Diff of the two buildlogs:

--
--- b1/build.log	2025-10-30 12:36:13.775331281 +0000
+++ b2/build.log	2025-10-30 12:46:48.299939876 +0000
@@ -1,2546 +1,8 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Thu Oct 30 00:31:13 -12 2025
-I: pbuilder-time-stamp: 1761827473
+I: Current time: Fri Oct 31 02:36:16 +14 2025
+I: pbuilder-time-stamp: 1761827776
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz]
-tar: ./build: time stamp 2026-11-30 05:47:35 is 34233381.56084771 s in the future
-tar: ./dev/null: time stamp 2026-11-30 05:47:21 is 34233367.56072411 s in the future
-tar: ./dev/zero: time stamp 2026-11-30 05:47:21 is 34233367.56071235 s in the future
-tar: ./dev/full: time stamp 2026-11-30 05:47:21 is 34233367.56070351 s in the future
-tar: ./dev/random: time stamp 2026-11-30 05:47:21 is 34233367.56069423 s in the future
-tar: ./dev/urandom: time stamp 2026-11-30 05:47:21 is 34233367.56068523 s in the future
-tar: ./dev/tty: time stamp 2026-11-30 05:47:21 is 34233367.56067587 s in the future
-tar: ./dev/console: time stamp 2026-11-30 05:47:21 is 34233367.56066759 s in the future
-tar: ./dev/pts: time stamp 2026-11-30 05:47:21 is 34233367.56065735 s in the future
-tar: ./dev/ptmx: time stamp 2026-11-30 05:47:21 is 34233367.56064995 s in the future
-tar: ./etc/ld.so.cache: time stamp 2026-12-01 22:29:40 is 34379906.56054823 s in the future
-tar: ./etc/default: time stamp 2026-11-30 05:47:39 is 34233385.56049095 s in the future
-tar: ./etc/dpkg/origins/default: time stamp 2026-11-30 05:47:21 is 34233367.56044691 s in the future
-tar: ./etc/dpkg/origins: time stamp 2026-11-30 05:47:25 is 34233371.56043467 s in the future
-tar: ./etc/dpkg/dpkg.cfg.d/02speedup: time stamp 2026-11-30 05:48:05 is 34233411.56040919 s in the future
-tar: ./etc/dpkg/dpkg.cfg.d: time stamp 2026-11-30 05:48:05 is 34233411.56040235 s in the future
-tar: ./etc/dpkg: time stamp 2026-11-30 05:47:35 is 34233381.56037679 s in the future
-tar: ./etc/skel: time stamp 2026-11-30 05:47:25 is 34233371.56029983 s in the future
-tar: ./etc/update-motd.d: time stamp 2026-11-30 05:47:25 is 34233371.56027539 s in the future
-tar: ./etc/apt/sources.list: time stamp 2026-11-30 05:48:05 is 34233411.56024703 s in the future
-tar: ./etc/apt/apt.conf.d/80proxy: time stamp 2026-11-30 05:48:05 is 34233411.56022635 s in the future
-tar: ./etc/apt/apt.conf.d/15pbuilder: time stamp 2026-11-30 05:47:35 is 34233381.56019523 s in the future
-tar: ./etc/apt/apt.conf.d: time stamp 2026-11-30 05:48:05 is 34233411.56018875 s in the future
-tar: ./etc/apt/trusted.gpg.d: time stamp 2026-11-30 05:47:35 is 34233381.55957179 s in the future
-tar: ./etc/apt: time stamp 2026-11-30 05:48:05 is 34233411.55954771 s in the future
-tar: ./etc/cron.daily: time stamp 2026-11-30 05:47:40 is 34233386.55894615 s in the future
-tar: ./etc/logrotate.d: time stamp 2026-11-30 05:47:40 is 34233386.55885619 s in the future
-tar: ./etc/ld.so.conf.d: time stamp 2026-11-30 05:47:40 is 34233386.55809775 s in the future
-tar: ./etc/security/opasswd: time stamp 2026-11-30 05:47:26 is 34233372.55794467 s in the future
-tar: ./etc/security: time stamp 2026-11-30 05:47:26 is 34233372.55792911 s in the future
-tar: ./etc/pam.d/common-auth: time stamp 2026-11-30 05:47:26 is 34233372.55750019 s in the future
-tar: ./etc/pam.d/common-account: time stamp 2026-11-30 05:47:26 is 34233372.55747351 s in the future
-tar: ./etc/pam.d/common-password: time stamp 2026-11-30 05:47:26 is 34233372.55746071 s in the future
-tar: ./etc/pam.d/common-session: time stamp 2026-11-30 05:47:26 is 34233372.55743147 s in the future
-tar: ./etc/pam.d/common-session-noninteractive: time stamp 2026-11-30 05:47:26 is 34233372.55741555 s in the future
-tar: ./etc/pam.d: time stamp 2026-12-01 16:41:49 is 34359035.55735271 s in the future
-tar: ./etc/terminfo: time stamp 2026-11-30 05:47:25 is 34233371.55732375 s in the future
-tar: ./etc/fstab: time stamp 2026-11-30 05:47:21 is 34233367.55731239 s in the future
-tar: ./etc/subuid: time stamp 2026-11-30 05:47:21 is 34233367.55729959 s in the future
-tar: ./etc/subgid: time stamp 2026-11-30 05:47:21 is 34233367.55729071 s in the future
-tar: ./etc/opt: time stamp 2026-11-30 05:47:21 is 34233367.55725403 s in the future
-tar: ./etc/shells: time stamp 2026-11-30 05:47:25 is 34233371.55724319 s in the future
-tar: ./etc/environment: time stamp 2026-11-30 05:47:26 is 34233372.55722507 s in the future
-tar: ./etc/kernel: time stamp 2026-11-30 05:47:26 is 34233372.55720879 s in the future
-tar: ./etc/perl/Net: time stamp 2026-11-30 05:47:35 is 34233381.55718507 s in the future
-tar: ./etc/perl: time stamp 2026-11-30 05:47:34 is 34233380.55717951 s in the future
-tar: ./etc/selinux: time stamp 2026-11-30 05:47:38 is 34233384.55713047 s in the future
-tar: ./etc/.pwd.lock: time stamp 2026-11-30 05:47:39 is 34233385.55711623 s in the future
-tar: ./etc/shadow: time stamp 2026-11-30 05:47:39 is 34233385.55706923 s in the future
-tar: ./etc/passwd-: time stamp 2026-11-30 05:47:21 is 34233367.55704071 s in the future
-tar: ./etc/passwd: time stamp 2026-11-30 05:47:39 is 34233385.55702931 s in the future
-tar: ./etc/gshadow: time stamp 2026-11-30 05:47:39 is 34233385.55700939 s in the future
-tar: ./etc/group-: time stamp 2026-11-30 05:47:21 is 34233367.55699211 s in the future
-tar: ./etc/group: time stamp 2026-11-30 05:47:39 is 34233385.55697871 s in the future
-tar: ./media: time stamp 2026-11-30 05:47:21 is 34233367.55691947 s in the future
-tar: ./mnt: time stamp 2026-11-30 05:47:21 is 34233367.55690387 s in the future
-tar: ./opt: time stamp 2026-11-30 05:47:21 is 34233367.55689555 s in the future
-tar: ./root: time stamp 2026-11-30 05:47:21 is 34233367.55686087 s in the future
-tar: ./run/lock: time stamp 2026-11-30 05:47:21 is 34233367.55684015 s in the future
-tar: ./srv: time stamp 2026-11-30 05:47:21 is 34233367.55682235 s in the future
-tar: ./usr/include/aarch64-linux-gnu/bits/types: time stamp 2026-11-30 05:47:32 is 34233377.94802875 s in the future
-tar: ./usr/include/aarch64-linux-gnu/bits: time stamp 2026-11-30 05:47:32 is 34233377.94194831 s in the future
-tar: ./usr/include/aarch64-linux-gnu/gnu: time stamp 2026-11-30 05:47:32 is 34233377.94184663 s in the future
-tar: ./usr/include/aarch64-linux-gnu/sys: time stamp 2026-11-30 05:47:32 is 34233377.93894943 s in the future
-tar: ./usr/include/aarch64-linux-gnu/c++/15/bits: time stamp 2026-12-01 22:29:39 is 34379904.93757959 s in the future
-tar: ./usr/include/aarch64-linux-gnu/c++/15/ext: time stamp 2026-12-01 22:29:39 is 34379904.93734447 s in the future
-tar: ./usr/include/aarch64-linux-gnu/c++/15: time stamp 2026-11-30 05:47:34 is 34233379.93732943 s in the future
-tar: ./usr/include/aarch64-linux-gnu/c++: time stamp 2026-11-30 05:47:34 is 34233379.93732363 s in the future
-tar: ./usr/include/arpa: time stamp 2026-11-30 05:47:32 is 34233377.93641183 s in the future
-tar: ./usr/include/finclude/aarch64-linux-gnu: time stamp 2026-11-30 05:47:32 is 34233377.93635267 s in the future
-tar: ./usr/include/finclude: time stamp 2026-11-30 05:47:32 is 34233377.93634535 s in the future
-tar: ./usr/include/net: time stamp 2026-11-30 05:47:32 is 34233377.93620651 s in the future
-tar: ./usr/include/netash: time stamp 2026-11-30 05:47:32 is 34233377.93617479 s in the future
-tar: ./usr/include/netatalk: time stamp 2026-11-30 05:47:32 is 34233377.93615611 s in the future
-tar: ./usr/include/netax25: time stamp 2026-11-30 05:47:32 is 34233377.93613447 s in the future
-tar: ./usr/include/neteconet: time stamp 2026-11-30 05:47:32 is 34233377.93611103 s in the future
-tar: ./usr/include/netinet: time stamp 2026-11-30 05:47:32 is 34233377.93538827 s in the future
-tar: ./usr/include/netipx: time stamp 2026-11-30 05:47:32 is 34233377.93534843 s in the future
-tar: ./usr/include/netiucv: time stamp 2026-11-30 05:47:32 is 34233377.93517255 s in the future
-tar: ./usr/include/netpacket: time stamp 2026-11-30 05:47:32 is 34233377.93514251 s in the future
-tar: ./usr/include/netrom: time stamp 2026-11-30 05:47:32 is 34233377.93511783 s in the future
-tar: ./usr/include/netrose: time stamp 2026-11-30 05:47:32 is 34233377.93509603 s in the future
-tar: ./usr/include/nfs: time stamp 2026-11-30 05:47:32 is 34233377.93507443 s in the future
-tar: ./usr/include/protocols: time stamp 2026-11-30 05:47:32 is 34233377.93470883 s in the future
-tar: ./usr/include/rpc: time stamp 2026-11-30 05:47:32 is 34233377.93465999 s in the future
-tar: ./usr/include/scsi/fc: time stamp 2026-11-30 05:47:34 is 34233379.93408519 s in the future
-tar: ./usr/include/scsi: time stamp 2026-11-30 05:47:34 is 34233379.93380535 s in the future
-tar: ./usr/include/c++/15/backward: time stamp 2026-12-01 22:29:39 is 34379904.91146599 s in the future
-tar: ./usr/include/c++/15/bits: time stamp 2026-12-01 22:29:39 is 34379904.88466203 s in the future
-tar: ./usr/include/c++/15/debug: time stamp 2026-12-01 22:29:39 is 34379904.88213143 s in the future
-tar: ./usr/include/c++/15/decimal: time stamp 2026-12-01 22:29:39 is 34379904.88198587 s in the future
-tar: ./usr/include/c++/15/experimental/bits: time stamp 2026-12-01 22:29:39 is 34379904.87522507 s in the future
-tar: ./usr/include/c++/15/experimental: time stamp 2026-12-01 22:29:39 is 34379904.87513447 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/bin_search_tree_: time stamp 2026-12-01 22:29:39 is 34379904.86926007 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/binary_heap_: time stamp 2026-12-01 22:29:39 is 34379904.86875907 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/binomial_heap_: time stamp 2026-12-01 22:29:39 is 34379904.86869463 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/binomial_heap_base_: time stamp 2026-12-01 22:29:39 is 34379904.86832943 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/branch_policy: time stamp 2026-12-01 22:29:39 is 34379904.86826695 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/cc_hash_table_map_: time stamp 2026-12-01 22:29:39 is 34379904.86730567 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/eq_fn: time stamp 2026-12-01 22:29:39 is 34379904.86723995 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/gp_hash_table_map_: time stamp 2026-12-01 22:29:39 is 34379904.86667123 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/hash_fn: time stamp 2026-12-01 22:29:39 is 34379904.86635599 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/left_child_next_sibling_heap_: time stamp 2026-12-01 22:29:39 is 34379904.86591939 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/list_update_map_: time stamp 2026-12-01 22:29:39 is 34379904.86549491 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/list_update_policy: time stamp 2026-12-01 22:29:39 is 34379904.86543399 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/ov_tree_map_: time stamp 2026-12-01 22:29:39 is 34379904.86500515 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/pairing_heap_: time stamp 2026-12-01 22:29:39 is 34379904.86476111 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/pat_trie_: time stamp 2026-12-01 22:29:39 is 34379904.86384871 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/rb_tree_map_: time stamp 2026-12-01 22:29:39 is 34379904.86342923 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/rc_binomial_heap_: time stamp 2026-12-01 22:29:39 is 34379904.86318363 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/resize_policy: time stamp 2026-12-01 22:29:39 is 34379904.86289163 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/splay_tree_: time stamp 2026-12-01 22:29:39 is 34379904.86244823 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/thin_heap_: time stamp 2026-12-01 22:29:39 is 34379904.86204383 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/tree_policy: time stamp 2026-12-01 22:29:39 is 34379904.86198607 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/trie_policy: time stamp 2026-12-01 22:29:39 is 34379904.86173883 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail/unordered_iterator: time stamp 2026-12-01 22:29:39 is 34379904.86167319 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds/detail: time stamp 2026-12-01 22:29:39 is 34379904.86166395 s in the future
-tar: ./usr/include/c++/15/ext/pb_ds: time stamp 2026-12-01 22:29:39 is 34379904.86165799 s in the future
-tar: ./usr/include/c++/15/ext: time stamp 2026-12-01 22:29:39 is 34379904.86165011 s in the future
-tar: ./usr/include/c++/15/parallel: time stamp 2026-12-01 22:29:39 is 34379904.85893943 s in the future
-tar: ./usr/include/c++/15/pstl: time stamp 2026-12-01 22:29:39 is 34379904.85685991 s in the future
-tar: ./usr/include/c++/15/tr1: time stamp 2026-12-01 22:29:39 is 34379904.85322659 s in the future
-tar: ./usr/include/c++/15/tr2: time stamp 2026-12-01 22:29:39 is 34379904.85299843 s in the future
-tar: ./usr/include/c++/15: time stamp 2026-12-01 22:29:39 is 34379904.85298703 s in the future
-tar: ./usr/include/c++: time stamp 2026-11-30 05:47:34 is 34233379.85298143 s in the future
-tar: ./usr/include/asm-generic: time stamp 2026-11-30 05:47:34 is 34233379.85144175 s in the future
-tar: ./usr/include/cxl: time stamp 2026-11-30 05:47:34 is 34233379.85130259 s in the future
-tar: ./usr/include/drm: time stamp 2026-11-30 05:47:34 is 34233379.84643659 s in the future
-tar: ./usr/include/fwctl: time stamp 2026-11-30 05:47:34 is 34233379.84617215 s in the future
-tar: ./usr/include/linux/android: time stamp 2026-11-30 05:47:34 is 34233379.84537367 s in the future
-tar: ./usr/include/linux/byteorder: time stamp 2026-11-30 05:47:34 is 34233379.84532871 s in the future
-tar: ./usr/include/linux/caif: time stamp 2026-11-30 05:47:34 is 34233379.84529507 s in the future
-tar: ./usr/include/linux/can: time stamp 2026-11-30 05:47:34 is 34233379.84518075 s in the future
-tar: ./usr/include/linux/cifs: time stamp 2026-11-30 05:47:34 is 34233379.84514807 s in the future
-tar: ./usr/include/linux/counter: time stamp 2026-11-30 05:47:34 is 34233379.84512807 s in the future
-tar: ./usr/include/linux/dvb: time stamp 2026-11-30 05:47:34 is 34233379.84467983 s in the future
-tar: ./usr/include/linux/genwqe: time stamp 2026-11-30 05:47:34 is 34233379.84449519 s in the future
-tar: ./usr/include/linux/hdlc: time stamp 2026-11-30 05:47:34 is 34233379.84431923 s in the future
-tar: ./usr/include/linux/hsi: time stamp 2026-11-30 05:47:34 is 34233379.84415287 s in the future
-tar: ./usr/include/linux/iio: time stamp 2026-11-30 05:47:34 is 34233379.84396267 s in the future
-tar: ./usr/include/linux/isdn: time stamp 2026-11-30 05:47:34 is 34233379.84380571 s in the future
-tar: ./usr/include/linux/media/amlogic: time stamp 2026-11-30 05:47:34 is 34233379.84361091 s in the future
-tar: ./usr/include/linux/media/raspberrypi: time stamp 2026-11-30 05:47:34 is 34233379.84336423 s in the future
-tar: ./usr/include/linux/media: time stamp 2026-11-30 05:47:34 is 34233379.84282499 s in the future
-tar: ./usr/include/linux/misc: time stamp 2026-11-30 05:47:34 is 34233379.84263991 s in the future
-tar: ./usr/include/linux/mmc: time stamp 2026-11-30 05:47:34 is 34233379.84249571 s in the future
-tar: ./usr/include/linux/netfilter/ipset: time stamp 2026-11-30 05:47:34 is 34233379.84231595 s in the future
-tar: ./usr/include/linux/netfilter: time stamp 2026-11-30 05:47:34 is 34233379.84080975 s in the future
-tar: ./usr/include/linux/netfilter_arp: time stamp 2026-11-30 05:47:34 is 34233379.84033955 s in the future
-tar: ./usr/include/linux/netfilter_bridge: time stamp 2026-11-30 05:47:34 is 34233379.84009079 s in the future
-tar: ./usr/include/linux/netfilter_ipv4: time stamp 2026-11-30 05:47:34 is 34233379.83985899 s in the future
-tar: ./usr/include/linux/netfilter_ipv6: time stamp 2026-11-30 05:47:34 is 34233379.83933455 s in the future
-tar: ./usr/include/linux/nfsd: time stamp 2026-11-30 05:47:34 is 34233379.83920903 s in the future
-tar: ./usr/include/linux/raid: time stamp 2026-11-30 05:47:34 is 34233379.83912119 s in the future
-tar: ./usr/include/linux/sched: time stamp 2026-11-30 05:47:34 is 34233379.83905967 s in the future
-tar: ./usr/include/linux/spi: time stamp 2026-11-30 05:47:34 is 34233379.83901799 s in the future
-tar: ./usr/include/linux/sunrpc: time stamp 2026-11-30 05:47:34 is 34233379.83899835 s in the future
-tar: ./usr/include/linux/surface_aggregator: time stamp 2026-11-30 05:47:34 is 34233379.83896059 s in the future
-tar: ./usr/include/linux/tc_act: time stamp 2026-11-30 05:47:34 is 34233379.83874359 s in the future
-tar: ./usr/include/linux/tc_ematch: time stamp 2026-11-30 05:47:34 is 34233379.83866503 s in the future
-tar: ./usr/include/linux/usb: time stamp 2026-11-30 05:47:34 is 34233379.83780307 s in the future
-tar: ./usr/include/linux: time stamp 2026-11-30 05:47:34 is 34233379.79879715 s in the future
-tar: ./usr/include/misc/uacce: time stamp 2026-11-30 05:47:34 is 34233379.79644223 s in the future
-tar: ./usr/include/misc: time stamp 2026-11-30 05:47:34 is 34233379.79632951 s in the future
-tar: ./usr/include/mtd: time stamp 2026-11-30 05:47:34 is 34233379.79598283 s in the future
-tar: ./usr/include/rdma/hfi: time stamp 2026-11-30 05:47:34 is 34233379.79394003 s in the future
-tar: ./usr/include/rdma: time stamp 2026-11-30 05:47:34 is 34233379.79274459 s in the future
-tar: ./usr/include/regulator: time stamp 2026-11-30 05:47:34 is 34233379.79270163 s in the future
-tar: ./usr/include/sound/intel/avs: time stamp 2026-11-30 05:47:34 is 34233379.79108367 s in the future
-tar: ./usr/include/sound/intel: time stamp 2026-11-30 05:47:34 is 34233379.79105339 s in the future
-tar: ./usr/include/sound/sof: time stamp 2026-11-30 05:47:34 is 34233379.79099395 s in the future
-tar: ./usr/include/sound: time stamp 2026-11-30 05:47:34 is 34233379.78947999 s in the future
-tar: ./usr/include/video: time stamp 2026-11-30 05:47:34 is 34233379.78852387 s in the future
-tar: ./usr/include/xen: time stamp 2026-11-30 05:47:34 is 34233379.78723867 s in the future
-tar: ./usr/include/rpcsvc: time stamp 2026-11-30 05:47:35 is 34233380.78566579 s in the future
-tar: ./usr/lib/systemd/system: time stamp 2026-12-01 16:41:49 is 34359034.78550451 s in the future
-tar: ./usr/lib/aarch64-linux-gnu/gconv/gconv-modules.d: time stamp 2026-11-30 05:47:23 is 34233368.49531215 s in the future
-tar: ./usr/lib/aarch64-linux-gnu/gconv: time stamp 2026-11-30 05:47:23 is 34233368.37342611 s in the future
-tar: ./usr/lib/aarch64-linux-gnu/security: time stamp 2026-11-30 05:47:24 is 34233369.35622399 s in the future
-tar: ./usr/lib/aarch64-linux-gnu/engines-3: time stamp 2026-11-30 05:47:24 is 34233369.35513739 s in the future
-tar: ./usr/lib/aarch64-linux-gnu/ossl-modules: time stamp 2026-11-30 05:47:24 is 34233369.35414295 s in the future
-tar: ./usr/lib/aarch64-linux-gnu/perl-base/Carp: time stamp 2026-11-30 05:47:24 is 34233369.35408391 s in the future
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-tar: ./usr/lib/locale/ar_YE/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37089463 s in the future
-tar: ./usr/lib/locale/ar_YE: time stamp 2026-11-30 05:47:40 is 34233381.37088391 s in the future
-tar: ./usr/lib/locale/ar_TN.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37087571 s in the future
-tar: ./usr/lib/locale/ar_TN.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37086935 s in the future
-tar: ./usr/lib/locale/ar_TN/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37086107 s in the future
-tar: ./usr/lib/locale/ar_TN: time stamp 2026-11-30 05:47:40 is 34233381.37085475 s in the future
-tar: ./usr/lib/locale/ar_SY.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37084683 s in the future
-tar: ./usr/lib/locale/ar_SY.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37084007 s in the future
-tar: ./usr/lib/locale/ar_SY/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37083299 s in the future
-tar: ./usr/lib/locale/ar_SY: time stamp 2026-11-30 05:47:40 is 34233381.37082671 s in the future
-tar: ./usr/lib/locale/ar_SS/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37081903 s in the future
-tar: ./usr/lib/locale/ar_SS: time stamp 2026-11-30 05:47:40 is 34233381.37081303 s in the future
-tar: ./usr/lib/locale/ar_SD.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37080603 s in the future
-tar: ./usr/lib/locale/ar_SD.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37079971 s in the future
-tar: ./usr/lib/locale/ar_SD/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37079227 s in the future
-tar: ./usr/lib/locale/ar_SD: time stamp 2026-11-30 05:47:40 is 34233381.37078615 s in the future
-tar: ./usr/lib/locale/ar_SA.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37077879 s in the future
-tar: ./usr/lib/locale/ar_SA.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37077271 s in the future
-tar: ./usr/lib/locale/ar_SA/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37076567 s in the future
-tar: ./usr/lib/locale/ar_SA: time stamp 2026-11-30 05:47:40 is 34233381.37075771 s in the future
-tar: ./usr/lib/locale/ar_QA.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37075051 s in the future
-tar: ./usr/lib/locale/ar_QA.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37074439 s in the future
-tar: ./usr/lib/locale/ar_QA/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37073691 s in the future
-tar: ./usr/lib/locale/ar_QA: time stamp 2026-11-30 05:47:40 is 34233381.37073103 s in the future
-tar: ./usr/lib/locale/ar_OM.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37072399 s in the future
-tar: ./usr/lib/locale/ar_OM.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37071791 s in the future
-tar: ./usr/lib/locale/ar_OM/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37071079 s in the future
-tar: ./usr/lib/locale/ar_OM: time stamp 2026-11-30 05:47:40 is 34233381.37070395 s in the future
-tar: ./usr/lib/locale/ar_MA.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37069675 s in the future
-tar: ./usr/lib/locale/ar_MA.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37069075 s in the future
-tar: ./usr/lib/locale/ar_MA/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37068367 s in the future
-tar: ./usr/lib/locale/ar_MA: time stamp 2026-11-30 05:47:40 is 34233381.37067763 s in the future
-tar: ./usr/lib/locale/ar_LY.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37067003 s in the future
-tar: ./usr/lib/locale/ar_LY.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37066399 s in the future
-tar: ./usr/lib/locale/ar_LY/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37065667 s in the future
-tar: ./usr/lib/locale/ar_LY: time stamp 2026-11-30 05:47:40 is 34233381.37065047 s in the future
-tar: ./usr/lib/locale/ar_LB.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37064323 s in the future
-tar: ./usr/lib/locale/ar_LB.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37063675 s in the future
-tar: ./usr/lib/locale/ar_LB/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37062919 s in the future
-tar: ./usr/lib/locale/ar_LB: time stamp 2026-11-30 05:47:40 is 34233381.37062291 s in the future
-tar: ./usr/lib/locale/ar_KW.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37061523 s in the future
-tar: ./usr/lib/locale/ar_KW.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37060811 s in the future
-tar: ./usr/lib/locale/ar_KW/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37060055 s in the future
-tar: ./usr/lib/locale/ar_KW: time stamp 2026-11-30 05:47:40 is 34233381.37059459 s in the future
-tar: ./usr/lib/locale/ar_JO.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37058699 s in the future
-tar: ./usr/lib/locale/ar_JO.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37058099 s in the future
-tar: ./usr/lib/locale/ar_JO/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37057379 s in the future
-tar: ./usr/lib/locale/ar_JO: time stamp 2026-11-30 05:47:40 is 34233381.37056779 s in the future
-tar: ./usr/lib/locale/ar_IQ.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37055995 s in the future
-tar: ./usr/lib/locale/ar_IQ.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37055383 s in the future
-tar: ./usr/lib/locale/ar_IQ/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37054643 s in the future
-tar: ./usr/lib/locale/ar_IQ: time stamp 2026-11-30 05:47:40 is 34233381.37054007 s in the future
-tar: ./usr/lib/locale/ar_IN/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37053251 s in the future
-tar: ./usr/lib/locale/ar_IN: time stamp 2026-11-30 05:47:40 is 34233381.37052627 s in the future
-tar: ./usr/lib/locale/ar_EG.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37051863 s in the future
-tar: ./usr/lib/locale/ar_EG.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37051159 s in the future
-tar: ./usr/lib/locale/ar_EG/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37050411 s in the future
-tar: ./usr/lib/locale/ar_EG: time stamp 2026-11-30 05:47:40 is 34233381.37049671 s in the future
-tar: ./usr/lib/locale/ar_DZ.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37048931 s in the future
-tar: ./usr/lib/locale/ar_DZ.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37048295 s in the future
-tar: ./usr/lib/locale/ar_DZ/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37047551 s in the future
-tar: ./usr/lib/locale/ar_DZ: time stamp 2026-11-30 05:47:40 is 34233381.37046871 s in the future
-tar: ./usr/lib/locale/ar_BH.utf8/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37046127 s in the future
-tar: ./usr/lib/locale/ar_BH.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37045531 s in the future
-tar: ./usr/lib/locale/ar_BH/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37044727 s in the future
-tar: ./usr/lib/locale/ar_BH: time stamp 2026-11-30 05:47:40 is 34233381.37044107 s in the future
-tar: ./usr/lib/locale/ar_AE.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37043443 s in the future
-tar: ./usr/lib/locale/anp_IN: time stamp 2026-11-30 05:47:40 is 34233381.37042787 s in the future
-tar: ./usr/lib/locale/an_ES.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37042063 s in the future
-tar: ./usr/lib/locale/am_ET: time stamp 2026-11-30 05:47:40 is 34233381.37041379 s in the future
-tar: ./usr/lib/locale/ak_GH: time stamp 2026-11-30 05:47:40 is 34233381.37040763 s in the future
-tar: ./usr/lib/locale/agr_PE: time stamp 2026-11-30 05:47:40 is 34233381.37040099 s in the future
-tar: ./usr/lib/locale/af_ZA.utf8: time stamp 2026-11-30 05:47:40 is 34233381.37039463 s in the future
-tar: ./usr/lib/locale/af_ZA: time stamp 2026-11-30 05:47:40 is 34233381.37038847 s in the future
-tar: ./usr/lib/locale/aa_ET/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37038123 s in the future
-tar: ./usr/lib/locale/aa_ET: time stamp 2026-11-30 05:47:40 is 34233381.37037471 s in the future
-tar: ./usr/lib/locale/aa_ER/LC_MESSAGES: time stamp 2026-11-30 05:47:40 is 34233381.37036747 s in the future
-tar: ./usr/lib/locale/aa_ER: time stamp 2026-11-30 05:47:40 is 34233381.37036155 s in the future
-tar: ./usr/lib/locale: time stamp 2026-11-30 05:47:40 is 34233381.37035531 s in the future
-tar: ./usr/lib/aarch64-linux-gnu/perl/cross-config-5.40.1: time stamp 2026-11-30 05:47:34 is 34233375.37034699 s in the future
-tar: ./usr/lib/aarch64-linux-gnu/perl: time stamp 2026-11-30 05:47:34 is 34233375.37034083 s in the future
-tar: ./usr/lib/aarch64-linux-gnu: time stamp 2026-12-01 22:29:40 is 34379901.37033487 s in the future
-tar: ./usr/lib: time stamp 2026-11-30 05:47:35 is 34233376.37032887 s in the future
-tar: ./usr/include/x86_64-linux-gnux32/asm: time stamp 2026-11-30 05:47:34 is 34233375.37032067 s in the future
-tar: ./usr/include/x86_64-linux-gnux32: time stamp 2026-11-30 05:47:34 is 34233375.37031483 s in the future
-tar: ./usr/include/x86_64-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37030715 s in the future
-tar: ./usr/include/x86_64-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37030095 s in the future
-tar: ./usr/include/sparc64-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37029371 s in the future
-tar: ./usr/include/sparc64-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37028771 s in the future
-tar: ./usr/include/sh4-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37027991 s in the future
-tar: ./usr/include/sh4-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37027419 s in the future
-tar: ./usr/include/s390x-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37026723 s in the future
-tar: ./usr/include/s390x-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37026127 s in the future
-tar: ./usr/include/riscv64-linux-gnu/asm/vendor: time stamp 2026-11-30 05:47:34 is 34233375.37025375 s in the future
-tar: ./usr/include/riscv64-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37024711 s in the future
-tar: ./usr/include/riscv64-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37024131 s in the future
-tar: ./usr/include/powerpc64le-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37023183 s in the future
-tar: ./usr/include/powerpc64le-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37022611 s in the future
-tar: ./usr/include/powerpc64-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37021891 s in the future
-tar: ./usr/include/powerpc64-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37021311 s in the future
-tar: ./usr/include/powerpc-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37020627 s in the future
-tar: ./usr/include/powerpc-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37020059 s in the future
-tar: ./usr/include/mipsisa64r6el-linux-gnuabi64/asm: time stamp 2026-11-30 05:47:34 is 34233375.37019367 s in the future
-tar: ./usr/include/mipsisa64r6el-linux-gnuabi64: time stamp 2026-11-30 05:47:34 is 34233375.37018731 s in the future
-tar: ./usr/include/mipsel-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37018019 s in the future
-tar: ./usr/include/mipsel-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37017391 s in the future
-tar: ./usr/include/mips64el-linux-gnuabi64/asm: time stamp 2026-11-30 05:47:34 is 34233375.37016683 s in the future
-tar: ./usr/include/mips64el-linux-gnuabi64: time stamp 2026-11-30 05:47:34 is 34233375.37016039 s in the future
-tar: ./usr/include/mips64-linux-gnuabi64/asm: time stamp 2026-11-30 05:47:34 is 34233375.37015339 s in the future
-tar: ./usr/include/mips64-linux-gnuabi64: time stamp 2026-11-30 05:47:34 is 34233375.37014699 s in the future
-tar: ./usr/include/mips-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37013887 s in the future
-tar: ./usr/include/mips-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37013291 s in the future
-tar: ./usr/include/m68k-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37012531 s in the future
-tar: ./usr/include/m68k-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37011907 s in the future
-tar: ./usr/include/loongarch64-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37011183 s in the future
-tar: ./usr/include/loongarch64-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37010603 s in the future
-tar: ./usr/include/i386-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37009835 s in the future
-tar: ./usr/include/i386-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37009231 s in the future
-tar: ./usr/include/hppa-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37008511 s in the future
-tar: ./usr/include/hppa-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37007899 s in the future
-tar: ./usr/include/arm-linux-gnueabihf/asm: time stamp 2026-11-30 05:47:34 is 34233375.37007123 s in the future
-tar: ./usr/include/arm-linux-gnueabihf: time stamp 2026-11-30 05:47:34 is 34233375.37006523 s in the future
-tar: ./usr/include/arm-linux-gnueabi/asm: time stamp 2026-11-30 05:47:34 is 34233375.37005811 s in the future
-tar: ./usr/include/arm-linux-gnueabi: time stamp 2026-11-30 05:47:34 is 34233375.37005191 s in the future
-tar: ./usr/include/alpha-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37004439 s in the future
-tar: ./usr/include/alpha-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37003831 s in the future
-tar: ./usr/include/aarch64-linux-gnu/asm: time stamp 2026-11-30 05:47:34 is 34233375.37003127 s in the future
-tar: ./usr/include/aarch64-linux-gnu: time stamp 2026-11-30 05:47:34 is 34233375.37002523 s in the future
-tar: ./usr/include: time stamp 2026-11-30 05:47:35 is 34233376.37001935 s in the future
-tar: ./usr/bin: time stamp 2026-12-01 22:29:40 is 34379901.37001295 s in the future
-tar: ./usr: time stamp 2026-11-30 05:47:21 is 34233362.37000691 s in the future
-tar: ./etc/systemd/system/timers.target.wants: time stamp 2026-11-30 05:47:35 is 34233376.36999395 s in the future
-tar: ./etc/systemd/system: time stamp 2026-11-30 05:47:21 is 34233362.36998787 s in the future
-tar: ./etc/alternatives: time stamp 2026-11-30 05:47:40 is 34233381.36997743 s in the future
 I: copying local configuration
 W: --override-config is not set; not updating apt.conf Read the manpage for details.
 I: mounting /proc filesystem
@@ -2560,53 +22,85 @@
 dpkg-source: info: unpacking garli_2.1-9.debian.tar.xz
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/3475926/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/3746721/tmp/hooks/D01_modify_environment starting
+debug: Running on codethink04-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 Oct 30 12:36 /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/3746721/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/3746721/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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
+  BASH_VERSION='5.3.3(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='forky'
-  HOME='/root'
-  HOST_ARCH='arm64'
+  DIRSTACK=()
+  DISTRIBUTION=forky
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=aarch64
+  HOST_ARCH=arm64
   IFS=' 	
   '
-  INVOCATION_ID='7fc55e45d39e4b718a148aef578c66f0'
-  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='3475926'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=8d621c3790e941bd8401788e260230a3
+  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=3746721
   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.PxGzuvva/pbuilderrc_dSpK --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PxGzuvva/b1 --logfile b1/build.log garli_2.1-9.dsc'
-  SUDO_GID='109'
-  SUDO_HOME='/var/lib/jenkins'
-  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.PxGzuvva/pbuilderrc_RXQk --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PxGzuvva/b2 --logfile b2/build.log garli_2.1-9.dsc'
+  SUDO_GID=109
+  SUDO_HOME=/var/lib/jenkins
+  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 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux
+  Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux
 I: ls -l /bin
   lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/3475926/tmp/hooks/D02_print_environment finished
+I: user script /srv/workspace/pbuilder/3746721/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -2753,7 +247,7 @@
 Get: 101 http://deb.debian.org/debian forky/main arm64 libopenmpi-dev arm64 5.0.8-10+b1 [1090 kB]
 Get: 102 http://deb.debian.org/debian forky/main arm64 mpi-default-dev arm64 1.19 [3432 B]
 Get: 103 http://deb.debian.org/debian forky/main arm64 ncl-tools arm64 2.1.21+git20210811.b1213a7-6 [166 kB]
-Fetched 88.1 MB in 1s (82.6 MB/s)
+Fetched 88.1 MB in 1s (91.7 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 ... 19971 files and directories currently installed.)
@@ -3188,7 +682,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/garli-2.1/ && 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  > ../garli_2.1-9_source.changes
+I: user script /srv/workspace/pbuilder/3746721/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for forky
+I: user script /srv/workspace/pbuilder/3746721/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/garli-2.1/ && 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  > ../garli_2.1-9_source.changes
 dpkg-buildpackage: info: source package garli
 dpkg-buildpackage: info: source version 2.1-9
 dpkg-buildpackage: info: source distribution unstable
@@ -3293,8 +791,8 @@
 checking whether make sets $(MAKE)... yes
 checking whether make supports nested variables... yes
 checking xargs -n works... yes
-checking whether UID '1111' is supported by ustar format... yes
-checking whether GID '1111' is supported by ustar format... yes
+checking whether UID '2222' is supported by ustar format... yes
+checking whether GID '2222' is supported by ustar format... yes
 checking how to create a ustar tar archive... gnutar
 checking whether ln -s works... yes
 checking for gcc... gcc
@@ -3458,58 +956,6 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-In file included from tree.h:35,
-                 from individual.h:21,
-                 from population.h:31,
-                 from garlimain.cpp:40:
-reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
-      |                         ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/15/string:51,
-                 from /usr/include/c++/15/bits/locale_classes.h:42,
-                 from /usr/include/c++/15/bits/ios_base.h:43,
-                 from /usr/include/c++/15/ios:46,
-                 from /usr/include/c++/15/bits/ostream.h:43,
-                 from /usr/include/c++/15/ostream:42,
-                 from /usr/include/c++/15/iostream:43,
-                 from population.h:23:
-/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-reconnode.h:65:41: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
-      |                                         ^~~~~~~~~~~~~~~
-/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
-      |                         ^~~~~~~~~~~~~~~
-/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)':
-reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
-   98 |                 return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist));
-      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/15/bits/stl_function.h:1441:
-/usr/include/c++/15/backward/binders.h:172:5: note: declared here
-  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
-      |     ^~~~~~~
-reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)':
-reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
-  102 |                 return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist));
-      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/include/c++/15/backward/binders.h:172:5: note: declared here
-  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
-      |     ^~~~~~~
-reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)':
-reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
-  202 |                 if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return;
-      |                                              ~~~~~~~^~~~~~~~~~~~~~~~~~
-/usr/include/c++/15/backward/binders.h:172:5: note: declared here
-  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
-      |     ^~~~~~~
 configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)':
 configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
   337 |                 sprintf(modName, "model%d", modelNum);
@@ -3526,16 +972,11 @@
       |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    32 |                                   __va_arg_pack ());
       |                                   ~~~~~~~~~~~~~~~~~
-In file included from garlimain.cpp:46:
-funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
-funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-  170 |         for(register int i=0;i<num;i++)
-      |                          ^
 In file included from tree.h:35,
                  from individual.h:21,
                  from population.h:31,
                  from funcs.h:25,
-                 from funcs.cpp:30:
+                 from configreader.cpp:30:
 reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
    58 | class DistEquals:public binary_function<ReconNode, int, bool>{
       |                         ^~~~~~~~~~~~~~~
@@ -3546,7 +987,7 @@
                  from /usr/include/c++/15/bits/ostream.h:43,
                  from /usr/include/c++/15/ostream:42,
                  from /usr/include/c++/15/iostream:43,
-                 from population.h:23:
+                 from configreader.cpp:21:
 /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -3584,6 +1025,11 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
+funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
+funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+  170 |         for(register int i=0;i<num;i++)
+      |                          ^
+mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp
 In file included from tree.h:35,
                  from individual.h:21,
                  from population.h:31,
@@ -3634,11 +1080,15 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
+funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
+funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+  170 |         for(register int i=0;i<num;i++)
+      |                          ^
 In file included from tree.h:35,
                  from individual.h:21,
                  from population.h:31,
                  from funcs.h:25,
-                 from configreader.cpp:30:
+                 from funcs.cpp:30:
 reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
    58 | class DistEquals:public binary_function<ReconNode, int, bool>{
       |                         ^~~~~~~~~~~~~~~
@@ -3649,7 +1099,7 @@
                  from /usr/include/c++/15/bits/ostream.h:43,
                  from /usr/include/c++/15/ostream:42,
                  from /usr/include/c++/15/iostream:43,
-                 from configreader.cpp:21:
+                 from population.h:23:
 /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -3680,29 +1130,20 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
-funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-  170 |         for(register int i=0;i<num;i++)
-      |                          ^
 reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)':
 reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
   202 |                 if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return;
       |                                              ~~~~~~~^~~~~~~~~~~~~~~~~~
-/usr/include/c++/15/backward/binders.h:172:5: note: declared here
-  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
-      |     ^~~~~~~
-funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
-funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-  170 |         for(register int i=0;i<num;i++)
-      |                          ^
 In file included from tree.h:35,
                  from individual.h:21,
                  from population.h:31,
-                 from funcs.h:25,
-                 from adaptation.cpp:25:
+                 from garlimain.cpp:40:
 reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
    58 | class DistEquals:public binary_function<ReconNode, int, bool>{
       |                         ^~~~~~~~~~~~~~~
+/usr/include/c++/15/backward/binders.h:172:5: note: declared here
+  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
+      |     ^~~~~~~
 In file included from /usr/include/c++/15/string:51,
                  from /usr/include/c++/15/bits/locale_classes.h:42,
                  from /usr/include/c++/15/bits/ios_base.h:43,
@@ -3710,7 +1151,7 @@
                  from /usr/include/c++/15/bits/ostream.h:43,
                  from /usr/include/c++/15/ostream:42,
                  from /usr/include/c++/15/iostream:43,
-                 from adaptation.cpp:18:
+                 from population.h:23:
 /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -3748,18 +1189,27 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
+In file included from garlimain.cpp:46:
 funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
 funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   170 |         for(register int i=0;i<num;i++)
       |                          ^
-mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp
 funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
 funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   170 |         for(register int i=0;i<num;i++)
       |                          ^
+configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)':
+configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  602 |         fread(&ch, sizeof(char), 1, file);
+      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
+configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  605 |                 fread(&ch, sizeof(char), 1, file);
+      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
 In file included from tree.h:35,
                  from individual.h:21,
-                 from model.cpp:26:
+                 from population.h:31,
+                 from funcs.h:25,
+                 from adaptation.cpp:25:
 reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
    58 | class DistEquals:public binary_function<ReconNode, int, bool>{
       |                         ^~~~~~~~~~~~~~~
@@ -3770,7 +1220,7 @@
                  from /usr/include/c++/15/bits/ostream.h:43,
                  from /usr/include/c++/15/ostream:42,
                  from /usr/include/c++/15/iostream:43,
-                 from model.cpp:17:
+                 from adaptation.cpp:18:
 /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -3808,25 +1258,25 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)':
-datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 1390 |         fscanf(inf, "%d  %d", &num_taxa, &num_chars);
-      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)':
-configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  602 |         fread(&ch, sizeof(char), 1, file);
-      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  605 |                 fread(&ch, sizeof(char), 1, file);
-      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
+mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp
+funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
+funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+  170 |         for(register int i=0;i<num;i++)
+      |                          ^
 In file included from tree.h:35,
-                 from optimization.cpp:19:
+                 from individual.h:21,
+                 from model.cpp:26:
 reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
    58 | class DistEquals:public binary_function<ReconNode, int, bool>{
       |                         ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/15/bits/refwrap.h:41,
-                 from /usr/include/c++/15/vector:70,
-                 from tree.h:24:
+In file included from /usr/include/c++/15/string:51,
+                 from /usr/include/c++/15/bits/locale_classes.h:42,
+                 from /usr/include/c++/15/bits/ios_base.h:43,
+                 from /usr/include/c++/15/ios:46,
+                 from /usr/include/c++/15/bits/ostream.h:43,
+                 from /usr/include/c++/15/ostream:42,
+                 from /usr/include/c++/15/iostream:43,
+                 from model.cpp:17:
 /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -3864,15 +1314,36 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-In file included from optimization.cpp:21:
-funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
-funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-  170 |         for(register int i=0;i<num;i++)
-      |                          ^
-optimization.cpp: In member function 'std::pair<double, double> Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)':
-optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
- 1099 | pair<FLOAT_TYPE, FLOAT_TYPE> Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){
-      |                                                                                       ^
+mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp
+datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)':
+datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 1390 |         fscanf(inf, "%d  %d", &num_taxa, &num_chars);
+      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/stdio.h:970,
+                 from /usr/include/c++/15/cstdio:47,
+                 from /usr/include/c++/15/ext/string_conversions.h:47,
