Diff of the two buildlogs:

--
--- b1/build.log	2025-03-29 02:08:52.167252124 +0000
+++ b2/build.log	2025-03-29 02:10:35.458613810 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Fri Mar 28 13:59:18 -12 2025
-I: pbuilder-time-stamp: 1743213558
+I: Current time: Fri May  1 22:31:54 +14 2026
+I: pbuilder-time-stamp: 1777624314
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
 I: copying local configuration
@@ -27,52 +27,84 @@
 dpkg-source: info: applying gcc-13-2.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/2773542/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/1579544/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos15-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 May  1 08:32 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/1579544/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/1579544/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='amd64'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
-  DISTRIBUTION='unstable'
-  HOME='/root'
-  HOST_ARCH='amd64'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.2.37(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=amd64
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
+  DIRSTACK=()
+  DISTRIBUTION=unstable
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='4bbd7c2425fe47cd97b93cad619c9198'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='2773542'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=f2c5553f7b7c4766b2b0c3342382ef19
+  LANG=C
+  LANGUAGE=et_EE:et
+  LC_ALL=C
+  MACHTYPE=x86_64-pc-linux-gnu
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnu
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=1579544
   PS4='+ '
-  PWD='/'
-  SHELL='/bin/bash'
-  SHLVL='2'
-  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4fM4RDle/pbuilderrc_Z33U --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4fM4RDle/b1 --logfile b1/build.log ivar_1.4.4+dfsg-1.dsc'
-  SUDO_GID='111'
-  SUDO_UID='106'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://46.16.76.132:3128'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.4fM4RDle/pbuilderrc_d4I9 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.4fM4RDle/b2 --logfile b2/build.log ivar_1.4.4+dfsg-1.dsc'
+  SUDO_GID=111
+  SUDO_UID=106
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://213.165.73.152:3128
 I: uname -a
-  Linux ionos11-amd64 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Mar  4 11:20 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/2773542/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Mar  4  2025 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/1579544/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -203,7 +235,7 @@
 Get: 91 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB]
 Get: 92 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.4-1 [323 kB]
 Get: 93 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB]
-Fetched 30.7 MB in 2s (14.0 MB/s)
+Fetched 30.7 MB in 1s (40.7 MB/s)
 Preconfiguring packages ...
 Selecting previously unselected package sensible-utils.
 (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19805 files and directories currently installed.)
@@ -590,7 +622,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/ivar-1.4.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../ivar_1.4.4+dfsg-1_source.changes
+I: user script /srv/workspace/pbuilder/1579544/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/1579544/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/ivar-1.4.4+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../ivar_1.4.4+dfsg-1_source.changes
 dpkg-buildpackage: info: source package ivar
 dpkg-buildpackage: info: source version 1.4.4+dfsg-1
 dpkg-buildpackage: info: source distribution unstable
@@ -677,7 +713,7 @@
 config.status: creating config.h
 config.status: executing depfiles commands
    dh_auto_build
-	make -j20
+	make -j42
 make[1]: Entering directory '/build/reproducible-path/ivar-1.4.4+dfsg'
 make  all-recursive
 make[2]: Entering directory '/build/reproducible-path/ivar-1.4.4+dfsg'
@@ -685,7 +721,9 @@
 make[3]: Entering directory '/build/reproducible-path/ivar-1.4.4+dfsg/src'
 g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o ivar.o ivar.cpp
 g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp
+g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o alignment.o alignment.cpp
 Using built-in specs.
+g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp
 COLLECT_GCC=g++
 OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
 OFFLOAD_TARGET_DEFAULT=1
@@ -694,11 +732,11 @@
 Thread model: posix
 Supported LTO compression algorithms: zlib zstd
 gcc version 14.2.0 (Debian 14.2.0-19) 
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccanY5YC.s
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o alignment.o alignment.cpp
 Using built-in specs.
-COLLECT_GCC=g++
+g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tablesCOLLECT_GCC=g++
+ -o /tmp/ccsaOidD.s
 OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
 OFFLOAD_TARGET_DEFAULT=1
 Target: x86_64-linux-gnu
@@ -706,55 +744,12 @@
 Thread model: posix
 Supported LTO compression algorithms: zlib zstd
 gcc version 14.2.0 (Debian 14.2.0-19) 
-GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
-	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
-
-warning: MPFR header version 4.2.1 differs from library version 4.2.2.
-GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
-ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
-ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
-ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
-ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed"
-ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include"
-#include "..." search starts here:
-#include <...> search starts here:
- .
- ..
- /usr/include/c++/14
- /usr/include/x86_64-linux-gnu/c++/14
- /usr/include/c++/14/backward
- /usr/lib/gcc/x86_64-linux-gnu/14/include
- /usr/local/include
- /usr/include/x86_64-linux-gnu
- /usr/include
-End of search list.
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccss6Wuf.s
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp
-GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
-	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
-
-warning: MPFR header version 4.2.1 differs from library version 4.2.2.
-GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
-ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
-ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
-ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
-ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed"
-ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include"
-#include "..." search starts here:
-#include <...> search starts here:
- .
- ..
- /usr/include/c++/14
- /usr/include/x86_64-linux-gnu/c++/14
- /usr/include/c++/14/backward
- /usr/lib/gcc/x86_64-linux-gnu/14/include
- /usr/local/include
- /usr/include/x86_64-linux-gnu
- /usr/include
-End of search list.
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp
+ call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/cczj3KHB.s
+Using built-in specs.
+g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp
 Using built-in specs.
-Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
 COLLECT_GCC=g++
 OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
 OFFLOAD_TARGET_DEFAULT=1
@@ -764,11 +759,31 @@
 Supported LTO compression algorithms: zlib zstd
 gcc version 14.2.0 (Debian 14.2.0-19) 
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/cc00UA8m.s
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp
+COLLECT_GCC=g++
+OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
+OFFLOAD_TARGET_DEFAULT=1
+Target: x86_64-linux-gnu
+Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-v /usr/libexec/gcc/x86_64-linux-gnu/14/cc1pluserify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list= -quietm32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without- -vcuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-co -Infig=bootstrap-lto-lean --enable-link-serialization=3
+ .Thread model: posix
+ -ISupported LTO compression algorithms: zlib .. zstd -imultiarch
+ x86_64-linux-gnugcc version 14.2.0 (Debian 14.2.0-19) 
+ -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cppg++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp
+ -quiet -dumpbase alignment.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64Using built-in specs.
+ -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccx2RGrR.s
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/cckUjz7c.s
+COLLECT_GCC=g++
 Using built-in specs.
-Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp
+OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
+OFFLOAD_TARGET_DEFAULT=1
+Target: x86_64-linux-gnu
+Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
+Thread model: posix
+Supported LTO compression algorithms: zlib zstd
+gcc version 14.2.0 (Debian 14.2.0-19) 
+g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccLQQVk9.s
 COLLECT_GCC=g++
 OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
 OFFLOAD_TARGET_DEFAULT=1
@@ -777,32 +792,8 @@
 Thread model: posix
 Supported LTO compression algorithms: zlib zstd
 gcc version 14.2.0 (Debian 14.2.0-19) 
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_tree.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccggw0Wj.s
-GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
-	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
-
-warning: MPFR header version 4.2.1 differs from library version 4.2.2.
-GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
-ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
-ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
-ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
-ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed"
-ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include"
-#include "..." search starts here:
-#include <...> search starts here:
- .
- ..
- /usr/include/c++/14
- /usr/include/x86_64-linux-gnu/c++/14
- /usr/include/c++/14/backward
- /usr/lib/gcc/x86_64-linux-gnu/14/include
- /usr/local/include
- /usr/include/x86_64-linux-gnu
- /usr/include
-End of search list.
 Using built-in specs.
+g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp
 COLLECT_GCC=g++
 OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
 OFFLOAD_TARGET_DEFAULT=1
@@ -811,10 +802,8 @@
 Thread model: posix
 Supported LTO compression algorithms: zlib zstd
 gcc version 14.2.0 (Debian 14.2.0-19) 
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccI5a4AI.s
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp
 Using built-in specs.
+g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp
 COLLECT_GCC=g++
 OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
 OFFLOAD_TARGET_DEFAULT=1
@@ -823,53 +812,89 @@
 Thread model: posix
 Supported LTO compression algorithms: zlib zstd
 gcc version 14.2.0 (Debian 14.2.0-19) 
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccRkBMXO.s
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp
+g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp
 Using built-in specs.
