PING google.com (216.58.206.78) 56(84) bytes of data. 64 bytes from lhr35s11-in-f14.1e100.net (216.58.206.78): icmp_seq=1 ttl=52 time=3.61 ms 64 bytes from lhr35s11-in-f14.1e100.net (216.58.206.78): icmp_seq=2 ttl=52 time=3.63 ms samtools 1.7 Using htslib 1.7 Copyright (C) 2018 Genome Research Ltd. Initialized empty Git repository in /gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/.git/ Submodule 'bwa' (https://github.com/jwalabroad/bwa) registered for path 'bwa' Submodule 'fermi-lite' (https://github.com/jwalabroad/fermi-lite) registered for path 'fermi-lite' Submodule 'htslib' (https://github.com/samtools/htslib) registered for path 'htslib' Initialized empty Git repository in /gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/bwa/.git/ Submodule path 'bwa': checked out 'c02766e3c34ac3f4af9842e20a54b7f9f4b36d0b' Initialized empty Git repository in /gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/fermi-lite/.git/ Submodule path 'fermi-lite': checked out '5bc90f8d70e2b66184eccbd223a3be714c914365' Initialized empty Git repository in /gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/htslib/.git/ Submodule path 'htslib': checked out '6c06833519551eb61d4e5b9aceb2383e21996930' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /users/flint/rwdavies/seqlib_test/SeqLib/missing: Unknown `--is-lightweight' option Try `/users/flint/rwdavies/seqlib_test/SeqLib/missing --help' for more information configure: WARNING: 'missing' script is too old or missing checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing gzopen... -lz checking for library containing lzma_code... -llzma checking for library containing BZ2_bzBuffToBuffDecompress... -lbz2 checking for library containing clock_gettime... -lrt checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/seqtools/Makefile config.status: creating config.h config.status: executing depfiles commands make all-recursive make[1]: Entering directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib' Making all in bwa make[2]: Entering directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/bwa' gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o ar -csru libbwa.a utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o is.o bwtindex.o rope.o rle.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o gcc -c -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o gcc -g -Wall -Wno-unused-function -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt make[2]: Leaving directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/bwa' Making all in htslib make[2]: Entering directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/htslib' echo '/* Default config.h generated by Makefile */' > config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.4.1"' > version.h gcc -g -Wall -O2 -I. -c -o hts.o hts.c gcc -g -Wall -O2 -I. -c -o md5.o md5.c gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c gcc -g -Wall -O2 -I. -c -o realn.o realn.c gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -I. -c -o sam.o sam.c gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -Wall -O2 -I. -c -o cram/vlen.o cram/vlen.c gcc -g -Wall -O2 -I. -c -o cram/zfio.o cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/vlen.o cram/zfio.o ranlib libhts.a gcc -g -Wall -O2 -I. -fpic -c -o kfunc.pico kfunc.c gcc -g -Wall -O2 -I. -fpic -c -o knetfile.pico knetfile.c gcc -g -Wall -O2 -I. -fpic -c -o kstring.pico