+                 from /usr/include/c++/15/bits/basic_string.h:4444,
+                 from /usr/include/c++/15/string:56,
+                 from /usr/include/c++/15/bits/locale_classes.h:42,
+                 from /usr/include/c++/15/bits/ios_base.h:43,
+                 from /usr/include/c++/15/ios:46,
+                 from /usr/include/c++/15/bits/ostream.h:43,
+                 from /usr/include/c++/15/ostream:42,
+                 from /usr/include/c++/15/iostream:43,
+                 from model.h:25,
+                 from clamanager.h:25,
+                 from condlike.cpp:22:
+In function 'int sprintf(char*, const char*, ...)',
+    inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
+   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
+      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   31 |                                   __glibc_objsize (__s), __fmt,
+      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   32 |                                   __va_arg_pack ());
+      |                                   ~~~~~~~~~~~~~~~~~
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
 adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)':
 adaptation.cpp:271:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   271 |         fread((char *) this, 1, scalarSize, in);
@@ -3934,7 +1405,52 @@
 adaptation.cpp:305:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   305 |         fread((char *) anyModelnum, sizeof(int), intervalsToStore, in);
       |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp
+mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp
+In file included from tree.h:35,
+                 from optimization.cpp:19:
+reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
+      |                         ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/15/bits/refwrap.h:41,
+                 from /usr/include/c++/15/vector:70,
+                 from tree.h:24:
+/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+reconnode.h:65:41: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
+      |                                         ^~~~~~~~~~~~~~~
+/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
+      |                         ^~~~~~~~~~~~~~~
+/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)':
+reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
+   98 |                 return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist));
+      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/15/bits/stl_function.h:1441:
+/usr/include/c++/15/backward/binders.h:172:5: note: declared here
+  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
+      |     ^~~~~~~
+reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)':
+reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
+  102 |                 return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist));
+      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+/usr/include/c++/15/backward/binders.h:172:5: note: declared here
+  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
+      |     ^~~~~~~
+reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)':
+reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
+  202 |                 if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return;
+      |                                              ~~~~~~~^~~~~~~~~~~~~~~~~~
+/usr/include/c++/15/backward/binders.h:172:5: note: declared here
+  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
+      |     ^~~~~~~
 model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)':
 model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  3666 |                         fread(r+i, sizeof(FLOAT_TYPE), 1, in);
@@ -3966,17 +1482,23 @@
 model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  3713 |                 fread((char*) &x, sizeof(FLOAT_TYPE), 1, in);
       |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from optimization.cpp:21:
+funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
+funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+  170 |         for(register int i=0;i<num;i++)
+      |                          ^
+optimization.cpp: In member function 'std::pair<double, double> Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)':
+optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
+ 1099 | pair<FLOAT_TYPE, FLOAT_TYPE> Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){
+      |                                                                                       ^
 model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)':
 model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  4956 |                         fread(dummy, sizeof(FLOAT_TYPE), 1, in);
       |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp
-mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
-                 from /usr/include/c++/15/ext/string_conversions.h:47,
-                 from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56:
+                 from /usr/include/ncl/ncl.h:27,
+                 from garlireader.cpp:41:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -3992,16 +1514,7 @@
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56,
-                 from /usr/include/c++/15/bits/locale_classes.h:42,
-                 from /usr/include/c++/15/bits/ios_base.h:43,
-                 from /usr/include/c++/15/ios:46,
-                 from /usr/include/c++/15/bits/ostream.h:43,
-                 from /usr/include/c++/15/ostream:42,
-                 from /usr/include/c++/15/iostream:43,
-                 from model.h:25,
-                 from clamanager.h:25,
-                 from condlike.cpp:22:
+                 from /usr/include/c++/15/string:56:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -4013,6 +1526,7 @@
       |                                   ~~~~~~~~~~~~~~~~~
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
+mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp
 In file included from tree.h:35,
                  from individual.h:21,
                  from population.h:31,
@@ -4053,6 +1567,7 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
+mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp
 reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)':
 reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
   202 |                 if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return;
@@ -4080,21 +1595,6 @@
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
-                 from /usr/include/ncl/ncl.h:27,
-                 from garlireader.cpp:41:
-In function 'int sprintf(char*, const char*, ...)',
-    inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
-   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
-      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   31 |                                   __glibc_objsize (__s), __fmt,
-      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   32 |                                   __va_arg_pack ());
-      |                                   ~~~~~~~~~~~~~~~~~
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
-In file included from /usr/include/stdio.h:970,
-                 from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
                  from /usr/include/c++/15/string:56:
@@ -4109,18 +1609,12 @@
       |                                   ~~~~~~~~~~~~~~~~~
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
+mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56,
-                 from /usr/include/c++/15/bits/locale_classes.h:42,
-                 from /usr/include/c++/15/bits/ios_base.h:43,
-                 from /usr/include/c++/15/ios:46,
-                 from /usr/include/c++/15/bits/ostream.h:43,
-                 from /usr/include/c++/15/ostream:42,
-                 from /usr/include/c++/15/iostream:43,
-                 from datamatr.cpp:20:
+                 from /usr/include/c++/15/string:56:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -4136,7 +1630,6 @@
 population.cpp:875:46: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
   875 |                 tree0->CalcDerivativesRateHet(nd->anc, nd);
       |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
-mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp
 reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)':
 reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   388 |                 fread(&unique, scalarSize, 1, in);
@@ -4161,25 +1654,6 @@
 population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  1896 |         fread(this, scalarSize, 1, pin);
       |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
-mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp
-mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp
-mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp
-In file included from /usr/include/stdio.h:970,
-                 from /usr/include/c++/15/cstdio:47,
-                 from /usr/include/c++/15/ext/string_conversions.h:47,
-                 from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56:
-In function 'int sprintf(char*, const char*, ...)',
-    inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
-   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
-      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   31 |                                   __glibc_objsize (__s), __fmt,
-      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   32 |                                   __va_arg_pack ());
-      |                                   ~~~~~~~~~~~~~~~~~
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
@@ -4200,7 +1674,14 @@
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56:
+                 from /usr/include/c++/15/string:56,
+                 from /usr/include/c++/15/bits/locale_classes.h:42,
+                 from /usr/include/c++/15/bits/ios_base.h:43,
+                 from /usr/include/c++/15/ios:46,
+                 from /usr/include/c++/15/bits/ostream.h:43,
+                 from /usr/include/c++/15/ostream:42,
+                 from /usr/include/c++/15/iostream:43,
+                 from datamatr.cpp:20:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -4260,6 +1741,8 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
+mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp
+mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp
 funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
 funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   170 |         for(register int i=0;i<num;i++)
@@ -4268,7 +1751,54 @@
 tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  8463 | pair<FLOAT_TYPE, FLOAT_TYPE> Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){
       |                                                                                       ^
-mpic++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp
+In file included from /usr/include/stdio.h:970,
+                 from /usr/include/c++/15/cstdio:47,
+                 from /usr/include/c++/15/ext/string_conversions.h:47,
+                 from /usr/include/c++/15/bits/basic_string.h:4444,
+                 from /usr/include/c++/15/string:56:
+In function 'int sprintf(char*, const char*, ...)',
+    inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
+   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
+      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   31 |                                   __glibc_objsize (__s), __fmt,
+      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   32 |                                   __va_arg_pack ());
+      |                                   ~~~~~~~~~~~~~~~~~
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
+garlimain.cpp: In function 'int SubGarliMain(int)':
+garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=]
+  323 |                         else sprintf(temp, ".run%d", rank);
+      |                                                 ^~
+garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647]
+  323 |                         else sprintf(temp, ".run%d", rank);
+      |                                            ^~~~~~~~
+In function 'int sprintf(char*, const char*, ...)',
+    inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16:
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 bytes into a destination of size 10
+   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
+      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   31 |                                   __glibc_objsize (__s), __fmt,
+      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   32 |                                   __va_arg_pack ());
+      |                                   ~~~~~~~~~~~~~~~~~
+garlimain.cpp: In function 'int SubGarliMain(int)':
+garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=]
+  322 |                         if(rank < 10) sprintf(temp, ".run0%d", rank);
+      |                                                           ^~
+garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9]
+  322 |                         if(rank < 10) sprintf(temp, ".run0%d", rank);
+      |                                                     ^~~~~~~~~
+In function 'int sprintf(char*, const char*, ...)',
+    inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25:
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10
+   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
+      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   31 |                                   __glibc_objsize (__s), __fmt,
+      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   32 |                                   __va_arg_pack ());
+      |                                   ~~~~~~~~~~~~~~~~~
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
@@ -4360,38 +1890,6 @@
 tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
  6881 |                 fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in);
       |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-garlimain.cpp: In function 'int SubGarliMain(int)':
-garlimain.cpp:323:49: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=]
-  323 |                         else sprintf(temp, ".run%d", rank);
-      |                                                 ^~
-garlimain.cpp:323:44: note: directive argument in the range [10, 2147483647]
-  323 |                         else sprintf(temp, ".run%d", rank);
-      |                                            ^~~~~~~~
-In function 'int sprintf(char*, const char*, ...)',
-    inlined from 'int SubGarliMain(int)' at garlimain.cpp:323:16:
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 15 bytes into a destination of size 10
-   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
-      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   31 |                                   __glibc_objsize (__s), __fmt,
-      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   32 |                                   __va_arg_pack ());
-      |                                   ~~~~~~~~~~~~~~~~~
-garlimain.cpp: In function 'int SubGarliMain(int)':
-garlimain.cpp:322:59: warning: '%d' directive writing between 1 and 11 bytes into a region of size 5 [-Wformat-overflow=]
-  322 |                         if(rank < 10) sprintf(temp, ".run0%d", rank);
-      |                                                           ^~
-garlimain.cpp:322:53: note: directive argument in the range [-2147483648, 9]
-  322 |                         if(rank < 10) sprintf(temp, ".run0%d", rank);
-      |                                                     ^~~~~~~~~
-In function 'int sprintf(char*, const char*, ...)',
-    inlined from 'int SubGarliMain(int)' at garlimain.cpp:322:25:
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 17 bytes into a destination of size 10
-   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
-      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   31 |                                   __glibc_objsize (__s), __fmt,
-      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   32 |                                   __va_arg_pack ());
-      |                                   ~~~~~~~~~~~~~~~~~
 In file included from tree.h:35,
                  from individual.h:21,
                  from population.h:31,
@@ -4454,6 +1952,24 @@
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
                  from /usr/include/c++/15/string:56,
+                 from translatetable.h:24,
+                 from translatetable.cpp:19:
+In function 'int sprintf(char*, const char*, ...)',
+    inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
+   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
+      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   31 |                                   __glibc_objsize (__s), __fmt,
+      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   32 |                                   __va_arg_pack ());
+      |                                   ~~~~~~~~~~~~~~~~~
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
+In file included from /usr/include/stdio.h:970,
+                 from /usr/include/c++/15/cstdio:47,
+                 from /usr/include/c++/15/ext/string_conversions.h:47,
+                 from /usr/include/c++/15/bits/basic_string.h:4444,
+                 from /usr/include/c++/15/string:56,
                  from datamatr.h:23,
                  from sequencedata.h:27,
                  from sequencedata.cpp:21:
@@ -4512,9 +2028,7 @@
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56,
-                 from translatetable.h:24,
-                 from translatetable.cpp:19:
+                 from /usr/include/c++/15/string:56:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -4530,7 +2044,10 @@
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56:
+                 from /usr/include/c++/15/string:56,
+                 from datamatr.h:23,
+                 from sequencedata.h:27,
+                 from tree.cpp:31:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -4558,25 +2075,6 @@
       |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    32 |                                   __va_arg_pack ());
       |                                   ~~~~~~~~~~~~~~~~~
-In file included from /usr/include/stdio.h:970,
-                 from /usr/include/c++/15/cstdio:47,
-                 from /usr/include/c++/15/ext/string_conversions.h:47,
-                 from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56,
-                 from datamatr.h:23,
-                 from sequencedata.h:27,
-                 from tree.cpp:31:
-In function 'int sprintf(char*, const char*, ...)',
-    inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
-   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
-      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   31 |                                   __glibc_objsize (__s), __fmt,
-      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   32 |                                   __va_arg_pack ());
-      |                                   ~~~~~~~~~~~~~~~~~
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
 mpic++  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o  -lncl -lncl
 make[4]: Leaving directory '/build/reproducible-path/garli-2.1/src'
 Making all in tests
@@ -4654,8 +2152,8 @@
 checking whether make sets $(MAKE)... yes
 checking whether make supports nested variables... yes
 checking xargs -n works... yes
-checking whether UID '1111' is supported by ustar format... yes
-checking whether GID '1111' is supported by ustar format... yes
+checking whether UID '2222' is supported by ustar format... yes
+checking whether GID '2222' is supported by ustar format... yes
 checking how to create a ustar tar archive... gnutar
 checking whether ln -s works... yes
 checking for gcc... gcc
@@ -4817,22 +2315,6 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)':
-configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
-  337 |                 sprintf(modName, "model%d", modelNum);
-      |                                        ^~
-configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647]
-  337 |                 sprintf(modName, "model%d", modelNum);
-      |                                  ^~~~~~~~~
-In function 'int sprintf(char*, const char*, ...)',
-    inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10:
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10
-   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
-      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   31 |                                   __glibc_objsize (__s), __fmt,
-      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   32 |                                   __va_arg_pack ());
-      |                                   ~~~~~~~~~~~~~~~~~
 In file included from tree.h:35,
                  from individual.h:21,
                  from population.h:31,
@@ -4887,9 +2369,27 @@
 funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   170 |         for(register int i=0;i<num;i++)
       |                          ^
+configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)':
+configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
+  337 |                 sprintf(modName, "model%d", modelNum);
+      |                                        ^~
+configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647]
+  337 |                 sprintf(modName, "model%d", modelNum);
+      |                                  ^~~~~~~~~
+In function 'int sprintf(char*, const char*, ...)',
+    inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10:
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10
+   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
+      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   31 |                                   __glibc_objsize (__s), __fmt,
+      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   32 |                                   __va_arg_pack ());
+      |                                   ~~~~~~~~~~~~~~~~~
 In file included from tree.h:35,
                  from individual.h:21,
-                 from model.cpp:26:
+                 from population.h:31,
+                 from funcs.h:25,
+                 from configreader.cpp:30:
 reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
    58 | class DistEquals:public binary_function<ReconNode, int, bool>{
       |                         ^~~~~~~~~~~~~~~
@@ -4900,7 +2400,7 @@
                  from /usr/include/c++/15/bits/ostream.h:43,
                  from /usr/include/c++/15/ostream:42,
                  from /usr/include/c++/15/iostream:43,
-                 from model.cpp:17:
+                 from configreader.cpp:21:
 /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -4938,11 +2438,15 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp
+funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
+funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+  170 |         for(register int i=0;i<num;i++)
+      |                          ^
 In file included from tree.h:35,
                  from individual.h:21,
                  from population.h:31,
-                 from garlimain.cpp:40:
+                 from funcs.h:25,
+                 from adaptation.cpp:25:
 reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
    58 | class DistEquals:public binary_function<ReconNode, int, bool>{
       |                         ^~~~~~~~~~~~~~~
@@ -4953,7 +2457,7 @@
                  from /usr/include/c++/15/bits/ostream.h:43,
                  from /usr/include/c++/15/ostream:42,
                  from /usr/include/c++/15/iostream:43,
-                 from population.h:23:
+                 from adaptation.cpp:18:
 /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -5044,7 +2548,6 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-In file included from garlimain.cpp:46:
 funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
 funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   170 |         for(register int i=0;i<num;i++)
@@ -5056,8 +2559,7 @@
 In file included from tree.h:35,
                  from individual.h:21,
                  from population.h:31,
-                 from funcs.h:25,
-                 from adaptation.cpp:25:
+                 from garlimain.cpp:40:
 reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
    58 | class DistEquals:public binary_function<ReconNode, int, bool>{
       |                         ^~~~~~~~~~~~~~~
@@ -5068,7 +2570,7 @@
                  from /usr/include/c++/15/bits/ostream.h:43,
                  from /usr/include/c++/15/ostream:42,
                  from /usr/include/c++/15/iostream:43,
-                 from adaptation.cpp:18:
+                 from population.h:23:
 /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -5106,15 +2608,10 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
-funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-  170 |         for(register int i=0;i<num;i++)
-      |                          ^
+g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp
 In file included from tree.h:35,
                  from individual.h:21,
-                 from population.h:31,
-                 from funcs.h:25,
-                 from configreader.cpp:30:
+                 from model.cpp:26:
 reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
    58 | class DistEquals:public binary_function<ReconNode, int, bool>{
       |                         ^~~~~~~~~~~~~~~
@@ -5125,7 +2622,7 @@
                  from /usr/include/c++/15/bits/ostream.h:43,
                  from /usr/include/c++/15/ostream:42,
                  from /usr/include/c++/15/iostream:43,
-                 from configreader.cpp:21:
+                 from model.cpp:17:
 /usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -5156,95 +2653,11 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)':
-reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
-  202 |                 if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return;
-      |                                              ~~~~~~~^~~~~~~~~~~~~~~~~~
-/usr/include/c++/15/backward/binders.h:172:5: note: declared here
-  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
-      |     ^~~~~~~
+In file included from garlimain.cpp:46:
 funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
 funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   170 |         for(register int i=0;i<num;i++)
       |                          ^
-datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)':
-datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 1390 |         fscanf(inf, "%d  %d", &num_taxa, &num_chars);
-      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)':
-model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 3666 |                         fread(r+i, sizeof(FLOAT_TYPE), 1, in);
-      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 3675 |                         fread(&o, sizeof(FLOAT_TYPE), 1, in);
-      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 3677 |                         fread(&o, sizeof(FLOAT_TYPE), 1, in);
-      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 3684 |                 fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in);
-      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 3691 |                         fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in);
-      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 3692 |                         fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in);
-      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 3699 |                         fread((char*) &a, sizeof(FLOAT_TYPE), 1, in);
-      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 3705 |                 fread((char*) &p, sizeof(FLOAT_TYPE), 1, in);
-      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 3710 |                 fread((char*) &x, sizeof(FLOAT_TYPE), 1, in);
-      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 3713 |                 fread((char*) &x, sizeof(FLOAT_TYPE), 1, in);
-      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)':
-model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 4956 |                         fread(dummy, sizeof(FLOAT_TYPE), 1, in);
-      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp
-In file included from tree.h:35,
-                 from optimization.cpp:19:
-reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
-      |                         ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/15/bits/refwrap.h:41,
-                 from /usr/include/c++/15/vector:70,
-                 from tree.h:24:
-/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-reconnode.h:65:41: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
-      |                                         ^~~~~~~~~~~~~~~
-/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
-      |                         ^~~~~~~~~~~~~~~
-/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)':
-reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
-   98 |                 return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist));
-      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/15/bits/stl_function.h:1441:
-/usr/include/c++/15/backward/binders.h:172:5: note: declared here
-  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
-      |     ^~~~~~~
-reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)':
-reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
-  102 |                 return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist));
-      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-/usr/include/c++/15/backward/binders.h:172:5: note: declared here
-  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
-      |     ^~~~~~~
 reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)':
 reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
   202 |                 if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return;
@@ -5252,22 +2665,14 @@
 /usr/include/c++/15/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-In file included from optimization.cpp:21:
-funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
-funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-  170 |         for(register int i=0;i<num;i++)
-      |                          ^
 configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)':
 configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   602 |         fread(&ch, sizeof(char), 1, file);
       |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-optimization.cpp: In member function 'std::pair<double, double> Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)':
-optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
- 1099 | pair<FLOAT_TYPE, FLOAT_TYPE> Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){
-      |                                                                                       ^
 configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   605 |                 fread(&ch, sizeof(char), 1, file);
       |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
+g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp
 adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)':
 adaptation.cpp:271:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   271 |         fread((char *) this, 1, scalarSize, in);
@@ -5329,6 +2734,99 @@
 adaptation.cpp:305:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
   305 |         fread((char *) anyModelnum, sizeof(int), intervalsToStore, in);
       |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from tree.h:35,
+                 from optimization.cpp:19:
+reconnode.h:58:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+   58 | class DistEquals:public binary_function<ReconNode, int, bool>{
+      |                         ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/15/bits/refwrap.h:41,
+                 from /usr/include/c++/15/vector:70,
+                 from tree.h:24:
+/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+reconnode.h:65:41: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+   65 | class DistEqualsWithinCutSubtree:public binary_function<ReconNode, int, bool>{
+      |                                         ^~~~~~~~~~~~~~~
+/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+reconnode.h:72:25: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+   72 | class NodeEquals:public binary_function<ReconNode, int, bool>{
+      |                         ^~~~~~~~~~~~~~~
+/usr/include/c++/15/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)':
+reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
+   98 |                 return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist));
+      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/15/bits/stl_function.h:1441:
+/usr/include/c++/15/backward/binders.h:172:5: note: declared here
+  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
+      |     ^~~~~~~
+reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDistWithinCutSubtree(int)':
+reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
+  102 |                 return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist));
+      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+/usr/include/c++/15/backward/binders.h:172:5: note: declared here
+  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
+      |     ^~~~~~~
+reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)':
+reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
+  202 |                 if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return;
+      |                                              ~~~~~~~^~~~~~~~~~~~~~~~~~
+/usr/include/c++/15/backward/binders.h:172:5: note: declared here
+  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
+      |     ^~~~~~~
+datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)':
+datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 1390 |         fscanf(inf, "%d  %d", &num_taxa, &num_chars);
+      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from optimization.cpp:21:
+funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)':
+funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+  170 |         for(register int i=0;i<num;i++)
+      |                          ^
+optimization.cpp: In member function 'std::pair<double, double> Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)':
+optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
+ 1099 | pair<FLOAT_TYPE, FLOAT_TYPE> Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){
+      |                                                                                       ^
+model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)':
+model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 3666 |                         fread(r+i, sizeof(FLOAT_TYPE), 1, in);
+      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 3675 |                         fread(&o, sizeof(FLOAT_TYPE), 1, in);
+      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 3677 |                         fread(&o, sizeof(FLOAT_TYPE), 1, in);
+      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 3684 |                 fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in);
+      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 3691 |                         fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in);
+      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 3692 |                         fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in);
+      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 3699 |                         fread((char*) &a, sizeof(FLOAT_TYPE), 1, in);
+      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 3705 |                 fread((char*) &p, sizeof(FLOAT_TYPE), 1, in);
+      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 3710 |                 fread((char*) &x, sizeof(FLOAT_TYPE), 1, in);
+      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 3713 |                 fread((char*) &x, sizeof(FLOAT_TYPE), 1, in);
+      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)':
+model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 4956 |                         fread(dummy, sizeof(FLOAT_TYPE), 1, in);
+      |                         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp
 g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp
 In file included from tree.h:35,
@@ -5387,16 +2885,7 @@
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56,
-                 from /usr/include/c++/15/bits/locale_classes.h:42,
-                 from /usr/include/c++/15/bits/ios_base.h:43,
-                 from /usr/include/c++/15/ios:46,
-                 from /usr/include/c++/15/bits/ostream.h:43,
-                 from /usr/include/c++/15/ostream:42,
-                 from /usr/include/c++/15/iostream:43,
-                 from model.h:25,
-                 from clamanager.h:25,
-                 from condlike.cpp:22:
+                 from /usr/include/c++/15/string:56:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -5408,34 +2897,6 @@
       |                                   ~~~~~~~~~~~~~~~~~
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
-population.cpp: In member function 'void Population::RunTests()':
-population.cpp:875:46: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
-  875 |                 tree0->CalcDerivativesRateHet(nd->anc, nd);
-      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
-reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)':
-reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  388 |                 fread(&unique, scalarSize, 1, in);
-      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
-reconnode.h: In constructor 'Swap::Swap(FILE*&)':
-reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  264 |                 fread(&count, scalarSize, 1, in);
-      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from treenode.h:30,
-                 from tree.h:31:
-bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)':
-bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  518 |                 fread((char*) rep, sizeof(unsigned int), nBlocks, in);
-      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-population.cpp: In member function 'void Population::ReadPopulationCheckpoint()':
-population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 1880 |         fread((char *) &seed, sizeof(seed), 1, pin);
-      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 1887 |         fread((char *) &t, sizeof(t), 1, pin);
-      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 1896 |         fread(this, scalarSize, 1, pin);
-      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
@@ -5453,10 +2914,7 @@
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
 In file included from /usr/include/stdio.h:970,
-                 from /usr/include/c++/15/cstdio:47,
-                 from /usr/include/c++/15/ext/string_conversions.h:47,
-                 from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56:
+                 from configreader.cpp:18:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -5466,13 +2924,26 @@
       |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    32 |                                   __va_arg_pack ());
       |                                   ~~~~~~~~~~~~~~~~~
+population.cpp: In member function 'void Population::RunTests()':
+population.cpp:875:46: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
+  875 |                 tree0->CalcDerivativesRateHet(nd->anc, nd);
+      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56:
+                 from /usr/include/c++/15/string:56,
+                 from /usr/include/c++/15/bits/locale_classes.h:42,
+                 from /usr/include/c++/15/bits/ios_base.h:43,
+                 from /usr/include/c++/15/ios:46,
+                 from /usr/include/c++/15/bits/ostream.h:43,
+                 from /usr/include/c++/15/ostream:42,
+                 from /usr/include/c++/15/iostream:43,
+                 from model.h:25,
+                 from clamanager.h:25,
+                 from condlike.cpp:22:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -5499,20 +2970,35 @@
       |                                   ~~~~~~~~~~~~~~~~~
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
-g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp
-g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp
+reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)':
+reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  388 |                 fread(&unique, scalarSize, 1, in);
+      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
+reconnode.h: In constructor 'Swap::Swap(FILE*&)':
+reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  264 |                 fread(&count, scalarSize, 1, in);
+      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from treenode.h:30,
+                 from tree.h:31:
+bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)':
+bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  518 |                 fread((char*) rep, sizeof(unsigned int), nBlocks, in);
+      |                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+population.cpp: In member function 'void Population::ReadPopulationCheckpoint()':
+population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 1880 |         fread((char *) &seed, sizeof(seed), 1, pin);
+      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 1887 |         fread((char *) &t, sizeof(t), 1, pin);
+      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 1896 |         fread(this, scalarSize, 1, pin);
+      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56,
-                 from /usr/include/c++/15/bits/locale_classes.h:42,
-                 from /usr/include/c++/15/bits/ios_base.h:43,
-                 from /usr/include/c++/15/ios:46,
-                 from /usr/include/c++/15/bits/ostream.h:43,
-                 from /usr/include/c++/15/ostream:42,
-                 from /usr/include/c++/15/iostream:43,
-                 from datamatr.cpp:20:
+                 from /usr/include/c++/15/string:56:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -5544,7 +3030,14 @@
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
                  from /usr/include/c++/15/bits/basic_string.h:4444,
-                 from /usr/include/c++/15/string:56:
+                 from /usr/include/c++/15/string:56,
+                 from /usr/include/c++/15/bits/locale_classes.h:42,
+                 from /usr/include/c++/15/bits/ios_base.h:43,
+                 from /usr/include/c++/15/ios:46,
+                 from /usr/include/c++/15/bits/ostream.h:43,
+                 from /usr/include/c++/15/ostream:42,
+                 from /usr/include/c++/15/iostream:43,
+                 from datamatr.cpp:20:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -5556,8 +3049,14 @@
       |                                   ~~~~~~~~~~~~~~~~~
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
+g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp
+g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp
+g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp
 In file included from /usr/include/stdio.h:970,
-                 from configreader.cpp:18:
+                 from /usr/include/c++/15/cstdio:47,
+                 from /usr/include/c++/15/ext/string_conversions.h:47,
+                 from /usr/include/c++/15/bits/basic_string.h:4444,
+                 from /usr/include/c++/15/string:56:
 In function 'int sprintf(char*, const char*, ...)',
     inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12:
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull]
@@ -5569,7 +3068,7 @@
       |                                   ~~~~~~~~~~~~~~~~~
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
-g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp
+g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
@@ -5594,7 +3093,6 @@
       |                                   ~~~~~~~~~~~~~~~~~
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
-g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp
 In file included from tree.h:35,
                  from individual.h:21,
                  from population.h:31,
@@ -5647,11 +3145,11 @@
 funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   170 |         for(register int i=0;i<num;i++)
       |                          ^
+g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp
 tree.cpp: In member function 'std::pair<double, double> Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE)':
 tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair<double, double>' when C++17 is enabled changed to match C++14 in GCC 10.1
  8463 | pair<FLOAT_TYPE, FLOAT_TYPE> Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){
       |                                                                                       ^
-g++ -DHAVE_CONFIG_H -I. -I..  -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT  -g -O2 -ffile-prefix-map=/build/reproducible-path/garli-2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
@@ -5773,22 +3271,6 @@
       |                                   ~~~~~~~~~~~~~~~~~
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
-population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)':
-population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
- 3066 |                                 sprintf(oStr, "R(%d)", d + 1);
-      |                                                  ^~
-population.cpp:3066:47: note: directive argument in the range [1, 2147483647]
- 3066 |                                 sprintf(oStr, "R(%d)", d + 1);
-      |                                               ^~~~~~~
-In function 'int sprintf(char*, const char*, ...)',
-    inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12:
-/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10
-   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
-      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   31 |                                   __glibc_objsize (__s), __fmt,
-      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-   32 |                                   __va_arg_pack ());
-      |                                   ~~~~~~~~~~~~~~~~~
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
@@ -5812,6 +3294,22 @@
       |                                   ~~~~~~~~~~~~~~~~~
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)'
 /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=]
+population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)':
+population.cpp:3066:50: warning: '%d' directive writing between 1 and 10 bytes into a region of size 8 [-Wformat-overflow=]
+ 3066 |                                 sprintf(oStr, "R(%d)", d + 1);
+      |                                                  ^~
+population.cpp:3066:47: note: directive argument in the range [1, 2147483647]
+ 3066 |                                 sprintf(oStr, "R(%d)", d + 1);
+      |                                               ^~~~~~~
+In function 'int sprintf(char*, const char*, ...)',
+    inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12:
+/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 14 bytes into a destination of size 10
+   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
+      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   31 |                                   __glibc_objsize (__s), __fmt,
+      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+   32 |                                   __va_arg_pack ());
+      |                                   ~~~~~~~~~~~~~~~~~
 In file included from /usr/include/stdio.h:970,
                  from /usr/include/c++/15/cstdio:47,
                  from /usr/include/c++/15/ext/string_conversions.h:47,
@@ -8814,7 +6312,7 @@
 pass 10: -12956.1235   (branch= 0.0000  omega= 0.0000)
 Looking for minimum length branches...
 Final score = -12956.1235
-Time used = 0 hours, 0 minutes and 7 seconds
+Time used = 0 hours, 0 minutes and 16 seconds
 Writing site likelihoods for tree 1 ...
 
