Mock Version: 2.11 Mock Version: 2.11 Mock Version: 2.11 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target s390x --nodeps /builddir/build/SPECS/samtools.spec'], chrootPath='/var/lib/mock/f35-build-29050408-3953142/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target s390x --nodeps /builddir/build/SPECS/samtools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1626998400 Wrote: /builddir/build/SRPMS/samtools-1.13-1.fc35.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target s390x --nodeps /builddir/build/SPECS/samtools.spec'], chrootPath='/var/lib/mock/f35-build-29050408-3953142/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target s390x --nodeps /builddir/build/SPECS/samtools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: s390x Building for target s390x setting SOURCE_DATE_EPOCH=1626998400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.SNxDLI + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf samtools-1.13 + /usr/bin/bzip2 -dc /builddir/build/SOURCES/samtools-1.13.tar.bz2 + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd samtools-1.13 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -f INSTALL + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.yR0jYn + umask 022 + cd /builddir/build/BUILD + cd samtools-1.13 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']' ++ find . -type f -name configure -print + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure + diff -u ./configure.backup ./configure + mv ./configure.backup ./configure + for file in $(find . -type f -name configure -print) + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./htslib-1.13/configure + diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure + mv ./htslib-1.13/configure.backup ./htslib-1.13/configure + /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./htslib-1.13/configure + diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure + mv ./htslib-1.13/configure.backup ./htslib-1.13/configure + /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./htslib-1.13/configure + diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure --- ./htslib-1.13/configure.backup 2021-07-07 18:06:34.000000000 +0000 +++ ./htslib-1.13/configure 2021-08-09 12:58:26.565892844 +0000 @@ -1697,7 +1697,7 @@ #ifdef __cplusplus extern "C" #endif -char $2 (); +__attribute__ ((used)) char $2 (); /* The GNU C library defines this for functions which it implements to always fail with ENOSYS. Some functions are actually named something starting with __ and the normal name is an alias. */ + /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./htslib-1.13/configure + diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure + mv ./htslib-1.13/configure.backup ./htslib-1.13/configure + /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./htslib-1.13/configure + diff -u ./htslib-1.13/configure.backup ./htslib-1.13/configure + mv ./htslib-1.13/configure.backup ./htslib-1.13/configure + '[' 1 = 1 ']' +++ dirname ./configure ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' ++ find . -name ltmain.sh + ./configure --build=s390x-redhat-linux-gnu --host=s390x-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/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection' 'LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 ' --prefix=/usr --with-htslib=system checking for gawk... gawk checking for s390x-redhat-linux-gnu-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 grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no 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 library containing cbreak... none required 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 -O -j2 V=1 VERBOSE=1 gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_index.o bam_index.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_view.o sam_view.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_plcmd.o bam_plcmd.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_fastq.o bam_fastq.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_cat.o bam_cat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_md.o bam_md.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_reheader.o bam_reheader.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_rmdup.o bam_rmdup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_rmdupse.o bam_rmdupse.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_mate.o bam_mate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_stat.o bam_stat.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_color.o bam_color.c echo '#define SAMTOOLS_VERSION "1.13"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h echo '#define SAMTOOLS_CPPFLAGS ""' >> version.h echo '#define SAMTOOLS_CFLAGS "-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection"' >> version.h echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 "' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h echo '#define SAMTOOLS_CURSES_LIB "-lncursesw"' >> version.h gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2bcf.o bam2bcf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_sort.o bam_sort.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sample.o sample.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o cut_target.o cut_target.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2bcf_indel.o bam2bcf_indel.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam2depth.o bam2depth.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o phase.o phase.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o coverage.o coverage.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o padding.o padding.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bedcov.o bedcov.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o faidx.o faidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o dict.o dict.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bamshuf.o bamshuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o stats_isize.o stats_isize.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_flags.o bam_flags.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_split.o bam_split.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview.o bam_tview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o stats.o stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview_curses.o bam_tview_curses.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_tview_html.o bam_tview_html.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_quickcheck.o bam_quickcheck.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_lpileup.o bam_lpileup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_addrprg.o bam_addrprg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o tmp_file.o tmp_file.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_ampliconclip.o bam_ampliconclip.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_markdup.o bam_markdup.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_import.o bam_import.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o amplicon_stats.o amplicon_stats.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_aux.o bam_aux.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam.o bam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam.o sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bam_plbuf.o bam_plbuf.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_opts.o sam_opts.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o sam_utils.o sam_utils.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bedidx.o bedidx.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o lz4/lz4.o lz4/lz4.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -DMAQ_LONGREADS -I. -I./lz4 -c -o misc/maq2sam-long.o misc/maq2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/ace2sam.o misc/ace2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/maq2sam-short.o misc/maq2sam.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/md5sum-lite.o misc/md5sum-lite.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/md5fa.o misc/md5fa.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o misc/wgsim.o misc/wgsim.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/test.o test/test.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_count_rg.o test/split/test_count_rg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/vcf-miniview.o test/vcf-miniview.c gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o bamtk.o bamtk.c ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=zEC12 -mtune=z13 -fasynchronous-unwind-tables -fstack-clash-protection -I. -I./lz4 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -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 -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -o samtools bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_reheader.o bam_sort.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 coverage.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 bam_ampliconclip.o amplicon_stats.o bam_import.o ./lz4/lz4.o libbam.a libst.a -lhts -lncursesw -lm -lz -lpthread + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.BEG5U7 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x '!