Diff of the two buildlogs:

--
--- b1/build.log	2024-05-31 11:29:55.869235122 +0000
+++ b2/build.log	2024-05-31 11:34:46.836855411 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Thu Jul  3 05:47:04 -12 2025
-I: pbuilder-time-stamp: 1751564824
+I: Current time: Fri Jul  4 07:53:06 +14 2025
+I: pbuilder-time-stamp: 1751565186
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
 I: copying local configuration
@@ -31,52 +31,84 @@
 dpkg-source: info: applying sphinx.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/1713694/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/572923/tmp/hooks/D01_modify_environment starting
+debug: Running on codethink01-arm64.
+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 Jul  3 17:53 /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/572923/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/572923/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='arm64'
-  DEBIAN_FRONTEND='noninteractive'
+  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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
+  BASH_VERSION='5.2.21(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=arm64
+  DEBIAN_FRONTEND=noninteractive
   DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
-  DISTRIBUTION='trixie'
-  HOME='/root'
-  HOST_ARCH='arm64'
+  DIRSTACK=()
+  DISTRIBUTION=trixie
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=aarch64
+  HOST_ARCH=arm64
   IFS=' 	
   '
-  INVOCATION_ID='4bb5ce09c5f44fac998070dd7634e73c'
-  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='1713694'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=602aed2770f24c848b06cc62d5a59c0d
+  LANG=C
+  LANGUAGE=nl_BE:nl
+  LC_ALL=C
+  MACHTYPE=aarch64-unknown-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=572923
   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.bXy4GrNd/pbuilderrc_VPYd --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bXy4GrNd/b1 --logfile b1/build.log salmon_1.10.2+ds1-1.dsc'
-  SUDO_GID='109'
-  SUDO_UID='104'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://192.168.101.4:3128'
+  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.bXy4GrNd/pbuilderrc_B6Xk --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bXy4GrNd/b2 --logfile b2/build.log salmon_1.10.2+ds1-1.dsc'
+  SUDO_GID=109
+  SUDO_UID=104
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://192.168.101.4:3128
 I: uname -a
-  Linux codethink03-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Jun 30 17:48 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/1713694/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Jun 28 17:47 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/572923/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -353,7 +385,7 @@
 Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-sphinx-rtd-theme all 2.0.0+dfsg-1 [28.3 kB]
 Get: 178 http://deb.debian.org/debian trixie/main arm64 rapmap-dev all 0.15.0+dfsg-4 [193 kB]
 Get: 179 http://deb.debian.org/debian trixie/main arm64 sphinx-doc all 7.2.6-8 [2371 kB]
-Fetched 120 MB in 1s (116 MB/s)
+Fetched 120 MB in 1s (179 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package fonts-lato.
 (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 ... 19744 files and directories currently installed.)
@@ -948,8 +980,8 @@
 Setting up tzdata (2024a-4) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Thu Jul  3 17:47:57 UTC 2025.
-Universal Time is now:  Thu Jul  3 17:47:57 UTC 2025.
+Local time is now:      Thu Jul  3 17:53:42 UTC 2025.
+Universal Time is now:  Thu Jul  3 17:53:42 UTC 2025.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up libboost-atomic1.83.0:arm64 (1.83.0-3) ...
@@ -1106,7 +1138,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/salmon-1.10.2+ds1/ && 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  > ../salmon_1.10.2+ds1-1_source.changes
+I: user script /srv/workspace/pbuilder/572923/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/572923/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/salmon-1.10.2+ds1/ && 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  > ../salmon_1.10.2+ds1-1_source.changes
 dpkg-buildpackage: info: source package salmon
 dpkg-buildpackage: info: source version 1.10.2+ds1-1
 dpkg-buildpackage: info: source distribution unstable
@@ -1227,8 +1263,8 @@
 TBB_LIBRARIES = 
 TBB_LIB_INSTALL_DIR = 
 TBBGLOBS = 
--- Configuring done (4.6s)
--- Generating done (0.0s)
+-- Configuring done (5.5s)
+-- Generating done (0.1s)
 CMake Warning:
   Manually-specified variables were not used by the project:
 
@@ -1254,205 +1290,173 @@
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+make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
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+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake "--color="
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+make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
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+make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
+make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
+make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
+make  -f external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build.make external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/build
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-[  2%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o
+make  -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build
+[  1%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o
+make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
 make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake "--color="
+make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
+make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
+make  -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/build
+make  -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o -MF CMakeFiles/graphdump.dir/graphdump.cpp.o.d -o CMakeFiles/graphdump.dir/graphdump.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/graphdump.cpp
 make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
+make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
+make  -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build
+[  2%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c
+make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
+make  -f src/CMakeFiles/UnitTestsMain.dir/build.make src/CMakeFiles/UnitTestsMain.dir/build
 [  3%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o
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-[  5%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -MF CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/dnachar.cpp
+[  4%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -MF CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/dnachar.cpp
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o -MF CMakeFiles/twopaco.dir/constructor.cpp.o.d -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp
+[  5%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o
 [  5%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o
 make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -MF CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o.d -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common/SignalHandler.cpp
 [  6%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c
+[  7%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o
+[  8%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/edlib.cpp.o -MF CMakeFiles/alevin_core.dir/edlib.cpp.o.d -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/edlib.cpp
+[  9%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -D__SSE4_1__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -MF CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o.d -o CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common/SignalHandler.cpp
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp
-[  7%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o
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-make  -f external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build.make external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/build
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -MF CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o.d -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common/Fcontrol.cpp
-[  8%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o
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-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -MF CMakeFiles/twopaco.dir/compressedstring.cpp.o.d -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp
-[  9%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c
-[ 10%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/kalloc.c
-[ 11%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o -MF CMakeFiles/ntcard.dir/nthll.cpp.o.d -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/nthll.cpp
-[ 12%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndexer.cpp
+[ 10%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -MF CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o.d -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/jellyfish/mer_dna.cc
+[ 10%] Building CXX object src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -MF CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o.d -o CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/UnitTests.cpp
+[ 11%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extd.c
+[ 11%] Building CXX object external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/../common -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump/. -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp
+[ 12%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -MF CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o.d -o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common/Fcontrol.cpp
 [ 13%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o
+[ 14%] Building CXX object external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/Common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -O3 -MD -MT external/pufferfish/external/ntcard/CMakeFiles/ntcard.dir/nthll.cpp.o -MF CMakeFiles/ntcard.dir/nthll.cpp.o.d -o CMakeFiles/ntcard.dir/nthll.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/ntcard/nthll.cpp
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz.c
-[ 14%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o
+[ 15%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c
+[ 15%] Building CXX object src/CMakeFiles/salmon_core.dir/backtrace.cc.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/backtrace.cc.o -MF CMakeFiles/salmon_core.dir/backtrace.cc.o.d -o CMakeFiles/salmon_core.dir/backtrace.cc.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/backtrace.cc
+[ 16%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o -MF CMakeFiles/twopaco.dir/constructor.cpp.o.d -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp
+[ 17%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o
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-[ 15%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp
