Diff of the two buildlogs:

--
--- b1/build.log	2025-02-24 03:14:40.018056660 +0000
+++ b2/build.log	2025-02-24 03:20:15.014944118 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Sun Feb 23 15:02:55 -12 2025
-I: pbuilder-time-stamp: 1740366175
+I: Current time: Sun Mar 29 23:37:42 +14 2026
+I: pbuilder-time-stamp: 1774777062
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
 I: copying local configuration
@@ -30,54 +30,86 @@
 dpkg-source: info: applying fix_linking.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/42323/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/74074/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos16-i386.
+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 Mar 29 09:37 /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/74074/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/74074/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='i386'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
-  DISTRIBUTION='unstable'
-  HOME='/root'
-  HOST_ARCH='i386'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
+  BASH_VERSION='5.2.37(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=i386
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 '
+  DIRSTACK=()
+  DISTRIBUTION=unstable
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=i686
+  HOST_ARCH=i386
   IFS=' 	
   '
-  INVOCATION_ID='e833ea61ef294dd1bf4c5d875357ba1c'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
-  LD_PRELOAD='libeatmydata.so'
-  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='42323'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=dc0b3c990a6745b0afd07b74f796519c
+  LANG=C
+  LANGUAGE=de_CH:de
+  LC_ALL=C
+  LD_LIBRARY_PATH=/usr/lib/libeatmydata
+  LD_PRELOAD=libeatmydata.so
+  MACHTYPE=i686-pc-linux-gnu
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnu
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=74074
   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.y5jc0evK/pbuilderrc_6prM --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.y5jc0evK/b1 --logfile b1/build.log mothur_1.48.1-1.dsc'
-  SUDO_GID='112'
-  SUDO_UID='107'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://46.16.76.132:3128'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.y5jc0evK/pbuilderrc_Zc1M --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.y5jc0evK/b2 --logfile b2/build.log mothur_1.48.1-1.dsc'
+  SUDO_GID=112
+  SUDO_UID=107
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://213.165.73.152:3128
 I: uname -a
-  Linux ionos12-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/42323/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/74074/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -170,7 +202,7 @@
 Get: 47 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB]
 Get: 48 http://deb.debian.org/debian unstable/main i386 libreadline-dev i386 8.2-6 [166 kB]
 Get: 49 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
-Fetched 59.1 MB in 1s (51.4 MB/s)
+Fetched 59.1 MB in 1s (92.5 MB/s)
 Preconfiguring packages ...
 Selecting previously unselected package readline-common.
 (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 ... 19761 files and directories currently installed.)
@@ -387,7 +419,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/mothur-1.48.1/ && 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  > ../mothur_1.48.1-1_source.changes
+I: user script /srv/workspace/pbuilder/74074/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/74074/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/mothur-1.48.1/ && 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  > ../mothur_1.48.1-1_source.changes
 dpkg-buildpackage: info: source package mothur
 dpkg-buildpackage: info: source version 1.48.1-1
 dpkg-buildpackage: info: source distribution unstable
@@ -413,7 +449,7 @@
    debian/rules override_dh_auto_build
 make[1]: Entering directory '/build/reproducible-path/mothur-1.48.1'
 dh_auto_build -- 64BIT_VERSION=no
-	make -j11 "INSTALL=install --strip-program=true" 64BIT_VERSION=no
+	make -j21 "INSTALL=install --strip-program=true" 64BIT_VERSION=no
 make[2]: Entering directory '/build/reproducible-path/mothur-1.48.1'
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/calculators/accuracy.o source/calculators/accuracy.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/calculators/ace.o source/calculators/ace.cpp
@@ -572,12 +608,12 @@
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp
 source/commands/alignmusclecommand.cpp: In member function 'void AlignMuscleCommand::wrapperFunction()':
 source/commands/alignmusclecommand.cpp:297:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   297 |         system(commandString.c_str());
       |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/chimerapintailcommand.o source/commands/chimerapintailcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/chimeraslayercommand.o source/commands/chimeraslayercommand.cpp
@@ -585,11 +621,11 @@
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/chimeravsearchcommand.o source/commands/chimeravsearchcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/chopseqscommand.o source/commands/chopseqscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/classifyotucommand.o source/commands/classifyotucommand.cpp
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp
 source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)':
 source/commands/chimerauchimecommand.cpp:517:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   517 |         system(commandString.c_str());
       |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp
 source/commands/chimeravsearchcommand.cpp: In function 'void driver(vsearchData*)':
@@ -598,10 +634,6 @@
       |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp
-source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::string, std::string, std::string)':
-source/commands/clustercommand.cpp:542:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  542 |         system(commandString.c_str());
-      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp
@@ -610,12 +642,16 @@
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/collectsharedcommand.o source/commands/collectsharedcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/consensusseqscommand.o source/commands/consensusseqscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/cooccurrencecommand.o source/commands/cooccurrencecommand.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp
+source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::string, std::string, std::string)':
+source/commands/clustercommand.cpp:542:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  542 |         system(commandString.c_str());
+      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
 source/commands/clustersplitcommand.cpp: In function 'int vsearchDriver(std::string, std::string, std::string, double, clusterData*)':