=' / ']' + rm -rf /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x ++ dirname /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x + cd samtools-1.13 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x 'INSTALL=/usr/bin/install -p' mkdir -p -m 755 /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/man/man1 /usr/bin/install -p samtools /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin /usr/bin/install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin /usr/bin/install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin /usr/bin/install -p -m 644 doc/samtools*.1 misc/wgsim.1 /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/man/man1 ++ grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/ace2sam /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/blast2sam.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/bowtie2sam.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/export2sam.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/fasta-sanitize.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/interpolate_sam.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/maq2sam-long /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/maq2sam-short /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/md5fa /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/md5sum-lite /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/novo2sam.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/plot-ampliconstats /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/plot-bamstats /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/psl2sam.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/sam2vcf.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/samtools /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/samtools.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/seq_cache_populate.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/soap2sam.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/wgsim /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/wgsim_eval.pl /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/zoom2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/blast2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/bowtie2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/export2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/fasta-sanitize.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/interpolate_sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/novo2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/plot-ampliconstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/plot-bamstats + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/psl2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/sam2vcf.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/samtools.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/seq_cache_populate.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/soap2sam.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/wgsim_eval.pl + for file in $(grep -l '^#!/usr/bin/env perl' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/*) + sed -i '1 s|/usr/bin/env perl|/usr/bin/perl|' /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/zoom2sam.pl + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.13-1.fc35 --unique-debug-suffix -1.13-1.fc35.s390x --unique-debug-src-base samtools-1.13-1.fc35.s390x --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/samtools-1.13 extracting debug info from /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/ace2sam extracting debug info from /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/maq2sam-long extracting debug info from /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/maq2sam-short extracting debug info from /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/md5fa extracting debug info from /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/md5sum-lite extracting debug info from /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/samtools extracting debug info from /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/bin/wgsim original debug info size: 2072kB, size after compression: 1884kB /usr/bin/sepdebugcrcfix: Updated 7 CRC32s, 0 CRC32s did match. 2373 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.nPBa2x + umask 022 + cd /builddir/build/BUILD + cd samtools-1.13 + ldd samtools + grep -E '/lib(64)?/libhts\.so\.' libhts.so.3 => /lib64/libhts.so.3 (0x000003ffa1180000) + make test test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args REF_PATH=: test/test.pl --exec bgzip= ${TEST_OPTS:-} bgzip -c -b 65272 -s 5 /tmp/oOB7QTsEIz/bgzip.dat.gz .. ok bgzip -c -b 979200 -s 6 /tmp/oOB7QTsEIz/bgzip.dat.gz .. ok bgzip -c -b 652804 -s 6 /tmp/oOB7QTsEIz/bgzip.dat.gz .. ok /builddir/build/BUILD/samtools-1.13/samtools faidx /tmp/oOB7QTsEIz/faidx.fa 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.13/samtools faidx /tmp/oOB7QTsEIz/faidx.fa.gz 3:11-13 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.13/samtools faidx /tmp/oOB7QTsEIz/faidx.fa 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.13/samtools faidx /tmp/oOB7QTsEIz/faidx.fa.gz 2:998-1003 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.13/samtools faidx /tmp/oOB7QTsEIz/faidx.fa 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.13/samtools faidx /tmp/oOB7QTsEIz/faidx.fa.gz 1:100-104 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.13/samtools faidx /tmp/oOB7QTsEIz/faidx.fa 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.13/samtools faidx /tmp/oOB7QTsEIz/faidx.fa.gz 1:99998-100007 | grep -v '^>' .. ok /builddir/build/BUILD/samtools-1.13/samtools fqidx /tmp/oOB7QTsEIz/fqidx.fq 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.13/samtools fqidx /tmp/oOB7QTsEIz/fqidx.fq.gz 3:11-13 .. ok .. ok /builddir/build/BUILD/samtools-1.13/samtools fqidx /tmp/oOB7QTsEIz/fqidx.fq 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.13/samtools fqidx /tmp/oOB7QTsEIz/fqidx.fq.gz 2:998-1003 .. ok .. ok /builddir/build/BUILD/samtools-1.13/samtools fqidx /tmp/oOB7QTsEIz/fqidx.fq 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.13/samtools fqidx /tmp/oOB7QTsEIz/fqidx.fq.gz 1:100-104 .. ok .. ok /builddir/build/BUILD/samtools-1.13/samtools fqidx /tmp/oOB7QTsEIz/fqidx.fq 1:99998-100007 .. ok .. ok /builddir/build/BUILD/samtools-1.13/samtools fqidx /tmp/oOB7QTsEIz/fqidx.fq.gz 1:99998-100007 .. ok .. ok test_dict: /builddir/build/BUILD/samtools-1.13/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /builddir/build/BUILD/samtools-1.13/test/dat/dict.fa .. ok test_dict: /builddir/build/BUILD/samtools-1.13/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz /tmp/oOB7QTsEIz/dict.fa.gz .. ok test_dict: cat /builddir/build/BUILD/samtools-1.13/test/dat/dict.fa | /builddir/build/BUILD/samtools-1.13/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://example.com/hf37d5.fa.gz .. ok test_dict: /builddir/build/BUILD/samtools-1.13/samtools dict -AH < /builddir/build/BUILD/samtools-1.13/test/dat/dict.alias.fa .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools view /tmp/oOB7QTsEIz/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools view /tmp/oOB7QTsEIz/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools index /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools view -X /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.bam /tmp/oOB7QTsEIz/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools merge -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam.bai /tmp/oOB7QTsEIz/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools index -c /builddir/build/BUILD/samtools-1.13/test/dat/auto_indexed.tmp.bam /tmp/oOB7QTsEIz/auto_indexed.csi && cat /tmp/oOB7QTsEIz/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools index /builddir/build/BUILD/samtools-1.13/test/dat/auto_indexed.tmp.cram /tmp/oOB7QTsEIz/auto_indexed.crai && cat /tmp/oOB7QTsEIz/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools index -c /builddir/build/BUILD/samtools-1.13/test/dat/auto_indexed.tmp.sam /tmp/oOB7QTsEIz/auto_indexed.csi && cat /tmp/oOB7QTsEIz/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools view -@ 2 /tmp/oOB7QTsEIz/large_chrom.bam ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools view -@ 2 /tmp/oOB7QTsEIz/large_chrom.bam ref2:1-541556283 .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools index -@ 2 /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam && cat /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools view -@ 2 -X /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.bam /tmp/oOB7QTsEIz/test_input_1_b.bam.bai ref2 .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -O sam - -X -cp -R ref2 /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam.bai /tmp/oOB7QTsEIz/test_input_1_b.bam.bai .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.13/test/dat/auto_indexed.tmp.bam /tmp/oOB7QTsEIz/auto_indexed.csi && cat /tmp/oOB7QTsEIz/auto_indexed.csi .