-[ 16%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o -MF CMakeFiles/twopaco.dir/test.cpp.o.d -o CMakeFiles/twopaco.dir/test.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp
-[ 17%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o
+[ 18%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -MF CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o.d -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp
+[ 19%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2.c
-[ 17%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c
-[ 18%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp
-[ 18%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -MF CMakeFiles/twopaco.dir/vertexenumerator.cpp.o.d -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp
-make  -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/depend
-make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src/CMakeFiles/puffer.dir/DependInfo.cmake "--color="
-[ 19%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -MF CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp
-make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-make  -f external/pufferfish/src/CMakeFiles/puffer.dir/build.make external/pufferfish/src/CMakeFiles/puffer.dir/build
-make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-[ 20%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndexer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndexer.cpp
-[ 21%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c
-[ 22%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o
+[ 20%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o
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+cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C
+cc1: warning: command-line option '-Wno-deprecated-copy' is valid for C++/ObjC++ but not for C
+[ 21%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o
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-[ 23%] Linking CXX static library libntcard.a
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/ntcard && /usr/bin/cmake -P CMakeFiles/ntcard.dir/cmake_clean_target.cmake
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+[ 22%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o
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+[ 22%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c
+[ 23%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o
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 [ 24%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o
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+[ 25%] Linking CXX static library libntcard.a
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 /usr/bin/ar qc libntcard.a CMakeFiles/ntcard.dir/Common/SignalHandler.cpp.o CMakeFiles/ntcard.dir/Common/Fcontrol.cpp.o CMakeFiles/ntcard.dir/nthll.cpp.o
 /usr/bin/ranlib libntcard.a
-[ 25%] Building C object external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -O3 -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -MF CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o.d -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c
-make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-[ 26%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp
-[ 26%] Built target ntcard
-make  -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend
-make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/salmon-1.10.2+ds1 /build/reproducible-path/salmon-1.10.2+ds1/src /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake "--color="
 make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
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-make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-[ 27%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -MF CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o.d -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/jellyfish/mer_dna.cc
-[ 27%] Building CXX object src/CMakeFiles/salmon_core.dir/backtrace.cc.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/backtrace.cc.o -MF CMakeFiles/salmon_core.dir/backtrace.cc.o.d -o CMakeFiles/salmon_core.dir/backtrace.cc.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/backtrace.cc
-[ 28%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/xxhash.c.o -MF CMakeFiles/salmon_core.dir/xxhash.c.o.d -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/xxhash.c
-cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C
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-[ 29%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -MF CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o.d -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/TranscriptGroup.cpp
-[ 30%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -MF CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o.d -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/EffectiveLengthStats.cpp
 make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-[ 31%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o
-[ 31%] Built target ksw2pp_basic
+[ 25%] Built target ksw2pp_sse2
+[ 25%] Built target ntcard
+[ 26%] Building CXX object external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_USE_ARM -D__SSE2__ -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -MF CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o.d -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp
+[ 27%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -MF CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o.d -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp
+[ 28%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -MF CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o.d -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp
-make  -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend
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-[ 32%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/edlib.cpp.o -MF CMakeFiles/alevin_core.dir/edlib.cpp.o.d -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/edlib.cpp
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-make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-[ 32%] Building CXX object src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -MF CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o.d -o CMakeFiles/UnitTestsMain.dir/__/tests/UnitTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/UnitTests.cpp
-[ 33%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o
+[ 29%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o
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-make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-[ 33%] Built target ksw2pp_sse2
-[ 34%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o
+[ 30%] Building CXX object src/CMakeFiles/salmon_core.dir/VersionChecker.cpp.o
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-[ 35%] Building CXX object src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -MF CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o.d -o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SingleCellProtocols.cpp
+[ 31%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SBModel.cpp.o -MF CMakeFiles/salmon_core.dir/SBModel.cpp.o.d -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SBModel.cpp
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-[ 35%] Built target ksw2pp_sse4
+[ 31%] Built target ksw2pp_basic
+[ 31%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o -MF CMakeFiles/salmon_core.dir/FastxParser.cpp.o.d -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp
+make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
+[ 31%] Built target ksw2pp_sse4
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-[ 36%] Linking CXX static library libksw2pp.a
+[ 32%] Linking CXX static library libksw2pp.a
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-[ 36%] Built target ksw2pp
-[ 37%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -MF CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o.d -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp
-[ 38%] Building CXX object src/CMakeFiles/salmon_core.dir/SBModel.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SBModel.cpp.o -MF CMakeFiles/salmon_core.dir/SBModel.cpp.o.d -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SBModel.cpp
-[ 38%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o -MF CMakeFiles/salmon_core.dir/FastxParser.cpp.o.d -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp
-[ 39%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o
+[ 32%] Built target ksw2pp
+[ 33%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp
+[ 34%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -MF CMakeFiles/salmon_core.dir/StadenUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/StadenUtils.cpp
-[ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o
+[ 35%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonUtils.cpp
-In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/FastxParser.hpp:15,
-                 from /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp:1:
-/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h: In instantiation of 'void moodycamel::details::swap_relaxed(std::atomic<_ITp>&, std::atomic<_ITp>&) [with T = std::thread::id]':
-/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:3302:26:   required from 'void moodycamel::ConcurrentQueue<T, Traits>::ImplicitProducerKVP::swap(moodycamel::ConcurrentQueue<T, Traits>::ImplicitProducerKVP&) [with T = std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]'
-/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:3295:4:   required from 'moodycamel::ConcurrentQueue<T, Traits>::ImplicitProducerKVP& moodycamel::ConcurrentQueue<T, Traits>::ImplicitProducerKVP::operator=(moodycamel::ConcurrentQueue<T, Traits>::ImplicitProducerKVP&&) [with T = std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]'
-/usr/include/c++/13/bits/move.h:198:11:   required from 'std::_Require<std::__not_<std::__is_tuple_like<_Tp> >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = moodycamel::ConcurrentQueue<unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; _Require<__not_<__is_tuple_like<_Tp> >, is_move_constructible<_Tp>, is_move_assignable<_Tp> > = void]'
-/usr/include/c++/13/bits/stl_algobase.h:185:11:   required from 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue<unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue<unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]'
-/usr/include/c++/13/bits/stl_algobase.h:215:16:   required from '_ForwardIterator2 std::swap_ranges(_ForwardIterator1, _ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue<unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue<unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]'
-/usr/include/c++/13/array:121:25:   required from 'void std::array<_Tp, _Nm>::swap(std::array<_Tp, _Nm>&) [with _Tp = moodycamel::ConcurrentQueue<std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; long unsigned int _Nm = 32]'
-/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:3343:43:   required from 'void moodycamel::ConcurrentQueue<T, Traits>::swap_implicit_producer_hashes(moodycamel::ConcurrentQueue<T, Traits>&) [with T = std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]'