 #######################################################
@@ -8966,7 +6464,7 @@
 pass 10: -13269.2298   (branch= 0.0000  rel rates= 0.0000)
 Looking for minimum length branches...
 Final score = -13269.2298
-Time used = 0 hours, 0 minutes and 5 seconds
+Time used = 0 hours, 0 minutes and 8 seconds
 Writing site likelihoods for tree 1 ...
 
 #######################################################
@@ -9170,7 +6668,7 @@
 pass 80: -3350.2333   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0001  subset rates= 0.0000)
 Looking for minimum length branches...
 Final score = -3350.2333
-Time used = 0 hours, 0 minutes and 0 seconds
+Time used = 0 hours, 0 minutes and 1 seconds
 Writing site likelihoods for tree 1 ...
 
 #######################################################
@@ -9861,7 +7359,7 @@
 pass 14: -14498.8854   (branch= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
 Looking for minimum length branches...
 Final score = -14498.8854
-Time used = 0 hours, 0 minutes and 2 seconds
+Time used = 0 hours, 0 minutes and 4 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -10115,7 +7613,7 @@
 pass 39: -13306.2061   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0002  subset rates= 0.0000)
 Looking for minimum length branches...
 Final score = -13306.2061
-Time used = 0 hours, 0 minutes and 3 seconds
+Time used = 0 hours, 0 minutes and 5 seconds
 Writing site likelihoods for tree 1 ...
 
 #######################################################
@@ -12085,7 +9583,7 @@
 pass 493: -208.3586   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
 Looking for minimum length branches...
 Final score = -208.3586
-Time used = 0 hours, 0 minutes and 2 seconds
+Time used = 0 hours, 0 minutes and 3 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -12349,7 +9847,7 @@
 pass 372: -208.1244   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
 Looking for minimum length branches...
 Final score = -208.1244
-Time used = 0 hours, 0 minutes and 2 seconds
+Time used = 0 hours, 0 minutes and 3 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -12641,7 +10139,7 @@
 pass 488: -208.3584   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0002)
 Looking for minimum length branches...
 Final score = -208.3584
-Time used = 0 hours, 0 minutes and 2 seconds
+Time used = 0 hours, 0 minutes and 3 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -12934,7 +10432,7 @@
 pass 492: -208.3584   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000)
 Looking for minimum length branches...
 Final score = -208.3584
-Time used = 0 hours, 0 minutes and 1 seconds
+Time used = 0 hours, 0 minutes and 2 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -15654,20 +13152,6 @@
 1100     -88.8475         0.010         879 
 1200     -88.8463         0.010         879 
 1300     -88.8312         0.010         879 
-1400     -88.8046         0.010         879 
-1500     -88.8000         0.010         879 
-1600     -88.7604         0.010         879 
-1700     -88.7532         0.010         879 
-1800     -88.7145         0.010         879 
-1900     -88.6979         0.010         879 
-2000     -88.6746         0.010         879 
-2100     -88.6394         0.010         879 
-2200     -88.6224         0.010         879 
-2300     -88.6154         0.010         879 
-2400     -88.6058         0.010         879 
-2500     -88.5913         0.010         879 
-2600     -88.5622         0.010         879 
-2700     -88.5467         0.010         879 
 NOTE: ****Specified time limit (5 seconds) reached...
 
 NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
@@ -15764,9 +13248,9 @@
 	Subset 1: Random seed for bootstrap reweighting: 42
 
 Restarting from checkpoint...
-Bootstrap rep 1 (of 1)  generation 2713, seed 87569617, best lnL -88.547
+Bootstrap rep 1 (of 1)  generation 1304, seed 86236595, best lnL -88.831
 gen      current_lnL    precision  last_tree_imp  
-2713     -88.5467         0.010         879 
+1304     -88.8312         0.010         879 
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -15780,33 +13264,33 @@
     0.0826 0.0496 0.0579 0.0083 0.0331 
   Rate Heterogeneity Model:
     3 discrete gamma distributed rate categories, alpha param estimated
-      2.7053
+      0.9984
     with an invariant (invariable) site category, proportion estimated
-      0.2785
+      0.1371
     Substitution rate categories under this model:
       rate	proportion
-      0.0000	0.2785
-      0.4254	0.2405
-      0.8872	0.2405
-      1.6874	0.2405
+      0.0000	0.1371
+      0.1887	0.2876
+      0.7119	0.2876
+      2.0994	0.2876
 
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    3 branches were collapsed.
+    1 branches were collapsed.
 
 
 #######################################################
 
 Completed 1 replicate search(es) (of 1).
 Results:
-Replicate 1 : -88.5467       
+Replicate 1 : -88.8312       
 
 Parameter estimates:
         alpha  pinv
-rep 1:  2.705 0.278
+rep 1:  0.998 0.137
 
 Treelengths:
           TL 
-rep 1:  2.394
+rep 1:  2.337
 
 Saving best tree to bootstrap file ch.a.G3.boot.tre
 
@@ -15941,15 +13425,6 @@
 800      -110.5642        0.010         707 
 900      -110.5555        0.010         707 
 1000     -110.5065        0.010         707 
-1100     -110.4789        0.010         707 
-1200     -110.4460        0.010         707 
-1300     -110.4042        0.010         707 
-1400     -110.3747        0.010         707 
-1500     -110.3652        0.010         707 
-1600     -110.2967        0.010         707 
-1700     -110.2780        0.010         707 
-1800     -110.2329        0.010         707 
-1900     -110.2137        0.010         707 
 NOTE: ****Specified time limit (5 seconds) reached...
 
 NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
@@ -16036,9 +13511,9 @@
 STARTING RUN
 
 Restarting from checkpoint...
- generation 1909, seed 392330819, best lnL -110.214
+ generation 1011, seed 1336803846, best lnL -110.506
 gen      current_lnL    precision  last_tree_imp  
-1909     -110.2137        0.010         707 
+1011     -110.5058        0.010         707 
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -16052,19 +13527,19 @@
     0.0826 0.0496 0.0579 0.0083 0.0331 
   Rate Heterogeneity Model:
     4 discrete gamma distributed rate categories, alpha param estimated
-      2.7149
+      1.3049
     with an invariant (invariable) site category, proportion estimated
-      0.1544
+      0.0988
     Substitution rate categories under this model:
       rate	proportion
-      0.0000	0.1544
-      0.3659	0.2114
-      0.7144	0.2114
-      1.0807	0.2114
-      1.8390	0.2114
+      0.0000	0.0988
+      0.1936	0.2253
+      0.5525	0.2253
+      1.0366	0.2253
+      2.2174	0.2253
 
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    No branches were short enough to be collapsed.
+    1 branches were collapsed.
 
 Saving site likelihoods to file ch.a.G4.sitelikes.log ...
 
@@ -16072,15 +13547,15 @@
 
 Completed 1 replicate search(es) (of 1).
 Results:
-Replicate 1 : -110.2137       
+Replicate 1 : -110.5058       
 
 Parameter estimates:
         alpha  pinv
-rep 1:  2.715 0.154
+rep 1:  1.305 0.099
 
 Treelengths:
           TL 
-rep 1:  2.692
+rep 1:  2.539
 
 Saving final tree from best search rep (#1) to ch.a.G4.best.tre
 Inferring internal state probabilities on best tree... saving to file ch.a.G4.internalstates.log
@@ -16226,48 +13701,15 @@
 2700     -111.6816        0.010         563 
 2800     -111.6816        0.010         563 
 2900     -111.6815        0.010         563 
-3000     -111.6815        0.010         563 
-3100     -111.6815        0.010         563 
-3200     -111.6815        0.010         563 
-Reached termination condition!
-last topological improvement at gen 563
-Improvement over last 500 gen = 0.00009
-
-MODEL REPORT - Parameter values are FINAL
-Model 1
-  Number of states = 20 (amino acid data)
-  Amino Acid Rate Matrix: Jones
-  Equilibrium State Frequencies: empirical (observed) values (+F)
-    (ACDEFGHIKLMNPQRSTVWY)
-    0.0165 0.0083 0.0496 0.0909 0.0909 
-    0.0083 0.0744 0.0083 0.0083 0.1074 
-    0.1157 0.0248 0.1240 0.0331 0.0083 
-    0.0826 0.0496 0.0579 0.0083 0.0331 
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    No branches were short enough to be collapsed.
-
-Saving site likelihoods to file ch.a.sitelikes.log ...
-
-#######################################################
-
-Completed 1 replicate search(es) (of 1).
-Results:
-Replicate 1 : -111.6815       
-
-Parameter estimates:
-	 Model contains no estimated parameters
-
-Treelengths:
-          TL 
-rep 1:  2.607
+NOTE: ****Specified time limit (5 seconds) reached...
 