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools index -@ 2 /builddir/build/BUILD/samtools-1.13/test/dat/auto_indexed.tmp.cram /tmp/oOB7QTsEIz/auto_indexed.crai && cat /tmp/oOB7QTsEIz/auto_indexed.crai .. ok test_index: /builddir/build/BUILD/samtools-1.13/samtools index -@ 2 -c /builddir/build/BUILD/samtools-1.13/test/dat/auto_indexed.tmp.sam /tmp/oOB7QTsEIz/auto_indexed.csi && cat /tmp/oOB7QTsEIz/auto_indexed.csi .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup -b /tmp/oOB7QTsEIz/mpileup.bam.list -f /tmp/oOB7QTsEIz/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup -b /tmp/oOB7QTsEIz/mpileup.cram.list -f /tmp/oOB7QTsEIz/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup -b /tmp/oOB7QTsEIz/mpileup.bam.urllist -f /tmp/oOB7QTsEIz/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup -b /tmp/oOB7QTsEIz/mpileup.cram.urllist -f /tmp/oOB7QTsEIz/mpileup.ref.fa.gz -r17:100-150 .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup -uvDV -b /tmp/oOB7QTsEIz/mpileup.bam.list -f /tmp/oOB7QTsEIz/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup -uvDV -b /tmp/oOB7QTsEIz/mpileup.cram.list -f /tmp/oOB7QTsEIz/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/oOB7QTsEIz/mpileup.cram.list -f /tmp/oOB7QTsEIz/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/oOB7QTsEIz/mpileup.cram.list -f /tmp/oOB7QTsEIz/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup -B --ff 0x14 -f /tmp/oOB7QTsEIz/mpileup.ref.fa.gz -r17:1050-1060 /tmp/oOB7QTsEIz/mpileup.1.bam | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup -B --ff 0x14 -f /tmp/oOB7QTsEIz/mpileup.ref.fa.gz -r17:1050-1060 /tmp/oOB7QTsEIz/mpileup.1.cram | grep -v mpileup .. ok test_mpileup: /builddir/build/BUILD/samtools-1.13/samtools mpileup /builddir/build/BUILD/samtools-1.13/test/mpileup/overlap.bam | grep 128814202 test/test.pl: no IO::Pty module or can't open pty; skipping usage tests .. ok test_usage: samtools test_view: Generating test data file .................. 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/oOB7QTsEIz/view.001.fogn (SAM input) .. ok 50: Count -R /tmp/oOB7QTsEIz/view.001.fogn (SAM input) .. ok 51: Filter -R /tmp/oOB7QTsEIz/view.001.fogn (BAM input) .. ok 52: Count -R /tmp/oOB7QTsEIz/view.001.fogn (BAM input) .. ok 53: Filter -R /tmp/oOB7QTsEIz/view.001.fogn (CRAM input) .. ok 54: Count -R /tmp/oOB7QTsEIz/view.001.fogn (CRAM input) .. ok 55: Filter -R /tmp/oOB7QTsEIz/view.001.fogn -r grp2 (SAM input).. ok 56: Count -R /tmp/oOB7QTsEIz/view.001.fogn -r grp2 (SAM input).. ok 57: Filter -R /tmp/oOB7QTsEIz/view.001.fogn -r grp2 (BAM input).. ok 58: Count -R /tmp/oOB7QTsEIz/view.001.fogn -r grp2 (BAM input).. ok 59: Filter -R /tmp/oOB7QTsEIz/view.001.fogn -r grp2 (CRAM input).. ok 60: Count -R /tmp/oOB7QTsEIz/view.001.fogn -r grp2 (CRAM input).. ok 61: Filter -r grp2 -R /tmp/oOB7QTsEIz/view.001.fogn (SAM input).. ok 62: Count -r grp2 -R /tmp/oOB7QTsEIz/view.001.fogn (SAM input).. ok 63: Filter -r grp2 -R /tmp/oOB7QTsEIz/view.001.fogn (BAM input).. ok 64: Count -r grp2 -R /tmp/oOB7QTsEIz/view.001.fogn (BAM input).. ok 65: Filter -r grp2 -R /tmp/oOB7QTsEIz/view.001.fogn (CRAM input).. ok 66: Count -r grp2 -R /tmp/oOB7QTsEIz/view.001.fogn (CRAM input).. ok 67: Filter -N /tmp/oOB7QTsEIz/view.001.forn (SAM input) .. ok 68: Count -N /tmp/oOB7QTsEIz/view.001.forn (SAM input) .. ok 69: Filter -N /tmp/oOB7QTsEIz/view.001.forn (BAM input) .. ok 70: Count -N /tmp/oOB7QTsEIz/view.001.forn (BAM input) .. ok 71: Filter -N /tmp/oOB7QTsEIz/view.001.forn (CRAM input) .. ok 72: Count -N /tmp/oOB7QTsEIz/view.001.forn (CRAM input) .. ok 73: Filter -d BC (SAM input) .. ok 74: Count -d BC (SAM input) .. ok 75: Filter -d BC (BAM input) .. ok 76: Count -d BC (BAM input) .. ok 77: Filter -d BC (CRAM input) .. ok 78: Count -d BC (CRAM input) .. ok 79: Filter -d BC:TGCA (SAM input) .. ok 80: Count -d BC:TGCA (SAM input) .. ok 81: Filter -d BC:TGCA (BAM input) .. ok 82: Count -d BC:TGCA (BAM input) .. ok 83: Filter -d BC:TGCA (CRAM input) .. ok 84: Count -d BC:TGCA (CRAM input) .. ok 85: Filter -D BC:/tmp/oOB7QTsEIz/view.001.fobc (SAM input) .. ok 86: Count -D BC:/tmp/oOB7QTsEIz/view.001.fobc (SAM input) .. ok 87: Filter -D BC:/tmp/oOB7QTsEIz/view.001.fobc (BAM input) .. ok 88: Count -D BC:/tmp/oOB7QTsEIz/view.001.fobc (BAM input) .. ok 89: Filter -D BC:/tmp/oOB7QTsEIz/view.001.fobc (CRAM input) .. ok 90: Count -D BC:/tmp/oOB7QTsEIz/view.001.fobc (CRAM input) .. ok 91: Filter -D BC:/tmp/oOB7QTsEIz/view.001.fobc -d BC:TGCA (SAM input).. ok 92: Count -D BC:/tmp/oOB7QTsEIz/view.001.fobc -d BC:TGCA (SAM input).. ok 93: Filter -D BC:/tmp/oOB7QTsEIz/view.001.fobc -d BC:TGCA (BAM input).. ok 94: Count -D BC:/tmp/oOB7QTsEIz/view.001.fobc -d BC:TGCA (BAM input).. ok 95: Filter -D BC:/tmp/oOB7QTsEIz/view.001.fobc -d BC:TGCA (CRAM input).. ok 96: Count -D BC:/tmp/oOB7QTsEIz/view.001.fobc -d BC:TGCA (CRAM input).. ok 97: Filter -d BC:TGCA -D BC:/tmp/oOB7QTsEIz/view.001.fobc (SAM input).. ok 98: Count -d BC:TGCA -D BC:/tmp/oOB7QTsEIz/view.001.fobc (SAM input).. ok 99: Filter -d BC:TGCA -D BC:/tmp/oOB7QTsEIz/view.001.fobc (BAM input).. ok 100: Count -d BC:TGCA -D BC:/tmp/oOB7QTsEIz/view.001.fobc (BAM input).. ok 101: Filter -d BC:TGCA -D BC:/tmp/oOB7QTsEIz/view.001.fobc (CRAM input).. ok 102: Count -d BC:TGCA -D BC:/tmp/oOB7QTsEIz/view.001.fobc (CRAM input).. ok 103: Filter -D RG:/tmp/oOB7QTsEIz/view.001.fogn (SAM input) .. ok 104: Count -D RG:/tmp/oOB7QTsEIz/view.001.fogn (SAM input) .. ok 105: Filter -D RG:/tmp/oOB7QTsEIz/view.001.fogn (BAM input) .. ok 106: Count -D RG:/tmp/oOB7QTsEIz/view.001.fogn (BAM input) .. ok 107: Filter -D RG:/tmp/oOB7QTsEIz/view.001.fogn (CRAM input).. ok 108: Count -D RG:/tmp/oOB7QTsEIz/view.001.fogn (CRAM input) .. ok 109: Filter -d NE:TGCA (SAM input) .. ok 110: Count -d NE:TGCA (SAM input) .. ok 111: Filter -d NE:TGCA (BAM input) .. ok 112: Count -d NE:TGCA (BAM input) .. ok 113: Filter -d NE:TGCA (CRAM input) .. ok 114: Count -d NE:TGCA (CRAM input) .. ok 115: Filter -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -o /tmp/oOB7QTsEIz/view.test115.sam -h -d TGCA /tmp/oOB7QTsEIz/view.001.sam --no-PG .. expected failure 116: Count -d TGCA (SAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -c -d TGCA /tmp/oOB7QTsEIz/view.001.sam --no-PG .. expected failure 117: Filter -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -o /tmp/oOB7QTsEIz/view.test117.sam -h -d TGCA /tmp/oOB7QTsEIz/view.test001.bam --no-PG .. expected failure 118: Count -d TGCA (BAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -c -d TGCA /tmp/oOB7QTsEIz/view.test001.bam --no-PG .. expected failure 119: Filter -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -o /tmp/oOB7QTsEIz/view.test119.sam -h -d TGCA /tmp/oOB7QTsEIz/view.test006.cram --no-PG .. expected failure 120: Count -d TGCA (CRAM input) samtools view: Invalid "tag:value" option: "TGCA" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -c -d TGCA /tmp/oOB7QTsEIz/view.test006.cram --no-PG .. expected failure 121: Filter -D BClong:/tmp/oOB7QTsEIz/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oOB7QTsEIz/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -o /tmp/oOB7QTsEIz/view.test121.sam -h -D BClong:/tmp/oOB7QTsEIz/view.001.fobc /tmp/oOB7QTsEIz/view.001.sam --no-PG .. expected failure 122: Count -D BClong:/tmp/oOB7QTsEIz/view.001.fobc (SAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oOB7QTsEIz/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -c -D BClong:/tmp/oOB7QTsEIz/view.001.fobc /tmp/oOB7QTsEIz/view.001.sam --no-PG .. expected failure 123: Filter -D BClong:/tmp/oOB7QTsEIz/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oOB7QTsEIz/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -o /tmp/oOB7QTsEIz/view.test123.sam -h -D BClong:/tmp/oOB7QTsEIz/view.001.fobc /tmp/oOB7QTsEIz/view.test001.bam --no-PG .. expected failure 124: Count -D BClong:/tmp/oOB7QTsEIz/view.001.fobc (BAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oOB7QTsEIz/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -c -D BClong:/tmp/oOB7QTsEIz/view.001.fobc /tmp/oOB7QTsEIz/view.test001.bam --no-PG .. expected failure 125: Filter -D BClong:/tmp/oOB7QTsEIz/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oOB7QTsEIz/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -o /tmp/oOB7QTsEIz/view.test125.sam -h -D BClong:/tmp/oOB7QTsEIz/view.001.fobc /tmp/oOB7QTsEIz/view.test006.cram --no-PG .. expected failure 126: Count -D BClong:/tmp/oOB7QTsEIz/view.001.fobc (CRAM input)samtools view: Invalid "tag:file" option: "BClong:/tmp/oOB7QTsEIz/view.001.fobc" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -c -D BClong:/tmp/oOB7QTsEIz/view.001.fobc /tmp/oOB7QTsEIz/view.test006.cram --no-PG .. expected failure 127: Filter -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -o /tmp/oOB7QTsEIz/view.test127.sam -h -d BC:ACGT -d RG:grp2 /tmp/oOB7QTsEIz/view.001.sam --no-PG .. expected failure 128: Count -d BC:ACGT -d RG:grp2 (SAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/oOB7QTsEIz/view.001.sam --no-PG .. expected failure 129: Filter -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -o /tmp/oOB7QTsEIz/view.test129.sam -h -d BC:ACGT -d RG:grp2 /tmp/oOB7QTsEIz/view.test001.bam --no-PG .. expected failure 130: Count -d BC:ACGT -d RG:grp2 (BAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/oOB7QTsEIz/view.test001.bam --no-PG .. expected failure 131: Filter -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -o /tmp/oOB7QTsEIz/view.test131.sam -h -d BC:ACGT -d RG:grp2 /tmp/oOB7QTsEIz/view.test006.cram --no-PG .. expected failure 132: Count -d BC:ACGT -d RG:grp2 (CRAM input) samtools view: Different tag "BC" was specified before: "RG:grp2" Failed command: /builddir/build/BUILD/samtools-1.13/samtools view -c -d BC:ACGT -d RG:grp2 /tmp/oOB7QTsEIz/view.test006.cram --no-PG .. expected failure 133: Filter -d NM:13 (SAM input) .. ok 134: Count -d NM:13 (SAM input) .. ok 135: Filter -d NM:13 (BAM input) .. ok 136: Count -d NM:13 (BAM input) .. ok 137: Filter -d NM:13 (CRAM input) .. ok 138: Count -d NM:13 (CRAM input) .. ok 139: Filter -d ab:z (SAM input) .. ok 140: Count -d ab:z (SAM input) .. ok 141: Filter -d ab:z (BAM input) .. ok 142: Count -d ab:z (BAM input) .. ok 143: Filter -d ab:z (CRAM input) .. ok 144: Count -d ab:z (CRAM input) .. ok 145: Filter -l Library 2 (SAM input) .. ok 146: Count -l Library 2 (SAM input) .. ok 147: Filter -l Library 2 (BAM input) .. ok 148: Count -l Library 2 (BAM input) .. ok 149: Filter -l Library 2 (CRAM input) .. ok 150: Count -l Library 2 (CRAM input) .. ok 151: Filter -l Library 3 (SAM input) .. ok 152: Count -l Library 3 (SAM input) .. ok 153: Filter -l Library 3 (BAM input) .. ok 154: Count -l Library 3 (BAM input) .. ok 155: Filter -l Library 3 (CRAM input) .. ok 156: Count -l Library 3 (CRAM input) .. ok 157: Filter -q 50 (SAM input) .. ok 158: Count -q 50 (SAM input) .. ok 159: Filter -q 50 (BAM input) .. ok 160: Count -q 50 (BAM input) .. ok 161: Filter -q 50 (CRAM input) .. ok 162: Count -q 50 (CRAM input) .. ok 163: Filter -q 99 (SAM input) .. ok 164: Count -q 99 (SAM input) .. ok 165: Filter -q 99 (BAM input) .. ok 166: Count -q 99 (BAM input) .. ok 167: Filter -q 99 (CRAM input) .. ok 168: Count -q 99 (CRAM input) .. ok 169: Filter -q 100 (SAM input) .. ok 170: Count -q 100 (SAM input) .. ok 171: Filter -q 100 (BAM input) .. ok 172: Count -q 100 (BAM input) .. ok 173: Filter -q 100 (CRAM input) .. ok 174: Count -q 100 (CRAM input) .. ok 175: Filter -x fa (SAM input) .. ok 176: Count -x fa (SAM input) .. ok 177: Filter -x fa (BAM input) .. ok 178: Count -x fa (BAM input) .. ok 179: Filter -x fa (CRAM input) .. ok 180: Count -x fa (CRAM input) .. ok 181: Filter -x fa -x ha (SAM input) .. ok 182: Count -x fa -x ha (SAM input) .. ok 183: Filter -x fa -x ha (BAM input) .. ok 184: Count -x fa -x ha (BAM input) .. ok 185: Filter -x fa -x ha (CRAM input) .. ok 186: Count -x fa -x ha (CRAM input) .. ok 187: Filter -x fa -r grp2 (SAM input) .. ok 188: Count -x fa -r grp2 (SAM input) .. ok 189: Filter -x fa -r grp2 (BAM input) .. ok 190: Count -x fa -r grp2 (BAM input) .. ok 191: Filter -x fa -r grp2 (CRAM input) .. ok 192: Count -x fa -r grp2 (CRAM input) .. ok 193: Filter -x RG -r grp2 (SAM input) .. ok 194: Count -x RG -r grp2 (SAM input) .. ok 195: Filter -x RG -r grp2 (BAM input) .. ok 196: Count -x RG -r grp2 (BAM input) .. ok 197: Filter -x RG -r grp2 (CRAM input) .. ok 198: Count -x RG -r grp2 (CRAM input) .. ok 199: Filter -m 10 (SAM input) .. ok 200: Count -m 10 (SAM input) .. ok 201: Filter -m 10 (BAM input) .. ok 202: Count -m 10 (BAM input) .. ok 203: Filter -m 10 (CRAM input) .. ok 204: Count -m 10 (CRAM input) .. ok 205: Filter -m 11 (SAM input) .. ok 206: Count -m 11 (SAM input) .. ok 207: Filter -m 11 (BAM input) .. ok 208: Count -m 11 (BAM input) .. ok 209: Filter -m 11 (CRAM input) .. ok 210: Count -m 11 (CRAM input) .. ok 211: Filter -m 15 (SAM input) .. ok 212: Count -m 15 (SAM input) .. ok 213: Filter -m 15 (BAM input) .. ok 214: Count -m 15 (BAM input) .. ok 215: Filter -m 15 (CRAM input) .. ok 216: Count -m 15 (CRAM input) .. ok 217: Filter -m 16 (SAM input) .. ok 218: Count -m 16 (SAM input) .. ok 219: Filter -m 16 (BAM input) .. ok 220: Count -m 16 (BAM input) .. ok 221: Filter -m 16 (CRAM input) .. ok 222: Count -m 16 (CRAM input) .. ok 223: Filter -e !(flag & 128) && (flag & 2) (SAM input) .. ok 224: Count -e !(flag & 128) && (flag & 2) (SAM input) .. ok 225: Filter -e !(flag & 128) && (flag & 2) (BAM input) .. ok 226: Count -e !(flag & 128) && (flag & 2) (BAM input) .. ok 227: Filter -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 228: Count -e !(flag & 128) && (flag & 2) (CRAM input) .. ok 229: Filter -e [BC] (SAM input) .. ok 230: Count -e [BC] (SAM input) .. ok 231: Filter -e [BC] (BAM input) .. ok 232: Count -e [BC] (BAM input) .. ok 233: Filter -e [BC] (CRAM input) .. ok 234: Count -e [BC] (CRAM input) .. ok 235: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 236: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (SAM input).. ok 237: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 238: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (BAM input).. ok 239: Filter -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 240: Count -e [BC] == "ACGT" || [BC] == "AATTCCGG" (CRAM input).. ok 241: Filter -e mapq >= 50 (SAM input) .. ok 242: Count -e mapq >= 50 (SAM input) .. ok 243: Filter -e mapq >= 50 (BAM input) .. ok 244: Count -e mapq >= 50 (BAM input) .. ok 245: Filter -e mapq >= 50 (CRAM input) .. ok 246: Count -e mapq >= 50 (CRAM input) .. ok 247: Filter -e mapq >= 99 (SAM input) .. ok 248: Count -e mapq >= 99 (SAM input) .. ok 249: Filter -e mapq >= 99 (BAM input) .. ok 250: Count -e mapq >= 99 (BAM input) .. ok 251: Filter -e mapq >= 99 (CRAM input) .. ok 252: Count -e mapq >= 99 (CRAM input) .. ok 253: Filter -e mapq >= 100 (SAM input) .. ok 254: Count -e mapq >= 100 (SAM input) .. ok 255: Filter -e mapq >= 100 (BAM input) .. ok 256: Count -e mapq >= 100 (BAM input) .. ok 257: Filter -e mapq >= 100 (CRAM input) .. ok 258: Count -e mapq >= 100 (CRAM input) .. ok 259: 1bp reads file SAM -> BAM -> SAM .. ok 260: 1bp reads file SAM -> CRAM -> SAM .. ok 260: Region Z (BAM input) .. ok 261: Count Z (BAM input) .. ok 262: Region Z (CRAM input) .. ok 263: Count Z (CRAM input) .. ok 264: Region Z:30 (BAM input) .. ok 265: Count Z:30 (BAM input) .. ok 266: Region Z:30 (CRAM input) .. ok 267: Count Z:30 (CRAM input) .. ok 268: Region Z:20-40 (BAM input) .. ok 269: Count Z:20-40 (BAM input) .. ok 270: Region Z:20-40 (CRAM input) .. ok 271: Count Z:20-40 (CRAM input) .. ok 272: Region ref1 (BAM input) .. ok 273: Count ref1 (BAM input) .. ok 274: Region ref1 (CRAM input) .. ok 275: Count ref1 (CRAM input) .. ok 276: Region ref1:15 (BAM input) .. ok 277: Count ref1:15 (BAM input) .. ok 278: Region ref1:15 (CRAM input) .. ok 279: Count ref1:15 (CRAM input) .. ok 280: Region ref1:15-45 (BAM input) .. ok 281: Count ref1:15-45 (BAM input) .. ok 282: Region ref1:15-45 (CRAM input) .. ok 283: Count ref1:15-45 (CRAM input) .. ok 284: Region ref1:15-45 ref2 (BAM input) .. ok 285: Count ref1:15-45 ref2 (BAM input) .. ok 286: Region ref1:15-45 ref2 (CRAM input) .. ok 287: Count ref1:15-45 ref2 (CRAM input) .. ok 288: Region ref1:15-45 ref2:16 (BAM input) .. ok 289: Count ref1:15-45 ref2:16 (BAM input) .. ok 290: Region ref1:15-45 ref2:16 (CRAM input) .. ok 291: Count ref1:15-45 ref2:16 (CRAM input) .. ok 292: Region ref1:15-45 ref2:16-31 (BAM input) .. ok 293: Count ref1:15-45 ref2:16-31 (BAM input) .. ok 294: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok 295: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok 296: Region ref1:15-15 ref1:45-45 (BAM input) .. ok 297: Count ref1:15-15 ref1:45-45 (BAM input) .. ok 298: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok 299: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok 300: Region -f 128 ref1 (BAM input) .. ok 301: Count -f 128 ref1 (BAM input) .. ok 302: Region -f 128 ref1 (CRAM input) .. ok 303: Count -f 128 ref1 (CRAM input) .. ok 304: Region -q 50 ref1:15-45 (BAM input) .. ok 305: Count -q 50 ref1:15-45 (BAM input) .. ok 306: Region -q 50 ref1:15-45 (CRAM input) .. ok 307: Count -q 50 ref1:15-45 (CRAM input) .. ok 308: Region -r grp2 ref1:15-45 (BAM input) .. ok 309: Count -r grp2 ref1:15-45 (BAM input) .. ok 310: Region -r grp2 ref1:15-45 (CRAM input) .. ok 311: Count -r grp2 ref1:15-45 (CRAM input) .. ok 312: Region * (BAM input) .. ok 313: Count * (BAM input) .. ok 314: Region * (CRAM input) .. ok 315: Count * (CRAM input) .. ok 316: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed (BAM input).. ok 317: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed (BAM input).. ok 318: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed (CRAM input).. ok 319: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed (CRAM input).. ok 320: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.02.bed (BAM input).. ok 321: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.02.bed (BAM input).. ok 322: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.02.bed (CRAM input).. ok 323: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.02.bed (CRAM input).. ok 324: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed (BAM input).. ok 325: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed (BAM input).. ok 326: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed (CRAM input).. ok 327: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed (CRAM input).. ok 328: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.02.bed (BAM input).. ok 329: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.02.bed (BAM input).. ok 330: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.02.bed (CRAM input).. ok 331: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.02.bed (CRAM input).. ok 332: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z (BAM input).. ok 333: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z (BAM input).. ok 334: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z (CRAM input).. ok 335: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z (CRAM input).. ok 336: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:30 (BAM input).. ok 337: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:30 (BAM input).. ok 338: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 339: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:30 (CRAM input).. ok 340: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 341: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok 342: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 343: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok 344: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 345: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok 346: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 347: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok 348: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 349: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok 350: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 351: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok 352: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref2 (BAM input).. ok 353: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref2 (BAM input).. ok 354: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref2 (CRAM input).. ok 355: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref2 (CRAM input).. ok 356: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 357: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (BAM input).. ok 358: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 359: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed ref1:1-15 ref1:44-45 (CRAM input).. ok 360: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 361: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -r grp1 (BAM input).. ok 362: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 363: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok 364: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -f 128 (BAM input).. ok 365: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -f 128 (BAM input).. ok 366: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 367: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -f 128 (CRAM input).. ok 368: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -q 5 (BAM input).. ok 369: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -q 5 (BAM input).. ok 370: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 371: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -q 5 (CRAM input).. ok 372: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 373: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok 374: Region -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 375: Count -L /builddir/build/BUILD/samtools-1.13/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok 376: Make BAM with no M5/UR tags .. ok 377: Add @SQ with -t (SAM -> SAM) .. ok 378: Add @SQ with -T (SAM -> SAM) .. ok 379: Add @SQ with -t (BAM -> SAM) .. ok 380: Add @SQ with -T (BAM -> SAM) .. ok 381: Add @SQ with -t (SAM -> BAM) .. ok 382: Add @SQ with -T (SAM -> BAM) .. ok 383: Add @SQ with -t (BAM -> BAM) .. ok 384: Add @SQ with -T (BAM -> BAM) .. ok 385: Add @SQ with -t (SAM -> CRAM) .. ok 386: Add @SQ with -T (SAM -> CRAM) .. ok 387: Add @SQ with -t (BAM -> CRAM) .. ok 388: Add @SQ with -T (BAM -> CRAM) .. ok 389: Make CRAM with no UR field .. ok 390: Decoding CRAM with no UR field via -T .. ok 391: CIGAR B-operator removal .. ok 392: Big SAM -> BAM .. ok 393: Big SAM -> BAM (2 threads) .. ok 394: Big SAM -> BAM (4 threads) .. ok 395: Big SAM -> CRAM .. ok 396: Big SAM -> CRAM (2 threads) .. ok 397: Big SAM -> CRAM (4 threads) .. ok 398: Subsample 0.2 (SAM input) ............ ok 399: Subsample 0.5 (SAM input) ............ ok 400: Subsample 0.8 (SAM input) ............ ok 401: Subsample 0.2 (BAM input) ............ ok 402: Subsample 0.5 (BAM input) ............ ok 403: Subsample 0.8 (BAM input) ............ ok 404: Subsample 0.2 (CRAM input) ............ ok 405: Subsample 0.5 (CRAM input) ............ ok 406: Subsample 0.8 (CRAM input) ............ ok 407: SAM add PG .. ok 408: Unset dup flag, remove dt and do tags .. 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_import: /builddir/build/BUILD/samtools-1.13/samtools import -0 test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.13/samtools fastq -0 /builddir/build/BUILD/samtools-1.13/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import -s test/bam2fq/1.1.fq.expected | /builddir/build/BUILD/samtools-1.13/samtools fastq -0 /builddir/build/BUILD/samtools-1.13/test/0.fq .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import -s test/bam2fq/5.s.fq.expected | /builddir/build/BUILD/samtools-1.13/samtools fastq -s /builddir/build/BUILD/samtools-1.13/test/s.fq .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected | /builddir/build/BUILD/samtools-1.13/samtools fastq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import test/bam2fq/5.1.fq.expected test/bam2fq/5.2.fq.expected | /builddir/build/BUILD/samtools-1.13/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.13/samtools fastq -i --index-format i*i* -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import --barcode-tag OX -i -1 test/bam2fq/12.1.fq.expected -2 test/bam2fq/12.2.fq.expected | /builddir/build/BUILD/samtools-1.13/samtools fastq --barcode-tag OX -i --index-format i*i* -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import -T "" -1 test/bam2fq/6.1.fq.expected -2 test/bam2fq/6.2.fq.expected | /builddir/build/BUILD/samtools-1.13/samtools fastq -N -T RG,BC,QT -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import -T "*" -1 test/bam2fq/7.1.fq.expected -2 test/bam2fq/7.2.fq.expected | /builddir/build/BUILD/samtools-1.13/samtools fastq -N -T RG,BC,QT,MD,ia -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -R rgid .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r ID:rgid .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import test/bam2fq/1.1.fq.expected test/bam2fq/1.2.fq.expected -r '@RG ID:rgid' .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import test/import/2.interleaved.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import test/import/3.interleaved.fq -i .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import test/import/4.aux.fq -T "*" .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import test/import/4.aux.fq -T "" .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import test/import/4.aux.fq -T XZ,XA,AA .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq .. ok test_import: /builddir/build/BUILD/samtools-1.13/samtools import --i1 test/import/5-i1.fq --i2 test/import/5-i2.fq --r1 test/import/5-r1.fq --r2 test/import/5-r2.fq --barcode-tag OX --quality-tag BZ .. 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-1.13/samtools fastq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.13/test/bc.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.13/test/bc.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.13/test/bc.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.13/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -N -t -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.13/test/i.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.13/test/i.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -N -1 /builddir/build/BUILD/samtools-1.13/test/o.fq -2 /builddir/build/BUILD/samtools-1.13/test/o.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fasta -N -1 /builddir/build/BUILD/samtools-1.13/test/o.fa -2 /builddir/build/BUILD/samtools-1.13/test/o.fa /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -N -o /builddir/build/BUILD/samtools-1.13/test/o.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -N -s /tmp/oOB7QTsEIz/bam2fq.discard.s.fq -0 /tmp/oOB7QTsEIz/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.013.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-1.13/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.002.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.003.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.13/test/bc.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.13/test/bc.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 --barcode-tag BC -O --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.13/test/bc.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.010.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /builddir/build/BUILD/samtools-1.13/test/bc_split.