-/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:955:3:   required from 'moodycamel::ConcurrentQueue<T, Traits>& moodycamel::ConcurrentQueue<T, Traits>::swap_internal(moodycamel::ConcurrentQueue<T, Traits>&) [with T = std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]'
-/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:926:10:   required from 'moodycamel::ConcurrentQueue<T, Traits>& moodycamel::ConcurrentQueue<T, Traits>::operator=(moodycamel::ConcurrentQueue<T, Traits>&&) [with T = std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp:43:14:   required from 'fastx_parser::FastxParser<T>::FastxParser(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, uint32_t, uint32_t, uint32_t) [with T = klibpp::KSeq; uint32_t = unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp:425:16:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:509:19: warning: moving a temporary object prevents copy elision [-Wpessimizing-move]
-  509 |                 T temp = std::move(left.load(std::memory_order_relaxed));
-      |                   ^~~~
-/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:509:19: note: remove 'std::move' call
-/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:510:27: warning: moving a temporary object prevents copy elision [-Wpessimizing-move]
-  510 |                 left.store(std::move(right.load(std::memory_order_relaxed)), std::memory_order_relaxed);
-      |                 ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:510:27: note: remove 'std::move' call
+[ 36%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -MF CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/DistributionUtils.cpp
 In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/PufferfishBinaryGFAReader.hpp:9,
                  from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:1,
                  from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndexer.cpp:20:
@@ -1484,35 +1488,67 @@
 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; row_it = spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*; col_it = std::pair<const std::vector<unsigned int>, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >]'
   946 |     Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
       |                                 ^~~~~~~~
-[ 41%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o
+In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/FastxParser.hpp:15,
+                 from /build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp:1:
+/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h: In instantiation of 'void moodycamel::details::swap_relaxed(std::atomic<_ITp>&, std::atomic<_ITp>&) [with T = std::thread::id]':
+/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:3302:26:   required from 'void moodycamel::ConcurrentQueue<T, Traits>::ImplicitProducerKVP::swap(moodycamel::ConcurrentQueue<T, Traits>::ImplicitProducerKVP&) [with T = std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]'
+/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:3295:4:   required from 'moodycamel::ConcurrentQueue<T, Traits>::ImplicitProducerKVP& moodycamel::ConcurrentQueue<T, Traits>::ImplicitProducerKVP::operator=(moodycamel::ConcurrentQueue<T, Traits>::ImplicitProducerKVP&&) [with T = std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]'
+/usr/include/c++/13/bits/move.h:198:11:   required from 'std::_Require<std::__not_<std::__is_tuple_like<_Tp> >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = moodycamel::ConcurrentQueue<unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; _Require<__not_<__is_tuple_like<_Tp> >, is_move_constructible<_Tp>, is_move_assignable<_Tp> > = void]'
+/usr/include/c++/13/bits/stl_algobase.h:185:11:   required from 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue<unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue<unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]'
+/usr/include/c++/13/bits/stl_algobase.h:215:16:   required from '_ForwardIterator2 std::swap_ranges(_ForwardIterator1, _ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = moodycamel::ConcurrentQueue<unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*; _ForwardIterator2 = moodycamel::ConcurrentQueue<unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP*]'
+/usr/include/c++/13/array:121:25:   required from 'void std::array<_Tp, _Nm>::swap(std::array<_Tp, _Nm>&) [with _Tp = moodycamel::ConcurrentQueue<std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >, moodycamel::ConcurrentQueueDefaultTraits>::ImplicitProducerKVP; long unsigned int _Nm = 32]'
+/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:3343:43:   required from 'void moodycamel::ConcurrentQueue<T, Traits>::swap_implicit_producer_hashes(moodycamel::ConcurrentQueue<T, Traits>&) [with T = std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]'
+/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:955:3:   required from 'moodycamel::ConcurrentQueue<T, Traits>& moodycamel::ConcurrentQueue<T, Traits>::swap_internal(moodycamel::ConcurrentQueue<T, Traits>&) [with T = std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]'
+/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:926:10:   required from 'moodycamel::ConcurrentQueue<T, Traits>& moodycamel::ConcurrentQueue<T, Traits>::operator=(moodycamel::ConcurrentQueue<T, Traits>&&) [with T = std::unique_ptr<fastx_parser::ReadChunk<klibpp::KSeq>, std::default_delete<fastx_parser::ReadChunk<klibpp::KSeq> > >; Traits = moodycamel::ConcurrentQueueDefaultTraits]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp:43:14:   required from 'fastx_parser::FastxParser<T>::FastxParser(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, uint32_t, uint32_t, uint32_t) [with T = klibpp::KSeq; uint32_t = unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/FastxParser.cpp:425:16:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:509:19: warning: moving a temporary object prevents copy elision [-Wpessimizing-move]
+  509 |                 T temp = std::move(left.load(std::memory_order_relaxed));
+      |                   ^~~~
+/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:509:19: note: remove 'std::move' call
+/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:510:27: warning: moving a temporary object prevents copy elision [-Wpessimizing-move]
+  510 |                 left.store(std::move(right.load(std::memory_order_relaxed)), std::memory_order_relaxed);
+      |                 ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+/build/reproducible-path/salmon-1.10.2+ds1/include/concurrentqueue.h:510:27: note: remove 'std::move' call
+[ 37%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -MF CMakeFiles/twopaco.dir/compressedstring.cpp.o.d -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp
+[ 38%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBaseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBaseIndex.cpp
-[ 42%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp
-[ 43%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -MF CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/DistributionUtils.cpp
-[ 44%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp
-[ 45%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o
+[ 39%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/streamfastaparser.cpp
+[ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonExceptions.cpp
-[ 46%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o
+[ 42%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -MF CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o.d -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonStringUtils.cpp
-[ 47%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o
+[ 41%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o -MF CMakeFiles/twopaco.dir/test.cpp.o.d -o CMakeFiles/twopaco.dir/test.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/test.cpp
+[ 43%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -MF CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o.d -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SimplePosBias.cpp
+[ 43%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -MF CMakeFiles/twopaco.dir/vertexenumerator.cpp.o.d -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp
 /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp: In function 'bool alevin::utils::extractBarcode(std::string&, std::string&, ProtocolT&, std::string&) [with ProtocolT = alevin::protocols::SciSeq3; std::string = std::__cxx11::basic_string<char>]':
 /build/reproducible-path/salmon-1.10.2+ds1/src/AlevinUtils.cpp:350:104: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
   350 |       if (pt.anchorPos != std::string::npos && ( pt.anchorPos == pt.maxHairpinIndexLen || pt.anchorPos == pt.maxHairpinIndexLen -1) // only 2 possible values of pt.anchorPos
       |                                                                                           ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
-[ 48%] Linking CXX static library libgraphdump.a
+[ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -MF CMakeFiles/salmon_core.dir/SGSmooth.cpp.o.d -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SGSmooth.cpp
+[ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -MF CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o.d -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/pufferfish/metro/metrohash64.cpp
+[ 45%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -MF CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp
+[ 46%] Building CXX object external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphconstructor && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -MD -MT external/pufferfish/external/twopaco/graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphconstructor/common.cpp
+[ 47%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishIndex.cpp
+[ 48%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishSparseIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishSparseIndex.cpp
+[ 49%] Linking CXX static library libgraphdump.a
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -P CMakeFiles/graphdump.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/external/twopaco/graphdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1
 /usr/bin/ar qc libgraphdump.a CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o
 /usr/bin/ranlib libgraphdump.a
 make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-[ 48%] Built target graphdump
-[ 49%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -MF CMakeFiles/salmon_core.dir/SGSmooth.cpp.o.d -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SGSmooth.cpp
-[ 49%] Building CXX object src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -MF CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o.d -o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/pufferfish/metro/metrohash64.cpp
+[ 49%] Built target graphdump
