Mock Version: 1.3.4 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/samtools.spec'], nspawn_args=[]shell=Falseuid=996env={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PS1': ' \\s-\\v\\$ '}chrootPath='/var/lib/mock/epel-1-armhfp-8c6a07d96d4098d25b86a7c2310c8a2586291fc0/root'gid=135user='mockbuild'timeout=0logger=printOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target armv7hl --nodeps /builddir/build/SPECS/samtools.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PS1': ' \\s-\\v\\$ '} and shell False Building target platforms: armv7hl Building for target armv7hl Wrote: /builddir/build/SRPMS/samtools-1.9-3.el7.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', u'/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/samtools.spec'], nspawn_args=[]shell=Falseuid=996env={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PS1': ' \\s-\\v\\$ '}chrootPath='/var/lib/mock/epel-1-armhfp-8c6a07d96d4098d25b86a7c2310c8a2586291fc0/root'gid=135user='mockbuild'timeout=0logger=printOutput=False) Executing command: ['bash', '--login', '-c', u'/usr/bin/rpmbuild -bb --target armv7hl --nodeps /builddir/build/SPECS/samtools.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOSTNAME': 'mock', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'HOME': '/builddir', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PS1': ' \\s-\\v\\$ '} and shell False Building target platforms: armv7hl Building for target armv7hl Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.WGX2am + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf samtools-1.9 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/samtools-1.9.tar.bz2 + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + cd samtools-1.9 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -f INSTALL + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.4mhasH + umask 022 + cd /builddir/build/BUILD + cd samtools-1.9 + CFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I/usr/lib/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro ' + export LDFLAGS + '[' 1 == 1 ']' + '[' arm == ppc64le ']' ++ find . -name config.guess -o -name config.sub + ./configure --build=armv7hl-redhat-linux-gnu --host=armv7hl-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard' 'LDFLAGS=-Wl,-z,relro ' --prefix=/usr --with-htslib=system checking for armv7hl-redhat-linux-gnu-gcc... no checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for NcursesW wide-character library... yes checking for working ncursesw/curses.h... yes checking for working ncursesw.h... no checking for working ncurses.h... yes checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h + /usr/bin/make -j4 gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_index.o bam_index.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_plcmd.o bam_plcmd.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o sam_view.o sam_view.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_cat.o bam_cat.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_md.o bam_md.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_reheader.o bam_reheader.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_sort.o bam_sort.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bedidx.o bedidx.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_rmdup.o bam_rmdup.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_rmdupse.o bam_rmdupse.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_mate.o bam_mate.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_stat.o bam_stat.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.9"' > version.h gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam2bcf.o bam2bcf.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o sample.o sample.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o cut_target.o cut_target.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o phase.o phase.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam2depth.o bam2depth.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o padding.o padding.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bedcov.o bedcov.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bamshuf.o bamshuf.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o faidx.o faidx.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o dict.o dict.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o stats.o stats.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o stats_isize.o stats_isize.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_flags.o bam_flags.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_split.o bam_split.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_tview.o bam_tview.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_tview_html.o bam_tview_html.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_lpileup.o bam_lpileup.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_quickcheck.o bam_quickcheck.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_addrprg.o bam_addrprg.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_markdup.o bam_markdup.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o tmp_file.o tmp_file.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o lz4/lz4.o lz4/lz4.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_aux.o bam_aux.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam.o bam.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_import.o bam_import.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o sam.o sam.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o sam_header.o sam_header.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bam_plbuf.o bam_plbuf.