 COLLECT_GCC=g++
 OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
 OFFLOAD_TARGET_DEFAULT=1
 Target: x86_64-linux-gnu
-Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
+Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/deg++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp
+bian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
 Thread model: posix
 Supported LTO compression algorithms: zlib zstd
 gcc version 14.2.0 (Debian 14.2.0-19) 
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -WallCOLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map -Wextra=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format- -Werrorsecurity' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccey3JY7.s
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccbVcT18.s
+Using built-in specs.
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccdwG7hp.s
-Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/cc4supQM.s
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+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=fullg++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp
+ -fasynchronous-unwind-tables -o /tmp/ccdJqtBs.s
+COLLECT_GCC=g++
+OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
+OFFLOAD_TARGET_DEFAULT=1
+Target: x86_64-linux-gnu
+Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
 Using built-in specs.
+Thread model: posix
+Supported LTO compression algorithms: zlib zstd
+gcc version 14.2.0 (Debian 14.2.0-19) 
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnuCOLLECT_GCC=g++
+ -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
+ get_masked_amplicons.cpp -quietOFFLOAD_TARGET_DEFAULT=1
+ -dumpbase get_masked_amplicons.cppTarget: x86_64-linux-gnu
+ -dumpbase-extConfigured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs .cpp --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettex -mtune=generict --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enabl -march=x86-64e-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto -g --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list= -gm32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without- -O2cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-co -Wdate-timenfig=bootstrap-lto-lean --enable-link-serialization=3
+ -Wformat=1Thread model: posix
+ -Werror=format-securitySupported LTO compression algorithms: zlib -Wall zstd -Wextra
+ -Werrorgcc version 14.2.0 (Debian 14.2.0-19) 
+ -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccdhkNlT.s
+Using built-in specs.
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccFta6rs.s
 COLLECT_GCC=g++
 OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
 OFFLOAD_TARGET_DEFAULT=1
+Using built-in specs.
 Target: x86_64-linux-gnu
 Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
 Thread model: posix
 Supported LTO compression algorithms: zlib zstd
 gcc version 14.2.0 (Debian 14.2.0-19) 
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- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/cc2kmfv9.s
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp
-GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
-	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
-
-warning: MPFR header version 4.2.1 differs from library version 4.2.2.
-GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
-	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
+	compiled by GNU C version 14.2.0,  /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plusCOLLECT_GCC=g++
+ -quiet -v -I . -IOFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
+ ..OFFLOAD_TARGET_DEFAULT=1
+ -imultiarch x86_64-linux-gnuTarget: x86_64-linux-gnu
+ -D_GNU_SOURCEGMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
 
-warning: MPFR header version 4.2.1 differs from library version 4.2.2.
-GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
+Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs -D --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 HAVE_CONFIG_H --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enabl -De-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-v _FORTIFY_SOURCE=2erify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list= parse_gff.cppm32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/de -quietbian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without- -dumpbasecuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-co parse_gff.cppnfig=bootstrap-lto-lean --enable-link-serialization=3
+Thread model: posix
+ -dumpbase-extSupported LTO compression algorithms: zlib .cpp zstd -mtune=generic
+ -march=x86-64gcc version 14.2.0 (Debian 14.2.0-19) 
+ -g -g -O2warning: MPFR header version 4.2.1 differs from library version 4.2.2.
+ -Wdate-time -Wformat=1 -Werror=format-security -WallGGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
+ -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccpNPvUe.s
+Using built-in specs.
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccw8oakr.s
 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
 ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include"
-#include "..." search starts here:
+GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
+	compiled by GNU C version 14.2.0, #include "..." search starts here:
 #include <...> search starts here:
  .
  ..
  /usr/include/c++/14
+GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
+
  /usr/include/x86_64-linux-gnu/c++/14
  /usr/include/c++/14/backward
  /usr/lib/gcc/x86_64-linux-gnu/14/include
@@ -877,6 +902,16 @@
  /usr/include/x86_64-linux-gnu
  /usr/include
 End of search list.
+warning: MPFR header version 4.2.1 differs from library version 4.2.2.
+GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
+COLLECT_GCC=g++
+OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
+OFFLOAD_TARGET_DEFAULT=1
+Target: x86_64-linux-gnu
+Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
+Thread model: posix
+Supported LTO compression algorithms: zlib zstd
+gcc version 14.2.0 (Debian 14.2.0-19) 
 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
 ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
@@ -884,7 +919,8 @@
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include"
 #include "..." search starts here:
 #include <...> search starts here:
- .
+GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
+	compiled by GNU C version 14.2.0,  .
  ..
  /usr/include/c++/14
  /usr/include/x86_64-linux-gnu/c++/14
@@ -894,10 +930,7 @@
  /usr/include/x86_64-linux-gnu
  /usr/include
 End of search list.
-Using built-in specs.
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp
-GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
-	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
+GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
 
 warning: MPFR header version 4.2.1 differs from library version 4.2.2.
 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
@@ -917,55 +950,53 @@
  /usr/local/include
  /usr/include/x86_64-linux-gnu
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-End of search list.
-COLLECT_GCC=g++
-OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
-OFFLOAD_TARGET_DEFAULT=1
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-Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
-Thread model: posix
-Supported LTO compression algorithms: zlib zstd
-gcc version 14.2.0 (Debian 14.2.0-19) 
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccC7fqhn.s
+GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
+	compiled by GNU C version 14.2.0, End of search list.
 GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
 	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
 
+GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
+
+warning: MPFR header version 4.2.1 differs from library version 4.2.2.
+GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
 warning: MPFR header version 4.2.1 differs from library version 4.2.2.
 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
+ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
+ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
+ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed"
+ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed"
+ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include"
 #include "..." search starts here:
 #include <...> search starts here:
+#include "..." search starts here:
  .
+#include <...> search starts here:
  ..
+ .
  /usr/include/c++/14
+ ..
  /usr/include/x86_64-linux-gnu/c++/14
+ /usr/include/c++/14
  /usr/include/c++/14/backward
+ /usr/include/x86_64-linux-gnu/c++/14
  /usr/lib/gcc/x86_64-linux-gnu/14/include
+ /usr/include/c++/14/backward
  /usr/local/include
+ /usr/lib/gcc/x86_64-linux-gnu/14/include
  /usr/include/x86_64-linux-gnu
+ /usr/local/include
  /usr/include
+ /usr/include/x86_64-linux-gnu
 End of search list.
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp
-Using built-in specs.
-COLLECT_GCC=g++
-OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
-OFFLOAD_TARGET_DEFAULT=1
-Target: x86_64-linux-gnu
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-Thread model: posix
-Supported LTO compression algorithms: zlib zstd
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-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccmxFfIz.s
-Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
-Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
-Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp
+ /usr/include
+End of search list.
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccYQZEfe.s
 GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
 	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
 
@@ -976,7 +1007,17 @@
 
 warning: MPFR header version 4.2.1 differs from library version 4.2.2.
 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
+GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
+	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
+
+warning: MPFR header version 4.2.1 differs from library version 4.2.2.
 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
+GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
+ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
+ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
+ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed"
+ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
+ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include"
 ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed"
@@ -986,22 +1027,39 @@
  .
  ..
  /usr/include/c++/14
+#include "..." search starts here:
  /usr/include/x86_64-linux-gnu/c++/14
+#include <...> search starts here:
  /usr/include/c++/14/backward
+ .
  /usr/lib/gcc/x86_64-linux-gnu/14/include
+ ..
+ /usr/include/c++/14
  /usr/local/include
+ /usr/include/x86_64-linux-gnu/c++/14
  /usr/include/x86_64-linux-gnu
+ /usr/include/c++/14/backward
  /usr/include
+ /usr/lib/gcc/x86_64-linux-gnu/14/include
+ /usr/local/include
 End of search list.
-ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
+ /usr/include/x86_64-linux-gnu
+ /usr/include
+End of search list.
+GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
+	compiled by GNU C version 14.2.0, ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
 ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
+GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
+
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include"
+warning: MPFR header version 4.2.1 differs from library version 4.2.2.
 #include "..." search starts here:
 #include <...> search starts here:
  .
  ..
+GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
  /usr/include/c++/14
  /usr/include/x86_64-linux-gnu/c++/14
  /usr/include/c++/14/backward
@@ -1010,46 +1068,11 @@
  /usr/include/x86_64-linux-gnu
  /usr/include
 End of search list.