-Saving final tree from best search rep (#1) to ch.a.best.tre
-Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log
+NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
+TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
+FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
+(set restart = 1 in the config file).  IF YOU WANT TO USE THE
+PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
+ADD "end;" TO THE TREE FILES.
 
-#######################################################
 Running GARLI Version 2.1. ()
 ->Single processor version for 64-bit OS<-
 ##############################################################
@@ -16344,9 +13786,9 @@
 STARTING RUN
 
 Restarting from checkpoint...
- generation 3200, seed 1669543796, best lnL -111.681
+ generation 2965, seed 626749801, best lnL -111.682
 gen      current_lnL    precision  last_tree_imp  
-3200     -111.6815        0.010         563 
+2965     -111.6815        0.010         563 
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -16377,7 +13819,7 @@
 
 Treelengths:
           TL 
-rep 1:  2.607
+rep 1:  2.606
 
 Saving final tree from best search rep (#1) to ch.a.best.tre
 Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log
@@ -16512,16 +13954,6 @@
 60       -205.5990        0.500          53 
 70       -205.5741        0.500          53 
 80       -205.4022        0.500          76 
-90       -205.3871        0.500          76 
-100      -205.3829        0.500          76 
-110      -205.3431        0.500         106 
-120      -205.3431        0.500         106 
-130      -205.2505        0.500         121 
-140      -205.2440        0.500         121 
-150      -205.1047        0.500         121 
-160      -205.0609        0.500         121 
-170      -204.9813        0.500         121 
-180      -204.9247        0.500         172 
 NOTE: ****Specified time limit (10 seconds) reached...
 
 NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
@@ -16608,15 +14040,18 @@
 STARTING RUN
 
 Restarting from checkpoint...
- generation 185, seed 1181261042, best lnL -204.925
+ generation 88, seed 530483715, best lnL -205.387
 gen      current_lnL    precision  last_tree_imp  
-185      -204.9247        0.500         172 
+88       -205.3871        0.500          76 
+90       -205.3871        0.500          76 
+100      -205.3829        0.500          76 
+NOTE: ****Specified generation limit (100) reached...
 
-MODEL REPORT - Parameter values are FINAL
+MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
 Model 1
   Number of states = 61 (codon data, standard code)
   Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
-    AC = 1.586, AG = 4.036, AT = 0.040, CG = 2.453, CT = 3.968, GT = 1.000
+    AC = 1.586, AG = 3.999, AT = 0.040, CG = 2.453, CT = 3.968, GT = 1.000
   Equilibrium State Frequencies: 
     empirical values calculated by F3x4 method (fixed)
     (AAA, AAC, AAG, AAT, ACA, ... etc)
@@ -16637,31 +14072,38 @@
     2 nonsynonymous rate categories, rate and proportion of each estimated
      (this is effectively the M3 model of PAML)
       dN/dS	Proportion
-      0.0473	0.5211
+      0.0490	0.5211
       0.4995	0.4789
 
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
     No branches were short enough to be collapsed.
 
 Saving site likelihoods to file ch.c.M3x2.sitelikes.log ...
+WARNING: Site likelihoods being output on prematurely terminated search ...
+
+NOTE: ***Search was terminated before full auto-termination condition was reached!
+Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
+
 
 #######################################################
 
 Completed 1 replicate search(es) (of 1).
 Results:
-Replicate 1 : -204.9247       
+Replicate 1 : -205.3829       
 
 Parameter estimates:
          w(0)  p(0)  w(1)  p(1)  r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT)
-rep 1:  0.047 0.521 0.499 0.479  1.586  4.036   0.04  2.453  3.968      1
+rep 1:  0.049 0.521 0.499 0.479  1.586  3.999   0.04  2.453  3.968      1
 
 Treelengths:
           TL 
-rep 1:  7.813
+rep 1:  7.371
 
 Saving final tree from best search rep (#1) to ch.c.M3x2.best.tre
 Inferring internal state probabilities on best tree... saving to file ch.c.M3x2.internalstates.log
 
+WARNING: Internal states inferred on tree from prematurely terminated search
+
 #######################################################
 TREEFILES PASS
 Running checkpoint test ./check/c.conf
@@ -16798,11 +14240,6 @@
 90       -194.9094        0.500           0 
 100      -194.9094        0.500           0 
 110      -194.8988        0.500           0 
-120      -194.8988        0.500           0 
-130      -194.8986        0.500           0 
-140      -194.8502        0.500           0 
-150      -194.7087        0.500           0 
-160      -194.7087        0.500           0 
 NOTE: ****Specified time limit (5 seconds) reached...
 
 NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
@@ -16890,16 +14327,16 @@
 	Subset 1: Random seed for bootstrap reweighting: 42
 
 Restarting from checkpoint...
-Bootstrap rep 1 (of 1)  generation 165, seed 1158429237, best lnL -194.709
+Bootstrap rep 1 (of 1)  generation 115, seed 1260723224, best lnL -194.899
 gen      current_lnL    precision  last_tree_imp  
-165      -194.7087        0.500           0 
+115      -194.8988        0.500           0 
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
   Number of states = 61 (codon data, standard code)
   One estimated dN/dS ratio (aka omega) = 0.120505
   Nucleotide Relative Rate Matrix Assumed by Codon Model:     6 rates 
-    AC = 1.637, AG = 5.802, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000
+    AC = 1.637, AG = 5.749, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000
   Equilibrium State Frequencies: 
     empirical values calculated by F3x4 method (fixed)
     (AAA, AAC, AAG, AAT, ACA, ... etc)
@@ -16927,15 +14364,15 @@
 
 Completed 1 replicate search(es) (of 1).
 Results:
-Replicate 1 : -194.7087       
+Replicate 1 : -194.8988       
 
 Parameter estimates:
          w(0)  p(0)  r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT)
-rep 1:  0.121 1.000  1.637  5.802 0.01146  4.174  2.324      1
+rep 1:  0.121 1.000  1.637  5.749 0.01146  4.174  2.324      1
 
 Treelengths:
           TL 
-rep 1:  9.839
+rep 1:  9.255
 
 Saving best tree to bootstrap file ch.c.boot.tre
 
@@ -17115,27 +14552,6 @@
 2300     -3351.2533       0.010           0 
 2400     -3351.2181       0.010           0 
 2500     -3351.1259       0.010           0 
-2600     -3351.0632       0.010           0 
-2700     -3351.0630       0.010           0 
-2800     -3351.0575       0.010           0 
-2900     -3351.0142       0.010           0 
-3000     -3351.0142       0.010           0 
-3100     -3351.0014       0.010           0 
-3200     -3350.9815       0.010           0 
-3300     -3350.9790       0.010           0 
-3400     -3350.9755       0.010           0 
-3500     -3350.9754       0.010           0 
-3600     -3350.9748       0.010           0 
-3700     -3350.9419       0.010           0 
-3800     -3350.9277       0.010           0 
-3900     -3350.8676       0.010           0 
-4000     -3350.8676       0.010           0 
-4100     -3350.8580       0.010           0 
-4200     -3350.8524       0.010           0 
-4300     -3350.8522       0.010           0 
-4400     -3350.8481       0.010           0 
-4500     -3350.8481       0.010           0 
-4600     -3350.8169       0.010           0 
 NOTE: ****Specified time limit (5 seconds) reached...
 
 NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
@@ -17239,112 +14655,88 @@
 STARTING RUN
 
 Restarting from checkpoint...
-Search rep 1 (of 2) generation 4699, seed 89606078, best lnL -3350.815
+Search rep 1 (of 2) generation 2507, seed 1174768858, best lnL -3351.126
 gen      current_lnL    precision  last_tree_imp  
-4699     -3350.8148       0.010           0 
+2507     -3351.1259       0.010           0 
+2600     -3351.0632       0.010           0 
+2700     -3351.0630       0.010           0 
+2800     -3351.0575       0.010           0 
+2900     -3351.0142       0.010           0 
+3000     -3351.0142       0.010           0 
+3100     -3351.0014       0.010           0 
+3200     -3350.9815       0.010           0 
+3300     -3350.9790       0.010           0 
+3400     -3350.9755       0.010           0 
+3500     -3350.9754       0.010           0 
+3600     -3350.9748       0.010           0 
+3700     -3350.9419       0.010           0 
+3800     -3350.9277       0.010           0 
+3900     -3350.8676       0.010           0 
+4000     -3350.8676       0.010           0 
+4100     -3350.8580       0.010           0 
+4200     -3350.8524       0.010           0 
+4300     -3350.8522       0.010           0 
+4400     -3350.8481       0.010           0 
+4500     -3350.8481       0.010           0 
+4600     -3350.8169       0.010           0 
 4700     -3350.8148       0.010           0 
 4800     -3350.8148       0.010           0 
-4900     -3350.8148       0.010           0 
-5000     -3350.8141       0.010           0 
-5100     -3350.7922       0.010           0 
-5200     -3350.7744       0.010           0 
-5300     -3350.7726       0.010           0 
-5400     -3350.7563       0.010           0 
-5500     -3350.7008       0.010           0 
-5600     -3350.6582       0.010           0 
-5700     -3350.6556       0.010           0 
-5800     -3350.6197       0.010           0 
-5900     -3350.6125       0.010           0 
-6000     -3350.6089       0.010           0 
-6100     -3350.5998       0.010           0 
-6200     -3350.5989       0.010           0 
-6300     -3350.5945       0.010           0 
-6400     -3350.5915       0.010           0 
-6500     -3350.5909       0.010           0 
-6600     -3350.5895       0.010           0 
-6700     -3350.5895       0.010           0 
-6800     -3350.5827       0.010           0 
-6900     -3350.5549       0.010           0 
-7000     -3350.5549       0.010           0 
-7100     -3350.5524       0.010           0 
-7200     -3350.5462       0.010           0 
-7300     -3350.5462       0.010           0 
-7400     -3350.5431       0.010           0 
-7500     -3350.5407       0.010           0 
-7600     -3350.5320       0.010           0 
-7700     -3350.5313       0.010           0 
-7800     -3350.5313       0.010           0 
-7900     -3350.5313       0.010           0 
-8000     -3350.5125       0.010           0 
-8100     -3350.5125       0.010           0 
-8200     -3350.5124       0.010           0 
-8300     -3350.5091       0.010           0 
-8400     -3350.5003       0.010           0 
-8500     -3350.4985       0.010           0 
-8600     -3350.4798       0.010           0 
-8700     -3350.4787       0.010           0 
-8800     -3350.4784       0.010           0 
-8900     -3350.4762       0.010           0 
-9000     -3350.4758       0.010           0 
-9100     -3350.4502       0.010           0 
-9200     -3350.4501       0.010           0 
-9300     -3350.4501       0.010           0 
-9400     -3350.4496       0.010           0 
-9500     -3350.4492       0.010           0 
-9600     -3350.4482       0.010           0 
-9700     -3350.4480       0.010           0 
 NOTE: ****Specified time limit (5 seconds) reached...
-Current score = -3350.4480
+Current score = -3350.8148
 Performing final optimizations...
-pass 1 : -3350.4376   (branch= 0.0000  alpha= 0.0000  pinv= 0.0103  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 2 : -3350.4154   (branch= 0.0000  alpha= 0.0120  pinv= 0.0102  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 3 : -3350.3923   (branch= 0.0000  alpha= 0.0107  pinv= 0.0092  eq freqs= 0.0000  rel rates= 0.0031  subset rates= 0.0000)
-pass 4 : -3350.3721   (branch= 0.0018  alpha= 0.0091  pinv= 0.0083  eq freqs= 0.0000  rel rates= 0.0010  subset rates= 0.0000)
-pass 5 : -3350.3537   (branch= 0.0004  alpha= 0.0096  pinv= 0.0073  eq freqs= 0.0000  rel rates= 0.0010  subset rates= 0.0000)
-pass 6 : -3350.3392   (branch= 0.0005  alpha= 0.0072  pinv= 0.0067  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 7 : -3350.3260   (branch= 0.0004  alpha= 0.0066  pinv= 0.0060  eq freqs= 0.0000  rel rates= 0.0002  subset rates= 0.0000)
-pass 8 : -3350.3142   (branch= 0.0002  alpha= 0.0059  pinv= 0.0053  eq freqs= 0.0001  rel rates= 0.0003  subset rates= 0.0000)
-pass 9 : -3350.3028   (branch= 0.0001  alpha= 0.0052  pinv= 0.0048  eq freqs= 0.0000  rel rates= 0.0001  subset rates= 0.0011)
-pass 10: -3350.2934   (branch= 0.0008  alpha= 0.0043  pinv= 0.0042  eq freqs= 0.0001  rel rates= 0.0000  subset rates= 0.0000)
-pass 11: -3350.2857   (branch= 0.0001  alpha= 0.0038  pinv= 0.0037  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 12: -3350.2786   (branch= 0.0000  alpha= 0.0037  pinv= 0.0033  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 13: -3350.2725   (branch= 0.0000  alpha= 0.0032  pinv= 0.0029  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 14: -3350.2671   (branch= 0.0000  alpha= 0.0028  pinv= 0.0025  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 15: -3350.2624   (branch= 0.0000  alpha= 0.0025  pinv= 0.0022  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 16: -3350.2583   (branch= 0.0000  alpha= 0.0022  pinv= 0.0019  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 17: -3350.2548   (branch= 0.0000  alpha= 0.0019  pinv= 0.0017  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 18: -3350.2517   (branch= 0.0000  alpha= 0.0016  pinv= 0.0014  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 19: -3350.2490   (branch= 0.0000  alpha= 0.0014  pinv= 0.0012  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
-pass 20: -3350.2467   (branch= 0.0000  alpha= 0.0012  pinv= 0.0011  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
+pass 1 : -3350.7662   (branch= 0.0000  alpha= 0.0000  pinv= 0.0241  eq freqs= 0.0001  rel rates= 0.0245  subset rates= 0.0000)
+pass 2 : -3350.7088   (branch= 0.0028  alpha= 0.0102  pinv= 0.0167  eq freqs= 0.0000  rel rates= 0.0263  subset rates= 0.0014)
+pass 3 : -3350.6535   (branch= 0.0073  alpha= 0.0163  pinv= 0.0149  eq freqs= 0.0000  rel rates= 0.0167  subset rates= 0.0000)
+pass 4 : -3350.5999   (branch= 0.0056  alpha= 0.0140  pinv= 0.0137  eq freqs= 0.0016  rel rates= 0.0155  subset rates= 0.0032)
+pass 5 : -3350.5569   (branch= 0.0046  alpha= 0.0120  pinv= 0.0127  eq freqs= 0.0000  rel rates= 0.0124  subset rates= 0.0014)
+pass 6 : -3350.5196   (branch= 0.0033  alpha= 0.0111  pinv= 0.0116  eq freqs= 0.0000  rel rates= 0.0113  subset rates= 0.0000)
+pass 7 : -3350.4850   (branch= 0.0009  alpha= 0.0106  pinv= 0.0104  eq freqs= 0.0001  rel rates= 0.0109  subset rates= 0.0017)
+pass 8 : -3350.4553   (branch= 0.0016  alpha= 0.0098  pinv= 0.0095  eq freqs= 0.0000  rel rates= 0.0089  subset rates= 0.0000)
+pass 9 : -3350.4281   (branch= 0.0002  alpha= 0.0087  pinv= 0.0085  eq freqs= 0.0000  rel rates= 0.0086  subset rates= 0.0011)
+pass 10: -3350.4043   (branch= 0.0010  alpha= 0.0081  pinv= 0.0077  eq freqs= 0.0000  rel rates= 0.0070  subset rates= 0.0000)
+pass 11: -3350.3836   (branch= 0.0001  alpha= 0.0071  pinv= 0.0069  eq freqs= 0.0000  rel rates= 0.0065  subset rates= 0.0000)
+pass 12: -3350.3647   (branch= 0.0000  alpha= 0.0068  pinv= 0.0061  eq freqs= 0.0000  rel rates= 0.0059  subset rates= 0.0000)
+pass 13: -3350.3480   (branch= 0.0000  alpha= 0.0061  pinv= 0.0055  eq freqs= 0.0000  rel rates= 0.0051  subset rates= 0.0000)
+pass 14: -3350.3332   (branch= 0.0000  alpha= 0.0055  pinv= 0.0049  eq freqs= 0.0000  rel rates= 0.0044  subset rates= 0.0000)
+pass 15: -3350.3202   (branch= 0.0000  alpha= 0.0049  pinv= 0.0043  eq freqs= 0.0000  rel rates= 0.0038  subset rates= 0.0000)
+pass 16: -3350.3087   (branch= 0.0000  alpha= 0.0043  pinv= 0.0038  eq freqs= 0.0000  rel rates= 0.0033  subset rates= 0.0000)
+pass 17: -3350.2986   (branch= 0.0000  alpha= 0.0038  pinv= 0.0034  eq freqs= 0.0000  rel rates= 0.0029  subset rates= 0.0000)
+pass 18: -3350.2898   (branch= 0.0000  alpha= 0.0033  pinv= 0.0030  eq freqs= 0.0000  rel rates= 0.0025  subset rates= 0.0000)
+pass 19: -3350.2821   (branch= 0.0000  alpha= 0.0029  pinv= 0.0026  eq freqs= 0.0000  rel rates= 0.0021  subset rates= 0.0000)
+pass 20: -3350.2754   (branch= 0.0000  alpha= 0.0026  pinv= 0.0023  eq freqs= 0.0000  rel rates= 0.0018  subset rates= 0.0000)
+ optimization up to ...
+pass 30: -3350.2423   (branch= 0.0000  alpha= 0.0127  pinv= 0.0115  eq freqs= 0.0000  rel rates= 0.0089  subset rates= 0.0000)
  optimization up to ...
-pass 30: -3350.2356   (branch= 0.0000  alpha= 0.0058  pinv= 0.0052  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
+pass 40: -3350.2349   (branch= 0.0000  alpha= 0.0027  pinv= 0.0025  eq freqs= 0.0000  rel rates= 0.0021  subset rates= 0.0000)
  optimization up to ...
-pass 40: -3350.2334   (branch= 0.0000  alpha= 0.0012  pinv= 0.0010  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
+pass 50: -3350.2335   (branch= 0.0000  alpha= 0.0005  pinv= 0.0005  eq freqs= 0.0000  rel rates= 0.0005  subset rates= 0.0000)
  optimization up to ...
-pass 50: -3350.2330   (branch= 0.0000  alpha= 0.0002  pinv= 0.0002  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
+pass 60: -3350.2332   (branch= 0.0000  alpha= 0.0001  pinv= 0.0001  eq freqs= 0.0000  rel rates= 0.0001  subset rates= 0.0000)
+ optimization up to ...
+pass 63: -3350.2332   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
-Final score = -3350.2330
+Final score = -3350.2332
 Time used so far = 0 hours, 0 minutes and 12 seconds
 
 MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT
 Model 1
   Number of states = 4 (nucleotide data)
   Nucleotide Relative Rate Matrix:     6 rates 
-    AC = 3.152, AG = 10.541, AT = 2.726, CG = 0.001, CT = 22.206, GT = 1.000
+    AC = 3.115, AG = 10.417, AT = 2.691, CG = 0.001, CT = 21.918, GT = 1.000
   Equilibrium State Frequencies: estimated
-    (ACGT) 0.3329 0.2222 0.1568 0.2882 
+    (ACGT) 0.3329 0.2222 0.1567 0.2882 
   Rate Heterogeneity Model:
     4 discrete gamma distributed rate categories, alpha param estimated
-      0.5745
+      0.5771
     with an invariant (invariable) site category, proportion estimated
-      0.3646
+      0.3655
     Substitution rate categories under this model:
       rate	proportion
-      0.0000	0.3646
-      0.0479	0.1588
-      0.2978	0.1588
-      0.8677	0.1588
-      2.7866	0.1588
+      0.0000	0.3655
+      0.0484	0.1586
+      0.2993	0.1586
+      0.8692	0.1586
+      2.7830	0.1586
 
 Model 2
   Number of states = 2 (binary data)
@@ -17369,20 +14761,20 @@
 
 Completed 1 replicate search(es) (of 2).
 Results:
-Replicate 1 : -3350.2330 (best) (TERMINATED PREMATURELY) 
+Replicate 1 : -3350.2332 (best) (TERMINATED PREMATURELY) 
 
 Parameter estimates across search replicates:
 
 Partition model subset 1:
          r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
-rep 1:   3.152  10.54  2.726  0.001  22.21      1 0.333 0.222 0.157 0.288 0.575 0.365
+rep 1:   3.115  10.42  2.691  0.001  21.92      1 0.333 0.222 0.157 0.288 0.577 0.365
 
 Partition model subset 2:
 	 Model contains no estimated parameters
 
 Treelengths and subset rate multipliers:
           TL   R(1)  R(2)
-rep 1:  0.790 1.821 0.179
+rep 1:  0.789 1.820 0.180
 
 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre
 #######################################################
@@ -17545,8 +14937,6 @@
 Optimization precision reduced 
    Optimizing parameters...    improved    0.583 lnL
    Optimizing branchlengths... improved    0.083 lnL
-1200     -3320.1074       0.010           1 
-1300     -3320.0585       0.010           1 
 NOTE: ****Specified time limit (5 seconds) reached...
 
 NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
@@ -17647,9 +15037,11 @@
 STARTING RUN
 
 Restarting from checkpoint...
-Search rep 1 (of 2) generation 1341, seed 1966262865, best lnL -3320.059
+Search rep 1 (of 2) generation 1136, seed 1550923747, best lnL -3320.184
 gen      current_lnL    precision  last_tree_imp  
-1341     -3320.0585       0.010           1 
+1136     -3320.1837       0.010           1 
+1200     -3320.1074       0.010           1 
+1300     -3320.0585       0.010           1 
 1400     -3320.0570       0.010           1 
 1500     -3320.0237       0.010           1 
 1600     -3320.0098       0.010           1 
@@ -17657,66 +15049,62 @@
 1800     -3319.8035       0.010           1 
 1900     -3319.5791       0.010           1 
 2000     -3319.5259       0.010           1 
-2100     -3319.5240       0.010           1 
-2200     -3319.4470       0.010           1 
-2300     -3319.3727       0.010           1 
-2400     -3319.3389       0.010           1 
 NOTE: ****Specified time limit (5 seconds) reached...
-Current score = -3319.3389
+Current score = -3319.5240
 Performing final optimizations...
-pass 1 : -3319.1341   (branch= 0.0079  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0001  rel rates= 0.1608  ins/del rates= 0.0361)
-pass 2 : -3318.9551   (branch= 0.0341  alpha= 0.0000  pinv= 0.0130  eq freqs= 0.0000  rel rates= 0.1211  ins/del rates= 0.0107)
-pass 3 : -3318.7779   (branch= 0.0343  alpha= 0.0102  pinv= 0.0153  eq freqs= 0.0041  rel rates= 0.1040  ins/del rates= 0.0093)
-pass 4 : -3318.6360   (branch= 0.0224  alpha= 0.0114  pinv= 0.0142  eq freqs= 0.0000  rel rates= 0.0863  ins/del rates= 0.0076)
-pass 5 : -3318.5199   (branch= 0.0125  alpha= 0.0101  pinv= 0.0136  eq freqs= 0.0015  rel rates= 0.0735  ins/del rates= 0.0049)
-pass 6 : -3318.4205   (branch= 0.0089  alpha= 0.0104  pinv= 0.0126  eq freqs= 0.0005  rel rates= 0.0634  ins/del rates= 0.0036)
-pass 7 : -3318.3371   (branch= 0.0058  alpha= 0.0099  pinv= 0.0117  eq freqs= 0.0001  rel rates= 0.0536  ins/del rates= 0.0023)
-pass 8 : -3318.2656   (branch= 0.0038  alpha= 0.0096  pinv= 0.0109  eq freqs= 0.0001  rel rates= 0.0455  ins/del rates= 0.0016)
-pass 9 : -3318.2039   (branch= 0.0025  alpha= 0.0091  pinv= 0.0100  eq freqs= 0.0001  rel rates= 0.0390  ins/del rates= 0.0011)
-pass 10: -3318.1495   (branch= 0.0016  alpha= 0.0086  pinv= 0.0091  eq freqs= 0.0001  rel rates= 0.0342  ins/del rates= 0.0007)
-pass 11: -3318.1026   (branch= 0.0012  alpha= 0.0079  pinv= 0.0083  eq freqs= 0.0000  rel rates= 0.0291  ins/del rates= 0.0005)
-pass 12: -3318.0619   (branch= 0.0007  alpha= 0.0076  pinv= 0.0075  eq freqs= 0.0001  rel rates= 0.0245  ins/del rates= 0.0003)
-pass 13: -3318.0266   (branch= 0.0005  alpha= 0.0069  pinv= 0.0068  eq freqs= 0.0000  rel rates= 0.0209  ins/del rates= 0.0002)
-pass 14: -3317.9957   (branch= 0.0003  alpha= 0.0063  pinv= 0.0061  eq freqs= 0.0000  rel rates= 0.0180  ins/del rates= 0.0001)
-pass 15: -3317.9688   (branch= 0.0002  alpha= 0.0057  pinv= 0.0055  eq freqs= 0.0000  rel rates= 0.0154  ins/del rates= 0.0001)
-pass 16: -3317.9452   (branch= 0.0001  alpha= 0.0052  pinv= 0.0049  eq freqs= 0.0000  rel rates= 0.0133  ins/del rates= 0.0000)
-pass 17: -3317.9246   (branch= 0.0001  alpha= 0.0047  pinv= 0.0044  eq freqs= 0.0000  rel rates= 0.0114  ins/del rates= 0.0000)
-pass 18: -3317.9066   (branch= 0.0000  alpha= 0.0042  pinv= 0.0039  eq freqs= 0.0000  rel rates= 0.0097  ins/del rates= 0.0000)
-pass 19: -3317.8909   (branch= 0.0000  alpha= 0.0038  pinv= 0.0035  eq freqs= 0.0000  rel rates= 0.0084  ins/del rates= 0.0000)
-pass 20: -3317.8772   (branch= 0.0000  alpha= 0.0034  pinv= 0.0031  eq freqs= 0.0000  rel rates= 0.0072  ins/del rates= 0.0000)
+pass 1 : -3319.1618   (branch= 0.0156  alpha= 0.0156  pinv= 0.0153  eq freqs= 0.0000  rel rates= 0.2555  ins/del rates= 0.0602)
+pass 2 : -3318.9401   (branch= 0.0352  alpha= 0.0167  pinv= 0.0139  eq freqs= 0.0092  rel rates= 0.1397  ins/del rates= 0.0071)
+pass 3 : -3318.7713   (branch= 0.0262  alpha= 0.0110  pinv= 0.0138  eq freqs= 0.0000  rel rates= 0.1095  ins/del rates= 0.0084)
+pass 4 : -3318.6244   (branch= 0.0197  alpha= 0.0098  pinv= 0.0133  eq freqs= 0.0012  rel rates= 0.0961  ins/del rates= 0.0069)
+pass 5 : -3318.5064   (branch= 0.0116  alpha= 0.0090  pinv= 0.0126  eq freqs= 0.0012  rel rates= 0.0793  ins/del rates= 0.0043)
+pass 6 : -3318.4086   (branch= 0.0074  alpha= 0.0099  pinv= 0.0117  eq freqs= 0.0000  rel rates= 0.0657  ins/del rates= 0.0031)
+pass 7 : -3318.3245   (branch= 0.0047  alpha= 0.0089  pinv= 0.0109  eq freqs= 0.0005  rel rates= 0.0571  ins/del rates= 0.0019)
+pass 8 : -3318.2531   (branch= 0.0033  alpha= 0.0091  pinv= 0.0100  eq freqs= 0.0001  rel rates= 0.0476  ins/del rates= 0.0014)
+pass 9 : -3318.1914   (branch= 0.0021  alpha= 0.0084  pinv= 0.0092  eq freqs= 0.0001  rel rates= 0.0410  ins/del rates= 0.0009)
+pass 10: -3318.1377   (branch= 0.0014  alpha= 0.0079  pinv= 0.0084  eq freqs= 0.0001  rel rates= 0.0354  ins/del rates= 0.0006)
+pass 11: -3318.0914   (branch= 0.0010  alpha= 0.0071  pinv= 0.0076  eq freqs= 0.0000  rel rates= 0.0301  ins/del rates= 0.0004)
+pass 12: -3318.0515   (branch= 0.0006  alpha= 0.0069  pinv= 0.0069  eq freqs= 0.0001  rel rates= 0.0252  ins/del rates= 0.0003)
+pass 13: -3318.0169   (branch= 0.0004  alpha= 0.0062  pinv= 0.0062  eq freqs= 0.0000  rel rates= 0.0216  ins/del rates= 0.0002)
+pass 14: -3317.9868   (branch= 0.0003  alpha= 0.0057  pinv= 0.0056  eq freqs= 0.0000  rel rates= 0.0184  ins/del rates= 0.0001)
+pass 15: -3317.9606   (branch= 0.0002  alpha= 0.0052  pinv= 0.0050  eq freqs= 0.0000  rel rates= 0.0158  ins/del rates= 0.0001)
+pass 16: -3317.9378   (branch= 0.0001  alpha= 0.0047  pinv= 0.0045  eq freqs= 0.0000  rel rates= 0.0135  ins/del rates= 0.0000)
+pass 17: -3317.9180   (branch= 0.0001  alpha= 0.0042  pinv= 0.0040  eq freqs= 0.0000  rel rates= 0.0116  ins/del rates= 0.0000)
+pass 18: -3317.9007   (branch= 0.0000  alpha= 0.0037  pinv= 0.0035  eq freqs= 0.0000  rel rates= 0.0099  ins/del rates= 0.0000)
+pass 19: -3317.8856   (branch= 0.0000  alpha= 0.0034  pinv= 0.0031  eq freqs= 0.0000  rel rates= 0.0085  ins/del rates= 0.0000)
+pass 20: -3317.8726   (branch= 0.0000  alpha= 0.0030  pinv= 0.0028  eq freqs= 0.0000  rel rates= 0.0073  ins/del rates= 0.0000)
  optimization up to ...
-pass 30: -3317.8082   (branch= 0.0000  alpha= 0.0177  pinv= 0.0162  eq freqs= 0.0001  rel rates= 0.0350  ins/del rates= 0.0000)
+pass 30: -3317.8070   (branch= 0.0000  alpha= 0.0156  pinv= 0.0144  eq freqs= 0.0001  rel rates= 0.0355  ins/del rates= 0.0000)
  optimization up to ...
-pass 40: -3317.7918   (branch= 0.0001  alpha= 0.0043  pinv= 0.0039  eq freqs= 0.0000  rel rates= 0.0081  ins/del rates= 0.0000)
+pass 40: -3317.7915   (branch= 0.0001  alpha= 0.0037  pinv= 0.0034  eq freqs= 0.0000  rel rates= 0.0082  ins/del rates= 0.0000)
  optimization up to ...
-pass 50: -3317.7880   (branch= 0.0000  alpha= 0.0009  pinv= 0.0008  eq freqs= 0.0000  rel rates= 0.0020  ins/del rates= 0.0000)
+pass 50: -3317.7880   (branch= 0.0000  alpha= 0.0008  pinv= 0.0007  eq freqs= 0.0000  rel rates= 0.0020  ins/del rates= 0.0000)
  optimization up to ...
 pass 60: -3317.7873   (branch= 0.0000  alpha= 0.0002  pinv= 0.0001  eq freqs= 0.0000  rel rates= 0.0004  ins/del rates= 0.0000)
  optimization up to ...
-pass 68: -3317.7871   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0001  ins/del rates= 0.0000)
+pass 67: -3317.7871   (branch= 0.0000  alpha= 0.0000  pinv= 0.0000  eq freqs= 0.0000  rel rates= 0.0001  ins/del rates= 0.0000)
 Looking for minimum length branches...
 Final score = -3317.7871
-Time used so far = 0 hours, 0 minutes and 12 seconds
+Time used so far = 0 hours, 0 minutes and 13 seconds
 
 MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT
 Model 1
   Number of states = 4 (nucleotide data)
   Nucleotide Relative Rate Matrix:     6 rates 
-    AC = 3.064, AG = 10.258, AT = 2.655, CG = 0.001, CT = 21.530, GT = 1.000
+    AC = 3.064, AG = 10.257, AT = 2.653, CG = 0.001, CT = 21.527, GT = 1.000
   Equilibrium State Frequencies: estimated
-    (ACGT) 0.3328 0.2223 0.1567 0.2882 
+    (ACGT) 0.3328 0.2223 0.1566 0.2882 
   Rate Heterogeneity Model:
     4 discrete gamma distributed rate categories, alpha param estimated
-      0.5738
+      0.5746
     with an invariant (invariable) site category, proportion estimated
-      0.3608
+      0.3613
     Substitution rate categories under this model:
       rate	proportion
-      0.0000	0.3608
-      0.0478	0.1598
-      0.2974	0.1598
-      0.8674	0.1598
-      2.7875	0.1598
+      0.0000	0.3613
+      0.0479	0.1597
+      0.2979	0.1597
+      0.8678	0.1597
+      2.7864	0.1597
 
 Model 2
   Number of states = 2 (0/1 coding of gaps)
@@ -17748,7 +15136,7 @@
 
 Partition model subset 1:
          r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
-rep 1:   3.064  10.26  2.655  0.001  21.53      1 0.333 0.222 0.157 0.288 0.574 0.361
+rep 1:   3.064  10.26  2.653  0.001  21.53      1 0.333 0.222 0.157 0.288 0.575 0.361
 
 Partition model subset 2:
           ins   del
@@ -17881,100 +15269,15 @@
 1400     -211.1316        0.010        1104 
 1600     -211.0217        0.010        1104 
 1800     -210.9996        0.010        1104 
-2000     -210.9459        0.010        1104 
-2200     -210.8945        0.010        1104 
-2400     -210.8863        0.010        1104 
-2600     -210.8436        0.010        1104 
-2800     -210.8252        0.010        1104 
-3000     -210.8190        0.010        1104 
-3200     -210.7906        0.010        1104 
-3400     -210.7554        0.010        1104 
-3600     -210.7287        0.010        1104 
-3800     -210.7083        0.010        1104 
-4000     -210.6947        0.010        1104 
-4200     -210.6742        0.010        1104 
-4400     -210.6493        0.010        1104 
-4600     -210.6258        0.010        1104 
-4800     -210.5949        0.010        1104 
-5000     -210.5740        0.010        1104 
-5200     -210.5694        0.010        1104 
-5400     -210.5462        0.010        1104 
-5600     -210.5152        0.010        1104 
-5800     -210.4823        0.010        1104 
-6000     -210.4633        0.010        1104 
-6200     -210.4597        0.010        1104 
-6400     -210.4469        0.010        1104 
-6600     -210.4215        0.010        1104 
-6800     -210.3965        0.010        1104 
-7000     -210.3384        0.010        1104 
-7200     -210.3218        0.010        1104 
-7400     -210.2808        0.010        1104 
-7600     -210.2625        0.010        1104 
-7800     -210.1873        0.010        1104 
-8000     -210.1733        0.010        1104 
-8200     -210.1282        0.010        1104 
-8400     -210.1102        0.010        1104 
-8600     -210.0896        0.010        1104 
-8800     -210.0543        0.010        1104 
-9000     -210.0431        0.010        1104 
-9200     -209.9790        0.010        1104 
-9400     -209.9603        0.010        1104 
-9600     -209.9463        0.010        1104 
-9800     -209.9221        0.010        1104 
-10000    -209.8836        0.010        1104 
-   Optimizing parameters...    improved    0.524 lnL
-   Optimizing branchlengths... improved    0.000 lnL
-NOTE: ****Specified generation limit (10000) reached...
-
-MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
-Model 1
-  Number of states = 4 (nucleotide data)
-  Nucleotide Relative Rate Matrix:     6 rates 
-    AC = 5.311, AG = 9.302, AT = 0.233, CG = 9.751, CT = 15.573, GT = 1.000
-  Equilibrium State Frequencies: estimated
-    (ACGT) 0.2351 0.3311 0.2101 0.2237 
-  Rate Heterogeneity Model:
-    3 discrete gamma distributed rate categories, alpha param estimated
-      4.1947
-    with an invariant (invariable) site category, proportion estimated
-      0.2927
-    Substitution rate categories under this model:
-      rate	proportion
-      0.0000	0.2927
-      0.5209	0.2358
-      0.9265	0.2358
-      1.5525	0.2358
-
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    No branches were short enough to be collapsed.
-
-Saving site likelihoods to file ch.n.G3.sitelikes.log ...
-WARNING: Site likelihoods being output on prematurely terminated search ...
-
-NOTE: ***Search was terminated before full auto-termination condition was reached!
-Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
-
-
-#######################################################
-
-Completed 1 replicate search(es) (of 1).
-Results:
-Replicate 1 : -209.3594       
-
-Parameter estimates:
-         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
-rep 1:   5.311  9.302 0.2334  9.751  15.57      1 0.235 0.331 0.210 0.224 4.195 0.293
-
-Treelengths:
-          TL 
-rep 1:  2.312
-
-Saving final tree from best search rep (#1) to ch.n.G3.best.tre
-Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log
+NOTE: ****Specified time limit (5 seconds) reached...
 
-WARNING: Internal states inferred on tree from prematurely terminated search
+NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
+TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
+FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
+(set restart = 1 in the config file).  IF YOU WANT TO USE THE
+PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
+ADD "end;" TO THE TREE FILES.
 
-#######################################################
 Running GARLI Version 2.1. ()
 ->Single processor version for 64-bit OS<-
 ##############################################################
@@ -18045,31 +15348,48 @@
 STARTING RUN
 
 Restarting from checkpoint...
- generation 10001, seed 447301326, best lnL -209.359
+ generation 1860, seed 1313195090, best lnL -210.978
 gen      current_lnL    precision  last_tree_imp  
-10001    -209.3594        0.010        1104 
+1860     -210.9783        0.010        1104 
+1900     -210.9491        0.010        1104 
+2000     -210.9459        0.010        1104 
+2100     -210.9365        0.010        1104 
+2200     -210.8945        0.010        1104 
+2300     -210.8921        0.010        1104 
+2400     -210.8863        0.010        1104 
+2500     -210.8674        0.010        1104 
+2600     -210.8436        0.010        1104 
+2700     -210.8340        0.010        1104 
+2800     -210.8252        0.010        1104 
+2900     -210.8230        0.010        1104 
+3000     -210.8190        0.010        1104 
+3100     -210.8050        0.010        1104 
+3200     -210.7906        0.010        1104 
+Reached termination condition!
+last topological improvement at gen 1104
+Improvement over last 500 gen = 0.04343
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
   Number of states = 4 (nucleotide data)
   Nucleotide Relative Rate Matrix:     6 rates 
-    AC = 5.311, AG = 9.302, AT = 0.233, CG = 9.751, CT = 15.573, GT = 1.000
+    AC = 2.253, AG = 4.312, AT = 0.229, CG = 3.799, CT = 6.511, GT = 1.000
   Equilibrium State Frequencies: estimated
-    (ACGT) 0.2351 0.3311 0.2101 0.2237 
+    (ACGT) 0.2299 0.3376 0.2132 0.2194 
   Rate Heterogeneity Model:
     3 discrete gamma distributed rate categories, alpha param estimated
-      4.1947
+      1.1008
     with an invariant (invariable) site category, proportion estimated
-      0.2927
+      0.1053
     Substitution rate categories under this model:
       rate	proportion
-      0.0000	0.2927
-      0.5209	0.2358
-      0.9265	0.2358
-      1.5525	0.2358
+      0.0000	0.1053
+      0.2110	0.2982
+      0.7362	0.2982
+      2.0528	0.2982
 
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    No branches were short enough to be collapsed.
+    1 branches were collapsed.
 
 Saving site likelihoods to file ch.n.G3.sitelikes.log ...
 
@@ -18077,15 +15397,15 @@
 
 Completed 1 replicate search(es) (of 1).
 Results:
-Replicate 1 : -209.3594       
+Replicate 1 : -210.7906       
 
 Parameter estimates:
          r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
-rep 1:   5.311  9.302 0.2334  9.751  15.57      1 0.235 0.331 0.210 0.224 4.195 0.293
+rep 1:   2.253  4.312 0.2288  3.799  6.511      1 0.230 0.338 0.213 0.219 1.101 0.105
 
 Treelengths:
           TL 
-rep 1:  2.312
+rep 1:  2.237
 
 Saving final tree from best search rep (#1) to ch.n.G3.best.tre
 Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log
@@ -18236,75 +15556,15 @@
 5800     -165.3719        0.010         843 
 6000     -165.3449        0.010         843 
 6200     -165.2640        0.010         843 
-6400     -165.1346        0.010         843 
-6600     -165.0582        0.010         843 
-6800     -165.0555        0.010         843 
-7000     -164.9207        0.010         843 
-7200     -164.7998        0.010         843 
-7400     -164.7200        0.010        7384 
-7600     -164.6617        0.010        7384 
-7800     -164.5208        0.010        7384 
-8000     -164.4381        0.010        7384 
-8200     -164.2988        0.010        7384 
-8400     -164.1759        0.010        7384 
-8600     -164.1241        0.010        7384 
-8800     -163.9560        0.010        7384 
-9000     -163.8539        0.010        7384 
-9200     -163.8476        0.010        7384 
-9400     -163.7481        0.010        7384 
-9600     -163.6368        0.010        7384 
-9800     -163.5998        0.010        7384 
-10000    -163.5758        0.010        7384 
-   Optimizing parameters...    improved    1.430 lnL
-   Optimizing branchlengths... improved    0.021 lnL
-NOTE: ****Specified generation limit (10000) reached...
-
-MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
-Model 1
-  Number of states = 4 (nucleotide data)
-  Nucleotide Relative Rate Matrix:     6 rates 
-    AC = 0.623, AG = 8.564, AT = 1.923, CG = 3.484, CT = 32.751, GT = 1.000
-  Equilibrium State Frequencies: estimated
-    (ACGT) 0.1298 0.4236 0.2357 0.2109 
-  Rate Heterogeneity Model:
-    4 discrete gamma distributed rate categories, alpha param estimated
-      53.5744
-    with an invariant (invariable) site category, proportion estimated
-      0.3606
-    Substitution rate categories under this model:
-      rate	proportion
-      0.0000	0.3606
-      0.8321	0.1599
-      0.9505	0.1599
-      1.0389	0.1599
-      1.1786	0.1599
-
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    3 branches were collapsed.
-
-
-NOTE: ***Search was terminated before full auto-termination condition was reached!
-Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
-
-
-#######################################################
-
-Completed 1 replicate search(es) (of 1).
-Results:
-Replicate 1 : -162.1251       
-
-Parameter estimates:
-         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
-rep 1:  0.6228  8.564  1.923  3.484  32.75      1 0.130 0.424 0.236 0.211 53.574 0.361
-
-Treelengths:
-          TL 
-rep 1:  3.164
+NOTE: ****Specified time limit (5 seconds) reached...
 
-Saving best tree to bootstrap file ch.n.G4.boot.tre
+NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
+TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
+FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
+(set restart = 1 in the config file).  IF YOU WANT TO USE THE
+PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
+ADD "end;" TO THE TREE FILES.
 
-WARNING: Tree from prematurely terminated search saved to bootstrap file
-#######################################################
 Running GARLI Version 2.1. ()
 ->Single processor version for 64-bit OS<-
 ##############################################################
@@ -18376,11 +15636,52 @@
 	Subset 1: Random seed for bootstrap reweighting: 42
 
 Restarting from checkpoint...
-Bootstrap rep 1 (of 1)  generation 10001, seed 172398639, best lnL -162.125
+Bootstrap rep 1 (of 1)  generation 6200, seed 1831900606, best lnL -165.264
 gen      current_lnL    precision  last_tree_imp  
-10001    -162.1251        0.010        7384 
+6200     -165.2640        0.010         843 
+6300     -165.1568        0.010         843 
+6400     -165.1346        0.010         843 
+6500     -165.1038        0.010         843 
+6600     -165.0582        0.010         843 
+6700     -165.0565        0.010         843 
+6800     -165.0555        0.010         843 
+6900     -164.9353        0.010         843 
+7000     -164.9207        0.010         843 
+7100     -164.8347        0.010         843 
+7200     -164.7998        0.010         843 
+7300     -164.7626        0.010         843 
+7400     -164.7200        0.010        7384 
+7500     -164.6619        0.010        7384 
+7600     -164.6617        0.010        7384 
+7700     -164.5339        0.010        7384 
+7800     -164.5208        0.010        7384 
+7900     -164.4744        0.010        7384 
+8000     -164.4381        0.010        7384 
+8100     -164.3291        0.010        7384 
+8200     -164.2988        0.010        7384 
+8300     -164.1852        0.010        7384 
+8400     -164.1759        0.010        7384 
+8500     -164.1671        0.010        7384 
+8600     -164.1241        0.010        7384 
+8700     -163.9937        0.010        7384 
+8800     -163.9560        0.010        7384 
+8900     -163.9223        0.010        7384 
+9000     -163.8539        0.010        7384 
+9100     -163.8505        0.010        7384 
+9200     -163.8476        0.010        7384 
+9300     -163.7792        0.010        7384 
+9400     -163.7481        0.010        7384 
+9500     -163.7087        0.010        7384 
+9600     -163.6368        0.010        7384 
+9700     -163.6117        0.010        7384 
+9800     -163.5998        0.010        7384 
+9900     -163.5962        0.010        7384 
+10000    -163.5758        0.010        7384 
+   Optimizing parameters...    improved    1.430 lnL
+   Optimizing branchlengths... improved    0.021 lnL
+NOTE: ****Specified generation limit (10000) reached...
 
-MODEL REPORT - Parameter values are FINAL
+MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
 Model 1
   Number of states = 4 (nucleotide data)
   Nucleotide Relative Rate Matrix:     6 rates 
@@ -18404,6 +15705,10 @@
     3 branches were collapsed.
 
 
+NOTE: ***Search was terminated before full auto-termination condition was reached!
+Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
+
+
 #######################################################
 
 Completed 1 replicate search(es) (of 1).
@@ -18420,7 +15725,7 @@
 
 Saving best tree to bootstrap file ch.n.G4.boot.tre
 
->>>Completed Bootstrap rep 1<<<
+WARNING: Tree from prematurely terminated search saved to bootstrap file
 #######################################################
 TREEFILES PASS
 Running checkpoint test ./check/n.conf
@@ -18564,57 +15869,15 @@
 8200     -212.6594        0.010        3769 
 8400     -212.6591        0.010        3769 
 8600     -212.6390        0.010        3769 
-8800     -212.5865        0.010        3769 
-9000     -212.5495        0.010        3769 
-9200     -212.5341        0.010        3769 
-9400     -212.5173        0.010        3769 
-9600     -212.4987        0.010        3769 
-9800     -212.4933        0.010        3769 
-10000    -212.4848        0.010        3769 
-   Optimizing parameters...    improved    0.000 lnL
-   Optimizing branchlengths... improved    0.000 lnL
-NOTE: ****Specified generation limit (10000) reached...
-
-MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
-Model 1
-  Number of states = 4 (nucleotide data)
-  Nucleotide Relative Rate Matrix:     6 rates 
-    AC = 8.254, AG = 15.546, AT = 0.648, CG = 15.522, CT = 10.081, GT = 1.000
-  Equilibrium State Frequencies: estimated
-    (ACGT) 0.2186 0.2862 0.1832 0.3120 
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    No branches were short enough to be collapsed.
-
-Saving site likelihoods to file ch.n.sitelikes.log ...
-WARNING: Site likelihoods being output on prematurely terminated search ...
-
-NOTE: ***Search was terminated before full auto-termination condition was reached!
-Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
-
-
-#######################################################
-
-Completed 1 replicate search(es) (of 1).
-Results:
-Replicate 1 : -212.4847       
-
-Parameter estimates:
-         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T)
-rep 1:   8.254  15.55 0.6481  15.52  10.08      1 0.219 0.286 0.183 0.312
-
-Treelengths:
-          TL 
-rep 1:  1.718
-
-Saving final tree from best search rep (#1) to ch.n.best.tre
-Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log
+NOTE: ****Specified time limit (5 seconds) reached...
 
-WARNING: Internal states inferred on tree from prematurely terminated search
+NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
+TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
+FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
+(set restart = 1 in the config file).  IF YOU WANT TO USE THE
+PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
+ADD "end;" TO THE TREE FILES.
 
-#######################################################
 Running GARLI Version 2.1. ()
 ->Single processor version for 64-bit OS<-
 ##############################################################
@@ -18685,22 +15948,33 @@
 STARTING RUN
 
 Restarting from checkpoint...
- generation 10001, seed 1459438551, best lnL -212.485
+ generation 8600, seed 822239336, best lnL -212.639
 gen      current_lnL    precision  last_tree_imp  
-10001    -212.4847        0.010        3769 
+8600     -212.6390        0.010        3769 
+8700     -212.6002        0.010        3769 
+8800     -212.5865        0.010        3769 
+8900     -212.5650        0.010        3769 
+9000     -212.5495        0.010        3769 
+9100     -212.5424        0.010        3769 
+9200     -212.5341        0.010        3769 
+9300     -212.5317        0.010        3769 
+9400     -212.5173        0.010        3769 
+Reached termination condition!
+last topological improvement at gen 3769
+Improvement over last 500 gen = 0.04770
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
   Number of states = 4 (nucleotide data)
   Nucleotide Relative Rate Matrix:     6 rates 
-    AC = 8.254, AG = 15.546, AT = 0.648, CG = 15.522, CT = 10.081, GT = 1.000
+    AC = 7.542, AG = 14.334, AT = 0.626, CG = 14.441, CT = 9.342, GT = 1.000
   Equilibrium State Frequencies: estimated
-    (ACGT) 0.2186 0.2862 0.1832 0.3120 
+    (ACGT) 0.2205 0.2887 0.1831 0.3078 
   Rate Heterogeneity Model:
     no rate heterogeneity
 
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    No branches were short enough to be collapsed.
+    1 branches were collapsed.
 
 Saving site likelihoods to file ch.n.sitelikes.log ...
 
@@ -18708,15 +15982,15 @@
 
 Completed 1 replicate search(es) (of 1).
 Results:
-Replicate 1 : -212.4847       
+Replicate 1 : -212.5173       
 
 Parameter estimates:
          r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T)
-rep 1:   8.254  15.55 0.6481  15.52  10.08      1 0.219 0.286 0.183 0.312
+rep 1:   7.542  14.33 0.6258  14.44  9.342      1 0.220 0.289 0.183 0.308
 
 Treelengths:
           TL 
-rep 1:  1.718
+rep 1:  1.727
 
 Saving final tree from best search rep (#1) to ch.n.best.tre
 Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log
@@ -18851,103 +16125,15 @@
 2000     -210.9688        0.010        1502 
 2200     -210.8961        0.010        1502 
 2400     -210.8906        0.010        1502 
-2600     -210.8173        0.010        1502 
-2800     -210.7848        0.010        1502 
-3000     -210.7511        0.010        2883 
-3200     -210.7244        0.010        2883 
-3400     -210.7006        0.010        2883 
-3600     -210.6993        0.010        2883 
-3800     -210.6779        0.010        2883 
-4000     -210.6776        0.010        2883 
-4200     -210.6505        0.010        2883 
-4400     -210.6306        0.010        2883 
-4600     -210.6208        0.010        2883 
-4800     -210.5769        0.010        2883 
-5000     -210.5647        0.010        2883 
-5200     -210.5368        0.010        2883 
-5400     -210.5093        0.010        2883 
-5600     -210.4833        0.010        2883 
-5800     -210.3736        0.010        2883 
-6000     -210.3398        0.010        2883 
-6200     -210.3306        0.010        2883 
-6400     -210.3132        0.010        2883 
-6600     -210.3007        0.010        2883 
-6800     -210.2825        0.010        2883 
-7000     -210.2752        0.010        2883 
-7200     -210.2750        0.010        2883 
-7400     -210.2439        0.010        2883 
-7600     -210.2321        0.010        2883 
-7800     -210.1861        0.010        2883 
-8000     -210.1813        0.010        2883 
-8200     -210.1599        0.010        2883 
-8400     -210.0780        0.010        2883 
-8600     -210.0377        0.010        2883 
-8800     -210.0091        0.010        2883 
-9000     -209.9765        0.010        2883 
-9200     -209.9496        0.010        2883 
-9400     -209.9483        0.010        2883 
-9600     -209.9457        0.010        2883 
-9800     -209.8760        0.010        2883 
-10000    -209.8543        0.010        2883 
-   Optimizing parameters...    improved    0.413 lnL
-   Optimizing branchlengths... improved    0.003 lnL
-NOTE: ****Specified generation limit (10000) reached...
-
-MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
-Model 1
-  Number of states = 4 (nucleotide data)
-  Nucleotide Relative Rate Matrix:     6 rates 
-    AC = 2.851, AG = 5.111, AT = 0.047, CG = 5.326, CT = 10.142, GT = 1.000
-  Equilibrium State Frequencies: estimated
-    (ACGT) 0.2408 0.3349 0.2137 0.2106 
-  Rate Heterogeneity Model:
-    4 discrete gamma distributed rate categories, alpha param estimated
-      3.7900
-    with an invariant (invariable) site category, proportion estimated
-      0.2957
-    Substitution rate categories under this model:
-      rate	proportion
-      0.0000	0.2957
-      0.4424	0.1761
-      0.7676	0.1761
-      1.0844	0.1761
-      1.7056	0.1761
-
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    No branches were short enough to be collapsed.
-
-
-NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with
-	a positive constraint, it is possible for a constrained branch itself to be collapsed.
-	If you care, be careful to check whether this has happened or turn off branch collapsing.
-
-Saving site likelihoods to file ch.n.const.sitelikes.log ...
-WARNING: Site likelihoods being output on prematurely terminated search ...
-
-NOTE: ***Search was terminated before full auto-termination condition was reached!
-Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
-
-
-#######################################################
-
-Completed 1 replicate search(es) (of 1).
-Results:
-Replicate 1 : -209.4385       
-
-Parameter estimates:
-         r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
-rep 1:   2.851  5.111 0.04734  5.326  10.14      1 0.241 0.335 0.214 0.211 3.790 0.296
-
-Treelengths:
-          TL 
-rep 1:  2.454
-
-Saving final tree from best search rep (#1) to ch.n.const.best.tre
-Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log
+NOTE: ****Specified time limit (5 seconds) reached...
 
-WARNING: Internal states inferred on tree from prematurely terminated search
+NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
+TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
+FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
+(set restart = 1 in the config file).  IF YOU WANT TO USE THE
+PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
+ADD "end;" TO THE TREE FILES.
 