 [ 49%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -MF CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishLossyIndex.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishLossyIndex.cpp
 [ 50%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/edlib.cpp.o
@@ -1537,22 +1573,26 @@
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -MF CMakeFiles/puffer.dir/PufferfishExamine.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishExamine.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishExamine.cpp
 [ 57%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -MF CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishKmerQuery.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishKmerQuery.cpp
-[ 58%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o -MF CMakeFiles/puffer.dir/FastxParser.cpp.o.d -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp
-[ 59%] Linking CXX static library libalevin_core.a
+[ 58%] Linking CXX static library libalevin_core.a
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1
 "/usr/bin/gcc-ar-13" qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/SingleCellProtocols.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o
 "/usr/bin/gcc-ranlib-13" libalevin_core.a
 make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-[ 59%] Built target alevin_core
+[ 58%] Built target alevin_core
+[ 59%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FastxParser.cpp.o -MF CMakeFiles/puffer.dir/FastxParser.cpp.o.d -o CMakeFiles/puffer.dir/FastxParser.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp
 [ 60%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp
 [ 61%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferFS.cpp.o -MF CMakeFiles/puffer.dir/PufferFS.cpp.o.d -o CMakeFiles/puffer.dir/PufferFS.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferFS.cpp
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -MF CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishBinaryGFAReader.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishBinaryGFAReader.cpp
 [ 62%] Building C object external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/cc  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/xxhash.c.o -MF CMakeFiles/puffer.dir/xxhash.c.o.d -o CMakeFiles/puffer.dir/xxhash.c.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/xxhash.c
 cc1: warning: command-line option '-Wno-reorder' is valid for C++/ObjC++ but not for C
+[ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -MF CMakeFiles/puffer.dir/FixFasta.cpp.o.d -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp
+[ 64%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -MF CMakeFiles/puffer.dir/MemCollector.cpp.o.d -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemCollector.cpp
 In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/FastxParser.hpp:15,
                  from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FastxParser.cpp:1:
 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h: In instantiation of 'void moodycamel::details::swap_relaxed(std::atomic<_ITp>&, std::atomic<_ITp>&) [with T = std::thread::id]':
@@ -1575,14 +1615,10 @@
   510 |                 left.store(std::move(right.load(std::memory_order_relaxed)), std::memory_order_relaxed);
       |                 ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/concurrentqueue.h:510:27: note: remove 'std::move' call
-[ 63%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/FixFasta.cpp.o -MF CMakeFiles/puffer.dir/FixFasta.cpp.o.d -o CMakeFiles/puffer.dir/FixFasta.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp
-[ 64%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemCollector.cpp.o -MF CMakeFiles/puffer.dir/MemCollector.cpp.o.d -o CMakeFiles/puffer.dir/MemCollector.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemCollector.cpp
 [ 64%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp
 [ 65%] Linking CXX static library libsalmon_core.a
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/MemChainer.cpp.o -MF CMakeFiles/puffer.dir/MemChainer.cpp.o.d -o CMakeFiles/puffer.dir/MemChainer.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/MemChainer.cpp
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1
 "/usr/bin/gcc-ar-13" qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/backtrace.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/__/external/install/src/pufferfish/metro/metrohash64.cpp.o
 "/usr/bin/gcc-ranlib-13" libsalmon_core.a
@@ -1620,10 +1656,6 @@
 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::pair<const std::vector<unsigned int>, unsigned int>, spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*, std::pair<const std::vector<unsigned int>, unsigned int>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::pair<const std::vector<unsigned int>, unsigned int>; row_it = spp::sparsegroup<std::pair<const std::vector<unsigned int>, unsigned int>, spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> > >*; col_it = std::pair<const std::vector<unsigned int>, unsigned int>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::pair<const std::vector<unsigned int>, unsigned int> >]'
   946 |     Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
       |                                 ^~~~~~~~
-[ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -MF CMakeFiles/puffer.dir/PufferfishAligner.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp
-[ 68%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp
 In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/FixFasta.cpp:4:
 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_mk_destructive_iterator(dest_it) const [with Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >*, std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >; dest_it = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >*, std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >]':
 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:2607:61:   required from 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_begin() [with Value = std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >; Key = long unsigned int; HashFcn = spp::spp_hash<long unsigned int>; ExtractKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SelectKey; SetKey = spp::sparse_hash_map<long unsigned int, std::vector<std::__cxx11::basic_string<char> > >::SetKey; EqualKey = std::equal_to<long unsigned int>; Alloc = spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::sparsegroup<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >*, std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > >*, std::input_iterator_tag, spp::libc_allocator<std::pair<const long unsigned int, std::vector<std::__cxx11::basic_string<char> > > > >]'
@@ -1653,6 +1685,14 @@
 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::__cxx11::basic_string<char>, spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*, std::__cxx11::basic_string<char>*, std::input_iterator_tag, spp::libc_allocator<std::__cxx11::basic_string<char> > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::__cxx11::basic_string<char>; row_it = spp::sparsegroup<std::__cxx11::basic_string<char>, spp::libc_allocator<std::__cxx11::basic_string<char> > >*; col_it = std::__cxx11::basic_string<char>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::__cxx11::basic_string<char> >]'
   946 |     Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
       |                                 ^~~~~~~~
+[ 67%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -MF CMakeFiles/puffer.dir/PufferfishAligner.cpp.o.d -o CMakeFiles/puffer.dir/PufferfishAligner.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/PufferfishAligner.cpp
+[ 68%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -MF CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o.d -o CMakeFiles/puffer.dir/RefSeqConstructor.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp
+[ 69%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/metro/metrohash64.cpp
+[ 70%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -MF CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o.d -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp
 In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/RefSeqConstructor.hpp:5,
                  from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/RefSeqConstructor.cpp:1:
 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h: In instantiation of 'spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::destructive_iterator spp::sparse_hashtable<Value, Key, HashFcn, ExtractKey, SetKey, EqualKey, Alloc>::_mk_destructive_iterator(dest_it) const [with Value = std::pair<const unsigned int, pufferfish::util::ContigBlock>; Key = unsigned int; HashFcn = spp::spp_hash<unsigned int>; ExtractKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SelectKey; SetKey = spp::sparse_hash_map<unsigned int, pufferfish::util::ContigBlock>::SetKey; EqualKey = std::equal_to<unsigned int>; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >; destructive_iterator = spp::Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*, std::pair<const unsigned int, pufferfish::util::ContigBlock>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >; dest_it = spp::Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*, std::pair<const unsigned int, pufferfish::util::ContigBlock>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >]':
@@ -1670,10 +1710,6 @@
 /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/sparsepp/spp.h:946:33: note: because 'spp::Two_d_destructive_iterator<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*, std::pair<const unsigned int, pufferfish::util::ContigBlock>*, std::input_iterator_tag, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >' has user-provided 'spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>& spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>::operator=(const spp::Two_d_destructive_iterator<T, row_it, col_it, iter_type, Alloc>&) [with T = std::pair<const unsigned int, pufferfish::util::ContigBlock>; row_it = spp::sparsegroup<std::pair<const unsigned int, pufferfish::util::ContigBlock>, spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> > >*; col_it = std::pair<const unsigned int, pufferfish::util::ContigBlock>*; iter_type = std::input_iterator_tag; Alloc = spp::libc_allocator<std::pair<const unsigned int, pufferfish::util::ContigBlock> >]'
   946 |     Two_d_destructive_iterator& operator=(const Two_d_destructive_iterator &o);
       |                                 ^~~~~~~~
-[ 69%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -MF CMakeFiles/puffer.dir/metro/metrohash64.cpp.o.d -o CMakeFiles/puffer.dir/metro/metrohash64.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/src/metro/metrohash64.cpp
-[ 70%] Building CXX object external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/external/pufferfish/src && /usr/bin/c++  -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -I/build/reproducible-path/salmon-1.10.2+ds1/include -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -MD -MT external/pufferfish/src/CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -MF CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o.d -o CMakeFiles/puffer.dir/__/__/__/src/LibraryFormat.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/LibraryFormat.cpp