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -N -t -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -N -t -T MD,ia -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'n2i2' --i1 /builddir/build/BUILD/samtools-1.13/test/i.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.004.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 --barcode-tag BC -i --index-format 'i*i*' --i1 /builddir/build/BUILD/samtools-1.13/test/i.fq -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -i --index-format 'i*i*' -s /builddir/build/BUILD/samtools-1.13/test/s.fq -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.005.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -1 /builddir/build/BUILD/samtools-1.13/test/1.fq -2 /builddir/build/BUILD/samtools-1.13/test/2.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.703.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -N -1 /builddir/build/BUILD/samtools-1.13/test/o.fq -2 /builddir/build/BUILD/samtools-1.13/test/o.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fasta -@ 2 -N -1 /builddir/build/BUILD/samtools-1.13/test/o.fa -2 /builddir/build/BUILD/samtools-1.13/test/o.fa /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -N -o /builddir/build/BUILD/samtools-1.13/test/o.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -N -s /tmp/oOB7QTsEIz/bam2fq.discard.s.fq -0 /tmp/oOB7QTsEIz/bam2fq.discard.0.fq /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.001.sam .. ok test_bam2fq: /builddir/build/BUILD/samtools-1.13/samtools fastq -@ 2 -T ba,bb,bc,bd,be,bf,bg /builddir/build/BUILD/samtools-1.13/test/dat/bam2fq.013.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-1.13/samtools stats -r /builddir/build/BUILD/samtools-1.13/test/stat/test.fa /builddir/build/BUILD/samtools-1.13/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/1_map_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -r /builddir/build/BUILD/samtools-1.13/test/stat/test.fa /builddir/build/BUILD/samtools-1.13/test/stat/2_equal_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/2_equal_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -r /builddir/build/BUILD/samtools-1.13/test/stat/test.fa /builddir/build/BUILD/samtools-1.13/test/stat/3_map_cigar_equal_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/3_map_cigar_equal_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -r /builddir/build/BUILD/samtools-1.13/test/stat/test.fa /builddir/build/BUILD/samtools-1.13/test/stat/4_X_cigar_full_seq.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/4_X_cigar_full_seq_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -r /builddir/build/BUILD/samtools-1.13/test/stat/test.fa /builddir/build/BUILD/samtools-1.13/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/5_insert_cigar_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -r /builddir/build/BUILD/samtools-1.13/test/stat/test.fa -i 0 /builddir/build/BUILD/samtools-1.13/test/stat/5_insert_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -r /builddir/build/BUILD/samtools-1.13/test/stat/test.fa /builddir/build/BUILD/samtools-1.13/test/stat/7_supp.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/7_supp_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -r /builddir/build/BUILD/samtools-1.13/test/stat/test.fa /builddir/build/BUILD/samtools-1.13/test/stat/8_secondary.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/8_secondary_large.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.13/test/stat/test.fa /builddir/build/BUILD/samtools-1.13/test/stat/1_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -S RG -r /builddir/build/BUILD/samtools-1.13/test/stat/test.fa /builddir/build/BUILD/samtools-1.13/test/stat/10_map_cigar.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -t /builddir/build/BUILD/samtools-1.13/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.13/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -g 4 -t /builddir/build/BUILD/samtools-1.13/test/stat/11.stats.targets /builddir/build/BUILD/samtools-1.13/test/stat/11_target.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats -g 4 /builddir/build/BUILD/samtools-1.13/test/stat/11_target.bam ref1:10-24 ref1:30-46 ref1:39-56 | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.13/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.13/test/stat/12_3reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/12_overlaps.bam -t /builddir/build/BUILD/samtools-1.13/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/12_overlaps.bam -p -t /builddir/build/BUILD/samtools-1.13/test/stat/12_2reads.bed | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/13_barcodes_ok.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/13_barcodes_ok_ox_bz.sam | tail -n+4 .. ok test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/13_barcodes_fail_bc_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.13/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/13_barcodes_fail_hyphen.sam | tail -n+4 /builddir/build/BUILD/samtools-1.13/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_stats: /builddir/build/BUILD/samtools-1.13/samtools stats /builddir/build/BUILD/samtools-1.13/test/stat/13_barcodes_fail_qt_length.sam | tail -n+4 /builddir/build/BUILD/samtools-1.13/test/stat/13.barcodes.fail.expected: No such file or directory .. expected failure test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -s 1 -O sam -b /tmp/0UdgXi7bp6 - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -s 1 -p -c -t PG -O SAM - /tmp/oOB7QTsEIz/merge.tag.1.bam /tmp/oOB7QTsEIz/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -s 1 -p -c -n -t PG -O SAM - /tmp/oOB7QTsEIz/merge.tag.3.bam /tmp/oOB7QTsEIz/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge --no-PG -O SAM - /builddir/build/BUILD/samtools-1.13/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.13/test/merge/merge.bed - /tmp/oOB7QTsEIz/merge.bed.1.bam /tmp/oOB7QTsEIz/merge.bed.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.bam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_c.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -s 1 -O sam -b /tmp/Xv9DV8o2Qf - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -r -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -cp -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -s 1 -O sam - /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a_regex.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b_regex.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -o - -s 1 -O sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_b.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_c.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -s 1 -p -c -t PG -O SAM - /tmp/oOB7QTsEIz/merge.tag.1.bam /tmp/oOB7QTsEIz/merge.tag.2.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 -s 1 -p -c -n -t PG -O SAM - /tmp/oOB7QTsEIz/merge.tag.3.bam /tmp/oOB7QTsEIz/merge.tag.4.bam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 --no-PG -O SAM - /builddir/build/BUILD/samtools-1.13/test/merge/test_no_pg_rg_co.sam .. ok test_merge: /builddir/build/BUILD/samtools-1.13/samtools merge -@ 2 --no-PG -O SAM -L /builddir/build/BUILD/samtools-1.13/test/merge/merge.bed - /tmp/oOB7QTsEIz/merge.bed.1.bam /tmp/oOB7QTsEIz/merge.bed.2.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam /tmp/oOB7QTsEIz/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -f /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam /tmp/oOB7QTsEIz/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -o /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam /tmp/oOB7QTsEIz/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -n -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -t RG -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -n -t RG -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -t AS -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -t FI -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -@ 2 /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam /tmp/oOB7QTsEIz/sortout .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -@ 2 -f /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam /tmp/oOB7QTsEIz/sortout.bam .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -@ 2 -o /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam /tmp/oOB7QTsEIz/sorttmp .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -@ 2 -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -@ 2 -n -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -@ 2 -t RG -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -@ 2 -n -t RG -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -@ 2 -t AS -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_sort: /builddir/build/BUILD/samtools-1.13/samtools sort -@ 2 -t FI -m 10M /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam -O SAM -o - .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate --output-fmt=sam -O /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate -o /builddir/build/BUILD/samtools-1.13/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate -o /builddir/build/BUILD/samtools-1.13/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.13/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate --output-fmt=sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.13/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate --output-fmt=sam -f /builddir/build/BUILD/samtools-1.13/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.13/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.13/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.13/test/collate/2_fast_collate_with_tmp.