-#######################################################
 Running GARLI Version 2.1. ()
 ->Single processor version for 64-bit OS<-
 ##############################################################
@@ -19026,29 +16212,71 @@
 STARTING RUN
 
 Restarting from checkpoint...
- generation 10001, seed 451797927, best lnL -209.439
+ generation 2400, seed 1282638830, best lnL -210.891
 gen      current_lnL    precision  last_tree_imp  
-10001    -209.4385        0.010        2883 
+2400     -210.8906        0.010        1502 
+2500     -210.8711        0.010        1502 
+2600     -210.8173        0.010        1502 
+2700     -210.8173        0.010        1502 
+2800     -210.7848        0.010        1502 
+2900     -210.7571        0.010        2883 
+3000     -210.7511        0.010        2883 
+3100     -210.7475        0.010        2883 
+3200     -210.7244        0.010        2883 
+3300     -210.7026        0.010        2883 
+3400     -210.7006        0.010        2883 
+3500     -210.7006        0.010        2883 
+3600     -210.6993        0.010        2883 
+3700     -210.6820        0.010        2883 
+3800     -210.6779        0.010        2883 
+3900     -210.6776        0.010        2883 
+4000     -210.6776        0.010        2883 
+4100     -210.6582        0.010        2883 
+4200     -210.6505        0.010        2883 
+4300     -210.6473        0.010        2883 
+4400     -210.6306        0.010        2883 
+4500     -210.6277        0.010        2883 
+4600     -210.6208        0.010        2883 
+4700     -210.5908        0.010        2883 
+4800     -210.5769        0.010        2883 
+4900     -210.5673        0.010        2883 
+5000     -210.5647        0.010        2883 
+5100     -210.5566        0.010        2883 
+5200     -210.5368        0.010        2883 
+5300     -210.5127        0.010        2883 
+5400     -210.5093        0.010        2883 
+5500     -210.5012        0.010        2883 
+5600     -210.4833        0.010        2883 
+5700     -210.4040        0.010        2883 
+5800     -210.3736        0.010        2883 
+5900     -210.3640        0.010        2883 
+6000     -210.3398        0.010        2883 
+6100     -210.3322        0.010        2883 
+6200     -210.3306        0.010        2883 
+6300     -210.3271        0.010        2883 
+Reached termination condition!
+last topological improvement at gen 2883
+Improvement over last 500 gen = 0.04654
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
   Number of states = 4 (nucleotide data)
   Nucleotide Relative Rate Matrix:     6 rates 
-    AC = 2.851, AG = 5.111, AT = 0.047, CG = 5.326, CT = 10.142, GT = 1.000
+    AC = 2.167, AG = 4.001, AT = 0.207, CG = 3.857, CT = 7.372, GT = 1.000
   Equilibrium State Frequencies: estimated
-    (ACGT) 0.2408 0.3349 0.2137 0.2106 
+    (ACGT) 0.2427 0.3358 0.2126 0.2089 
   Rate Heterogeneity Model:
     4 discrete gamma distributed rate categories, alpha param estimated
-      3.7900
+      1.4302
     with an invariant (invariable) site category, proportion estimated
-      0.2957
+      0.1984
     Substitution rate categories under this model:
       rate	proportion
-      0.0000	0.2957
-      0.4424	0.1761
-      0.7676	0.1761
-      1.0844	0.1761
-      1.7056	0.1761
+      0.0000	0.1984
+      0.2143	0.2004
+      0.5765	0.2004
+      1.0460	0.2004
+      2.1631	0.2004
 
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
     No branches were short enough to be collapsed.
@@ -19064,15 +16292,15 @@
 
 Completed 1 replicate search(es) (of 1).
 Results:
-Replicate 1 : -209.4385       
+Replicate 1 : -210.3271       
 
 Parameter estimates:
          r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
-rep 1:   2.851  5.111 0.04734  5.326  10.14      1 0.241 0.335 0.214 0.211 3.790 0.296
+rep 1:   2.167  4.001 0.2071  3.857  7.372      1 0.243 0.336 0.213 0.209 1.430 0.198
 
 Treelengths:
           TL 
-rep 1:  2.454
+rep 1:  2.432
 
 Saving final tree from best search rep (#1) to ch.n.const.best.tre
 Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log
@@ -19290,32 +16518,6 @@
 1200     -13370.5241      0.304           0 
 1300     -13370.5103      0.304           0 
 1400     -13370.5063      0.304           0 
-1500     -13370.4967      0.304           0 
-Optimization precision reduced 
-   Optimizing parameters...    improved    0.015 lnL
-   Optimizing branchlengths... improved    0.000 lnL
-1600     -13370.4816      0.206           0 
-1700     -13370.4688      0.206           0 
-1800     -13370.4569      0.206           0 
-1900     -13370.4339      0.206           0 
-2000     -13370.4174      0.206           0 
-Optimization precision reduced 
-   Optimizing parameters...    improved    0.006 lnL
-   Optimizing branchlengths... improved    0.000 lnL
-2100     -13370.4112      0.108           0 
-2200     -13370.3996      0.108           0 
-2300     -13370.3996      0.108           0 
-2400     -13370.3947      0.108           0 
-2500     -13370.3792      0.108           0 
-Optimization precision reduced 
-   Optimizing parameters...    improved    0.001 lnL
-   Optimizing branchlengths... improved    0.000 lnL
-2600     -13370.3703      0.010           0 
-2700     -13370.3695      0.010           0 
-2800     -13370.3692      0.010           0 
-2900     -13370.3688      0.010           0 
-3000     -13370.3644      0.010           0 
-3100     -13370.3583      0.010           0 
 NOTE: ****Specified time limit (5 seconds) reached...
 
 NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
@@ -19438,18 +16640,31 @@
 	Subset 3: Random seed for bootstrap reweighting: 486988955
 
 Restarting from checkpoint...
-Bootstrap rep 1 (of 1)  generation 3159, seed 259937768, best lnL -13370.353
+Bootstrap rep 1 (of 1)  generation 1431, seed 1520349315, best lnL -13370.499
 gen      current_lnL    precision  last_tree_imp  
-3159     -13370.3526      0.010           0 
+1431     -13370.4986      0.304           0 
+1500     -13370.4967      0.304           0 
+Optimization precision reduced 
+   Optimizing parameters...    improved    0.015 lnL
+   Optimizing branchlengths... improved    0.000 lnL
+1600     -13370.4816      0.206           0 
+1700     -13370.4688      0.206           0 
+1800     -13370.4569      0.206           0 
+1900     -13370.4339      0.206           0 
+2000     -13370.4174      0.206           0 
+Optimization precision reduced 
+   Optimizing parameters...    improved    0.006 lnL
+   Optimizing branchlengths... improved    0.000 lnL
+NOTE: ****Specified generation limit (2000) reached...
 
-MODEL REPORT - Parameter values are FINAL
+MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT
 Model 1
   Number of states = 4 (nucleotide data)
   Nucleotide Relative Rate Matrix: 
     User specified matrix type: ( 0 1 2 2 3 4 ) 
-    AC = 1.717, AG = 2.662, AT = 1.270, CG = 1.270, CT = 4.337, GT = 1.000
+    AC = 1.663, AG = 2.558, AT = 1.235, CG = 1.235, CT = 4.221, GT = 1.000
   Equilibrium State Frequencies: estimated
-    (ACGT) 0.3076 0.1804 0.3103 0.2017 
+    (ACGT) 0.3082 0.1810 0.3087 0.2020 
   Rate Heterogeneity Model:
     4 discrete gamma distributed rate categories, alpha param estimated
       0.3662
@@ -19457,45 +16672,45 @@
       rate	proportion
       0.0122	0.2500
       0.1561	0.2500
-      0.6920	0.2500
-      3.1397	0.2500
+      0.6919	0.2500
+      3.1398	0.2500
 
 Model 2
   Number of states = 4 (nucleotide data)
   Nucleotide Relative Rate Matrix: 
     User specified matrix type: ( 0 1 2 1 0 3 ) 
-    AC = 2.631, AG = 4.225, AT = 0.813, CG = 4.225, CT = 2.631, GT = 1.000
+    AC = 2.621, AG = 4.245, AT = 0.820, CG = 4.245, CT = 2.621, GT = 1.000
   Equilibrium State Frequencies: estimated
-    (ACGT) 0.2819 0.1752 0.1596 0.3832 
+    (ACGT) 0.2814 0.1768 0.1593 0.3825 
   Rate Heterogeneity Model:
     4 discrete gamma distributed rate categories, alpha param estimated
-      0.2452
+      0.2457
     Substitution rate categories under this model:
       rate	proportion
       0.0019	0.2500
-      0.0632	0.2500
-      0.4912	0.2500
-      3.4437	0.2500
+      0.0636	0.2500
+      0.4923	0.2500
+      3.4422	0.2500
 
 Model 3
   Number of states = 4 (nucleotide data)
   Nucleotide Relative Rate Matrix: 
     User specified matrix type: ( 0 1 2 3 1 0 ) 
-    AC = 1.000, AG = 5.303, AT = 4.268, CG = 0.630, CT = 5.303, GT = 1.000
+    AC = 1.000, AG = 5.311, AT = 4.291, CG = 0.629, CT = 5.311, GT = 1.000
   Equilibrium State Frequencies: estimated
-    (ACGT) 0.1555 0.3463 0.2762 0.2219 
+    (ACGT) 0.1554 0.3464 0.2763 0.2219 
   Rate Heterogeneity Model:
     4 discrete gamma distributed rate categories, alpha param estimated
-      4.1990
+      4.1264
     with an invariant (invariable) site category, proportion estimated
-      0.0491
+      0.0487
     Substitution rate categories under this model:
       rate	proportion
-      0.0000	0.0491
-      0.4650	0.2377
-      0.7818	0.2377
-      1.0843	0.2377
-      1.6689	0.2377
+      0.0000	0.0487
+      0.4612	0.2378
+      0.7795	0.2378
+      1.0844	0.2378
+      1.6750	0.2378
 
 Subset rate multipliers:
     0.53  0.29  2.18
@@ -19503,33 +16718,37 @@
     No branches were short enough to be collapsed.
 
 
+NOTE: ***Search was terminated before full auto-termination condition was reached!
+Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
+
+
 #######################################################
 
 Completed 1 replicate search(es) (of 1).
 Results:
-Replicate 1 : -13370.3526       
+Replicate 1 : -13370.4112       
 
 Parameter estimates:
 
 Partition model subset 1:
          r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha
-rep 1:   1.717  2.662   1.27   1.27  4.337      1 0.308 0.180 0.310 0.202 0.366
+rep 1:   1.663  2.558  1.235  1.235  4.221      1 0.308 0.181 0.309 0.202 0.366
 
 Partition model subset 2:
          r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha
-rep 1:   2.631  4.225  0.813  4.225  2.631      1 0.282 0.175 0.160 0.383 0.245
+rep 1:   2.621  4.245 0.8204  4.245  2.621      1 0.281 0.177 0.159 0.382 0.246
 
 Partition model subset 3:
          r(AC)  r(AG)  r(AT)  r(CG)  r(CT)  r(GT) pi(A) pi(C) pi(G) pi(T) alpha  pinv
-rep 1:       1  5.303  4.268 0.6297  5.303      1 0.155 0.346 0.276 0.222 4.199 0.049
+rep 1:       1  5.311  4.291 0.6292  5.311      1 0.155 0.346 0.276 0.222 4.126 0.049
 
 Treelengths and subset rate multipliers:
           TL   R(1)  R(2)  R(3)
-rep 1:  1.767 0.530 0.287 2.183
+rep 1:  1.762 0.530 0.287 2.183
 
 Saving best tree to bootstrap file ch.p.3diff.boot.tre
 
->>>Completed Bootstrap rep 1<<<
+WARNING: Tree from prematurely terminated search saved to bootstrap file
 #######################################################
 TREEFILES PASS
 Running checkpoint test ./check/p.mk.ssr.conf
@@ -19749,7 +16968,7 @@
 pass 17: -467.6783   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
 Final score = -467.6783
-Time used so far = 0 hours, 0 minutes and 1 seconds
+Time used so far = 0 hours, 0 minutes and 5 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -19831,6 +17050,134 @@
 400      -467.7467        0.010           0 
 500      -467.7423        0.010           0 
 600      -467.7395        0.010           0 
+NOTE: ****Specified time limit (5 seconds) reached...
+
+NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
+TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
+FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
+(set restart = 1 in the config file).  IF YOU WANT TO USE THE
+PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
+ADD "end;" TO THE TREE FILES.
+
+Running GARLI Version 2.1. ()
+->Single processor version for 64-bit OS<-
+##############################################################
+ This is GARLI 2.1: maximum likelihood phylogenetic inference
+ using nucleotide, amino acid, codon and morphology-like data,
+             as well as partitioned models.
+   General program usage is extensively documented here:
+            http://www.nescent.org/wg/garli/
+   See this page for details on partitioned model usage:
+  http://www.nescent.org/wg_garli/Using_partitioned_models
+   and this page for details on Mkv mophology model usage:
+    http://www.nescent.org/wg_garli/Mkv_morphology_model
+         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
+                garli.support@gmail.com
+##############################################################
+Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0
+Using NCL version 2.1.17
+
+#######################################################
+Reading config file ./restart/p.mk.ssr.conf
+###################################################
+READING OF DATA
+Attempting to read data file in Nexus format (using NCL):
+	data/L2001.30x52.nex ...
+Reading CHARACTERS block...
+Warning:  
+ Skipping command: OPTIONS
+at line 23, column (approximately) 9 (file position 611)
+storing implied block: TAXA
+storing read block: CHARACTERS
+ found standard data... successful
+Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
+ successful
+
+###################################################
+PARTITIONING OF DATA AND MODELS
+GARLI data subset 1
+	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
+	Data read as Standard k-state data,
+	modeled as Standard k-state data
+NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
+Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
+	
+	Subset of data with 2 states:
+	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
+	Summary of data:
+	  30 sequences.
+	  0 constant characters.
+	  39 parsimony-informative characters.
+	  0 uninformative variable characters.
+	  39 total characters.
+	  39 unique patterns in compressed data matrix.
+NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
+Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
+	
+	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
+	  char  90 
+	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
+	  char  90 
+	Subset of data with 3 states:
+	  chars 54 61 62 64 71 72 83 90-102 \ 6
+	Summary of data:
+	  30 sequences.
+	  0 constant characters.
+	  10 parsimony-informative characters.
+	  0 uninformative variable characters.
+	  10 total characters.
+	  10 unique patterns in compressed data matrix.
+NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
+Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
+	
+	Subset of data with 4 states:
+	  chars 52 59 73
+	Summary of data:
+	  30 sequences.
+	  0 constant characters.
+	  0 parsimony-informative characters.
+	  3 uninformative variable characters.
+	  3 total characters.
+	  3 unique patterns in compressed data matrix.
+NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
+Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
+	
+NOTE: No characters found with 5 observed states.
+NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
+Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
+	
+NOTE: No characters found with 6 observed states.
+
+###################################################
+NOTE: Unlike many programs, the amount of system memory that Garli will
+use can be controlled by the user.
+(This comes from the availablememory setting in the configuration file.
+Availablememory should NOT be set to more than the actual amount of 
+physical memory that your computer has installed)
+
+For this dataset:
+ Mem level		availablememory setting
+  great			    >= 1 MB
+  good			approx 0 MB to 1 MB
+  low			approx 0 MB to 1 MB
+  very low		approx 0 MB to 1 MB
+the minimum required availablememory is 1 MB
+
+You specified that Garli should use at most 512.0 MB of memory.
+
+Garli will actually use approx. 0.5 MB of memory
+**Your memory level is: great (you don't need to change anything)**
+
+#######################################################
+Loading starting model and/or tree from file data/L.start
+Reading TREES block...storing read block: TREES
+ successful
+STARTING RUN
+
+Restarting from checkpoint...
+Search rep 2 (of 5) generation 600, seed 1680473931, best lnL -467.740
+gen      current_lnL    precision  last_tree_imp  
+600      -467.7395        0.010           0 
 700      -467.7359        0.010           0 
 800      -467.7330        0.010           0 
 900      -467.7316        0.010           0 
@@ -19889,7 +17236,7 @@
 pass 12: -467.6782   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
 Final score = -467.6782
-Time used so far = 0 hours, 0 minutes and 3 seconds
+Time used so far = 0 hours, 0 minutes and 9 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -20026,7 +17373,7 @@
 pass 17: -467.6782   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
 Final score = -467.6782
-Time used so far = 0 hours, 0 minutes and 5 seconds
+Time used so far = 0 hours, 0 minutes and 11 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -20114,190 +17461,29 @@
 1000     -467.7499        0.010           0 
 1100     -467.7459        0.010           0 
 1200     -467.7457        0.010           0 
-NOTE: ****Specified time limit (5 seconds) reached...
-
-NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
-TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
-FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
-(set restart = 1 in the config file).  IF YOU WANT TO USE THE
-PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
-ADD "end;" TO THE TREE FILES.
-
-Running GARLI Version 2.1. ()
-->Single processor version for 64-bit OS<-
-##############################################################
- This is GARLI 2.1: maximum likelihood phylogenetic inference
- using nucleotide, amino acid, codon and morphology-like data,
-             as well as partitioned models.
-   General program usage is extensively documented here:
-            http://www.nescent.org/wg/garli/
-   See this page for details on partitioned model usage:
-  http://www.nescent.org/wg_garli/Using_partitioned_models
-   and this page for details on Mkv mophology model usage:
-    http://www.nescent.org/wg_garli/Mkv_morphology_model
-         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
-                garli.support@gmail.com
-##############################################################
-Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0
-Using NCL version 2.1.17
-
-#######################################################
-Reading config file ./restart/p.mk.ssr.conf
-###################################################
-READING OF DATA
-Attempting to read data file in Nexus format (using NCL):
-	data/L2001.30x52.nex ...
-Reading CHARACTERS block...
-Warning:  
- Skipping command: OPTIONS
-at line 23, column (approximately) 9 (file position 611)
-storing implied block: TAXA
-storing read block: CHARACTERS
- found standard data... successful
-Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
- successful
-
-###################################################
-PARTITIONING OF DATA AND MODELS
-GARLI data subset 1
-	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
-	Data read as Standard k-state data,
-	modeled as Standard k-state data
-NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
-Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
-	
-	Subset of data with 2 states:
-	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
-	Summary of data:
-	  30 sequences.
-	  0 constant characters.
-	  39 parsimony-informative characters.
-	  0 uninformative variable characters.
-	  39 total characters.
-	  39 unique patterns in compressed data matrix.
-NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
-Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
-	
-	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
-	  char  90 
-	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
-	  char  90 
-	Subset of data with 3 states:
-	  chars 54 61 62 64 71 72 83 90-102 \ 6
-	Summary of data:
-	  30 sequences.
-	  0 constant characters.
-	  10 parsimony-informative characters.
-	  0 uninformative variable characters.
-	  10 total characters.
-	  10 unique patterns in compressed data matrix.
-NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
-Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
-	
-	Subset of data with 4 states:
-	  chars 52 59 73
-	Summary of data:
-	  30 sequences.
-	  0 constant characters.
-	  0 parsimony-informative characters.
-	  3 uninformative variable characters.
-	  3 total characters.
-	  3 unique patterns in compressed data matrix.
-NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
-Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
-	
-NOTE: No characters found with 5 observed states.
-NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
-Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
-	
-NOTE: No characters found with 6 observed states.
-
-###################################################
-NOTE: Unlike many programs, the amount of system memory that Garli will
-use can be controlled by the user.
-(This comes from the availablememory setting in the configuration file.
-Availablememory should NOT be set to more than the actual amount of 
-physical memory that your computer has installed)
-
-For this dataset:
- Mem level		availablememory setting
-  great			    >= 1 MB
-  good			approx 0 MB to 1 MB
-  low			approx 0 MB to 1 MB
-  very low		approx 0 MB to 1 MB
-the minimum required availablememory is 1 MB
-
-You specified that Garli should use at most 512.0 MB of memory.
-
-Garli will actually use approx. 0.5 MB of memory
-**Your memory level is: great (you don't need to change anything)**
-
-#######################################################
-Loading starting model and/or tree from file data/L.start
-Reading TREES block...storing read block: TREES
- successful
-STARTING RUN
-
-Restarting from checkpoint...
-Search rep 4 (of 5) generation 1251, seed 1866500990, best lnL -467.746
-gen      current_lnL    precision  last_tree_imp  
-1251     -467.7456        0.010           0 
 1300     -467.7450        0.010           0 
-1400     -467.7445        0.010           0 
-1500     -467.7424        0.010           0 
-1600     -467.7392        0.010           0 
-1700     -467.7366        0.010           0 
-1800     -467.7357        0.010           0 
-1900     -467.7340        0.010           0 
-2000     -467.7322        0.010           0 
-2100     -467.7321        0.010           0 
-2200     -467.7314        0.010           0 
-2300     -467.7269        0.010           0 
-2400     -467.7239        0.010           0 
-2500     -467.7234        0.010           0 
-2600     -467.7227        0.010           0 
-2700     -467.7227        0.010           0 
-2800     -467.7225        0.010           0 
-2900     -467.7210        0.010           0 
-3000     -467.7183        0.010           0 
-3100     -467.7179        0.010           0 
-3200     -467.7177        0.010           0 
-3300     -467.7172        0.010           0 
-3400     -467.7169        0.010           0 
-3500     -467.7164        0.010           0 
-3600     -467.7159        0.010           0 
-3700     -467.7148        0.010           0 
-3800     -467.7148        0.010           0 
-3900     -467.7132        0.010           0 
-4000     -467.7131        0.010           0 
-4100     -467.7127        0.010           0 
-4200     -467.7127        0.010           0 
-4300     -467.7123        0.010           0 
-4400     -467.7122        0.010           0 
-Reached termination condition!
-last topological improvement at gen 0
-Improvement over last 500 gen = 0.00098
-Current score = -467.7122
+NOTE: ****Specified time limit (5 seconds) reached...
+Current score = -467.7445
 Performing final optimizations...
-pass 1 : -467.7122   (branch= 0.0000  subset rates= 0.0000)
-pass 2 : -467.7036   (branch= 0.0086  subset rates= 0.0000)
-pass 3 : -467.6999   (branch= 0.0036  subset rates= 0.0000)
-pass 4 : -467.6991   (branch= 0.0008  subset rates= 0.0000)
-pass 5 : -467.6968   (branch= 0.0023  subset rates= 0.0000)
-pass 6 : -467.6956   (branch= 0.0012  subset rates= 0.0000)
-pass 7 : -467.6948   (branch= 0.0008  subset rates= 0.0000)
-pass 8 : -467.6939   (branch= 0.0006  subset rates= 0.0003)
-pass 9 : -467.6935   (branch= 0.0003  subset rates= 0.0000)
-pass 10: -467.6933   (branch= 0.0002  subset rates= 0.0000)
-pass 11: -467.6932   (branch= 0.0001  subset rates= 0.0000)
-pass 12: -467.6931   (branch= 0.0000  subset rates= 0.0000)
-pass 13: -467.6931   (branch= 0.0000  subset rates= 0.0000)
-pass 14: -467.6931   (branch= 0.0000  subset rates= 0.0000)
+pass 1 : -467.7294   (branch= 0.0151  subset rates= 0.0000)
+pass 2 : -467.7162   (branch= 0.0132  subset rates= 0.0000)
+pass 3 : -467.7065   (branch= 0.0097  subset rates= 0.0000)
+pass 4 : -467.7007   (branch= 0.0057  subset rates= 0.0000)
+pass 5 : -467.6981   (branch= 0.0027  subset rates= 0.0000)
+pass 6 : -467.6963   (branch= 0.0017  subset rates= 0.0000)
+pass 7 : -467.6948   (branch= 0.0016  subset rates= 0.0000)
+pass 8 : -467.6939   (branch= 0.0009  subset rates= 0.0000)
+pass 9 : -467.6934   (branch= 0.0005  subset rates= 0.0000)
+pass 10: -467.6933   (branch= 0.0001  subset rates= 0.0000)
+pass 11: -467.6932   (branch= 0.0000  subset rates= 0.0000)
+pass 12: -467.6932   (branch= 0.0000  subset rates= 0.0000)
+pass 13: -467.6932   (branch= 0.0000  subset rates= 0.0000)
+pass 14: -467.6932   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
-Final score = -467.6931
-Time used so far = 0 hours, 0 minutes and 7 seconds
+Final score = -467.6932
+Time used so far = 0 hours, 0 minutes and 12 seconds
 
-MODEL REPORT - Parameter values are FINAL
+MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT
 Model 1
   Number of states = 2 (standard data)
   Character change matrix:
@@ -20323,161 +17509,19 @@
     no rate heterogeneity
 
 Subset rate multipliers:
-    0.78  1.49  2.19
+    0.78  1.49  2.18
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
     8 branches were collapsed.
 
->>>Completed Search rep 4 (of 5)<<<
-
->>>Search rep 5 (of 5)<<<
-Obtained starting tree 1 from Nexus
-MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
-Model 1
-  Number of states = 2 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 3
-  Number of states = 4 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    1.00  1.00  1.00
-Starting with seed=1825473762
+>>>Terminated Search rep 4 (of 5)<<<
 
-Initial ln Likelihood: -611.8261
-optimizing: starting branch lengths, subset rates...
-pass 1:+  128.630 (branch= 123.24 scale=  0.39 subset rates=  4.99)
-pass 2:+   10.941 (branch=   9.80 scale=  0.05 subset rates=  1.10)
-pass 3:+    4.121 (branch=   3.92 scale=  0.00 subset rates=  0.20)
-pass 4:+    0.225 (branch=   0.23 scale=  0.00 subset rates=  0.00)
-pass 5:+    0.029 (branch=   0.03 scale=  0.00 subset rates=  0.00)
-pass 6:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
-lnL after optimization: -467.8803
-gen      current_lnL    precision  last_tree_imp  
-0        -467.8803        0.010           0 
-100      -467.8393        0.010           0 
-200      -467.8200        0.010           0 
-300      -467.7990        0.010         291 
-400      -467.7853        0.010         291 
-500      -467.7724        0.010         291 
-600      -467.7655        0.010         291 
-700      -467.7587        0.010         291 
-800      -467.7573        0.010         291 
-900      -467.7566        0.010         291 
-1000     -467.7532        0.010         291 
-1100     -467.7463        0.010         291 
-1200     -467.7454        0.010         291 
-1300     -467.7449        0.010         291 
-1400     -467.7416        0.010         291 
-1500     -467.7375        0.010         291 
-1600     -467.7374        0.010         291 
-1700     -467.7336        0.010         291 
-1800     -467.7313        0.010         291 
-1900     -467.7287        0.010         291 
-2000     -467.7240        0.010         291 
-2100     -467.7240        0.010         291 
-2200     -467.7231        0.010         291 
-2300     -467.7223        0.010         291 
-2400     -467.7184        0.010         291 
-2500     -467.7174        0.010         291 
-2600     -467.7161        0.010         291 
-2700     -467.7145        0.010         291 
-2800     -467.7144        0.010         291 
-2900     -467.7142        0.010         291 
-3000     -467.7134        0.010         291 
-3100     -467.7131        0.010         291 
-3200     -467.7130        0.010         291 
-3300     -467.7121        0.010         291 
-3400     -467.7119        0.010         291 
-3500     -467.7111        0.010         291 
-3600     -467.7100        0.010         291 
-3700     -467.7093        0.010         291 
-3800     -467.7087        0.010         291 
-3900     -467.7083        0.010         291 
-4000     -467.7080        0.010         291 
-4100     -467.7078        0.010         291 
-4200     -467.7070        0.010         291 
-4300     -467.7065        0.010         291 
-4400     -467.7060        0.010         291 
-4500     -467.7060        0.010         291 
-4600     -467.7056        0.010         291 
-4700     -467.7055        0.010         291 
-4800     -467.7050        0.010         291 
-4900     -467.7050        0.010         291 
-Reached termination condition!
-last topological improvement at gen 291
-Improvement over last 500 gen = 0.00097
-Current score = -467.7050
-Performing final optimizations...
-pass 1 : -467.7045   (branch= 0.0000  subset rates= 0.0005)
-pass 2 : -467.6902   (branch= 0.0142  subset rates= 0.0000)
-pass 3 : -467.6859   (branch= 0.0043  subset rates= 0.0000)
-pass 4 : -467.6832   (branch= 0.0019  subset rates= 0.0008)
-pass 5 : -467.6818   (branch= 0.0013  subset rates= 0.0001)
-pass 6 : -467.6805   (branch= 0.0013  subset rates= 0.0000)
-pass 7 : -467.6798   (branch= 0.0007  subset rates= 0.0000)
-pass 8 : -467.6789   (branch= 0.0009  subset rates= 0.0000)
-pass 9 : -467.6786   (branch= 0.0003  subset rates= 0.0000)
-pass 10: -467.6784   (branch= 0.0003  subset rates= 0.0000)
-pass 11: -467.6783   (branch= 0.0001  subset rates= 0.0000)
-pass 12: -467.6782   (branch= 0.0000  subset rates= 0.0000)
-pass 13: -467.6782   (branch= 0.0000  subset rates= 0.0000)
-pass 14: -467.6782   (branch= 0.0000  subset rates= 0.0000)
-Looking for minimum length branches...
-Final score = -467.6782
-Time used = 0 hours, 0 minutes and 9 seconds
-
-MODEL REPORT - Parameter values are FINAL
-Model 1
-  Number of states = 2 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 3
-  Number of states = 4 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    0.79  1.48  2.18
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    8 branches were collapsed.
+NOTE: ***Search was terminated before full auto-termination condition was reached!
+Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
 
->>>Completed Search rep 5 (of 5)<<<
 
 #######################################################
 
-Completed 5 replicate search(es) (of 5).
+Completed 4 replicate search(es) (of 5).
 