 [ 71%] Linking CXX static library libUnitTestsMain.a
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/UnitTestsMain.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/UnitTestsMain.dir/link.txt --verbose=1
@@ -1687,14 +1723,14 @@
 make[4]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
 make  -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build
 make[4]: Entering directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
-[ 72%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp
+[ 73%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/LibraryTypeTests.cpp.o
 [ 73%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -MF CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o.d -o CMakeFiles/unitTests.dir/__/tests/GCSampleTests.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/tests/GCSampleTests.cpp
-[ 74%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -MF CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o.d -o CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/external/install/src/pufferfish/rank9b.cpp
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+[ 74%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o
+[ 75%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/pufferfish/rank9b.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_CHRONO_DYN_LINK -DBOOST_CHRONO_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_TIMER_DYN_LINK -DBOOST_TIMER_NO_LIB -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -fsigned-char -ftree-vectorize -funroll-loops -fPIC -fomit-frame-pointer -O3 -DNDEBUG -DSTX_NO_STD_STRING_VIEW -D__STDC_FORMAT_MACROS -static-libstdc++ -DHAVE_NUMERIC_LIMITS128 -Wall -Wno-unknown-pragmas -Wno-reorder -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-function -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp
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 In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/algorithm/sha2.hpp:9,
                  from /build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/include/digestpp/digestpp.hpp:6,
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+[ 79%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o
+[ 79%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedEMOptimizer.cpp.o
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+[ 81%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o
+[ 82%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o
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-[ 85%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o
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 [ 86%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o
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-[ 87%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o
-[ 88%] Building CXX object src/CMakeFiles/salmon.dir/AlevinHash.cpp.o
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+[ 86%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o
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+[ 88%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -MF CMakeFiles/salmon.dir/SalmonAlevin.cpp.o.d -o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/WhiteList.cpp.o -MF CMakeFiles/salmon.dir/WhiteList.cpp.o.d -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/WhiteList.cpp
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/DedupUMI.cpp.o -MF CMakeFiles/salmon.dir/DedupUMI.cpp.o.d -o CMakeFiles/salmon.dir/DedupUMI.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/DedupUMI.cpp
 In file included from /build/reproducible-path/salmon-1.10.2+ds1/include/pcg_random.hpp:104,
                  from /build/reproducible-path/salmon-1.10.2+ds1/src/CollapsedGibbsSampler.cpp:22:
 /build/reproducible-path/salmon-1.10.2+ds1/include/pcg_extras.hpp:563:51: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
@@ -2429,8 +2465,6 @@
       |                                                            ^~~~~~~~
 [ 89%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantify.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantify.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantify.cpp
-[ 90%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o
-cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp
 In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:65,
                  from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47,
                  from /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:8,
@@ -2470,10 +2504,140 @@
   168 |         for(const std::string trueBarcode: trueBarcodes){
       |                               ^~~~~~~~~~~
       |                               &
+[ 90%] Building CXX object src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentLengthDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentLengthDistribution.cpp
 [ 91%] Building CXX object src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -MF CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o.d -o CMakeFiles/salmon.dir/FragmentStartPositionDistribution.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/FragmentStartPositionDistribution.cpp
 [ 92%] Building CXX object src/CMakeFiles/salmon.dir/GZipWriter.cpp.o
 cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/GZipWriter.cpp.o -MF CMakeFiles/salmon.dir/GZipWriter.cpp.o.d -o CMakeFiles/salmon.dir/GZipWriter.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/GZipWriter.cpp
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::DropSeq; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::DropSeq; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1084:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::InDropV2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::InDropV2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::InDropV2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1094:25:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CITESeq; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CITESeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CITESeq; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1110:25:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::ChromiumV3; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::ChromiumV3; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::ChromiumV3; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1122:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Chromium; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Chromium; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Chromium; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1129:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Gemcode; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Gemcode; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Gemcode; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1136:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CELSeq; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1143:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CELSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1150:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV1; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV1; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SplitSeqV1; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1157:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SplitSeqV2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1164:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::QuartzSeq2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::QuartzSeq2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::QuartzSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1171:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SciSeq3; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SciSeq3; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SciSeq3; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1177:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Custom; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Custom; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Custom; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1183:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CustomGeometry; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CustomGeometry; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CustomGeometry; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1189:23:   required from here
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
+/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
+  488 |   for (const auto trueBarcode: trueBarcodes){
+      |                   ^~~~~~~~~~~
+      |                   &
 In file included from /build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/sparsepp/spp.h:65,
                  from /build/reproducible-path/salmon-1.10.2+ds1/include/AlevinUtils.hpp:47,
                  from /build/reproducible-path/salmon-1.10.2+ds1/include/Graph.hpp:8,
@@ -2508,6 +2672,8 @@
 /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair<const std::pair<unsigned int, unsigned int>, unsigned int>' declared here
   187 |     struct pair
       |            ^~~~
+[ 93%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -MF CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o.d -o CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonQuantMerge.cpp
 /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::DropSeq; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
 /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33:   required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::DropSeq>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::DropSeq>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
 /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23:   required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::DropSeq; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
@@ -2724,6 +2890,8 @@
 /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
   397 |                        IndexT* qidx, std::vector<Transcript>& transcripts,
       |                                      ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
+[ 94%] Building CXX object src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o
+cd /build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DKSW_USE_ARM=1 -DPUFFERFISH_SALMON_SUPPORT=1 -DRAPMAP_SALMON_SUPPORT=1 -DSTX_NO_STD_STRING_VIEW=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/build/reproducible-path/salmon-1.10.2+ds1/include -I/usr/include/eigen3 -I/build/reproducible-path/salmon-1.10.2+ds1/external -I/build/reproducible-path/salmon-1.10.2+ds1/external/cereal/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish -I/build/reproducible-path/salmon-1.10.2+ds1/external/install/include/pufferfish/digestpp -I/build/reproducible-path/salmon-1.10.2+ds1/external/pufferfish/external/twopaco/graphdump -g -O2 -ffile-prefix-map=/build/reproducible-path/salmon-1.10.2+ds1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=c++14 -flto=auto -fno-fat-lto-objects -fsigned-char -DHAVE_KALLOC -W -Wall -Wextra -Wpointer-arith -Wunused -Wwrite-strings -Wno-unknown-pragmas -Wno-unused-function -Wno-reorder -DPUFFERFISH_SALMON_SUPPORT -DHAVE_NUMERIC_LIMITS128 -DHAVE_SIMDE -D__STDC_FORMAT_MACROS -DSTX_NO_STD_STRING_VIEW -O3 -fPIC -DNDEBUG -funroll-loops -ftree-vectorize -fno-strict-aliasing -fomit-frame-pointer -static-libstdc++ -Wno-unused-variable -Wreturn-type -Werror=return-type -Wno-unused-local-typedefs -Wno-int-in-bool-context -Wno-deprecated-copy -MD -MT src/CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -MF CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o.d -o CMakeFiles/salmon.dir/ProgramOptionsGenerator.cpp.o -c /build/reproducible-path/salmon-1.10.2+ds1/src/ProgramOptionsGenerator.cpp