 source/commands/clustersplitcommand.cpp:1050:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  1050 |         system(commandString.c_str());
       |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/corraxescommand.o source/commands/corraxescommand.cpp
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/countgroupscommand.o source/commands/countgroupscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/countseqscommand.o source/commands/countseqscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/createdatabasecommand.o source/commands/createdatabasecommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/degapseqscommand.o source/commands/degapseqscommand.cpp
@@ -623,13 +659,13 @@
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/distsharedcommand.o source/commands/distsharedcommand.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/diversityestimatorcommand.o source/commands/diversityestimatorcommand.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/fastaqinfocommand.o source/commands/fastaqinfocommand.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp
 source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()':
 source/commands/distancecommand.cpp:323:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   323 |                         system(("gzip -v " + outputFile).c_str());
       |                         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/diversityestimatorcommand.o source/commands/diversityestimatorcommand.cpp
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/fastaqinfocommand.o source/commands/fastaqinfocommand.cpp
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/getcoremicrobiomecommand.o source/commands/getcoremicrobiomecommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/getcurrentcommand.o source/commands/getcurrentcommand.cpp
@@ -664,11 +700,11 @@
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/makefastqcommand.o source/commands/makefastqcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp
 source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::string)':
 source/commands/makefilecommand.cpp:473:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   473 |         system(findCommand.c_str());
       |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/makesharedcommand.o source/commands/makesharedcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp
@@ -688,15 +724,15 @@
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/otuassociationcommand.o source/commands/otuassociationcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/otuhierarchycommand.o source/commands/otuhierarchycommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp
-source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()':
-source/commands/pairwiseseqscommand.cpp:339:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  339 |             system(("gzip -v " + outputFile).c_str());
-      |             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp
+source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()':
+source/commands/pairwiseseqscommand.cpp:339:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  339 |             system(("gzip -v " + outputFile).c_str());
+      |             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/preclustercommand.o source/commands/preclustercommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/primerdesigncommand.o source/commands/primerdesigncommand.cpp
@@ -730,22 +766,22 @@
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/splitgroupscommand.o source/commands/splitgroupscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/sracommand.o source/commands/sracommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/srainfocommand.o source/commands/srainfocommand.cpp
-source/commands/srainfocommand.cpp: In member function 'void SRAInfoCommand::runSystemCommand(std::string)':
-source/commands/srainfocommand.cpp:487:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  487 |         system(inputString.c_str());
-      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/subsamplecommand.o source/commands/subsamplecommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp
+source/commands/srainfocommand.cpp: In member function 'void SRAInfoCommand::runSystemCommand(std::string)':
+source/commands/srainfocommand.cpp:487:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  487 |         system(inputString.c_str());
+      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/systemcommand.o source/commands/systemcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/translateseqscommand.o source/commands/translateseqscommand.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/treesharedcommand.o source/commands/treesharedcommand.cpp
 source/commands/systemcommand.cpp: In member function 'virtual int SystemCommand::execute()':
 source/commands/systemcommand.cpp:97:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
    97 |         system(command.c_str());
       |         ~~~~~~^~~~~~~~~~~~~~~~~
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/treesharedcommand.o source/commands/treesharedcommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/trimflowscommand.o source/commands/trimflowscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/trimseqscommand.o source/commands/trimseqscommand.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/commands/unifracunweightedcommand.o source/commands/unifracunweightedcommand.cpp
@@ -871,6 +907,25 @@
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/trialSwap2.o source/trialSwap2.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/trimoligos.o source/trimoligos.cpp
 g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/utils.o source/utils.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/validcalculator.o source/validcalculator.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/validparameter.o source/validparameter.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/venn.o source/venn.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/weightedlinkage.o source/weightedlinkage.cpp
+g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/wilcox.o source/wilcox.cpp
+source/utils.cpp: In member function 'bool Utils::findTool(std::string&, std::string&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::vector<std::__cxx11::basic_string<char> > >)':
+source/utils.cpp:952:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  952 |             system(versionTestCommand.c_str());
+      |             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
+source/utils.cpp: In member function 'std::string Utils::sortFile(std::string, std::string)':
+source/utils.cpp:1514:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 1514 |         system(command.c_str());
+      |         ~~~~~~^~~~~~~~~~~~~~~~~
+cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd ..