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o sam_opts.o sam_opts.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o sam_utils.o sam_utils.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o misc/ace2sam.o misc/ace2sam.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -DMAQ_LONGREADS -I. -I./lz4 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o misc/md5fa.o misc/md5fa.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o misc/wgsim.o misc/wgsim.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o test/test.o test/test.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -march=armv7-a -mfpu=vfpv3-d16 -mfloat-abi=hard -I. -I./lz4 -c -o bamtk.o bamtk.c ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o ar -rcs libst.a sam_opts.o sam_utils.o gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o ./lz4/lz4.o libbam.a libst.a -lhts -lncursesw -lm -lz -lpthread gcc -L./lz4 -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o libst.a -lhts -lz -lpthread Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.FFb63A + exit 0 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm ++ dirname /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm + cd samtools-1.9 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.9-3.el7.arm mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/man/man1 install -p samtools /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin install -p -m 644 samtools.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/man/man1 + rm -f /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/varfilter.py ++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/zoom2sam.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/blast2sam.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/bowtie2sam.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/export2sam.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/interpolate_sam.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/novo2sam.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/plot-bamstats + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/psl2sam.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/sam2vcf.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/samtools.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/seq_cache_populate.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/soap2sam.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/wgsim_eval.pl + for file in '$(grep -l '\''^#!/usr/bin/env perl'\'' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/*)' + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/zoom2sam.pl + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 /builddir/build/BUILD/samtools-1.9 extracting debug info from /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/md5fa extracting debug info from /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/ace2sam extracting debug info from /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/samtools extracting debug info from /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/maq2sam-long extracting debug info from /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/maq2sam-short extracting debug info from /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/wgsim extracting debug info from /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/bin/md5sum-lite /usr/lib/rpm/sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match. 1860 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-compress + /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.QNSyS6 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.9 + ldd samtools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.2 => /lib/libhts.so.2 (0xb6f43000) + make test REF_PATH=: test/test.pl --exec bgzip= ${TEST_OPTS:-} bgzip -c -b 65272 -s 5 /tmp/aVzH4GV3rq/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/aVzH4GV3rq/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/aVzH4GV3rq/bgzip.dat.gz .. ok /builddir/build/BUILD/samtools-1.9/samtools faidx /tmp/aVzH4GV3rq/faidx.fa 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.9/samtools faidx /tmp/aVzH4GV3rq/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.9/samtools faidx /tmp/aVzH4GV3rq/faidx.fa 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.9/samtools faidx /tmp/aVzH4GV3rq/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.9/samtools faidx /tmp/aVzH4GV3rq/faidx.fa 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.9/samtools faidx /tmp/aVzH4GV3rq/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.9/samtools faidx /tmp/aVzH4GV3rq/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.9/samtools faidx /tmp/aVzH4GV3rq/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.9/samtools fqidx /tmp/aVzH4GV3rq/fqidx.fq 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.9/samtools fqidx /tmp/aVzH4GV3rq/fqidx.fq.gz 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.9/samtools fqidx /tmp/aVzH4GV3rq/fqidx.fq 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.9/samtools fqidx /tmp/aVzH4GV3rq/fqidx.fq.gz 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.9/samtools fqidx /tmp/aVzH4GV3rq/fqidx.fq 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.9/samtools fqidx /tmp/aVzH4GV3rq/fqidx.fq.gz 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.9/samtools fqidx /tmp/aVzH4GV3rq/fqidx.fq 1:99998-100007 .. ok .. ok /builddir/build/BUILD/samtools-1.9/samtools fqidx /tmp/aVzH4GV3rq/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /builddir/build/BUILD/samtools-1.9/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /builddir/build/BUILD/samtools-1.9/test/dat/dict.fa .. ok test_dict: /builddir/build/BUILD/samtools-1.9/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/aVzH4GV3rq/dict.fa.gz .. ok test_dict: cat /builddir/build/BUILD/samtools-1.9/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.9/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_index: /builddir/build/BUILD/samtools-1.9/samtools view /tmp/aVzH4GV3rq/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.9/samtools view /tmp/aVzH4GV3rq/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.9/samtools index /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.9/samtools view -@ 2 /tmp/aVzH4GV3rq/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.9/samtools view -@ 2 /tmp/aVzH4GV3rq/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.9/samtools index -@ 2 /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam.bai .. ok test_mpileup: /builddir/build/BUILD/samtools-1.9/samtools mpileup -b /tmp/aVzH4GV3rq/mpileup.bam.list -f /tmp/aVzH4GV3rq/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.9/samtools mpileup -b /tmp/aVzH4GV3rq/mpileup.cram.list -f /tmp/aVzH4GV3rq/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.9/samtools mpileup -b /tmp/aVzH4GV3rq/mpileup.bam.urllist -f /tmp/aVzH4GV3rq/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.9/samtools mpileup -b /tmp/aVzH4GV3rq/mpileup.cram.urllist -f /tmp/aVzH4GV3rq/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.9/samtools mpileup -uvDV -b /tmp/aVzH4GV3rq/mpileup.bam.list -f /tmp/aVzH4GV3rq/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /builddir/build/BUILD/samtools-1.9/samtools mpileup -uvDV -b /tmp/aVzH4GV3rq/mpileup.cram.list -f /tmp/aVzH4GV3rq/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /builddir/build/BUILD/samtools-1.9/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/aVzH4GV3rq/mpileup.cram.list -f /tmp/aVzH4GV3rq/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /builddir/build/BUILD/samtools-1.9/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/aVzH4GV3rq/mpileup.cram.list -f /tmp/aVzH4GV3rq/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /builddir/build/BUILD/samtools-1.9/samtools mpileup -B --ff 0x14 -f /tmp/aVzH4GV3rq/mpileup.ref.fa.gz -r17:1050-1060 /tmp/aVzH4GV3rq/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.9/samtools mpileup -B --ff 0x14 -f /tmp/aVzH4GV3rq/mpileup.ref.fa.gz -r17:1050-1060 /tmp/aVzH4GV3rq/mpileup.1.cram | grep -v mpileup .. ok test_usage: samtools test_view: Generating test data file test/test.pl: no IO::Pty module or can't open pty; skipping usage tests .................. done 1: SAM -> BAM -> SAM .. ok 2: SAM -> uncompressed BAM .. ok 3: uncompressed BAM -> SAM and compare .. ok 4: SAM -> fast compressed BAM .. ok 5: fast compressed BAM -> SAM and compare .. ok 6: SAM -> CRAM -> SAM (UR header tags) .. ok 7: SAM -> CRAM -> SAM (M5 header tags) .. ok 8: BAM -> CRAM with UR -> SAM .. ok 9: SAM -> BAM (M5 header tags) .. ok 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok 11: CRAM -> BAM with UR .. ok 12: CRAM -> BAM with M5 .. ok 13: SAM -> SAM via stdout .. ok 14: SAM -> BAM via stdout .. ok 15: SAM -> CRAM via stdout .. ok 16: SAM from stdin -> SAM .. ok 17: BAM from stdin -> SAM .. ok 18: CRAM from stdin -> SAM .. ok 19: samtools view -H (SAM input) .. ok 20: samtools view -H (BAM input) .. ok 21: samtools view -H (CRAM input) .. ok 22: No headers (SAM input) .. ok 23: No headers (BAM input) .. ok 24: No headers (CRAM input) .. ok 25: Filter -f 128 (SAM input) .. ok 26: Count -f 128 (SAM input) .. ok 27: Filter -f 128 (BAM input) .. ok 28: Count -f 128 (BAM input) .. ok 29: Filter -f 128 (CRAM input) .. ok 30: Count -f 128 (CRAM input) .. ok 31: Filter -F 128 (SAM input) .. ok 32: Count -F 128 (SAM input) .. ok 33: Filter -F 128 (BAM input) .. ok 34: Count -F 128 (BAM input) .. ok 35: Filter -F 128 (CRAM input) .. ok 36: Count -F 128 (CRAM input) .. ok 37: Filter -F 128 -f 2 (SAM input) .. ok 38: Count -F 128 -f 2 (SAM input) .. ok 39: Filter -F 128 -f 2 (BAM input) .. ok 40: Count -F 128 -f 2 (BAM input) .. ok 41: Filter -F 128 -f 2 (CRAM input) .. ok 42: Count -F 128 -f 2 (CRAM input) .. ok 43: Filter -r grp2 (SAM input) .. ok 44: Count -r grp2 (SAM input) .. ok 45: Filter -r grp2 (BAM input) .. ok 46: Count -r grp2 (BAM input) .. ok 47: Filter -r grp2 (CRAM input) .. ok 48: Count -r grp2 (CRAM input) .. ok 49: Filter -R /tmp/aVzH4GV3rq/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/aVzH4GV3rq/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/aVzH4GV3rq/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/aVzH4GV3rq/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/aVzH4GV3rq/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/aVzH4GV3rq/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/aVzH4GV3rq/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/aVzH4GV3rq/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/aVzH4GV3rq/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/aVzH4GV3rq/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/aVzH4GV3rq/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/aVzH4GV3rq/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/aVzH4GV3rq/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/aVzH4GV3rq/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/aVzH4GV3rq/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/aVzH4GV3rq/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/aVzH4GV3rq/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/aVzH4GV3rq/view.001.fogn (CRAM input).. ok 67: Filter -l Library 2 (SAM input) .. ok 68: Count -l Library 2 (SAM input) .. ok 69: Filter -l Library 2 (BAM input) .. ok 