kstring.c gcc -g -Wall -O2 -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c gcc -g -Wall -O2 -I. -fpic -c -o bgzf.pico bgzf.c gcc -g -Wall -O2 -I. -fpic -c -o errmod.pico errmod.c gcc -g -Wall -O2 -I. -fpic -c -o faidx.pico faidx.c gcc -g -Wall -O2 -I. -fpic -c -o hfile.pico hfile.c gcc -g -Wall -O2 -I. -fpic -c -o hfile_net.pico hfile_net.c gcc -g -Wall -O2 -I. -fpic -c -o hts.pico hts.c gcc -g -Wall -O2 -I. -fpic -c -o md5.pico md5.c gcc -g -Wall -O2 -I. -fpic -c -o multipart.pico multipart.c gcc -g -Wall -O2 -I. -fpic -c -o probaln.pico probaln.c gcc -g -Wall -O2 -I. -fpic -c -o realn.pico realn.c gcc -g -Wall -O2 -I. -fpic -c -o regidx.pico regidx.c gcc -g -Wall -O2 -I. -fpic -c -o sam.pico sam.c gcc -g -Wall -O2 -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c gcc -g -Wall -O2 -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c gcc -g -Wall -O2 -I. -fpic -c -o tbx.pico tbx.c gcc -g -Wall -O2 -I. -fpic -c -o textutils.pico textutils.c gcc -g -Wall -O2 -I. -fpic -c -o thread_pool.pico thread_pool.c gcc -g -Wall -O2 -I. -fpic -c -o vcf.pico vcf.c gcc -g -Wall -O2 -I. -fpic -c -o vcfutils.pico vcfutils.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c gcc -g -Wall -O2 -I. -fpic -c -o cram/files.pico cram/files.c gcc -g -Wall -O2 -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c gcc -g -Wall -O2 -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c gcc -g -Wall -O2 -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c gcc -g -Wall -O2 -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c gcc -g -Wall -O2 -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c gcc -g -Wall -O2 -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c gcc -g -Wall -O2 -I. -fpic -c -o cram/vlen.pico cram/vlen.c gcc -g -Wall -O2 -I. -fpic -c -o cram/zfio.pico cram/zfio.c gcc -shared -Wl,-soname,libhts.so.2 -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico cram/vlen.pico cram/zfio.pico -lz -lm -lbz2 -llzma -lpthread ln -sf libhts.so libhts.so.2 gcc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o tabix.o tabix.c gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/hts_endian.o test/hts_endian.c test/hts_endian.c: In function 't_double': ./htslib/hts_endian.h:152: warning: dereferencing pointer 'buf.17' does break strict-aliasing rules ./htslib/hts_endian.h:152: note: initialized from here ./htslib/hts_endian.h:152: warning: dereferencing pointer 'buf.17' does break strict-aliasing rules ./htslib/hts_endian.h:152: note: initialized from here test/hts_endian.c: In function 't_float': ./htslib/hts_endian.h:136: warning: dereferencing pointer 'buf.16' does break strict-aliasing rules ./htslib/hts_endian.h:136: note: initialized from here ./htslib/hts_endian.h:136: warning: dereferencing pointer 'buf.16' does break strict-aliasing rules ./htslib/hts_endian.h:136: note: initialized from here gcc -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma gcc -g -Wall -O2 -I. -c -o test/fieldarith.o test/fieldarith.c gcc -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/hfile.o test/hfile.c gcc -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/sam.o test/sam.c gcc -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test-regidx.o test/test-regidx.c gcc -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test_view.o test/test_view.c gcc -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread gcc -g -Wall -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread make[2]: Leaving directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/htslib' Making all in fermi-lite make[2]: Entering directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/fermi-lite' gcc -c -g -Wall -O2 -Wno-unused-function kthread.c -o kthread.o gcc -c -g -Wall -O2 -Wno-unused-function misc.c -o misc.o gcc -c -g -Wall -O2 -Wno-unused-function bseq.c -o bseq.o gcc -c -g -Wall -O2 -Wno-unused-function htab.c -o htab.o gcc -c -g -Wall -O2 -Wno-unused-function bfc.c -o bfc.o gcc -c -g -Wall -O2 -Wno-unused-function rle.c -o rle.o gcc -c -g -Wall -O2 -Wno-unused-function rope.c -o rope.o gcc -c -g -Wall -O2 -Wno-unused-function mrope.c -o mrope.o gcc -c -g -Wall -O2 -Wno-unused-function rld0.c -o rld0.o gcc -c -g -Wall -O2 -Wno-unused-function unitig.c -o unitig.o gcc -c -g -Wall -O2 -Wno-unused-function mag.c -o mag.o gcc -c -g -Wall -O2 -Wno-unused-function bubble.c -o bubble.o gcc -c -g -Wall -O2 -Wno-unused-function f_ksw.c -o f_ksw.o ar -csru libfml.a kthread.o misc.o bseq.o htab.o bfc.o rle.o rope.o mrope.o rld0.o unitig.o mag.o bubble.o f_ksw.o gcc -c -g -Wall -O2 -Wno-unused-function example.c -o example.o gcc -g -Wall -O2 -Wno-unused-function libfml.a example.o -o fml-asm -L. -lfml -lm -lz -lpthread make[2]: Leaving directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/fermi-lite' Making all in src make[2]: Entering directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/src' g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-FastqReader.o -MD -MP -MF .deps/libseqlib_a-FastqReader.Tpo -c -o libseqlib_a-FastqReader.o `test -f 'FastqReader.cpp' || echo './'`FastqReader.cpp mv -f .deps/libseqlib_a-FastqReader.Tpo .deps/libseqlib_a-FastqReader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-BFC.o -MD -MP -MF .deps/libseqlib_a-BFC.Tpo -c -o libseqlib_a-BFC.o `test -f 'BFC.cpp' || echo './'`BFC.cpp mv -f .deps/libseqlib_a-BFC.Tpo .deps/libseqlib_a-BFC.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-ReadFilter.o -MD -MP -MF .deps/libseqlib_a-ReadFilter.Tpo -c -o libseqlib_a-ReadFilter.o `test -f 'ReadFilter.cpp' || echo './'`ReadFilter.cpp mv -f .deps/libseqlib_a-ReadFilter.Tpo .deps/libseqlib_a-ReadFilter.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-SeqPlot.o -MD -MP -MF .deps/libseqlib_a-SeqPlot.Tpo -c -o libseqlib_a-SeqPlot.o `test -f 'SeqPlot.cpp' || echo './'`SeqPlot.cpp mv -f .deps/libseqlib_a-SeqPlot.Tpo .deps/libseqlib_a-SeqPlot.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-jsoncpp.o -MD -MP -MF .deps/libseqlib_a-jsoncpp.Tpo -c -o libseqlib_a-jsoncpp.o `test -f 'jsoncpp.cpp' || echo './'`jsoncpp.cpp mv -f .deps/libseqlib_a-jsoncpp.Tpo .deps/libseqlib_a-jsoncpp.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-ssw_cpp.o -MD -MP -MF .deps/libseqlib_a-ssw_cpp.Tpo -c -o libseqlib_a-ssw_cpp.o `test -f 'ssw_cpp.cpp' || echo './'`ssw_cpp.cpp mv -f .deps/libseqlib_a-ssw_cpp.Tpo .deps/libseqlib_a-ssw_cpp.Po gcc -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -O2 -MT libseqlib_a-ssw.o -MD -MP -MF .deps/libseqlib_a-ssw.Tpo -c -o libseqlib_a-ssw.o `test -f 'ssw.c' || echo './'`ssw.c mv -f .deps/libseqlib_a-ssw.Tpo .deps/libseqlib_a-ssw.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-GenomicRegion.o -MD -MP -MF .deps/libseqlib_a-GenomicRegion.Tpo -c -o libseqlib_a-GenomicRegion.o `test -f 'GenomicRegion.cpp' || echo './'`GenomicRegion.cpp mv -f .deps/libseqlib_a-GenomicRegion.Tpo .deps/libseqlib_a-GenomicRegion.