+make[3]: Entering directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src'
+make[3]: Leaving directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src'
+make[3]: Entering directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src'
+g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c -o addtargets2.o addtargets2.cpp
 In file included from /usr/include/i386-linux-gnu/c++/14/bits/c++allocator.h:33,
                  from /usr/include/c++/14/bits/allocator.h:46,
                  from /usr/include/c++/14/string:43,
@@ -902,25 +957,6 @@
 /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)'
   151 |         return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
       |                                                       ^
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/validcalculator.o source/validcalculator.cpp
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/validparameter.o source/validparameter.cpp
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/venn.o source/venn.cpp
-source/utils.cpp: In member function 'bool Utils::findTool(std::string&, std::string&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::vector<std::__cxx11::basic_string<char> > >)':
-source/utils.cpp:952:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  952 |             system(versionTestCommand.c_str());
-      |             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-source/utils.cpp: In member function 'std::string Utils::sortFile(std::string, std::string)':
-source/utils.cpp:1514:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 1514 |         system(command.c_str());
-      |         ~~~~~~^~~~~~~~~~~~~~~~~
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/weightedlinkage.o source/weightedlinkage.cpp
-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.48.1\"" -DRELEASE_DATE="\"5/15/24\"" -DUSE_READLINE -Isource  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/engines/  -I source/metastats/  -I source/read/  -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2  -c -o source/wilcox.o source/wilcox.cpp
-cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd ..
-make[3]: Entering directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src'
-make[3]: Leaving directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src'
-make[3]: Entering directory '/build/reproducible-path/mothur-1.48.1/source/uchime_src'
-g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c -o addtargets2.o addtargets2.cpp
 g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c -o alignchime.o alignchime.cpp
 g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c -o alignchimel.o alignchimel.cpp
 g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -std=c++14 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c -o alnparams.o alnparams.cpp
@@ -1074,8 +1110,8 @@
    dh_gencontrol
    dh_md5sums
    dh_builddeb
-dpkg-deb: building package 'mothur' in '../mothur_1.48.1-1_i386.deb'.
 dpkg-deb: building package 'mothur-dbgsym' in '../mothur-dbgsym_1.48.1-1_i386.deb'.
+dpkg-deb: building package 'mothur' in '../mothur_1.48.1-1_i386.deb'.
  dpkg-genbuildinfo --build=binary -O../mothur_1.48.1-1_i386.buildinfo
  dpkg-genchanges --build=binary -O../mothur_1.48.1-1_i386.changes
 dpkg-genchanges: info: binary-only upload (no source code included)
@@ -1083,12 +1119,14 @@
 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/74074/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/74074/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/42323 and its subdirectories
-I: Current time: Sun Feb 23 15:14:39 -12 2025
-I: pbuilder-time-stamp: 1740366879
+I: removing directory /srv/workspace/pbuilder/74074 and its subdirectories
+I: Current time: Sun Mar 29 23:43:13 +14 2026
+I: pbuilder-time-stamp: 1774777393