70: Count -l Library 2 (BAM input) .. ok 71: Filter -l Library 2 (CRAM input) .. ok 72: Count -l Library 2 (CRAM input) .. ok 73: Filter -l Library 3 (SAM input) .. ok 74: Count -l Library 3 (SAM input) .. ok 75: Filter -l Library 3 (BAM input) .. ok 76: Count -l Library 3 (BAM input) .. ok 77: Filter -l Library 3 (CRAM input) .. ok 78: Count -l Library 3 (CRAM input) .. ok 79: Filter -q 50 (SAM input) .. ok 80: Count -q 50 (SAM input) .. ok 81: Filter -q 50 (BAM input) .. ok 82: Count -q 50 (BAM input) .. ok 83: Filter -q 50 (CRAM input) .. ok 84: Count -q 50 (CRAM input) .. ok 85: Filter -q 99 (SAM input) .. ok 86: Count -q 99 (SAM input) .. ok 87: Filter -q 99 (BAM input) .. ok 88: Count -q 99 (BAM input) .. ok 89: Filter -q 99 (CRAM input) .. ok 90: Count -q 99 (CRAM input) .. ok 91: Filter -q 100 (SAM input) .. ok 92: Count -q 100 (SAM input) .. ok 93: Filter -q 100 (BAM input) .. ok 94: Count -q 100 (BAM input) .. ok 95: Filter -q 100 (CRAM input) .. ok 96: Count -q 100 (CRAM input) .. ok 97: Filter -x fa (SAM input) .. ok 98: Count -x fa (SAM input) .. ok 99: Filter -x fa (BAM input) .. ok 100: Count -x fa (BAM input) .. ok 101: Filter -x fa (CRAM input) .. ok 102: Count -x fa (CRAM input) .. ok 103: Filter -x fa -x ha (SAM input) .. ok 104: Count -x fa -x ha (SAM input) .. ok 105: Filter -x fa -x ha (BAM input) .. ok 106: Count -x fa -x ha (BAM input) .. ok 107: Filter -x fa -x ha (CRAM input) .. ok 108: Count -x fa -x ha (CRAM input) .. ok 109: Filter -x fa -r grp2 (SAM input) .. ok 110: Count -x fa -r grp2 (SAM input) .. ok 111: Filter -x fa -r grp2 (BAM input) .. ok 112: Count -x fa -r grp2 (BAM input) .. ok 113: Filter -x fa -r grp2 (CRAM input) .. ok 114: Count -x fa -r grp2 (CRAM input) .. ok 115: Filter -x RG -r grp2 (SAM input) .. ok 116: Count -x RG -r grp2 (SAM input) .. ok 117: Filter -x RG -r grp2 (BAM input) .. ok 118: Count -x RG -r grp2 (BAM input) .. ok 119: Filter -x RG -r grp2 (CRAM input) .. ok 120: Count -x RG -r grp2 (CRAM input) .. ok 121: Filter -m 10 (SAM input) .. ok 122: Count -m 10 (SAM input) .. ok 123: Filter -m 10 (BAM input) .. ok 124: Count -m 10 (BAM input) .. ok 125: Filter -m 10 (CRAM input) .. ok 126: Count -m 10 (CRAM input) .. ok 127: Filter -m 11 (SAM input) .. ok 128: Count -m 11 (SAM input) .. ok 129: Filter -m 11 (BAM input) .. ok 130: Count -m 11 (BAM input) .. ok 131: Filter -m 11 (CRAM input) .. ok 132: Count -m 11 (CRAM input) .. ok 133: Filter -m 15 (SAM input) .. ok 134: Count -m 15 (SAM input) .. ok 135: Filter -m 15 (BAM input) .. ok 136: Count -m 15 (BAM input) .. ok 137: Filter -m 15 (CRAM input) .. ok 138: Count -m 15 (CRAM input) .. ok 139: Filter -m 16 (SAM input) .. ok 140: Count -m 16 (SAM input) .. ok 141: Filter -m 16 (BAM input) .. ok 142: Count -m 16 (BAM input) .. ok 143: Filter -m 16 (CRAM input) .. ok 144: Count -m 16 (CRAM input) .. ok 145: 1bp reads file SAM -> BAM -> SAM .. ok 146: 1bp reads file SAM -> CRAM -> SAM .. ok 146: Region Z (BAM input) .. ok 147: Count Z (BAM input) .. ok 148: Region Z (CRAM input) .. ok 149: Count Z (CRAM input) .. ok 150: Region Z:30 (BAM input) .. ok 151: Count Z:30 (BAM input) .. ok 152: Region Z:30 (CRAM input) .. ok 153: Count Z:30 (CRAM input) .. ok 154: Region Z:20-40 (BAM input) .. ok 155: Count Z:20-40 (BAM input) .. ok 156: Region Z:20-40 (CRAM input) .. ok 157: Count Z:20-40 (CRAM input) .. ok 158: Region ref1 (BAM input) .. ok 159: Count ref1 (BAM input) .. ok 160: Region ref1 (CRAM input) .. ok 161: Count ref1 (CRAM input) .. ok 162: Region ref1:15 (BAM input) .. ok 163: Count ref1:15 (BAM input) .. ok 164: Region ref1:15 (CRAM input) .. ok 165: Count ref1:15 (CRAM input) .. ok 166: Region ref1:15-45 (BAM input) .. ok 167: Count ref1:15-45 (BAM input) .. ok 168: Region ref1:15-45 (CRAM input) .. ok 169: Count ref1:15-45 (CRAM input) .. ok 170: Region ref1:15-45 ref2 (BAM input) .. ok 171: Count ref1:15-45 ref2 (BAM input) .. ok 172: Region ref1:15-45 ref2 (CRAM input) .. ok 173: Count ref1:15-45 ref2 (CRAM input) .. ok 174: Region ref1:15-45 ref2:16 (BAM input) .. ok 175: Count ref1:15-45 ref2:16 (BAM input) .. ok 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 186: Region -f 128 ref1 (BAM input) .. ok 187: Count -f 128 ref1 (BAM input) .. ok 188: Region -f 128 ref1 (CRAM input) .. ok 189: Count -f 128 ref1 (CRAM input) .. ok 190: Region -q 50 ref1:15-45 (BAM input) .. ok 191: Count -q 50 ref1:15-45 (BAM input) .. ok 192: Region -q 50 ref1:15-45 (CRAM input) .. ok 193: Count -q 50 ref1:15-45 (CRAM input) .. ok 194: Region -r grp2 ref1:15-45 (BAM input) .. ok 195: Count -r grp2 ref1:15-45 (BAM input) .. ok 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok 198: Region * (BAM input) .. ok 199: Count * (BAM input) .. ok 200: Region * (CRAM input) .. ok 201: Count * (CRAM input) .. ok 202: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed (BAM input).. ok 203: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed (BAM input).. ok 204: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed (CRAM input).. ok 205: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed (CRAM input).. ok 206: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.02.bed (BAM input).. ok 207: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.02.bed (BAM input).. ok 208: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.02.bed (CRAM input).. ok 209: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.02.bed (CRAM input).. ok 210: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed (BAM input).. ok 211: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed (BAM input).. ok 212: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed (CRAM input).. ok 213: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed (CRAM input).. ok 214: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.02.bed (BAM input).. ok 215: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.02.bed (BAM input).. ok 216: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.02.bed (CRAM input).. ok 217: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.02.bed (CRAM input).. ok 218: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z (BAM input).. ok 219: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z (BAM input).. ok 220: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z (CRAM input).. ok 221: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z (CRAM input).. ok 222: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:30 (BAM input).. ok 223: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:30 (BAM input).. ok 224: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 225: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 226: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 227: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 228: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 229: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 230: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 231: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 232: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 233: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 234: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 235: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 236: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 237: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 238: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref2 (BAM input).. ok 239: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref2 (BAM input).. ok 240: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref2 (CRAM input).. ok 241: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref2 (CRAM input).. ok 242: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 243: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 244: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 245: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 246: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 247: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 248: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 249: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 250: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -f 128 (BAM input).. ok 251: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -f 128 (BAM input).. ok 252: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 253: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 254: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -q 5 (BAM input).. ok 255: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -q 5 (BAM input).. ok 256: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 257: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 258: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 259: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 260: Region -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 261: Count -L /builddir/build/BUILD/samtools-1.9/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 262: Make BAM with no M5/UR tags .. ok 263: Add @SQ with -t (SAM -> SAM) .. ok 264: Add @SQ with -T (SAM -> SAM) .. ok 265: Add @SQ with -t (BAM -> SAM) .. ok 266: Add @SQ with -T (BAM -> SAM) .. ok 267: Add @SQ with -t (SAM -> BAM) .. ok 268: Add @SQ with -T (SAM -> BAM) .. ok 269: Add @SQ with -t (BAM -> BAM) .. ok 270: Add @SQ with -T (BAM -> BAM) .. ok 271: Add @SQ with -t (SAM -> CRAM) .. ok 272: Add @SQ with -T (SAM -> CRAM) .. ok 273: Add @SQ with -t (BAM -> CRAM) .. ok 274: Add @SQ with -T (BAM -> CRAM) .. ok 275: Make CRAM with no UR field .. ok 276: Decoding CRAM with no UR field via -T .. ok 277: CIGAR B-operator removal .. ok 278: Big SAM -> BAM .. ok 279: Big SAM -> BAM (2 threads) .. ok 280: Big SAM -> BAM (4 threads) .. ok 281: Big SAM -> CRAM .. ok 282: Big SAM -> CRAM (2 threads) .. ok 283: Big SAM -> CRAM (4 threads) .. ok 284: Subsample 0.2 (SAM input) ............ ok 285: Subsample 0.5 (SAM input) ............ ok 286: Subsample 0.8 (SAM input) ............ ok 287: Subsample 0.2 (BAM input) ............ ok 288: Subsample 0.5 (BAM input) ............ ok 289: Subsample 0.8 (BAM input) ............ ok 290: Subsample 0.2 (CRAM input) ............ ok 291: Subsample 0.5 (CRAM input) ............ ok 292: Subsample 0.8 (CRAM input) ............ ok test_cat: Generating test data file .................. done Generate BAM file #1 .. ok Generate CRAM file #1 .. ok Generating test data file .................. done Generate BAM file #2 .. ok Generate CRAM file #2 .. ok Generating test data file .................. done Generate BAM file #3 .. ok Generate CRAM file #3 .. ok Generating test data file .................. done Generate BAM file #4 .. ok Generate CRAM file #4 .. ok 1: cat BAM files .. ok 2: cat recompressed BAM files .. ok 3: cat CRAM files .. ok 4: cat BAM files to stdout .. ok 5: cat recompressed BAM files to stdout .. ok 6: cat CRAM files to stdout .. ok 7: cat BAM files with new header .. ok 8: cat recompressed BAM files with new header .. ok 9: cat CRAM files with new header .. ok test_bam2fq: Generate BAM file .. ok Generate CRAM file .. ok 1: fastq (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.9/test/bc.fq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.9/test/bc.fq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.9/test/bc.fq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.9/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -N -t -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -N -t -i -T MD,ia -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.9/test/i.fq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.703.sam .. ok test_bam2fq: Generate BAM file (2 threads) .. ok Generate CRAM file (2 threads) .. ok 1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok 6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] discarded 0 singletons [M::bam2fq_mainloop] processed 36 reads .