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate -@ 2 --output-fmt=sam -O /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.13/test/collate/collate1.tmp.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate -@ 2 -o /builddir/build/BUILD/samtools-1.13/test/collate/collate2.tmp.sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.13/test/collate/collate2.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate -@ 2 --output-fmt=sam /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_d.sam /builddir/build/BUILD/samtools-1.13/test/collate/collate3.tmp .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate -@ 2 --output-fmt=sam -f /builddir/build/BUILD/samtools-1.13/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.13/test/collate/1_fast_collate.sam .. ok test_collate: /builddir/build/BUILD/samtools-1.13/samtools collate -@ 2 --output-fmt=sam -f -r 4 /builddir/build/BUILD/samtools-1.13/test/collate/fast_collate.sam -o /builddir/build/BUILD/samtools-1.13/test/collate/2_fast_collate_with_tmp.sam .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.13/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-1.13/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.13/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.13/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.13/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.13/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -cO sam /builddir/build/BUILD/samtools-1.13/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.13/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -O sam /builddir/build/BUILD/samtools-1.13/test/fixmate/8_isize_overflow_64bit.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.13/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-1.13/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.13/test/fixmate/2_isize_overflow.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.13/test/fixmate/3_reverse_read_pp_lt.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.13/test/fixmate/4_reverse_read_pp_equal.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.13/test/fixmate/5_ct.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -@ 2 -cO sam /builddir/build/BUILD/samtools-1.13/test/fixmate/6_ct_replace.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.13/test/fixmate/7_two_read_mapped.sam - .. ok test_fixmate: /builddir/build/BUILD/samtools-1.13/samtools fixmate -@ 2 -O sam /builddir/build/BUILD/samtools-1.13/test/fixmate/8_isize_overflow_64bit.sam - .. ok /builddir/build/BUILD/samtools-1.13/samtools calmd -uAr /builddir/build/BUILD/samtools-1.13/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.13/test/dat/mpileup.ref.fa .. ok /builddir/build/BUILD/samtools-1.13/samtools calmd -@ 2 -uAr /builddir/build/BUILD/samtools-1.13/test/dat/mpileup.1.sam /builddir/build/BUILD/samtools-1.13/test/dat/mpileup.ref.fa .. ok test_idxstat: /builddir/build/BUILD/samtools-1.13/samtools idxstats /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.bam .. ok test_idxstat: /builddir/build/BUILD/samtools-1.13/samtools idxstats /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.cram .. ok test_idxstat: /builddir/build/BUILD/samtools-1.13/samtools idxstats /builddir/build/BUILD/samtools-1.13/test/dat/test_input_1_a.sam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck /builddir/build/BUILD/samtools-1.13/test/quickcheck/1.quickcheck.badeof.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck /builddir/build/BUILD/samtools-1.13/test/quickcheck/2.quickcheck.badheader.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck /builddir/build/BUILD/samtools-1.13/test/quickcheck/3.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck /builddir/build/BUILD/samtools-1.13/test/quickcheck/4.quickcheck.ok.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck /builddir/build/BUILD/samtools-1.13/test/quickcheck/5.quickcheck.scramble30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck /builddir/build/BUILD/samtools-1.13/test/quickcheck/6.quickcheck.cram21.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck /builddir/build/BUILD/samtools-1.13/test/quickcheck/7.quickcheck.cram30.ok.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck /builddir/build/BUILD/samtools-1.13/test/quickcheck/8.quickcheck.cram21.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck /builddir/build/BUILD/samtools-1.13/test/quickcheck/9.quickcheck.cram30.truncated.cram .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck /builddir/build/BUILD/samtools-1.13/test/quickcheck/10.quickcheck.notargets.bam .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck -v /builddir/build/BUILD/samtools-1.13/test/quickcheck/1.quickcheck.badeof.bam /builddir/build/BUILD/samtools-1.13/test/quickcheck/2.quickcheck.badheader.bam /builddir/build/BUILD/samtools-1.13/test/quickcheck/3.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.13/test/quickcheck/4.quickcheck.ok.bam /builddir/build/BUILD/samtools-1.13/test/quickcheck/5.quickcheck.scramble30.truncated.cram /builddir/build/BUILD/samtools-1.13/test/quickcheck/6.quickcheck.cram21.ok.cram /builddir/build/BUILD/samtools-1.13/test/quickcheck/7.quickcheck.cram30.ok.cram /builddir/build/BUILD/samtools-1.13/test/quickcheck/8.quickcheck.cram21.truncated.cram /builddir/build/BUILD/samtools-1.13/test/quickcheck/9.quickcheck.cram30.truncated.cram /builddir/build/BUILD/samtools-1.13/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_quickcheck: /builddir/build/BUILD/samtools-1.13/samtools quickcheck -uv /builddir/build/BUILD/samtools-1.13/test/quickcheck/10.quickcheck.notargets.bam | sed 's,.*/quickcheck/,,' .. ok test_reheader: /builddir/build/BUILD/samtools-1.13/samtools reheader /builddir/build/BUILD/samtools-1.13/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.13/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.13/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.13/samtools reheader /builddir/build/BUILD/samtools-1.13/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.13/test/dat/view.001.tmp.v21.cram | /builddir/build/BUILD/samtools-1.13/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.13/samtools reheader /builddir/build/BUILD/samtools-1.13/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.13/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.13/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.13/samtools reheader --in-place /builddir/build/BUILD/samtools-1.13/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.13/test/dat/view.001.tmp.v21.cram && /builddir/build/BUILD/samtools-1.13/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.13/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.13/samtools reheader --in-place /builddir/build/BUILD/samtools-1.13/test/reheader/hdr.sam /builddir/build/BUILD/samtools-1.13/test/dat/view.001.tmp.v30.cram && /builddir/build/BUILD/samtools-1.13/samtools view -h --no-PG /builddir/build/BUILD/samtools-1.13/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.13/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.13/test/dat/view.001.tmp.bam | /builddir/build/BUILD/samtools-1.13/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_reheader: /builddir/build/BUILD/samtools-1.13/samtools reheader -c "sed 's/2014 Genome/2019 Genome/g'" /builddir/build/BUILD/samtools-1.13/test/dat/view.001.tmp.v30.cram | /builddir/build/BUILD/samtools-1.13/samtools view -h --no-PG | perl -pe 's/ VN:.*//' .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.13/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -O sam -m orphan_only /builddir/build/BUILD/samtools-1.13/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -O sam -R '1#9' /builddir/build/BUILD/samtools-1.13/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.13/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.13/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.13/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.13/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -@ 2 -O sam -m overwrite_all /builddir/build/BUILD/samtools-1.13/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -@ 2 -O sam -m orphan_only /builddir/build/BUILD/samtools-1.13/test/addrprg/2_fixup_orphan.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -@ 2 -O sam -R '1#9' /builddir/build/BUILD/samtools-1.13/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /builddir/build/BUILD/samtools-1.13/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /builddir/build/BUILD/samtools-1.13/test/addrprg/1_fixup.