-Using built-in specs.
-COLLECT_GCC=g++
-OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
-OFFLOAD_TARGET_DEFAULT=1
-Target: x86_64-linux-gnu
-Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
-Thread model: posix
-Supported LTO compression algorithms: zlib zstd
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- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccgVkILm.s
-g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -O2 -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -v -g -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp
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-Target: x86_64-linux-gnu
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-Thread model: posix
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-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/ccU8CpuI.s
-Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
-Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
-Using built-in specs.
-Using built-in specs.
 GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
 	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
 
 warning: MPFR header version 4.2.1 differs from library version 4.2.2.
 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
-COLLECT_GCC=g++
-OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
-OFFLOAD_TARGET_DEFAULT=1
-Target: x86_64-linux-gnu
-Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
-Thread model: posix
-Supported LTO compression algorithms: zlib zstd
-gcc version 14.2.0 (Debian 14.2.0-19) 
 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
 ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
@@ -1067,24 +1090,6 @@
  /usr/include/x86_64-linux-gnu
  /usr/include
 End of search list.
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- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/cc9ECfdL.s
-Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
-COLLECT_GCC=g++
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-OFFLOAD_TARGET_DEFAULT=1
-Target: x86_64-linux-gnu
-Configured with: ../src/configure -v --with-pkgversion='Debian 14.2.0-19' --with-bugurl=file:///usr/share/doc/gcc-14/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2,rust --prefix=/usr --with-gcc-major-version-only --program-suffix=-14 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/reproducible-path/gcc-14-14.2.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=3
-Thread model: posix
-Supported LTO compression algorithms: zlib zstd
-gcc version 14.2.0 (Debian 14.2.0-19) 
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- /usr/libexec/gcc/x86_64-linux-gnu/14/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -fcf-protection=full -fasynchronous-unwind-tables -o /tmp/cc22Wcyb.s
-GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
-	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
-
-warning: MPFR header version 4.2.1 differs from library version 4.2.2.
-GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
 ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
@@ -1129,6 +1134,11 @@
 
 warning: MPFR header version 4.2.1 differs from library version 4.2.2.
 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
+GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
+	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
+
+warning: MPFR header version 4.2.1 differs from library version 4.2.2.
+GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
 ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
 ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
@@ -1145,11 +1155,32 @@
  /usr/local/include
  /usr/include/x86_64-linux-gnu
  /usr/include
+ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
+End of search list.
+ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
+ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed/x86_64-linux-gnu"
+ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/include-fixed"
+ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/14/../../../../x86_64-linux-gnu/include"
+#include "..." search starts here:
+#include <...> search starts here:
+ .
+ ..
+ /usr/include/c++/14
+ /usr/include/x86_64-linux-gnu/c++/14
+ /usr/include/c++/14/backward
+ /usr/lib/gcc/x86_64-linux-gnu/14/include
+ /usr/local/include
+ /usr/include/x86_64-linux-gnu
+ /usr/include
 End of search list.
 Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
-GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
-	compiled by GNU C version 14.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
+Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
+Compiler executable checksum: a0Compiler executable checksum: e1d70aa04b6ce150d7c70aed4b1b6c3d5036c7dfedd31bf93da436df
+d3f9a4
+Compiler executable checksum: GNU C++17 (Debian 14.2.0-19) version 14.2.0 (x86_64-linux-gnu)
+	compiled by GNU C version 14.2.0, a0e1d70a4b6c50c7ed1b3d36dfGMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.27-GMP
 
+d3f9a4
 warning: MPFR header version 4.2.1 differs from library version 4.2.2.
 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
 ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/14"
@@ -1170,53 +1201,49 @@
  /usr/include
 End of search list.
 Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
+Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9Compiler executable checksum: a4
+a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
+Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
+Compiler executable checksum: a0e1d70a4b6c50c7edCompiler executable checksum: 1b3da036e1dfd7d30af94b6ca450c7ed
+1b3d36dfd3f9a4
 Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
 Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
 Compiler executable checksum: a0e1d70a4b6c50c7ed1b3d36dfd3f9a4
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o interval_tree.o /tmp/cc9ECfdL.s
+ as -v -I . -I .. --gdwarf-5 --64 -o interval_tree.o /tmp/ccYQZEfe.s
 GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'interval_tree.'