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.9/test/bc.fq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.9/test/bc.fq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.9/test/bc.fq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.9/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 -N -t -i -T MD,ia -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.9/test/i.fq -s /builddir/build/BUILD/samtools-1.9/test/s.fq -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.9/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.9/test/1.fq -2 /builddir/build/BUILD/samtools-1.9/test/2.fq /builddir/build/BUILD/samtools-1.9/test/dat/bam2fq.703.sam .. ok test_depad: Generate BAM file .. ok depad (SAM input) .. ok depad -s (SAM input) .. ok depad -u (SAM input) .. ok depad -1 (SAM input) .. ok depad (BAM input) .. ok depad -s (BAM input) .. ok depad -u (BAM input) .. ok depad -1 (BAM input) .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -r /builddir/build/BUILD/samtools-1.9/test/stat/test.fa /builddir/build/BUILD/samtools-1.9/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -r /builddir/build/BUILD/samtools-1.9/test/stat/test.fa /builddir/build/BUILD/samtools-1.9/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -r /builddir/build/BUILD/samtools-1.9/test/stat/test.fa /builddir/build/BUILD/samtools-1.9/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -r /builddir/build/BUILD/samtools-1.9/test/stat/test.fa /builddir/build/BUILD/samtools-1.9/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -r /builddir/build/BUILD/samtools-1.9/test/stat/test.fa /builddir/build/BUILD/samtools-1.9/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -r /builddir/build/BUILD/samtools-1.9/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.9/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -r /builddir/build/BUILD/samtools-1.9/test/stat/test.fa /builddir/build/BUILD/samtools-1.9/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -r /builddir/build/BUILD/samtools-1.9/test/stat/test.fa /builddir/build/BUILD/samtools-1.9/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.9/test/stat/test.fa /builddir/build/BUILD/samtools-1.9/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.9/test/stat/test.fa /builddir/build/BUILD/samtools-1.9/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -t /builddir/build/BUILD/samtools-1.9/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.9/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats /builddir/build/BUILD/samtools-1.9/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.9/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.9/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats -g 4 /builddir/build/BUILD/samtools-1.9/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats /builddir/build/BUILD/samtools-1.9/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.9/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats /builddir/build/BUILD/samtools-1.9/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.9/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats /builddir/build/BUILD/samtools-1.9/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.9/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.9/samtools stats /builddir/build/BUILD/samtools-1.9/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.9/test/stat/12_2reads.bed | tail -n+4 .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -s 1 -O sam -b /tmp/DmSH8aZr3q - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/aVzH4GV3rq/merge.tag.1.bam /tmp/aVzH4GV3rq/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/aVzH4GV3rq/merge.tag.3.bam /tmp/aVzH4GV3rq/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -@ 2 -s 1 -O sam -b /tmp/RB3vJ4khnC - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/aVzH4GV3rq/merge.tag.1.bam /tmp/aVzH4GV3rq/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.9/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/aVzH4GV3rq/merge.tag.3.bam /tmp/aVzH4GV3rq/merge.tag.4.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam /tmp/aVzH4GV3rq/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -f /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam /tmp/aVzH4GV3rq/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -o /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam /tmp/aVzH4GV3rq/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -n /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -t RG /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -n -t RG /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -t AS /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -t FI /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam /tmp/aVzH4GV3rq/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam /tmp/aVzH4GV3rq/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam /tmp/aVzH4GV3rq/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -@ 2 -n /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -@ 2 -t RG /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -@ 2 -n -t RG /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -@ 2 -t AS /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.9/samtools sort -@ 2 -t FI /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate -o /builddir/build/BUILD/samtools-1.9/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate -o /builddir/build/BUILD/samtools-1.9/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.9/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.9/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.9/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.9/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.9/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.9/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.9/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.9/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.9/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.9/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.9/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.9/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.9/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.9/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.9/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.9/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.9/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.9/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.9/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.9/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.9/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.9/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.9/test/fixmate/1_coord_sort.sam - ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname. .. expected failure test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.9/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.9/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.9/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.9/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.9/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.9/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.9/test/fixmate/7_two_read_mapped.sam - .. ok /builddir/build/BUILD/samtools-1.9/samtools calmd -uAr /builddir/build/BUILD/samtools-1.9/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.9/test/dat/mpileup.ref.fa .. ok /builddir/build/BUILD/samtools-1.9/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.9/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.9/test/dat/mpileup.ref.fa .. ok test_idxstat: /builddir/build/BUILD/samtools-1.9/samtools idxstats /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.bam .. ok test_idxstat: /builddir/build/BUILD/samtools-1.9/samtools idxstats /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.cram .. ok test_idxstat: /builddir/build/BUILD/samtools-1.9/samtools idxstats /builddir/build/BUILD/samtools-1.9/test/dat/test_input_1_a.sam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.9/samtools quickcheck /builddir/build/BUILD/samtools-1.9/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.9/samtools quickcheck /builddir/build/BUILD/samtools-1.9/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.9/samtools quickcheck /builddir/build/BUILD/samtools-1.9/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.9/samtools quickcheck /builddir/build/BUILD/samtools-1.9/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.9/samtools quickcheck /builddir/build/BUILD/samtools-1.9/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.9/samtools quickcheck /builddir/build/BUILD/samtools-1.9/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.9/samtools quickcheck /builddir/build/BUILD/samtools-1.9/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.9/samtools quickcheck /builddir/build/BUILD/samtools-1.9/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.9/samtools quickcheck /builddir/build/BUILD/samtools-1.9/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.9/samtools quickcheck -v /builddir/build/BUILD/samtools-1.9/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.9/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.9/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.9/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.9/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.9/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.9/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.9/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.9/test/quickcheck/9.quickcheck.cram30.truncated.cram | sed 's,.*/quickcheck/,,' .. ok test_reheader: /builddir/build/BUILD/samtools-1.9/samtools reheader /builddir/build/BUILD/samtools-1.9/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.9/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.9/samtools view -h | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.9/samtools reheader /builddir/build/BUILD/samtools-1.9/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.9/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.9/samtools view -h | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.9/samtools reheader /builddir/build/BUILD/samtools-1.9/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.9/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.9/samtools view -h | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.9/samtools reheader --in-place /builddir/build/BUILD/samtools-1.9/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.9/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.9/samtools view -h /builddir/build/BUILD/samtools-1.9/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.9/samtools