 /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp: In instantiation of 'void process_reads_sc_sketch(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec<pufferfish::util::QuasiAlignment>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, IndexT*, std::vector<Transcript>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with IndexT = PufferfishSparseIndex; ProtocolT = alevin::protocols::SplitSeqV2; alevin::paired_parser = fastx_parser::FastxParser<fastx_parser::ReadPair>; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; alevin::AlnGroupVec<pufferfish::util::QuasiAlignment> = std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >; std::ofstream = std::basic_ofstream<char>]':
 /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1730:33:   required from 'sc_align_read_library<pufferfish::util::QuasiAlignment, alevin::protocols::SplitSeqV2>(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > >, std::allocator<std::vector<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int>, std::allocator<AlignmentGroup<pufferfish::util::QuasiAlignment, unsigned int, long unsigned int> > > > >&, AlevinOpts<alevin::protocols::SplitSeqV2>&, MappingStatistics&)::<lambda(size_t, auto:7*, auto:8*)> [with auto:7 = fastx_parser::FastxParser<fastx_parser::ReadPair>; auto:8 = PufferfishSparseIndex; size_t = long unsigned int]'
 /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:1751:23:   required from 'void sc_align_read_library(ReadExperimentT&, ReadLibrary&, SalmonIndex*, std::vector<Transcript>&, std::atomic<long unsigned int>&, std::atomic<long unsigned int>&, std::atomic<unsigned int>&, std::atomic<unsigned int>&, std::atomic<bool>&, FragmentLengthDistribution&, SalmonOpts&, std::atomic<long unsigned int>&, std::ofstream&, std::ofstream&, std::mutex&, std::mutex&, std::mutex&, size_t, std::vector<std::vector<AlignmentGroup<AlnT, unsigned int, long unsigned int> > >&, AlevinOpts<ProtocolT>&, MappingStatistics&) [with AlnT = pufferfish::util::QuasiAlignment; ProtocolT = alevin::protocols::SplitSeqV2; ReadExperimentT = ReadExperiment<EquivalenceClassBuilder<SCTGValue> >; std::ofstream = std::basic_ofstream<char>; size_t = long unsigned int]'
@@ -2844,138 +3012,6 @@
 /build/reproducible-path/salmon-1.10.2+ds1/src/SalmonAlevin.cpp:397:63: warning: unused parameter 'transcripts' [-Wunused-parameter]
   397 |                        IndexT* qidx, std::vector<Transcript>& transcripts,
       |                                      ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::DropSeq; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::DropSeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::DropSeq; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1084:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::InDropV2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::InDropV2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::InDropV2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1094:25:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CITESeq; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CITESeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CITESeq; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1110:25:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::ChromiumV3; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::ChromiumV3; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::ChromiumV3; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1122:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Chromium; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Chromium; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Chromium; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1129:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Gemcode; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Gemcode; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Gemcode; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1136:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CELSeq; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1143:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CELSeq2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CELSeq2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CELSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1150:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV1; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV1; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SplitSeqV1; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1157:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SplitSeqV2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SplitSeqV2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SplitSeqV2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1164:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::QuartzSeq2; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::QuartzSeq2; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::QuartzSeq2; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1171:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::SciSeq3; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::SciSeq3; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::SciSeq3; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1177:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::Custom; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::Custom; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::Custom; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1183:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp: In instantiation of 'void indexBarcodes(AlevinOpts<ProtocolT>&, CFreqMapT&, TrueBcsT&, SoftMapT&) [with ProtocolT = alevin::protocols::CustomGeometry; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >]':
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:780:16:   required from 'void processBarcodes(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, AlevinOpts<ProtocolT>&, SoftMapT&, TrueBcsT&, CFreqMapT&, size_t&) [with ProtocolT = alevin::protocols::CustomGeometry; SoftMapT = std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::__cxx11::basic_string<char>, double> > >; TrueBcsT = std::unordered_set<std::__cxx11::basic_string<char> >; CFreqMapT = tsl::array_map<char, unsigned int, BarcodeGroupStringHasherMetro>; size_t = long unsigned int]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:938:20:   required from 'void initiatePipeline(AlevinOpts<ProtocolT>&, SalmonOpts&, OrderedOptionsT&, boost::program_options::variables_map&, std::string, bool, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::unique_ptr<SalmonIndex>&) [with ProtocolT = alevin::protocols::CustomGeometry; OrderedOptionsT = boost::program_options::basic_parsed_options<char>; std::string = std::__cxx11::basic_string<char>]'
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:1189:23:   required from here
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: warning: loop variable 'trueBarcode' creates a copy from type 'const std::__cxx11::basic_string<char>' [-Wrange-loop-construct]
-/build/reproducible-path/salmon-1.10.2+ds1/src/Alevin.cpp:488:19: note: use reference type to prevent copying
-  488 |   for (const auto trueBarcode: trueBarcodes){
-      |                   ^~~~~~~~~~~
-      |                   &
-[ 93%] Building CXX object src/CMakeFiles/salmon.dir/SalmonQuantMerge.cpp.o
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@@ -3190,9 +3226,9 @@
 1: Test timeout computed to be: 10000000
 1: -- For unit tests, will set working directory to /build/reproducible-path/salmon-1.10.2+ds1/tests
 1: ===============================================================================
-1: All tests passed (1996306 assertions in 4 test cases)
+1: All tests passed (1979050 assertions in 4 test cases)
 1: 
-1/2 Test #1: unit_tests .......................   Passed    0.22 sec
+1/2 Test #1: unit_tests .......................   Passed    0.26 sec
 test 2
     Start 2: salmon_read_test_quasi
 
@@ -3205,18 +3241,18 @@
 2: sample_data/transcripts.fasta
 2: sample_data/reads_1.fastq
 2: index ["sample_salmon_quasi_index"] did not previously exist  . . . creating it
-2: [2025-07-03 05:52:24.907] [jLog] [warning] The salmon index is being built without any decoy sequences.  It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
-2: [2025-07-03 05:52:24.907] [jLog] [info] building index
+2: [2025-07-04 07:57:11.535] [jLog] [warning] The salmon index is being built without any decoy sequences.  It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.
+2: [2025-07-04 07:57:11.535] [jLog] [info] building index
 2: out : sample_salmon_quasi_index
-2: [2025-07-03 05:52:24.907] [puff::index::jointLog] [info] Running fixFasta
+2: [2025-07-04 07:57:11.536] [puff::index::jointLog] [info] Running fixFasta
 2: 
 2: [Step 1 of 4] : counting k-mers
 2: 
-2: [2025-07-03 05:52:24.918] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
-2: [2025-07-03 05:52:24.918] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts
+2: [2025-07-04 07:57:11.541] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides
+2: [2025-07-04 07:57:11.541] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts
 2: wrote 15 cleaned references
-2: [2025-07-03 05:52:24.919] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
-2: [2025-07-03 05:52:24.919] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20
+2: [2025-07-04 07:57:11.541] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers
+2: [2025-07-04 07:57:11.543] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20
 2: Threads = 2
 2: Vertex length = 31
 2: Hash functions = 5
@@ -3230,9 +3266,9 @@
 2: 1	0	0	
 2: 2	0	0
 2: True junctions count = 14
-2: False junctions count = 17
-2: Hash table size = 31
-2: Candidate marks count = 54
+2: False junctions count = 19
+2: Hash table size = 33
+2: Candidate marks count = 58
 2: --------------------------------------------------------------------------------
 2: Reallocating bifurcations time: 0
 2: True marks count: 51
@@ -3250,44 +3286,44 @@
 2: (prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0
 2: contig count: 24 element count: 19592 complex nodes: 0
 2: # of ones in rank vector: 23
-2: [2025-07-03 05:52:24.965] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
-2: [2025-07-03 05:52:24.965] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory sample_salmon_quasi_index
+2: [2025-07-04 07:57:11.579] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.