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o alignment.o /tmp/cc00UA8m.s
+ as -v -I . -I .. --gdwarf-5 --64 -o alignment.o /tmp/ccx2RGrR.s
 GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'alignment.'
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o get_masked_amplicons.o /tmp/ccmxFfIz.s
-GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
-COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
-LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'get_masked_amplicons.'
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o remove_reads_from_amplicon.o /tmp/cc2kmfv9.s
+ as -v -I . -I .. --gdwarf-5 --64 -o remove_reads_from_amplicon.o /tmp/ccey3JY7.s
 GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'remove_reads_from_amplicon.'
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o primer_bed.o /tmp/ccdwG7hp.s
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o call_variants.o /tmp/ccRkBMXO.s
-GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ as -v -I . -I .. --gdwarf-5 --64 -o get_masked_amplicons.o /tmp/ccdhkNlT.s
 GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_variants.'
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o allele_functions.o /tmp/ccC7fqhn.s
-GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'get_masked_amplicons.'
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o ref_seq.o /tmp/cc22Wcyb.s
+ as -v -I . -I .. --gdwarf-5 --64 -o ref_seq.o /tmp/ccw8oakr.s
 GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
-COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
-LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'primer_bed.'
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ as -v -I . -I .. --gdwarf-5 --64 -o allele_functions.o /tmp/ccdJqtBs.s
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o get_common_variants.o /tmp/ccU8CpuI.s
+ as -v -I . -I .. --gdwarf-5 --64 -o get_common_variants.o /tmp/ccFta6rs.s
+GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
+GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ as -v -I . -I .. --gdwarf-5 --64 -o call_variants.o /tmp/ccbVcT18.s
 GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
@@ -1227,32 +1254,41 @@
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'get_common_variants.'
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o ivar.o /tmp/ccanY5YC.s
+COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
+LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_variants.'
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ as -v -I . -I .. --gdwarf-5 --64 -o primer_bed.o /tmp/cc4supQM.s
 GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o call_consensus_pileup.o /tmp/ccss6Wuf.s
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ as -v -I . -I .. --gdwarf-5 --64 -o ivar.o /tmp/ccsaOidD.s
 GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.'
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'primer_bed.'
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_consensus_pileup.'
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.'
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ as -v -I . -I .. --gdwarf-5 --64 -o suffix_tree.o /tmp/cckUjz7c.s
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
+ as -v -I . -I .. --gdwarf-5 --64 -o call_consensus_pileup.o /tmp/cczj3KHB.s
+GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
+GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o trim_primer_quality.o /tmp/ccI5a4AI.s
+ as -v -I . -I .. --gdwarf-5 --64 -o trim_primer_quality.o /tmp/ccLQQVk9.s
 GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
+COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_consensus_pileup.'
+COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
+LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'trim_primer_quality.'
-COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o suffix_tree.o /tmp/ccggw0Wj.s
-GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'suffix_tree.'
 COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
- as -v -I . -I .. --gdwarf-5 --64 -o parse_gff.o /tmp/ccgVkILm.s
+ as -v -I . -I .. --gdwarf-5 --64 -o parse_gff.o /tmp/ccpNPvUe.s
 GNU assembler version 2.44 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.44
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
@@ -1271,7 +1307,7 @@
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
 COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-foffload-options=-l_GCC_m' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.'
- /usr/libexec/gcc/x86_64-linux-gnu/14/collect2 -plugin /usr/libexec/gcc/x86_64-linux-gnu/14/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper -plugin-opt=-fresolution=/tmp/ccdunfoJ.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o
+ /usr/libexec/gcc/x86_64-linux-gnu/14/collect2 -plugin /usr/libexec/gcc/x86_64-linux-gnu/14/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper -plugin-opt=-fresolution=/tmp/cc9IhOKZ.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o
 COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-foffload-options=-l_GCC_m' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.'
 make[3]: Leaving directory '/build/reproducible-path/ivar-1.4.4+dfsg/src'
 Making all in tests
@@ -1394,7 +1430,7 @@
    create-stamp debian/debhelper-build-stamp
    dh_prep
    dh_auto_install
-	make -j20 install DESTDIR=/build/reproducible-path/ivar-1.4.4\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no
+	make -j42 install DESTDIR=/build/reproducible-path/ivar-1.4.4\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no
 make[1]: Entering directory '/build/reproducible-path/ivar-1.4.4+dfsg'
 Making install in src
 make[2]: Entering directory '/build/reproducible-path/ivar-1.4.4+dfsg/src'
@@ -1412,7 +1448,7 @@
 COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/14/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/
 LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/14/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/14/../../../:/lib/:/usr/lib/
 COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-foffload-options=-l_GCC_m' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.'