reheader --in-place /builddir/build/BUILD/samtools-1.9/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.9/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.9/samtools view -h /builddir/build/BUILD/samtools-1.9/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.9/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -O sam -R '1#7' /builddir/build/BUILD/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.9/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.9/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.9/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -@ 2 -O sam -R '1#7' /builddir/build/BUILD/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.9/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.9/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.9/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.9/test/addrprg/4_fixup_norg.sam .. ok test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/2_bad_order.sam - ERR: [markdup] error: bad coordinate order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -O sam -r /builddir/build/BUILD/samtools-1.9/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -S -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -@ 2 -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -@ 2 -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/2_bad_order.sam - ERR: [markdup] error: bad coordinate order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -@ 2 -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/3_missing_mc.sam - ERR: [markdup] error: no MC tag. Please run samtools fixmate on file first. [markdup] error: unable to assign pair hash key. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -@ 2 -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/4_missing_ms.sam - ERR: [markdup] error: no ms score tag. Please run samtools fixmate on file first. [markdup] error: no ms score tag. Please run samtools fixmate on file first. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -@ 2 -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -@ 2 -O sam -r /builddir/build/BUILD/samtools-1.9/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.9/samtools markdup -@ 2 -S -O sam /builddir/build/BUILD/samtools-1.9/test/markdup/7_mark_supp_dup.sam - .. ok test_bedcov: /builddir/build/BUILD/samtools-1.9/samtools bedcov /builddir/build/BUILD/samtools-1.9/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.9/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.9/samtools bedcov -j /builddir/build/BUILD/samtools-1.9/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.9/test/bedcov/bedcov.bam .. ok Number of tests: total .. 535 passed .. 525 failed .. 0 expected failure .. 10 unexpected pass .. 0 test/merge/test_bam_translate test/merge/test_bam_translate.tmp test/merge/test_rtrans_build test/merge/test_trans_tbl_init cd test/mpileup && ./regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -Q0 -x -f c1.fa c1#pad1.bam EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -Q0 -x -f c1.fa c1#pad2.bam EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 153 Unexpected passes: 0 Expected failures: 3 Unexpected failures: 0 => PASS cd test/mpileup && ./regression.sh depth.reg === Testing depth.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools depth -a -b xx.bed3 xx#depth3.bam Expected passes: 43 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args + exit 0 Processing files: samtools-1.9-3.el7.armv7hl Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.MXoomA + umask 022 + cd /builddir/build/BUILD + cd samtools-1.9 + DOCDIR=/builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/doc/samtools-1.9 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/doc/samtools-1.9 + cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/doc/samtools-1.9 + cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/doc/samtools-1.9 + cp -pr NEWS /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/doc/samtools-1.9 + cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/doc/samtools-1.9 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.qOZW08 + exit 0 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.9 + LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/licenses/samtools-1.9 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/licenses/samtools-1.9 + cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm/usr/share/licenses/samtools-1.9 + exit 0 Provides: samtools = 1.9-3.el7 samtools(armv7hl-32) = 1.9-3.el7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl ld-linux-armhf.so.3 ld-linux-armhf.so.3(GLIBC_2.4) libc.so.6 libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libgcc_s.so.1 libgcc_s.so.1(GCC_3.5) libhts.so.2 libm.so.6 libm.so.6(GLIBC_2.4) libncursesw.so.5 libpthread.so.0 libpthread.so.0(GLIBC_2.4) libtinfo.so.5 libz.so.1 libz.so.1(ZLIB_1.2.3.3) perl(Carp) perl(Data::Dumper) perl(Digest::MD5) perl(File::Find) perl(File::Path) perl(File::Spec) perl(File::Spec::Functions) perl(File::Temp) perl(Getopt::Long) perl(Getopt::Std) perl(IO::Handle) perl(List::Util) perl(constant) perl(strict) perl(warnings) rtld(GNU_HASH) Processing files: samtools-debuginfo-1.9-3.el7.armv7hl Provides: samtools-debuginfo = 1.9-3.el7 samtools-debuginfo(armv7hl-32) = 1.9-3.el7 Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm Wrote: /builddir/build/RPMS/samtools-1.9-3.el7.armv7hl.rpm Wrote: /builddir/build/RPMS/samtools-debuginfo-1.9-3.el7.armv7hl.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.7mBCUa + umask 022 + cd /builddir/build/BUILD + cd samtools-1.9 + /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.9-3.el7.arm + exit 0 Child return code was: 0