+2: [2025-07-04 07:57:11.579] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory sample_salmon_quasi_index
 2: size = 19592
 2: -----------------------------------------
-2: | Loading contigs | Time = 43.84 us
+2: | Loading contigs | Time = 96.2 us
 2: -----------------------------------------
 2: size = 19592
 2: -----------------------------------------
-2: | Loading contig boundaries | Time = 32.28 us
+2: | Loading contig boundaries | Time = 49.64 us
 2: -----------------------------------------
 2: Number of ones: 23
 2: Number of ones per inventory item: 512
 2: Inventory entries filled: 1
 2: 23
-2: [2025-07-03 05:52:24.966] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
-2: [2025-07-03 05:52:24.966] [puff::index::jointLog] [info] contig count for validation: 23
-2: [2025-07-03 05:52:24.966] [puff::index::jointLog] [info] Total # of Contigs : 23
-2: [2025-07-03 05:52:24.966] [puff::index::jointLog] [info] Total # of numerical Contigs : 23
-2: [2025-07-03 05:52:24.966] [puff::index::jointLog] [info] Total # of contig vec entries: 36
-2: [2025-07-03 05:52:24.966] [puff::index::jointLog] [info] bits per offset entry 6
-2: [2025-07-03 05:52:24.966] [puff::index::jointLog] [info] Done constructing the contig vector. 24
-2: [2025-07-03 05:52:24.966] [puff::index::jointLog] [info] # segments = 23
-2: [2025-07-03 05:52:24.966] [puff::index::jointLog] [info] total length = 19,592
-2: [2025-07-03 05:52:24.966] [puff::index::jointLog] [info] Reading the reference files ...
-2: [2025-07-03 05:52:24.969] [puff::index::jointLog] [info] positional integer width = 15
-2: [2025-07-03 05:52:24.969] [puff::index::jointLog] [info] seqSize = 19,592
-2: [2025-07-03 05:52:24.969] [puff::index::jointLog] [info] rankSize = 19,592
-2: [2025-07-03 05:52:24.969] [puff::index::jointLog] [info] edgeVecSize = 0
-2: [2025-07-03 05:52:24.969] [puff::index::jointLog] [info] num keys = 18,902
-2: 
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-2: [2025-07-03 05:52:24.977] [puff::index::jointLog] [info] mphf size = 0.0125198 MB
-2: [2025-07-03 05:52:24.977] [puff::index::jointLog] [info] chunk size = 9,796
-2: [2025-07-03 05:52:24.977] [puff::index::jointLog] [info] chunk 0 = [0, 9,796)
-2: [2025-07-03 05:52:24.977] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562)
-2: [2025-07-03 05:52:24.979] [puff::index::jointLog] [info] finished populating pos vector
-2: [2025-07-03 05:52:24.979] [puff::index::jointLog] [info] writing index components
-2: [2025-07-03 05:52:24.979] [puff::index::jointLog] [info] finished writing dense pufferfish index
-2: [2025-07-03 05:52:24.979] [jLog] [info] done building index
+2: [2025-07-04 07:57:11.579] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.
+2: [2025-07-04 07:57:11.579] [puff::index::jointLog] [info] contig count for validation: 23
+2: [2025-07-04 07:57:11.579] [puff::index::jointLog] [info] Total # of Contigs : 23
+2: [2025-07-04 07:57:11.579] [puff::index::jointLog] [info] Total # of numerical Contigs : 23
+2: [2025-07-04 07:57:11.579] [puff::index::jointLog] [info] Total # of contig vec entries: 36
+2: [2025-07-04 07:57:11.579] [puff::index::jointLog] [info] bits per offset entry 6
+2: [2025-07-04 07:57:11.579] [puff::index::jointLog] [info] Done constructing the contig vector. 24
+2: [2025-07-04 07:57:11.580] [puff::index::jointLog] [info] # segments = 23
+2: [2025-07-04 07:57:11.580] [puff::index::jointLog] [info] total length = 19,592
+2: [2025-07-04 07:57:11.580] [puff::index::jointLog] [info] Reading the reference files ...
+2: [2025-07-04 07:57:11.582] [puff::index::jointLog] [info] positional integer width = 15
+2: [2025-07-04 07:57:11.582] [puff::index::jointLog] [info] seqSize = 19,592
+2: [2025-07-04 07:57:11.582] [puff::index::jointLog] [info] rankSize = 19,592
+2: [2025-07-04 07:57:11.582] [puff::index::jointLog] [info] edgeVecSize = 0
+2: [2025-07-04 07:57:11.582] [puff::index::jointLog] [info] num keys = 18,902
+2: 
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+2: [2025-07-04 07:57:11.600] [puff::index::jointLog] [info] mphf size = 0.0125198 MB
+2: [2025-07-04 07:57:11.600] [puff::index::jointLog] [info] chunk size = 9,796
+2: [2025-07-04 07:57:11.600] [puff::index::jointLog] [info] chunk 0 = [0, 9,796)
+2: [2025-07-04 07:57:11.600] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562)
+2: [2025-07-04 07:57:11.603] [puff::index::jointLog] [info] finished populating pos vector
+2: [2025-07-04 07:57:11.603] [puff::index::jointLog] [info] writing index components
+2: [2025-07-04 07:57:11.603] [puff::index::jointLog] [info] finished writing dense pufferfish index
+2: [2025-07-04 07:57:11.603] [jLog] [info] done building index
 2: for info, total work write each  : 2.331    total work inram from level 3 : 4.322  total work raw : 25.000 
 2: Bitarray          105024  bits (100.00 %)   (array + ranks )
 2: final hash             0  bits (0.00 %) (nb in final hash 0)
@@ -3300,52 +3336,52 @@
 2: ### [ mates2 ] => { reads_2.fastq }
 2: ### [ output ] => { sample_salmon_quasi_quant }
 2: Logs will be written to sample_salmon_quasi_quant/logs
-2: [2025-07-03 05:52:25.006] [jointLog] [info] setting maxHashResizeThreads to 12
+2: [2025-07-04 07:57:11.650] [jointLog] [info] setting maxHashResizeThreads to 12
+2: [2025-07-04 07:57:11.650] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
+2: [2025-07-04 07:57:11.650] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
+2: [2025-07-04 07:57:11.650] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
+2: [2025-07-04 07:57:11.650] [jointLog] [info] parsing read library format
+2: [2025-07-04 07:57:11.650] [jointLog] [info] There is 1 library.
+2: [2025-07-04 07:57:11.651] [jointLog] [info] Loading pufferfish index
+2: [2025-07-04 07:57:11.651] [jointLog] [info] Loading dense pufferfish index.
