir/realign/Realign.cpp.o [ 71%] Building CXX object src/CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/VCFPrinter.cpp: In member function ‘virtual void VCFPrinter::print_body(Breakpoint*&, BamTools::RefVector)’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/VCFPrinter.cpp:154:41: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf(file, "%i", SV->get_length()); ^ [ 72%] Building CXX object src/CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp: In member function ‘virtual void BedpePrinter::print_body(Breakpoint*&, BamTools::RefVector)’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:35:89: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] file, "%i", IPrinter::calc_pos(SV->get_coordinates().start.max_pos, ref, chr)); ^ /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:42:88: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] (file, "%i", IPrinter::calc_pos(SV->get_coordinates().stop.max_pos, ref, chr)); ^ /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:70:41: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf(file, "%i", SV->get_length()); ^ [ 73%] Building CXX object src/CMakeFiles/sniffles.dir/print/IPrinter.cpp.o [ 74%] Building CXX object src/CMakeFiles/sniffles.dir/tree/BinTree.cpp.o [ 75%] Building CXX object src/CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o [ 76%] Building CXX object src/CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o [ 77%] Building CXX object src/CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/cluster/Cluster_SVs.cpp: In member function ‘void Cluster_SVS::update_SVs(std::vector<combine_str>&)’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/cluster/Cluster_SVs.cpp:87:22: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(move.c_str()); ^ /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/cluster/Cluster_SVs.cpp: In member function ‘void Cluster_SVS::update_SVs()’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/cluster/Cluster_SVs.cpp:159:21: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system(del.c_str()); ^ [ 78%] Linking CXX executable ../../bin/sniffles-core-1.0.5/sniffles [ 78%] Built target sniffles Scanning dependencies of target sniffles-debug [ 79%] Building CXX object src/CMakeFiles/sniffles-debug.dir/tree/Breakpoint_Tree.cpp.o [ 80%] Building CXX object src/CMakeFiles/sniffles-debug.dir/Genotyper/Genotyper.cpp.o [ 81%] Building CXX object src/CMakeFiles/sniffles-debug.dir/Alignment.cpp.o [ 82%] Building CXX object src/CMakeFiles/sniffles-debug.dir/BamParser.cpp.o [ 83%] Building CXX object src/CMakeFiles/sniffles-debug.dir/Sniffles.cpp.o [ 84%] Building CXX object src/CMakeFiles/sniffles-debug.dir/Ignore_Regions.cpp.o [ 85%] Building CXX object src/CMakeFiles/sniffles-debug.dir/tree/Intervall_bed.cpp.o [ 86%] Building CXX object src/CMakeFiles/sniffles-debug.dir/tree/IntervallList.cpp.o [ 87%] Building CXX object src/CMakeFiles/sniffles-debug.dir/sub/Detect_Breakpoints.cpp.o [ 88%] Building CXX object src/CMakeFiles/sniffles-debug.dir/sub/Breakpoint.cpp.o [ 89%] Building CXX object src/CMakeFiles/sniffles-debug.dir/tree/IntervallTree.cpp.o [ 90%] Building CXX object src/CMakeFiles/sniffles-debug.dir/realign/SWCPU.cpp.o /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/realign/SWCPU.cpp: In constructor ‘SWCPUCor::SWCPUCor(int)’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/realign/SWCPU.cpp:30:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] fprintf(stderr, "Allocationg: %llu\n", maxLen * sizeof(MatrixElement)); ^ [ 91%] Building CXX object src/CMakeFiles/sniffles-debug.dir/realign/Realign.cpp.o [ 92%] Building CXX object src/CMakeFiles/sniffles-debug.dir/print/VCFPrinter.cpp.o /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/VCFPrinter.cpp: In member function ‘virtual void VCFPrinter::print_body(Breakpoint*&, BamTools::RefVector)’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/VCFPrinter.cpp:154:41: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf(file, "%i", SV->get_length()); ^ [ 93%] Building CXX object src/CMakeFiles/sniffles-debug.dir/print/BedpePrinter.cpp.o /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp: In member function ‘virtual void BedpePrinter::print_body(Breakpoint*&, BamTools::RefVector)’: /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:35:89: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] file, "%i", IPrinter::calc_pos(SV->get_coordinates().start.max_pos, ref, chr)); ^ /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:42:88: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] (file, "%i", IPrinter::calc_pos(SV->get_coordinates().stop.max_pos, ref, chr)); ^ /home/urbe/Tools/nextsv/aligners_and_callers/Sniffles-1.0.5/src/print/BedpePrinter.cpp:70:41: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] fprintf(file, "%i", SV->get_length()); ^ [ 94%] Building CXX object src/CMakeFiles/sniffles-debug.dir/print/IPrinter.cpp.o [ 95%] Building CXX object src/CMakeFiles/sniffles-debug.dir/tree/BinTree.cpp.o [ 96%] Building CXX object src/CMakeFiles/sniffles-debug.dir/print/NGMPrinter.cpp.o [ 97%] Building CXX object src/CMakeFiles/sniffles-debug.dir/plane-sweep/PlaneSweep_slim.cpp.o [ 98%] Building CXX object src/CMakeFiles/sniffles-debug.dir/cluster/Cluster_SVs.cpp.o [100%] Linking CXX executable ../../bin/sniffles-core-1.0.5/sniffles-debug [100%] Built target sniffles-debug Installation of Sniffles finished ➜ nextsv git:(master) ✗]]> Jit