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /builddir/build/BUILD/samtools-1.13/test/addrprg/4_fixup_norg.sam .. ok test_addrprg: /builddir/build/BUILD/samtools-1.13/samtools addreplacerg -@ 2 -O sam -w -r '@RG\tID:1#8\tCN:Sanger\tDS:Testing the editing code.' /builddir/build/BUILD/samtools-1.13/test/addrprg/1_fixup.sam .. ok test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.13/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-1.13/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.13/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-1.13/samtools markdup -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -O sam -r --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -S -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/9_optical_dup_qcfail.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/1_name_sort.sam - ERR: [markdup] error: queryname sorted, must be sorted by coordinate. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/2_bad_order.sam - ERR: [markdup] error: not in coordinate sorted order. .. expected failure test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.13/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-1.13/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.13/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-1.13/samtools markdup -@ 2 -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/5_markdup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -@ 2 -O sam -r --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/6_remove_dups.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -@ 2 -S -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/7_mark_supp_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -@ 2 -S -d 100 --mode s -t -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/8_optical_dup.sam - .. ok test_markdup: /builddir/build/BUILD/samtools-1.13/samtools markdup -@ 2 -S -d 2500 --mode s -t --include-fails -O sam --no-PG /builddir/build/BUILD/samtools-1.13/test/markdup/9_optical_dup_qcfail.sam - .. ok test_bedcov: /builddir/build/BUILD/samtools-1.13/samtools bedcov /builddir/build/BUILD/samtools-1.13/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.13/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.13/samtools bedcov -j /builddir/build/BUILD/samtools-1.13/test/bedcov/bedcov.bed /builddir/build/BUILD/samtools-1.13/test/bedcov/bedcov.bam .. ok test_bedcov: /builddir/build/BUILD/samtools-1.13/samtools bedcov -g512 -G2048 /builddir/build/BUILD/samtools-1.13/test/bedcov/bedcov_gG.bed /builddir/build/BUILD/samtools-1.13/test/bedcov/bedcov.bam .. ok test_split: /builddir/build/BUILD/samtools-1.13/samtools split --output-fmt sam -u /builddir/build/BUILD/samtools-1.13/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.13/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.13/test/split/split.sam .. ok test_split: /builddir/build/BUILD/samtools-1.13/samtools split -@ 2 --output-fmt sam -u /builddir/build/BUILD/samtools-1.13/test/split/split.tmp.unk.sam -f /builddir/build/BUILD/samtools-1.13/test/split/split.tmp.%!.%. /builddir/build/BUILD/samtools-1.13/test/split/split.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.13/samtools view -h --no-PG /tmp/oOB7QTsEIz/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.13/samtools view -h --no-PG /tmp/oOB7QTsEIz/longref.sam.gz CHROMOSOME_I:10000000114-10000000168 .. ok test_large_positions: /builddir/build/BUILD/samtools-1.13/samtools view -h --no-PG -L /builddir/build/BUILD/samtools-1.13/test/large_pos/test.bed /tmp/oOB7QTsEIz/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.13/samtools sort -O sam --no-PG -m 10M /builddir/build/BUILD/samtools-1.13/test/large_pos/longref_name.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.13/samtools merge -O sam --no-PG - /builddir/build/BUILD/samtools-1.13/test/large_pos/longref.sam /builddir/build/BUILD/samtools-1.13/test/large_pos/longref2.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.13/samtools depth /builddir/build/BUILD/samtools-1.13/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.13/samtools depth -b /builddir/build/BUILD/samtools-1.13/test/large_pos/test.bed /builddir/build/BUILD/samtools-1.13/test/large_pos/longref.sam .. ok test_large_positions: /builddir/build/BUILD/samtools-1.13/samtools tview -d T -p CHROMOSOME_I:10000000000 /tmp/oOB7QTsEIz/longref.sam.gz .. ok test_large_positions: /builddir/build/BUILD/samtools-1.13/samtools sort -O sam --no-PG -n -m 10M test/large_pos/longref3.sam | /builddir/build/BUILD/samtools-1.13/samtools fixmate -O sam --no-PG - - | /builddir/build/BUILD/samtools-1.13/samtools sort -O sam --no-PG -m 10M .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --hard-clip -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --filter-len 185 -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --fail-len 185 -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --original -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip -@ 2 --no-PG --output-fmt=sam -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_test_data.sam .. ok test_ampliconclip: /builddir/build/BUILD/samtools-1.13/samtools ampliconclip -@ 2 --no-PG --keep-tag --output-fmt=sam --strand --both-ends -b /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/2_both_test_data.sam .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.13/samtools ampliconstats -@ 2 -S -t 50 -d 1,20,100 /builddir/build/BUILD/samtools-1.13/test/ampliconclip/ac_test.bed /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_hard_clipped.expected.sam /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_soft_clipped.expected.sam /builddir/build/BUILD/samtools-1.13/test/ampliconclip/1_soft_clipped_strand.expected.sam /builddir/build/BUILD/samtools-1.13/test/ampliconclip/2_both_clipped.expected.sam | egrep -v 'Samtools version|Command line' .. ok test_ampliconstats: /builddir/build/BUILD/samtools-1.13/samtools ampliconstats -@ 2 -c 0 /builddir/build/BUILD/samtools-1.13/test/ampliconclip/multi_ref.bed /builddir/build/BUILD/samtools-1.13/test/ampliconstats/mixed_clipped.sam | egrep -v 'Samtools version|Command line' .. ok Number of tests: total .. 754 passed .. 723 failed .. 0 expected failure .. 31 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 && AWK="gawk" ./regression.sh mpileup.reg === Testing mpileup.reg regressions === EXPECTED FAIL: Task failed, but expected to fail; when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam Expected passes: 163 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS cd test/mpileup && AWK="gawk" ./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: 47 Unexpected passes: 0 Expected failures: 1 Unexpected failures: 0 => PASS + RPM_EC=0 ++ jobs -p + exit 0 Processing files: samtools-1.13-1.fc35.s390x Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.1MA8r4 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.13 + DOCDIR=/builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/doc/samtools + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/doc/samtools + cp -pr AUTHORS /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/doc/samtools + cp -pr ChangeLog.old /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/doc/samtools + cp -pr NEWS /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/doc/samtools + cp -pr examples/ /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/doc/samtools + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.eHP0Wk + umask 022 + cd /builddir/build/BUILD + cd samtools-1.13 + LICENSEDIR=/builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/licenses/samtools + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/licenses/samtools + cp -pr LICENSE /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x/usr/share/licenses/samtools + RPM_EC=0 ++ jobs -p + exit 0 Provides: samtools = 1.13-1.fc35 samtools(s390-64) = 1.13-1.fc35 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/perl libc.so.6()(64bit) libc.so.6(GLIBC_2.2)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2)(64bit) libm.so.6(GLIBC_2.29)(64bit) libncursesw.so.6()(64bit) libtinfo.so.6()(64bit) libz.so.1()(64bit) rtld(GNU_HASH) Processing files: samtools-debugsource-1.13-1.fc35.s390x Provides: samtools-debugsource = 1.13-1.fc35 samtools-debugsource(s390-64) = 1.13-1.fc35 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: samtools-debuginfo-1.13-1.fc35.s390x Provides: debuginfo(build-id) = 32d30adde0af2e0986de72369a831cf44ecf6409 debuginfo(build-id) = 42348a69b8dcf4bef182983b021cd21ba39873ec debuginfo(build-id) = 632a09ab2d28fa06e6e3134c27249244d68899c8 debuginfo(build-id) = 81a9ee6cbef18379b981c6ee9c5674156134a609 debuginfo(build-id) = 8384914fdb85ce5b50a36eef16ba288ef2ab7ff5 debuginfo(build-id) = 91ac7b7cd0e619427cee0b4990c174e149dab337 debuginfo(build-id) = e38524903b16f1b44ed83119a81e9f97dd3216f8 samtools-debuginfo = 1.13-1.fc35 samtools-debuginfo(s390-64) = 1.13-1.fc35 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: samtools-debugsource(s390-64) = 1.13-1.fc35 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x Wrote: /builddir/build/RPMS/samtools-1.13-1.fc35.s390x.rpm Wrote: /builddir/build/RPMS/samtools-debuginfo-1.13-1.fc35.s390x.rpm Wrote: /builddir/build/RPMS/samtools-debugsource-1.13-1.fc35.s390x.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.qLR572 + umask 022 + cd /builddir/build/BUILD + cd samtools-1.13 + /usr/bin/rm -rf /builddir/build/BUILDROOT/samtools-1.13-1.fc35.s390x + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0