 2: -----------------------------------------
-2: | Loading contig table | Time = 12.04 us
+2: | Loading contig table | Time = 23.12 us
 2: -----------------------------------------
 2: size = 24
 2: -----------------------------------------
-2: | Loading contig offsets | Time = 44.56 us
+2: | Loading contig offsets | Time = 81.68 us
 2: -----------------------------------------
 2: -----------------------------------------
-2: | Loading reference lengths | Time = 2.16 us
+2: | Loading reference lengths | Time = 5.4 us
 2: -----------------------------------------
 2: -----------------------------------------
-2: | Loading mphf table | Time = 909.76 us
+2: | Loading mphf table | Time = 70.72 us
 2: -----------------------------------------
 2: size = 19592
 2: Number of ones: 23
 2: Number of ones per inventory item: 512
 2: Inventory entries filled: 1
 2: -----------------------------------------
-2: | Loading contig boundaries | Time = 101.72 us
+2: | Loading contig boundaries | Time = 132.64 us
 2: -----------------------------------------
 2: size = 19592
 2: -----------------------------------------
-2: | Loading sequence | Time = 22.52 us
+2: | Loading sequence | Time = 51.68 us
 2: -----------------------------------------
 2: size = 18902
 2: -----------------------------------------
-2: | Loading positions | Time = 55.92 us
+2: | Loading positions | Time = 97 us
 2: -----------------------------------------
 2: size = 28562
 2: -----------------------------------------
-2: | Loading reference sequence | Time = 22.04 us
+2: | Loading reference sequence | Time = 56.48 us
 2: -----------------------------------------
 2: -----------------------------------------
-2: | Loading reference accumulative lengths | Time = 3.2 us
+2: | Loading reference accumulative lengths | Time = 4.84 us
 2: -----------------------------------------
-2: [2025-07-03 05:52:25.006] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
-2: [2025-07-03 05:52:25.006] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
-2: [2025-07-03 05:52:25.006] [jointLog] [info] Setting consensusSlack to selective-alignment default of 0.35.
-2: [2025-07-03 05:52:25.006] [jointLog] [info] parsing read library format
-2: [2025-07-03 05:52:25.006] [jointLog] [info] There is 1 library.
-2: [2025-07-03 05:52:25.006] [jointLog] [info] Loading pufferfish index
-2: [2025-07-03 05:52:25.006] [jointLog] [info] Loading dense pufferfish index.
-2: [2025-07-03 05:52:25.007] [jointLog] [info] done
-2: [2025-07-03 05:52:25.047] [jointLog] [info] Index contained 15 targets
-2: [2025-07-03 05:52:25.047] [jointLog] [info] Number of decoys : 0
+2: [2025-07-04 07:57:11.652] [jointLog] [info] done
+2: [2025-07-04 07:57:11.683] [jointLog] [info] Index contained 15 targets
+2: [2025-07-04 07:57:11.683] [jointLog] [info] Number of decoys : 0
 2: 
 2: 
 2: 
@@ -3358,31 +3394,31 @@
 2: 
 2: 
 2: 
-2: [2025-07-03 05:52:25.227] [jointLog] [info] Computed 28 rich equivalence classes for further processing
-2: [2025-07-03 05:52:25.227] [jointLog] [info] Counted 10,000 total reads in the equivalence classes 
-2: [2025-07-03 05:52:25.230] [jointLog] [info] Number of mappings discarded because of alignment score : 67
-2: [2025-07-03 05:52:25.230] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0
-2: [2025-07-03 05:52:25.230] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
-2: [2025-07-03 05:52:25.230] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
-2: [2025-07-03 05:52:25.230] [jointLog] [warning] Only 10000 fragments were mapped, but the number of burn-in fragments was set to 5000000.
+2: [2025-07-04 07:57:11.845] [jointLog] [info] Computed 28 rich equivalence classes for further processing
+2: [2025-07-04 07:57:11.845] [jointLog] [info] Counted 10,000 total reads in the equivalence classes 
+2: [2025-07-04 07:57:11.850] [jointLog] [info] Number of mappings discarded because of alignment score : 67
+2: [2025-07-04 07:57:11.850] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0
+2: [2025-07-04 07:57:11.850] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
+2: [2025-07-04 07:57:11.850] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0
+2: [2025-07-04 07:57:11.850] [jointLog] [warning] Only 10000 fragments were mapped, but the number of burn-in fragments was set to 5000000.
 2: The effective lengths have been computed using the observed mappings.
 2: 
-2: [2025-07-03 05:52:25.230] [jointLog] [info] Mapping rate = 100%
+2: [2025-07-04 07:57:11.850] [jointLog] [info] Mapping rate = 100%
 2: 
-2: [2025-07-03 05:52:25.230] [jointLog] [info] finished quantifyLibrary()
-2: [2025-07-03 05:52:25.230] [jointLog] [info] Starting optimizer
-2: [2025-07-03 05:52:25.231] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
-2: [2025-07-03 05:52:25.232] [jointLog] [info] iteration = 0 | max rel diff. = 14.87
-2: [2025-07-03 05:52:25.234] [jointLog] [info] iteration = 100 | max rel diff. = 2.94688e-05
-2: [2025-07-03 05:52:25.234] [jointLog] [info] Finished optimizer
-2: [2025-07-03 05:52:25.234] [jointLog] [info] writing output 
+2: [2025-07-04 07:57:11.850] [jointLog] [info] finished quantifyLibrary()
+2: [2025-07-04 07:57:11.850] [jointLog] [info] Starting optimizer
+2: [2025-07-04 07:57:11.852] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
+2: [2025-07-04 07:57:11.852] [jointLog] [info] iteration = 0 | max rel diff. = 14.87
+2: [2025-07-04 07:57:11.855] [jointLog] [info] iteration = 100 | max rel diff. = 3.27924e-05
+2: [2025-07-04 07:57:11.855] [jointLog] [info] Finished optimizer
+2: [2025-07-04 07:57:11.855] [jointLog] [info] writing output 
 2: 
 2: Salmon (read) ran successfully
-2/2 Test #2: salmon_read_test_quasi ...........   Passed    1.14 sec
+2/2 Test #2: salmon_read_test_quasi ...........   Passed    1.16 sec
 
 100% tests passed, 0 tests failed out of 2
 
-Total Test time (real) =   1.37 sec
+Total Test time (real) =   1.42 sec
 make[2]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1/obj-aarch64-linux-gnu'
 make[1]: Leaving directory '/build/reproducible-path/salmon-1.10.2+ds1'
    create-stamp debian/debhelper-build-stamp
@@ -3439,10 +3475,10 @@
    dh_install
    dh_installdocs
    dh_sphinxdoc
-dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/search-focus.js
+dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/themetoggle.js
 dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/copybutton.js
+dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/search-focus.js
 dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/menu.js
-dh_sphinxdoc: warning: ignoring unknown JavaScript code: debian/salmon/usr/share/doc/salmon/html/_static/themetoggle.js
    dh_installchangelogs
    dh_installexamples
    dh_installman
@@ -3460,8 +3496,8 @@
    dh_gencontrol
    dh_md5sums
    dh_builddeb
-dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.10.2+ds1-1_arm64.deb'.
 dpkg-deb: building package 'salmon' in '../salmon_1.10.2+ds1-1_arm64.deb'.
+dpkg-deb: building package 'salmon-dbgsym' in '../salmon-dbgsym_1.10.2+ds1-1_arm64.deb'.
  dpkg-genbuildinfo --build=binary -O../salmon_1.10.2+ds1-1_arm64.buildinfo
  dpkg-genchanges --build=binary -O../salmon_1.10.2+ds1-1_arm64.changes
 dpkg-genchanges: info: binary-only upload (no source code included)
@@ -3469,12 +3505,14 @@
 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/572923/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/572923/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/1713694 and its subdirectories
-I: Current time: Thu Jul  3 05:52:54 -12 2025
-I: pbuilder-time-stamp: 1751565174
+I: removing directory /srv/workspace/pbuilder/572923 and its subdirectories
+I: Current time: Fri Jul  4 07:57:45 +14 2025
+I: pbuilder-time-stamp: 1751565465