- /usr/libexec/gcc/x86_64-linux-gnu/14/collect2 -plugin /usr/libexec/gcc/x86_64-linux-gnu/14/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper -plugin-opt=-fresolution=/tmp/cc76lcyQ.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o
+ /usr/libexec/gcc/x86_64-linux-gnu/14/collect2 -plugin /usr/libexec/gcc/x86_64-linux-gnu/14/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/x86_64-linux-gnu/14/lto-wrapper -plugin-opt=-fresolution=/tmp/ccAXL9Lc.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ivar /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/14/crtbeginS.o -L/usr/lib/gcc/x86_64-linux-gnu/14 -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/14/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/14/../../.. -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/14/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/14/../../../x86_64-linux-gnu/crtn.o
 COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/build/reproducible-path/ivar-1.4.4+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-fcf-protection=full' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-foffload-options=-l_GCC_m' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.'
 make[3]: Entering directory '/build/reproducible-path/ivar-1.4.4+dfsg/src'
 make[3]: Nothing to be done for 'install-data-am'.
@@ -1448,7 +1484,7 @@
 if [ -x /build/reproducible-path/ivar-1.4.4+dfsg/debian/ivar/usr/share/doc/ivar/examples/data/primer_pair_test/test_primer_pair.bed ] \
 ; then chmod -v -x /build/reproducible-path/ivar-1.4.4+dfsg/debian/ivar/usr/share/doc/ivar/examples/data/primer_pair_test/test_primer_pair.bed \
 ; fi
-mode of '/build/reproducible-path/ivar-1.4.4+dfsg/debian/ivar/usr/share/doc/ivar/examples/data/primer_pair_test/test_primer_pair.bed' changed from 0755 (rwxr-xr-x) to 0644 (rw-r--r--)
+mode of '/build/reproducible-path/ivar-1.4.4+dfsg/debian/ivar/usr/share/doc/ivar/examples/data/primer_pair_test/test_primer_pair.bed' changed from 0775 (rwxrwxr-x) to 0664 (rw-rw-r--)
 make[1]: Leaving directory '/build/reproducible-path/ivar-1.4.4+dfsg'
    dh_fixperms
    dh_missing
@@ -1460,8 +1496,8 @@
    dh_gencontrol
    dh_md5sums
    dh_builddeb
-dpkg-deb: building package 'ivar-dbgsym' in '../ivar-dbgsym_1.4.4+dfsg-1_amd64.deb'.
 dpkg-deb: building package 'ivar' in '../ivar_1.4.4+dfsg-1_amd64.deb'.
+dpkg-deb: building package 'ivar-dbgsym' in '../ivar-dbgsym_1.4.4+dfsg-1_amd64.deb'.
 dpkg-deb: building package 'ivar-doc' in '../ivar-doc_1.4.4+dfsg-1_all.deb'.
  dpkg-genbuildinfo --build=binary -O../ivar_1.4.4+dfsg-1_amd64.buildinfo
  dpkg-genchanges --build=binary -O../ivar_1.4.4+dfsg-1_amd64.changes
@@ -1470,12 +1506,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: including full source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/1579544/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/1579544/tmp/hooks/B01_cleanup finished
 I: unmounting dev/ptmx filesystem
 I: unmounting dev/pts filesystem
 I: unmounting dev/shm filesystem
 I: unmounting proc filesystem
 I: unmounting sys filesystem
 I: cleaning the build env 
-I: removing directory /srv/workspace/pbuilder/2773542 and its subdirectories
-I: Current time: Fri Mar 28 14:08:51 -12 2025
-I: pbuilder-time-stamp: 1743214131
+I: removing directory /srv/workspace/pbuilder/1579544 and its subdirectories
+I: Current time: Fri May  1 22:33:34 +14 2026
+I: pbuilder-time-stamp: 1777624414