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-RefGenome.o -MD -MP -MF .deps/libseqlib_a-RefGenome.Tpo -c -o libseqlib_a-RefGenome.o `test -f 'RefGenome.cpp' || echo './'`RefGenome.cpp mv -f .deps/libseqlib_a-RefGenome.Tpo .deps/libseqlib_a-RefGenome.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-BamWriter.o -MD -MP -MF .deps/libseqlib_a-BamWriter.Tpo -c -o libseqlib_a-BamWriter.o `test -f 'BamWriter.cpp' || echo './'`BamWriter.cpp mv -f .deps/libseqlib_a-BamWriter.Tpo .deps/libseqlib_a-BamWriter.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-BamReader.o -MD -MP -MF .deps/libseqlib_a-BamReader.Tpo -c -o libseqlib_a-BamReader.o `test -f 'BamReader.cpp' || echo './'`BamReader.cpp mv -f .deps/libseqlib_a-BamReader.Tpo .deps/libseqlib_a-BamReader.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-BWAWrapper.o -MD -MP -MF .deps/libseqlib_a-BWAWrapper.Tpo -c -o libseqlib_a-BWAWrapper.o `test -f 'BWAWrapper.cpp' || echo './'`BWAWrapper.cpp mv -f .deps/libseqlib_a-BWAWrapper.Tpo .deps/libseqlib_a-BWAWrapper.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-BamRecord.o -MD -MP -MF .deps/libseqlib_a-BamRecord.Tpo -c -o libseqlib_a-BamRecord.o `test -f 'BamRecord.cpp' || echo './'`BamRecord.cpp mv -f .deps/libseqlib_a-BamRecord.Tpo .deps/libseqlib_a-BamRecord.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-FermiAssembler.o -MD -MP -MF .deps/libseqlib_a-FermiAssembler.Tpo -c -o libseqlib_a-FermiAssembler.o `test -f 'FermiAssembler.cpp' || echo './'`FermiAssembler.cpp mv -f .deps/libseqlib_a-FermiAssembler.Tpo .deps/libseqlib_a-FermiAssembler.Po g++ -DHAVE_CONFIG_H -I. -I.. -I../ -I../htslib -Wno-sign-compare -g -Wno-unknown-pragmas -g -O2 -MT libseqlib_a-BamHeader.o -MD -MP -MF .deps/libseqlib_a-BamHeader.Tpo -c -o libseqlib_a-BamHeader.o `test -f 'BamHeader.cpp' || echo './'`BamHeader.cpp mv -f .deps/libseqlib_a-BamHeader.Tpo .deps/libseqlib_a-BamHeader.Po rm -f libseqlib.a ar cru libseqlib.a libseqlib_a-FastqReader.o libseqlib_a-BFC.o libseqlib_a-ReadFilter.o libseqlib_a-SeqPlot.o libseqlib_a-jsoncpp.o libseqlib_a-ssw_cpp.o libseqlib_a-ssw.o libseqlib_a-GenomicRegion.o libseqlib_a-RefGenome.o libseqlib_a-BamWriter.o libseqlib_a-BamReader.o libseqlib_a-BWAWrapper.o libseqlib_a-BamRecord.o libseqlib_a-FermiAssembler.o libseqlib_a-BamHeader.o ranlib libseqlib.a make[2]: Leaving directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/src' make[2]: Entering directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib' make[2]: Leaving directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib' make[1]: Leaving directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib' mkdir -p bin && cd src/seqtools && make && mv seqtools ../../bin make[1]: Entering directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/src/seqtools' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../htslib -I../.. -g -Wno-unknown-pragmas -g -O2 -MT seqtools-seqtools.o -MD -MP -MF .deps/seqtools-seqtools.Tpo -c -o seqtools-seqtools.o `test -f 'seqtools.cpp' || echo './'`seqtools.cpp mv -f .deps/seqtools-seqtools.Tpo .deps/seqtools-seqtools.Po g++ -g -Wno-unknown-pragmas -g -O2 -o seqtools seqtools-seqtools.o ../libseqlib.a ../../htslib/libhts.a ../../bwa/libbwa.a ../../fermi-lite/libfml.a -lrt -lbz2 -llzma -lz -pthread make[1]: Leaving directory `/gpfs0/users/flint/rwdavies/seqlib_test/SeqLib/src/seqtools'