 NOTE: Unless the following output indicates that search replicates found the
 	same topology, you should assume that they found different topologies.
@@ -20485,8 +17529,7 @@
 Replicate 1 : -467.6783       
 Replicate 2 : -467.6782        (same topology as 1)
 Replicate 3 : -467.6782 (best) (same topology as 1)
-Replicate 4 : -467.6931       
-Replicate 5 : -467.6782        (same topology as 1)
+Replicate 4 : -467.6932        (TERMINATED PREMATURELY) 
 
 Parameter estimates across search replicates:
 
@@ -20504,10 +17547,7 @@
 rep 1:  3.843 0.786 1.480 2.178
 rep 2:  3.842 0.786 1.478 2.185
 rep 3:  3.844 0.786 1.479 2.186
-rep 4:  3.883 0.782 1.493 2.189
-rep 5:  3.844 0.786 1.480 2.183
-
-Saving final trees from all search reps to ch.p.mk.ssr.best.all.tre
+rep 4:  3.882 0.783 1.492 2.184
 
 Saving final tree from best search rep (#3) to ch.p.mk.ssr.best.tre
 #######################################################
@@ -20727,7 +17767,7 @@
 pass 15: -477.4316   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
 Final score = -477.4316
-Time used so far = 0 hours, 0 minutes and 1 seconds
+Time used so far = 0 hours, 0 minutes and 5 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -20815,6 +17855,134 @@
 900      -477.6923        0.010         102 
 1000     -477.6923        0.010         102 
 1100     -477.6865        0.010         102 
+NOTE: ****Specified time limit (5 seconds) reached...
+
+NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
+TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
+FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
+(set restart = 1 in the config file).  IF YOU WANT TO USE THE
+PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
+ADD "end;" TO THE TREE FILES.
+
+Running GARLI Version 2.1. ()
+->Single processor version for 64-bit OS<-
+##############################################################
+ This is GARLI 2.1: maximum likelihood phylogenetic inference
+ using nucleotide, amino acid, codon and morphology-like data,
+             as well as partitioned models.
+   General program usage is extensively documented here:
+            http://www.nescent.org/wg/garli/
+   See this page for details on partitioned model usage:
+  http://www.nescent.org/wg_garli/Using_partitioned_models
+   and this page for details on Mkv mophology model usage:
+    http://www.nescent.org/wg_garli/Mkv_morphology_model
+         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
+                garli.support@gmail.com
+##############################################################
+Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0
+Using NCL version 2.1.17
+
+#######################################################
+Reading config file ./restart/p.mkO.ssr.conf
+###################################################
+READING OF DATA
+Attempting to read data file in Nexus format (using NCL):
+	data/L2001.30x52.nex ...
+Reading CHARACTERS block...
+Warning:  
+ Skipping command: OPTIONS
+at line 23, column (approximately) 9 (file position 611)
+storing implied block: TAXA
+storing read block: CHARACTERS
+ found standard data... successful
+Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
+ successful
+
+###################################################
+PARTITIONING OF DATA AND MODELS
+GARLI data subset 1
+	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
+	Data read as Standard ordered k-state data,
+	modeled as Standard ordered k-state data
+NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
+Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
+	
+	Subset of data with 2 states:
+	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
+	Summary of data:
+	  30 sequences.
+	  0 constant characters.
+	  39 parsimony-informative characters.
+	  0 uninformative variable characters.
+	  39 total characters.
+	  39 unique patterns in compressed data matrix.
+NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
+Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
+	
+	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
+	  char  90 
+	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
+	  char  90 
+	Subset of data with 3 states:
+	  chars 54 61 62 64 71 72 83 90-102 \ 6
+	Summary of data:
+	  30 sequences.
+	  0 constant characters.
+	  10 parsimony-informative characters.
+	  0 uninformative variable characters.
+	  10 total characters.
+	  10 unique patterns in compressed data matrix.
+NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
+Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
+	
+	Subset of data with 4 states:
+	  chars 52 59 73
+	Summary of data:
+	  30 sequences.
+	  0 constant characters.
+	  0 parsimony-informative characters.
+	  3 uninformative variable characters.
+	  3 total characters.
+	  3 unique patterns in compressed data matrix.
+NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
+Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
+	
+NOTE: No characters found with 5 observed states.
+NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
+Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
+	
+NOTE: No characters found with 6 observed states.
+
+###################################################
+NOTE: Unlike many programs, the amount of system memory that Garli will
+use can be controlled by the user.
+(This comes from the availablememory setting in the configuration file.
+Availablememory should NOT be set to more than the actual amount of 
+physical memory that your computer has installed)
+
+For this dataset:
+ Mem level		availablememory setting
+  great			    >= 1 MB
+  good			approx 0 MB to 1 MB
+  low			approx 0 MB to 1 MB
+  very low		approx 0 MB to 1 MB
+the minimum required availablememory is 1 MB
+
+You specified that Garli should use at most 512.0 MB of memory.
+
+Garli will actually use approx. 0.5 MB of memory
+**Your memory level is: great (you don't need to change anything)**
+
+#######################################################
+Loading starting model and/or tree from file data/L.start
+Reading TREES block...storing read block: TREES
+ successful
+STARTING RUN
+
+Restarting from checkpoint...
+Search rep 2 (of 5) generation 1133, seed 462598386, best lnL -477.686
+gen      current_lnL    precision  last_tree_imp  
+1133     -477.6863        0.010         102 
 1200     -477.6862        0.010         102 
 1300     -477.6839        0.010         102 
 1400     -477.6824        0.010         102 
@@ -20891,7 +18059,7 @@
 pass 16: -477.4320   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
 Final score = -477.4320
-Time used so far = 0 hours, 0 minutes and 4 seconds
+Time used so far = 0 hours, 0 minutes and 9 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -21020,7 +18188,7 @@
 pass 14: -477.2121   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
 Final score = -477.2121
-Time used so far = 0 hours, 0 minutes and 5 seconds
+Time used so far = 0 hours, 0 minutes and 11 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -21100,210 +18268,31 @@
 200      -477.7818        0.010         127 
 300      -477.7724        0.010         127 
 400      -477.7685        0.010         127 
-NOTE: ****Specified time limit (5 seconds) reached...
-
-NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
-TERMINATED.  OUTPUT FILES (tree files, etc.) WILL NOT BE
-FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF
-(set restart = 1 in the config file).  IF YOU WANT TO USE THE
-PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY
-ADD "end;" TO THE TREE FILES.
-
-Running GARLI Version 2.1. ()
-->Single processor version for 64-bit OS<-
-##############################################################
- This is GARLI 2.1: maximum likelihood phylogenetic inference
- using nucleotide, amino acid, codon and morphology-like data,
-             as well as partitioned models.
-   General program usage is extensively documented here:
-            http://www.nescent.org/wg/garli/
-   See this page for details on partitioned model usage:
-  http://www.nescent.org/wg_garli/Using_partitioned_models
-   and this page for details on Mkv mophology model usage:
-    http://www.nescent.org/wg_garli/Mkv_morphology_model
-         PLEASE LET ME KNOW OF ANY PROBLEMS AT:
-                garli.support@gmail.com
-##############################################################
-Compiled Dec 19 2024 19:44:33 using GNU gcc compiler version 15.2.0
-Using NCL version 2.1.17
-
-#######################################################
-Reading config file ./restart/p.mkO.ssr.conf
-###################################################
-READING OF DATA
-Attempting to read data file in Nexus format (using NCL):
-	data/L2001.30x52.nex ...
-Reading CHARACTERS block...
-Warning:  
- Skipping command: OPTIONS
-at line 23, column (approximately) 9 (file position 611)
-storing implied block: TAXA
-storing read block: CHARACTERS
- found standard data... successful
-Reading ASSUMPTIONS block...storing read block: ASSUMPTIONS
- successful
-
-###################################################
-PARTITIONING OF DATA AND MODELS
-GARLI data subset 1
-	CHARACTERS block #1 ("Untitled CHARACTERS Block 1")
-	Data read as Standard ordered k-state data,
-	modeled as Standard ordered k-state data
-NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
-Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
-	
-	Subset of data with 2 states:
-	  chars 46-51 53 55-58 60 63 65-70 84 87-89 91-95 97-101 103 104 106 107 113 115
-	Summary of data:
-	  30 sequences.
-	  0 constant characters.
-	  39 parsimony-informative characters.
-	  0 uninformative variable characters.
-	  39 total characters.
-	  39 unique patterns in compressed data matrix.
-NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
-Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
-	
-	Part ambig. char's of taxon Chelonus_sp. converted to full ambiguity:
-	  char  90 
-	Part ambig. char's of taxon Alysia_lucicola converted to full ambiguity:
-	  char  90 
-	Subset of data with 3 states:
-	  chars 54 61 62 64 71 72 83 90-102 \ 6
-	Summary of data:
-	  30 sequences.
-	  0 constant characters.
-	  10 parsimony-informative characters.
-	  0 uninformative variable characters.
-	  10 total characters.
-	  10 unique patterns in compressed data matrix.
-NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
-Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
-	
-	Subset of data with 4 states:
-	  chars 52 59 73
-	Summary of data:
-	  30 sequences.
-	  0 constant characters.
-	  0 parsimony-informative characters.
-	  3 uninformative variable characters.
-	  3 total characters.
-	  3 unique patterns in compressed data matrix.
-NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
-Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
-	
-NOTE: No characters found with 5 observed states.
-NOTE: Default wtsets cannot currently be used with non-sequence data! Wtset "equal" ignored.
-Excluded characters:  1-45 74-82 85 86 105 108-112 114 116-118
-	
-NOTE: No characters found with 6 observed states.
-
-###################################################
-NOTE: Unlike many programs, the amount of system memory that Garli will
-use can be controlled by the user.
-(This comes from the availablememory setting in the configuration file.
-Availablememory should NOT be set to more than the actual amount of 
-physical memory that your computer has installed)
-
-For this dataset:
- Mem level		availablememory setting
-  great			    >= 1 MB
-  good			approx 0 MB to 1 MB
-  low			approx 0 MB to 1 MB
-  very low		approx 0 MB to 1 MB
-the minimum required availablememory is 1 MB
-
-You specified that Garli should use at most 512.0 MB of memory.
-
-Garli will actually use approx. 0.5 MB of memory
-**Your memory level is: great (you don't need to change anything)**
-
-#######################################################
-Loading starting model and/or tree from file data/L.start
-Reading TREES block...storing read block: TREES
- successful
-STARTING RUN
-
-Restarting from checkpoint...
-Search rep 4 (of 5) generation 447, seed 589049812, best lnL -477.761
-gen      current_lnL    precision  last_tree_imp  
-447      -477.7611        0.010         127 
 500      -477.7333        0.010         493 
 600      -477.7164        0.010         514 
-700      -477.7079        0.010         514 
-800      -477.7007        0.010         514 
-900      -477.6911        0.010         514 
-1000     -477.6861        0.010         514 
-1100     -477.6778        0.010         514 
-1200     -477.5009        0.010        1183 
-1300     -477.4970        0.010        1183 
-1400     -477.4945        0.010        1183 
-1500     -477.4926        0.010        1183 
-1600     -477.4896        0.010        1183 
-1700     -477.4864        0.010        1183 
-1800     -477.4846        0.010        1183 
-1900     -477.4819        0.010        1183 
-2000     -477.4799        0.010        1183 
-2100     -477.4779        0.010        1183 
-2200     -477.4774        0.010        1183 
-2300     -477.4766        0.010        1183 
-2400     -477.4755        0.010        1183 
-2500     -477.4745        0.010        1183 
-2600     -477.4721        0.010        1183 
-2700     -477.4702        0.010        1183 
-2800     -477.4686        0.010        1183 
-2900     -477.4684        0.010        1183 
-3000     -477.4669        0.010        1183 
-3100     -477.4668        0.010        1183 
-3200     -477.4655        0.010        1183 
-3300     -477.4648        0.010        1183 
-3400     -477.4643        0.010        1183 
-3500     -477.4640        0.010        1183 
-3600     -477.4639        0.010        1183 
-3700     -477.4639        0.010        1183 
-3800     -477.4627        0.010        1183 
-3900     -477.4621        0.010        1183 
-4000     -477.4621        0.010        1183 
-4100     -477.4618        0.010        1183 
-4200     -477.4614        0.010        1183 
-4300     -477.4610        0.010        1183 
-4400     -477.4609        0.010        1183 
-4500     -477.4607        0.010        1183 
-4600     -477.4605        0.010        1183 
-4700     -477.4603        0.010        1183 
-4800     -477.4594        0.010        1183 
-4900     -477.4591        0.010        1183 
-5000     -477.4589        0.010        1183 
-   Optimizing parameters...    improved    0.000 lnL
-   Optimizing branchlengths... improved    0.000 lnL
-5100     -477.4589        0.010        1183 
-5200     -477.4587        0.010        1183 
-5300     -477.4586        0.010        1183 
-Reached termination condition!
-last topological improvement at gen 1183
-Improvement over last 500 gen = 0.00080
-Current score = -477.4586
+NOTE: ****Specified time limit (5 seconds) reached...
+Current score = -477.7164
 Performing final optimizations...
-pass 1 : -477.4586   (branch= 0.0000  subset rates= 0.0000)
-pass 2 : -477.4484   (branch= 0.0097  subset rates= 0.0005)
-pass 3 : -477.4401   (branch= 0.0079  subset rates= 0.0004)
-pass 4 : -477.4371   (branch= 0.0030  subset rates= 0.0000)
-pass 5 : -477.4351   (branch= 0.0020  subset rates= 0.0000)
-pass 6 : -477.4340   (branch= 0.0011  subset rates= 0.0000)
-pass 7 : -477.4328   (branch= 0.0011  subset rates= 0.0000)
-pass 8 : -477.4324   (branch= 0.0004  subset rates= 0.0000)
-pass 9 : -477.4321   (branch= 0.0003  subset rates= 0.0000)
-pass 10: -477.4320   (branch= 0.0001  subset rates= 0.0000)
-pass 11: -477.4319   (branch= 0.0001  subset rates= 0.0000)
-pass 12: -477.4319   (branch= 0.0000  subset rates= 0.0000)
-pass 13: -477.4318   (branch= 0.0000  subset rates= 0.0000)
-pass 14: -477.4318   (branch= 0.0000  subset rates= 0.0000)
-pass 15: -477.4318   (branch= 0.0000  subset rates= 0.0000)
+pass 1 : -477.6958   (branch= 0.0198  subset rates= 0.0008)
+pass 2 : -477.6595   (branch= 0.0347  subset rates= 0.0017)
+pass 3 : -477.6408   (branch= 0.0187  subset rates= 0.0000)
+pass 4 : -477.6284   (branch= 0.0124  subset rates= 0.0000)
+pass 5 : -477.6215   (branch= 0.0069  subset rates= 0.0000)
+pass 6 : -477.6198   (branch= 0.0017  subset rates= 0.0000)
+pass 7 : -477.6183   (branch= 0.0010  subset rates= 0.0005)
+pass 8 : -477.6176   (branch= 0.0007  subset rates= 0.0000)
+pass 9 : -477.6173   (branch= 0.0003  subset rates= 0.0000)
+pass 10: -477.6171   (branch= 0.0002  subset rates= 0.0000)
+pass 11: -477.6171   (branch= 0.0001  subset rates= 0.0000)
+pass 12: -477.6170   (branch= 0.0001  subset rates= 0.0000)
+pass 13: -477.6170   (branch= 0.0000  subset rates= 0.0000)
+pass 14: -477.6170   (branch= 0.0000  subset rates= 0.0000)
+pass 15: -477.6170   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
-Final score = -477.4318
-Time used so far = 0 hours, 0 minutes and 8 seconds
+Final score = -477.6170
+Time used so far = 0 hours, 0 minutes and 12 seconds
 
-MODEL REPORT - Parameter values are FINAL
+MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT
 Model 1
   Number of states = 2 (ordered standard data)
   Character change matrix:
@@ -21329,176 +18318,19 @@
     no rate heterogeneity
 
 Subset rate multipliers:
-    0.63  1.91  2.74
+    0.63  1.90  2.74
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    7 branches were collapsed.
-
->>>Completed Search rep 4 (of 5)<<<
-
->>>Search rep 5 (of 5)<<<
-Obtained starting tree 1 from Nexus
-MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
-Model 1
-  Number of states = 2 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 3
-  Number of states = 4 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    1.00  1.00  1.00
-Starting with seed=1041576089
-
-Initial ln Likelihood: -651.4568
-optimizing: starting branch lengths, subset rates...
-pass 1:+  152.391 (branch= 140.86 scale=  1.50 subset rates= 10.03)
-pass 2:+   15.704 (branch=  11.85 scale=  0.05 subset rates=  3.80)
-pass 3:+    2.824 (branch=   1.56 scale=  0.00 subset rates=  1.27)
-pass 4:+    1.328 (branch=   1.01 scale=  0.00 subset rates=  0.32)
-pass 5:+    1.072 (branch=   1.06 scale=  0.00 subset rates=  0.01)
-pass 6:+    0.279 (branch=   0.28 scale=  0.00 subset rates=  0.00)
-pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
-lnL after optimization: -477.8605
-gen      current_lnL    precision  last_tree_imp  
-0        -477.8605        0.010           0 
-100      -477.7343        0.010           9 
-200      -477.7022        0.010         193 
-300      -477.5491        0.010         269 
-400      -477.5287        0.010         269 
-500      -477.5243        0.010         269 
-600      -477.5188        0.010         269 
-700      -477.5125        0.010         269 
-800      -477.5074        0.010         269 
-900      -477.5008        0.010         269 
-1000     -477.4953        0.010         269 
-1100     -477.4918        0.010         269 
-1200     -477.4893        0.010         269 
-1300     -477.4880        0.010         269 
-1400     -477.4860        0.010         269 
-1500     -477.4857        0.010         269 
-1600     -477.4844        0.010         269 
-1700     -477.4801        0.010         269 
-1800     -477.4783        0.010         269 
-1900     -477.4751        0.010         269 
-2000     -477.4732        0.010         269 
-2100     -477.4707        0.010         269 
-2200     -477.4693        0.010         269 
-2300     -477.4671        0.010         269 
-2400     -477.4670        0.010         269 
-2500     -477.4666        0.010         269 
-2600     -477.4664        0.010         269 
-2700     -477.4653        0.010         269 
-2800     -477.4653        0.010         269 
-2900     -477.4651        0.010         269 
-3000     -477.4641        0.010         269 
-3100     -477.4637        0.010         269 
-3200     -477.4630        0.010         269 
-3300     -477.4626        0.010         269 
-3400     -477.4622        0.010         269 
-3500     -477.4621        0.010         269 
-3600     -477.4619        0.010         269 
-3700     -477.4614        0.010         269 
-3800     -477.4611        0.010         269 
-3900     -477.4607        0.010         269 
-4000     -477.4606        0.010         269 
-4100     -477.4603        0.010         269 
-4200     -477.4596        0.010         269 
-4300     -477.4593        0.010         269 
-4400     -477.4590        0.010         269 
-4500     -477.4589        0.010         269 
-4600     -477.4586        0.010         269 
-4700     -477.4582        0.010         269 
-4800     -477.4582        0.010         269 
-4900     -477.4579        0.010         269 
-5000     -477.4576        0.010         269 
-   Optimizing parameters...    improved    0.000 lnL
-   Optimizing branchlengths... improved    0.000 lnL
-5100     -477.4576        0.010         269 
-5200     -477.4568        0.010         269 
-5300     -477.4564        0.010         269 
-5400     -477.4563        0.010         269 
-5500     -477.4561        0.010         269 
-5600     -477.4560        0.010         269 
-5700     -477.4555        0.010         269 
-5800     -477.4555        0.010         269 
-Reached termination condition!
-last topological improvement at gen 269
-Improvement over last 500 gen = 0.00090
-Current score = -477.4555
-Performing final optimizations...
-pass 1 : -477.4545   (branch= 0.0000  subset rates= 0.0009)
-pass 2 : -477.4454   (branch= 0.0092  subset rates= 0.0000)
-pass 3 : -477.4363   (branch= 0.0087  subset rates= 0.0004)
-pass 4 : -477.4355   (branch= 0.0007  subset rates= 0.0000)
-pass 5 : -477.4351   (branch= 0.0005  subset rates= 0.0000)
-pass 6 : -477.4344   (branch= 0.0007  subset rates= 0.0000)
-pass 7 : -477.4334   (branch= 0.0010  subset rates= 0.0000)
-pass 8 : -477.4330   (branch= 0.0003  subset rates= 0.0000)
-pass 9 : -477.4324   (branch= 0.0007  subset rates= 0.0000)
-pass 10: -477.4322   (branch= 0.0002  subset rates= 0.0000)
-pass 11: -477.4320   (branch= 0.0001  subset rates= 0.0000)
-pass 12: -477.4320   (branch= 0.0000  subset rates= 0.0000)
-pass 13: -477.4319   (branch= 0.0000  subset rates= 0.0000)
-pass 14: -477.4318   (branch= 0.0001  subset rates= 0.0000)
-pass 15: -477.4318   (branch= 0.0000  subset rates= 0.0000)
-pass 16: -477.4318   (branch= 0.0000  subset rates= 0.0000)
-pass 17: -477.4317   (branch= 0.0000  subset rates= 0.0000)
-Looking for minimum length branches...
-Final score = -477.4317
-Time used = 0 hours, 0 minutes and 10 seconds
-
-MODEL REPORT - Parameter values are FINAL
-Model 1
-  Number of states = 2 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
+    8 branches were collapsed.
 
-Model 2
-  Number of states = 3 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
+>>>Terminated Search rep 4 (of 5)<<<
 
-Model 3
-  Number of states = 4 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mk model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    0.63  1.92  2.75
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    7 branches were collapsed.
+NOTE: ***Search was terminated before full auto-termination condition was reached!
+Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
 
->>>Completed Search rep 5 (of 5)<<<
 
 #######################################################
 
-Completed 5 replicate search(es) (of 5).
+Completed 4 replicate search(es) (of 5).
 
 NOTE: Unless the following output indicates that search replicates found the
 	same topology, you should assume that they found different topologies.
@@ -21506,8 +18338,7 @@
 Replicate 1 : -477.4316       
 Replicate 2 : -477.4320        (same topology as 1)
 Replicate 3 : -477.2121 (best)
-Replicate 4 : -477.4318        (same topology as 1)
-Replicate 5 : -477.4317        (same topology as 1)
+Replicate 4 : -477.6170        (TERMINATED PREMATURELY) 
 
 Parameter estimates across search replicates:
 
@@ -21525,10 +18356,7 @@
 rep 1:  4.930 0.631 1.916 2.739
 rep 2:  4.935 0.630 1.915 2.762
 rep 3:  4.672 0.643 1.904 2.631
-rep 4:  4.925 0.633 1.909 2.740
-rep 5:  4.933 0.630 1.917 2.750
-
-Saving final trees from all search reps to ch.p.mkO.ssr.best.all.tre
+rep 4:  4.889 0.635 1.903 2.737
 
 Saving final tree from best search rep (#3) to ch.p.mkO.ssr.best.tre
 #######################################################
@@ -21756,7 +18584,7 @@
 pass 14: -425.5486   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
 Final score = -425.5486
-Time used so far = 0 hours, 0 minutes and 2 seconds
+Time used so far = 0 hours, 0 minutes and 5 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -21813,237 +18641,6 @@
 lnL after optimization: -439.2274
 gen      current_lnL    precision  last_tree_imp  
 0        -439.2274        0.010           0 
-100      -428.8677        0.010          98 
-200      -428.0499        0.010         164 
-300      -427.6003        0.010         249 
-400      -427.5648        0.010         249 
-500      -427.4910        0.010         499 
-600      -427.3863        0.010         511 
-700      -425.7187        0.010         668 
-800      -425.6951        0.010         722 
-900      -425.6795        0.010         722 
-1000     -425.6689        0.010         722 
-1100     -425.6640        0.010         722 
-1200     -425.6430        0.010         722 
-1300     -425.6381        0.010         722 
-1400     -425.6345        0.010         722 
-1500     -425.6341        0.010         722 
-1600     -425.6274        0.010         722 
-1700     -425.6239        0.010         722 
-1800     -425.6236        0.010         722 
-1900     -425.6225        0.010         722 
-2000     -425.6202        0.010         722 
-2100     -425.6197        0.010         722 
-2200     -425.6174        0.010         722 
-2300     -425.6146        0.010         722 
-2400     -425.6135        0.010         722 
-2500     -425.6104        0.010         722 
-2600     -425.6099        0.010         722 
-2700     -425.6088        0.010         722 
-2800     -425.6077        0.010         722 
-2900     -425.6073        0.010         722 
-3000     -425.6059        0.010         722 
-3100     -425.6056        0.010         722 
-3200     -425.6055        0.010         722 
-3300     -425.6051        0.010         722 
-3400     -425.6049        0.010         722 
-3500     -425.6048        0.010         722 
-3600     -425.6048        0.010         722 
-Reached termination condition!
-last topological improvement at gen 722
-Improvement over last 500 gen = 0.00084
-Current score = -425.6048
-Performing final optimizations...
-pass 1 : -425.6048   (branch= 0.0000  subset rates= 0.0000)
-pass 2 : -425.5577   (branch= 0.0188  subset rates= 0.0282)
-pass 3 : -425.5536   (branch= 0.0041  subset rates= 0.0000)
-pass 4 : -425.5523   (branch= 0.0012  subset rates= 0.0000)
-pass 5 : -425.5511   (branch= 0.0013  subset rates= 0.0000)
-pass 6 : -425.5498   (branch= 0.0007  subset rates= 0.0005)
-pass 7 : -425.5492   (branch= 0.0007  subset rates= 0.0000)
-pass 8 : -425.5489   (branch= 0.0003  subset rates= 0.0000)
-pass 9 : -425.5488   (branch= 0.0001  subset rates= 0.0000)
-pass 10: -425.5487   (branch= 0.0001  subset rates= 0.0000)
-pass 11: -425.5487   (branch= 0.0000  subset rates= 0.0000)
-pass 12: -425.5486   (branch= 0.0000  subset rates= 0.0000)
-pass 13: -425.5486   (branch= 0.0000  subset rates= 0.0000)
-Looking for minimum length branches...
-Final score = -425.5486
-Time used so far = 0 hours, 0 minutes and 3 seconds
-
-MODEL REPORT - Parameter values are FINAL
-Model 1
-  Number of states = 2 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 3
-  Number of states = 4 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    0.87  1.53  1.12
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    9 branches were collapsed.
-
->>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<<
-
->>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<<
-Obtained starting tree 1 from Nexus
-Starting with seed=2129292874
-
-Initial ln Likelihood: -588.2493
-optimizing: starting branch lengths, subset rates...
-pass 1:+  141.030 (branch= 140.49 scale=  0.38 subset rates=  0.17)
-pass 2:+    6.535 (branch=   6.52 scale=  0.00 subset rates=  0.02)
-pass 3:+    1.052 (branch=   1.03 scale=  0.00 subset rates=  0.02)
-pass 4:+    0.061 (branch=   0.06 scale=  0.00 subset rates=  0.00)
-pass 5:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
-lnL after optimization: -439.5713
-gen      current_lnL    precision  last_tree_imp  
-0        -439.5713        0.010           0 
-100      -431.1390        0.010          95 
-200      -428.6585        0.010         167 
-300      -427.6515        0.010         295 
-400      -427.2441        0.010         295 
-500      -427.2139        0.010         295 
-600      -427.1680        0.010         568 
-700      -427.1488        0.010         568 
-800      -425.4819        0.010         762 
-900      -425.4264        0.010         803 
-1000     -425.4085        0.010         803 
-1100     -425.4058        0.010         803 
-1200     -425.3915        0.010         803 
-1300     -425.3912        0.010         803 
-1400     -425.3886        0.010         803 
-1500     -425.3865        0.010         803 
-1600     -425.3820        0.010         803 
-1700     -425.3760        0.010         803 
-1800     -425.3758        0.010         803 
-1900     -425.3750        0.010         803 
-2000     -425.3712        0.010         803 
-2100     -425.3702        0.010         803 
-2200     -425.3666        0.010         803 
-2300     -425.3654        0.010         803 
-2400     -425.3634        0.010         803 
-2500     -425.3629        0.010         803 
-2600     -425.3622        0.010         803 
-2700     -425.3619        0.010         803 
-2800     -425.3613        0.010         803 
-2900     -425.3592        0.010         803 
-3000     -425.3583        0.010         803 
-3100     -425.3581        0.010         803 
-3200     -425.3571        0.010         803 
-3300     -425.3567        0.010         803 
-3400     -425.3566        0.010         803 
-3500     -425.3562        0.010         803 
-3600     -425.3554        0.010         803 
-3700     -425.3549        0.010         803 
-3800     -425.3546        0.010         803 
-3900     -425.3537        0.010         803 
-4000     -425.3536        0.010         803 
-4100     -425.3533        0.010         803 
-4200     -425.3531        0.010         803 
-4300     -425.3531        0.010         803 
-4400     -425.3531        0.010         803 
-Reached termination condition!
-last topological improvement at gen 803
-Improvement over last 500 gen = 0.00059
-Current score = -425.3531
-Performing final optimizations...
-pass 1 : -425.3485   (branch= 0.0000  subset rates= 0.0045)
-pass 2 : -425.3316   (branch= 0.0161  subset rates= 0.0009)
-pass 3 : -425.3247   (branch= 0.0069  subset rates= 0.0000)
-pass 4 : -425.3221   (branch= 0.0026  subset rates= 0.0000)
-pass 5 : -425.3221   (branch= 0.0000  subset rates= 0.0000)
-pass 6 : -425.3219   (branch= 0.0002  subset rates= 0.0000)
-pass 7 : -425.3209   (branch= 0.0009  subset rates= 0.0000)
-pass 8 : -425.3203   (branch= 0.0007  subset rates= 0.0000)
-pass 9 : -425.3202   (branch= 0.0000  subset rates= 0.0000)
-pass 10: -425.3201   (branch= 0.0001  subset rates= 0.0000)
-pass 11: -425.3201   (branch= 0.0000  subset rates= 0.0000)
-pass 12: -425.3201   (branch= 0.0000  subset rates= 0.0000)
-pass 13: -425.3201   (branch= 0.0000  subset rates= 0.0000)
-Looking for minimum length branches...
-Final score = -425.3201
-Time used so far = 0 hours, 0 minutes and 5 seconds
-
-MODEL REPORT - Parameter values are FINAL
-Model 1
-  Number of states = 2 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 3
-  Number of states = 4 (standard data)
-  Character change matrix:
-    One rate (symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    0.86  1.54  1.15
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    9 branches were collapsed.
-
->>>Completed Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<<
-
->>>Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<<
-Obtained starting tree 1 from Nexus
-Starting with seed=1573911897
-
-Initial ln Likelihood: -585.3657
-optimizing: starting branch lengths, subset rates...
-pass 1:+  128.924 (branch= 128.21 scale=  0.69 subset rates=  0.02)
-pass 2:+   11.724 (branch=  11.59 scale=  0.02 subset rates=  0.11)
-pass 3:+    4.613 (branch=   4.49 scale=  0.00 subset rates=  0.12)
-pass 4:+    0.819 (branch=   0.80 scale=  0.00 subset rates=  0.02)
-pass 5:+    0.057 (branch=   0.06 scale=  0.00 subset rates=  0.00)
-pass 6:+    0.012 (branch=   0.01 scale=  0.00 subset rates=  0.00)
-pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
-lnL after optimization: -439.2170
-gen      current_lnL    precision  last_tree_imp  
-0        -439.2170        0.010           0 
-100      -428.1644        0.010          88 
-200      -427.4929        0.010         189 
-300      -425.8887        0.010         242 
-400      -425.6742        0.010         351 
-500      -425.6722        0.010         351 
-600      -425.6693        0.010         351 
-700      -425.6634        0.010         351 
-800      -425.6287        0.010         772 
-900      -425.6222        0.010         772 
-1000     -425.6141        0.010         772 
-1100     -425.6073        0.010         772 
-1200     -425.6061        0.010         772 
-1300     -425.6034        0.010         772 
 NOTE: ****Specified time limit (5 seconds) reached...
 
 NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
@@ -22172,60 +18769,66 @@
 	Subset 3: Random seed for bootstrap reweighting: 974568031
 
 Restarting from checkpoint...
-Bootstrap rep 1 (of 1) Search rep 4 (of 5) generation 1388, seed 949530989, best lnL -425.601
+Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 1, seed 255600397, best lnL -439.223
 gen      current_lnL    precision  last_tree_imp  
-1388     -425.6013        0.010         772 
-1400     -425.6009        0.010         772 
-1500     -425.5980        0.010         772 
-1600     -425.5952        0.010         772 
-1700     -425.5948        0.010         772 
-1800     -425.5929        0.010         772 
-1900     -425.5920        0.010         772 
-2000     -425.5918        0.010         772 
-2100     -425.5908        0.010         772 
-2200     -425.5905        0.010         772 
-2300     -425.5903        0.010         772 
-2400     -425.5896        0.010         772 
-2500     -425.5894        0.010         772 
-2600     -425.5871        0.010         772 
-2700     -425.5869        0.010         772 
-2800     -425.5863        0.010         772 
-2900     -425.5859        0.010         772 
-3000     -425.5856        0.010         772 
-3100     -425.5847        0.010         772 
-3200     -425.5847        0.010         772 
-3300     -425.5842        0.010         772 
-3400     -425.5842        0.010         772 
-3500     -425.5838        0.010         772 
-3600     -425.5832        0.010         772 
-3700     -425.5827        0.010         772 
-3800     -425.5826        0.010         772 
-3900     -425.5823        0.010         772 
-4000     -425.5823        0.010         772 
-4100     -425.5816        0.010         772 
-4200     -425.5815        0.010         772 
-4300     -425.5815        0.010         772 
-4400     -425.5813        0.010         772 
+1        -439.2231        0.010           0 
+100      -428.8677        0.010          98 
+200      -428.0499        0.010         164 
+300      -427.6003        0.010         249 
+400      -427.5648        0.010         249 
+500      -427.4910        0.010         499 
+600      -427.3863        0.010         511 
+700      -425.7187        0.010         668 
+800      -425.6951        0.010         722 
+900      -425.6795        0.010         722 
+1000     -425.6689        0.010         722 
+1100     -425.6640        0.010         722 
+1200     -425.6430        0.010         722 
+1300     -425.6381        0.010         722 
+1400     -425.6345        0.010         722 
+1500     -425.6341        0.010         722 
+1600     -425.6274        0.010         722 
+1700     -425.6239        0.010         722 
+1800     -425.6236        0.010         722 
+1900     -425.6225        0.010         722 
+2000     -425.6202        0.010         722 
+2100     -425.6197        0.010         722 
+2200     -425.6174        0.010         722 
+2300     -425.6146        0.010         722 
+2400     -425.6135        0.010         722 
+2500     -425.6104        0.010         722 
+2600     -425.6099        0.010         722 
+2700     -425.6088        0.010         722 
+2800     -425.6077        0.010         722 
+2900     -425.6073        0.010         722 
+3000     -425.6059        0.010         722 
+3100     -425.6056        0.010         722 
+3200     -425.6055        0.010         722 
+3300     -425.6051        0.010         722 
+3400     -425.6049        0.010         722 
+3500     -425.6048        0.010         722 
+3600     -425.6048        0.010         722 
 Reached termination condition!
-last topological improvement at gen 772
-Improvement over last 500 gen = 0.00098
-Current score = -425.5813
+last topological improvement at gen 722
+Improvement over last 500 gen = 0.00084
+Current score = -425.6048
 Performing final optimizations...
-pass 1 : -425.5707   (branch= 0.0000  subset rates= 0.0106)
-pass 2 : -425.5552   (branch= 0.0128  subset rates= 0.0026)
-pass 3 : -425.5518   (branch= 0.0034  subset rates= 0.0000)
-pass 4 : -425.5506   (branch= 0.0012  subset rates= 0.0000)
-pass 5 : -425.5506   (branch= 0.0000  subset rates= 0.0000)
-pass 6 : -425.5499   (branch= 0.0006  subset rates= 0.0000)
-pass 7 : -425.5498   (branch= 0.0001  subset rates= 0.0000)
-pass 8 : -425.5497   (branch= 0.0002  subset rates= 0.0000)
-pass 9 : -425.5495   (branch= 0.0002  subset rates= 0.0000)
-pass 10: -425.5494   (branch= 0.0001  subset rates= 0.0000)
-pass 11: -425.5494   (branch= 0.0000  subset rates= 0.0000)
-pass 12: -425.5494   (branch= 0.0000  subset rates= 0.0000)
+pass 1 : -425.6048   (branch= 0.0000  subset rates= 0.0000)
+pass 2 : -425.5577   (branch= 0.0188  subset rates= 0.0282)
+pass 3 : -425.5536   (branch= 0.0041  subset rates= 0.0000)
+pass 4 : -425.5523   (branch= 0.0012  subset rates= 0.0000)
+pass 5 : -425.5511   (branch= 0.0013  subset rates= 0.0000)
+pass 6 : -425.5498   (branch= 0.0007  subset rates= 0.0005)
+pass 7 : -425.5492   (branch= 0.0007  subset rates= 0.0000)
+pass 8 : -425.5489   (branch= 0.0003  subset rates= 0.0000)
+pass 9 : -425.5488   (branch= 0.0001  subset rates= 0.0000)
+pass 10: -425.5487   (branch= 0.0001  subset rates= 0.0000)
+pass 11: -425.5487   (branch= 0.0000  subset rates= 0.0000)
+pass 12: -425.5486   (branch= 0.0000  subset rates= 0.0000)
+pass 13: -425.5486   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
-Final score = -425.5494
-Time used so far = 0 hours, 0 minutes and 7 seconds
+Final score = -425.5486
+Time used so far = 0 hours, 0 minutes and 10 seconds
 
 MODEL REPORT - Parameter values are FINAL
 Model 1
@@ -22253,88 +18856,57 @@
     no rate heterogeneity
 
 Subset rate multipliers:
-    0.87  1.53  1.11
+    0.87  1.53  1.12
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    10 branches were collapsed.
+    9 branches were collapsed.
 
->>>Completed Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<<
+>>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<<
 
->>>Bootstrap rep 1 (of 1) Search rep 5 (of 5)<<<
+>>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<<
 Obtained starting tree 1 from Nexus
-Starting with seed=168869522
+Starting with seed=2129292874
 
-Initial ln Likelihood: -579.0195
+Initial ln Likelihood: -588.2493
 optimizing: starting branch lengths, subset rates...
-pass 1:+  123.488 (branch= 121.41 scale=  1.88 subset rates=  0.20)
-pass 2:+   14.572 (branch=  14.50 scale=  0.00 subset rates=  0.08)
-pass 3:+    1.641 (branch=   1.62 scale=  0.02 subset rates=  0.00)
-pass 4:+    0.124 (branch=   0.12 scale=  0.00 subset rates=  0.00)
+pass 1:+  141.030 (branch= 140.49 scale=  0.38 subset rates=  0.17)
+pass 2:+    6.535 (branch=   6.52 scale=  0.00 subset rates=  0.02)
+pass 3:+    1.052 (branch=   1.03 scale=  0.00 subset rates=  0.02)
+pass 4:+    0.061 (branch=   0.06 scale=  0.00 subset rates=  0.00)
 pass 5:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
-lnL after optimization: -439.1943
+lnL after optimization: -439.5713
 gen      current_lnL    precision  last_tree_imp  
-0        -439.1943        0.010           0 
-100      -434.6851        0.010          38 
-200      -432.5357        0.010         130 
-300      -432.5139        0.010         263 
-400      -432.5121        0.010         263 
-500      -432.5109        0.010         263 
-600      -427.8690        0.010         536 
-700      -427.0560        0.010         659 
-800      -427.0182        0.010         714 
-900      -427.0122        0.010         714 
-1000     -426.9995        0.010         714 
-1100     -426.9914        0.010         714 
-1200     -426.9867        0.010         714 
-1300     -426.9864        0.010         714 
-1400     -426.8164        0.010        1382 
-1500     -425.8924        0.010        1454 
-1600     -425.8579        0.010        1454 
-1700     -425.4428        0.010        1643 
-1800     -425.3860        0.010        1717 
-1900     -425.3791        0.010        1717 
-2000     -425.3756        0.010        1717 
-2100     -425.3739        0.010        1717 
-2200     -425.3699        0.010        1717 
-2300     -425.3683        0.010        1717 
-2400     -425.3643        0.010        1717 
-2500     -425.3605        0.010        1717 
-2600     -425.3551        0.010        1717 
-2700     -425.3532        0.010        1717 
-2800     -425.3528        0.010        1717 
-2900     -425.3520        0.010        1717 
-3000     -425.3517        0.010        1717 
-3100     -425.3515        0.010        1717 
-3200     -425.3494        0.010        1717 
-3300     -425.3493        0.010        1717 
-3400     -425.3489        0.010        1717 
-3500     -425.3487        0.010        1717 
-3600     -425.3483        0.010        1717 
-3700     -425.3481        0.010        1717 
-3800     -425.3479        0.010        1717 
-3900     -425.3478        0.010        1717 
-4000     -425.3477        0.010        1717 
-Reached termination condition!
-last topological improvement at gen 1717
-Improvement over last 500 gen = 0.00100
-Current score = -425.3477
+0        -439.5713        0.010           0 
+100      -431.1390        0.010          95 
+200      -428.6585        0.010         167 
+300      -427.6515        0.010         295 
+400      -427.2441        0.010         295 
+500      -427.2139        0.010         295 
+600      -427.1680        0.010         568 
+700      -427.1488        0.010         568 
+800      -425.4819        0.010         762 
+900      -425.4264        0.010         803 
+1000     -425.4085        0.010         803 
+NOTE: ****Specified time limit (5 seconds) reached...
+Current score = -425.4064
 Performing final optimizations...
-pass 1 : -425.3467   (branch= 0.0000  subset rates= 0.0009)
-pass 2 : -425.3314   (branch= 0.0142  subset rates= 0.0012)
-pass 3 : -425.3253   (branch= 0.0061  subset rates= 0.0000)
-pass 4 : -425.3242   (branch= 0.0011  subset rates= 0.0000)
-pass 5 : -425.3231   (branch= 0.0008  subset rates= 0.0003)
-pass 6 : -425.3225   (branch= 0.0006  subset rates= 0.0000)
-pass 7 : -425.3217   (branch= 0.0008  subset rates= 0.0000)
-pass 8 : -425.3215   (branch= 0.0002  subset rates= 0.0000)
-pass 9 : -425.3212   (branch= 0.0002  subset rates= 0.0000)
-pass 10: -425.3211   (branch= 0.0001  subset rates= 0.0000)
-pass 11: -425.3203   (branch= 0.0000  subset rates= 0.0008)
-pass 12: -425.3203   (branch= 0.0000  subset rates= 0.0000)
+pass 1 : -425.3809   (branch= 0.0202  subset rates= 0.0053)
+pass 2 : -425.3510   (branch= 0.0299  subset rates= 0.0000)
+pass 3 : -425.3353   (branch= 0.0157  subset rates= 0.0000)
+pass 4 : -425.3262   (branch= 0.0091  subset rates= 0.0000)
+pass 5 : -425.3222   (branch= 0.0040  subset rates= 0.0000)
+pass 6 : -425.3213   (branch= 0.0010  subset rates= 0.0000)
+pass 7 : -425.3209   (branch= 0.0004  subset rates= 0.0000)
+pass 8 : -425.3207   (branch= 0.0001  subset rates= 0.0000)
+pass 9 : -425.3206   (branch= 0.0001  subset rates= 0.0000)
+pass 10: -425.3206   (branch= 0.0000  subset rates= 0.0000)
+pass 11: -425.3206   (branch= 0.0000  subset rates= 0.0000)
+pass 12: -425.3206   (branch= 0.0000  subset rates= 0.0000)
+pass 13: -425.3205   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
-Final score = -425.3203
-Time used = 0 hours, 0 minutes and 8 seconds
+Final score = -425.3205
+Time used so far = 0 hours, 0 minutes and 12 seconds
 
-MODEL REPORT - Parameter values are FINAL
+MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT
 Model 1
   Number of states = 2 (standard data)
   Character change matrix:
@@ -22360,24 +18932,26 @@
     no rate heterogeneity
 
 Subset rate multipliers:
-    0.87  1.54  1.14
+    0.86  1.54  1.15
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    9 branches were collapsed.
+    10 branches were collapsed.
+
+>>>Terminated Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<<
+
+NOTE: ***Search was terminated before full auto-termination condition was reached!
+Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
 
->>>Completed Bootstrap rep 1 (of 1) Search rep 5 (of 5)<<<
 
 #######################################################
 
-Completed 5 replicate search(es) (of 5).
+Completed 3 replicate search(es) (of 5).
 
 NOTE: Unless the following output indicates that search replicates found the
 	same topology, you should assume that they found different topologies.
 Results:
 Replicate 1 : -425.5486       
 Replicate 2 : -425.5486       
-Replicate 3 : -425.3201 (best)
-Replicate 4 : -425.5494        (same topology as 1)
-Replicate 5 : -425.3203        (same topology as 3)
+Replicate 3 : -425.3205 (best) (TERMINATED PREMATURELY) 
 
 Parameter estimates across search replicates:
 
@@ -22394,13 +18968,11 @@
           TL   R(1)  R(2)  R(3)
 rep 1:  3.040 0.869 1.528 1.121
 rep 2:  3.039 0.869 1.527 1.119
-rep 3:  2.978 0.864 1.543 1.148
-rep 4:  3.040 0.868 1.533 1.106
-rep 5:  2.982 0.866 1.536 1.138
+rep 3:  2.979 0.863 1.544 1.145
 
 Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre
 
->>>Completed Bootstrap rep 1<<<
+WARNING: Tree from prematurely terminated search saved to bootstrap file
 #######################################################
 TREEFILES PASS
 Running checkpoint test ./check/p.mkvO.ssr.conf
@@ -22592,271 +19164,6 @@
 2600     -473.9778        0.010         663 
 2700     -473.9772        0.010         663 
 2800     -473.9768        0.010         663 
-2900     -473.9767        0.010         663 
-3000     -473.9767        0.010         663 
-3100     -473.9765        0.010         663 
-3200     -473.9765        0.010         663 
-Reached termination condition!
-last topological improvement at gen 663
-Improvement over last 500 gen = 0.00073
-Current score = -473.9765
-Performing final optimizations...
-pass 1 : -473.9764   (branch= 0.0001  subset rates= 0.0000)
-pass 2 : -473.9596   (branch= 0.0153  subset rates= 0.0015)
-pass 3 : -473.9548   (branch= 0.0024  subset rates= 0.0024)
-pass 4 : -473.9540   (branch= 0.0008  subset rates= 0.0000)
-pass 5 : -473.9529   (branch= 0.0012  subset rates= 0.0000)
-pass 6 : -473.9522   (branch= 0.0007  subset rates= 0.0000)
-pass 7 : -473.9518   (branch= 0.0004  subset rates= 0.0000)
-pass 8 : -473.9513   (branch= 0.0005  subset rates= 0.0000)
-pass 9 : -473.9509   (branch= 0.0002  subset rates= 0.0001)
-pass 10: -473.9508   (branch= 0.0001  subset rates= 0.0000)
-pass 11: -473.9508   (branch= 0.0000  subset rates= 0.0000)
-pass 12: -473.9508   (branch= 0.0000  subset rates= 0.0000)
-pass 13: -473.9508   (branch= 0.0000  subset rates= 0.0000)
-Looking for minimum length branches...
-Final score = -473.9508
-Time used so far = 0 hours, 0 minutes and 2 seconds
-
-MODEL REPORT - Parameter values are FINAL
-Model 1
-  Number of states = 2 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 3
-  Number of states = 4 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    0.59  2.07  2.80
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    8 branches were collapsed.
-
->>>Completed Search rep 1 (of 5)<<<
-
->>>Search rep 2 (of 5)<<<
-Obtained starting tree 1 from Nexus
-MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
-Model 1
-  Number of states = 2 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 3
-  Number of states = 4 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    1.00  1.00  1.00
-Starting with seed=2102612689
-
-Initial ln Likelihood: -621.4204
-optimizing: starting branch lengths, subset rates...
-pass 1:+  126.879 (branch= 115.75 scale=  0.84 subset rates= 10.29)
-pass 2:+   14.864 (branch=   9.78 scale=  0.00 subset rates=  5.08)
-pass 3:+    3.762 (branch=   2.04 scale=  0.00 subset rates=  1.72)
-pass 4:+    0.945 (branch=   0.32 scale=  0.02 subset rates=  0.61)
-pass 5:+    0.062 (branch=   0.04 scale=  0.00 subset rates=  0.02)
-pass 6:+    0.038 (branch=   0.04 scale=  0.00 subset rates=  0.00)
-pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
-lnL after optimization: -474.8703
-gen      current_lnL    precision  last_tree_imp  
-0        -474.8703        0.010           0 
-100      -474.8246        0.010           0 
-200      -474.8160        0.010           0 
-300      -474.7392        0.010         224 
-400      -474.7245        0.010         224 
-500      -474.5290        0.010         429 
-600      -474.4732        0.010         502 
-700      -474.4649        0.010         502 
-800      -474.4584        0.010         502 
-900      -474.4515        0.010         502 
-1000     -474.4453        0.010         502 
-1100     -474.4357        0.010         502 
-1200     -474.4236        0.010         502 
-1300     -474.4207        0.010         502 
-1400     -474.4150        0.010         502 
-1500     -474.4128        0.010         502 
-1600     -474.4091        0.010         502 
-1700     -474.4058        0.010         502 
-1800     -474.4028        0.010         502 
-1900     -474.4021        0.010         502 
-2000     -474.4005        0.010         502 
-2100     -474.3986        0.010         502 
-2200     -474.3951        0.010         502 
-2300     -474.3926        0.010         502 
-2400     -474.3879        0.010         502 
-2500     -474.3877        0.010         502 
-2600     -474.3853        0.010         502 
-2700     -474.3828        0.010         502 
-2800     -474.3827        0.010         502 
-2900     -474.3813        0.010         502 
-3000     -474.3803        0.010         502 
-3100     -474.3782        0.010         502 
-3200     -474.3770        0.010         502 
-3300     -474.3752        0.010         502 
-3400     -474.3715        0.010         502 
-3500     -474.3703        0.010         502 
-3600     -474.3694        0.010         502 
-3700     -474.3684        0.010         502 
-3800     -474.3679        0.010         502 
-3900     -474.3676        0.010         502 
-4000     -474.3668        0.010         502 
-4100     -474.3664        0.010         502 
-4200     -474.3661        0.010         502 
-4300     -474.3660        0.010         502 
-4400     -474.3659        0.010         502 
-4500     -474.3643        0.010         502 
-4600     -474.3642        0.010         502 
-4700     -474.3637        0.010         502 
-4800     -474.3634        0.010         502 
-4900     -474.3630        0.010         502 
-5000     -474.3627        0.010         502 
-   Optimizing parameters...    improved    0.000 lnL
-   Optimizing branchlengths... improved    0.000 lnL
-5100     -474.3627        0.010         502 
-5200     -474.3627        0.010         502 
-5300     -474.3624        0.010         502 
-5400     -474.3624        0.010         502 
-Reached termination condition!
-last topological improvement at gen 502
-Improvement over last 500 gen = 0.00065
-Current score = -474.3624
-Performing final optimizations...
-pass 1 : -474.3573   (branch= 0.0000  subset rates= 0.0051)
-pass 2 : -474.3411   (branch= 0.0150  subset rates= 0.0012)
-pass 3 : -474.3373   (branch= 0.0037  subset rates= 0.0000)
-pass 4 : -474.3348   (branch= 0.0025  subset rates= 0.0000)
-pass 5 : -474.3334   (branch= 0.0014  subset rates= 0.0000)
-pass 6 : -474.3327   (branch= 0.0007  subset rates= 0.0000)
-pass 7 : -474.3322   (branch= 0.0005  subset rates= 0.0000)
-pass 8 : -474.3320   (branch= 0.0002  subset rates= 0.0000)
-pass 9 : -474.3317   (branch= 0.0003  subset rates= 0.0000)
-pass 10: -474.3317   (branch= 0.0000  subset rates= 0.0000)
-pass 11: -474.3317   (branch= 0.0000  subset rates= 0.0000)
-pass 12: -474.3317   (branch= 0.0000  subset rates= 0.0000)
-Looking for minimum length branches...
-Final score = -474.3317
-Time used so far = 0 hours, 0 minutes and 5 seconds
-
-MODEL REPORT - Parameter values are FINAL
-Model 1
-  Number of states = 2 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 3
-  Number of states = 4 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    0.62  1.94  2.82
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    7 branches were collapsed.
-
->>>Completed Search rep 2 (of 5)<<<
-
->>>Search rep 3 (of 5)<<<
-Obtained starting tree 1 from Nexus
-MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
-Model 1
-  Number of states = 2 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 3
-  Number of states = 4 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    1.00  1.00  1.00
-Starting with seed=506017183
-
-Initial ln Likelihood: -631.6760
-optimizing: starting branch lengths, subset rates...
-pass 1:+  133.891 (branch= 123.05 scale=  0.38 subset rates= 10.46)
-pass 2:+   17.845 (branch=  13.02 scale=  0.00 subset rates=  4.83)
-pass 3:+    3.961 (branch=   2.25 scale=  0.02 subset rates=  1.69)
-pass 4:+    1.002 (branch=   0.40 scale=  0.00 subset rates=  0.60)
-pass 5:+    0.093 (branch=   0.06 scale=  0.00 subset rates=  0.03)
-pass 6:+    0.019 (branch=   0.02 scale=  0.00 subset rates=  0.00)
-pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
-lnL after optimization: -474.8655
-gen      current_lnL    precision  last_tree_imp  
-0        -474.8655        0.010           0 
-100      -474.6907        0.010          98 
-200      -474.1114        0.010         198 
-300      -474.0445        0.010         265 
-400      -474.0307        0.010         265 
-500      -474.0301        0.010         265 
-600      -474.0268        0.010         265 
-700      -474.0181        0.010         265 
-800      -474.0146        0.010         265 
-900      -474.0095        0.010         265 
-1000     -474.0050        0.010         265 
-1100     -474.0016        0.010         265 
-1200     -474.0005        0.010         265 
 NOTE: ****Specified time limit (5 seconds) reached...
 
 NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY
@@ -22982,49 +19289,33 @@
 STARTING RUN
 
 Restarting from checkpoint...
-Search rep 3 (of 5) generation 1280, seed 371618343, best lnL -473.999
+Search rep 1 (of 5) generation 2800, seed 234954222, best lnL -473.977
 gen      current_lnL    precision  last_tree_imp  
-1280     -473.9992        0.010         265 
-1300     -473.9990        0.010         265 
-1400     -473.9948        0.010         265 
-1500     -473.9947        0.010         265 
-1600     -473.9938        0.010         265 
-1700     -473.9924        0.010         265 
-1800     -473.9916        0.010         265 
-1900     -473.9913        0.010         265 
-2000     -473.9908        0.010         265 
-2100     -473.9898        0.010         265 
-2200     -473.9895        0.010         265 
-2300     -473.9889        0.010         265 
-2400     -473.9883        0.010         265 
-2500     -473.9871        0.010         265 
-2600     -473.9869        0.010         265 
-2700     -473.9865        0.010         265 
-2800     -473.9864        0.010         265 
-2900     -473.9858        0.010         265 
-3000     -473.9856        0.010         265 
-3100     -473.9856        0.010         265 
-3200     -473.9855        0.010         265 
+2800     -473.9768        0.010         663 
+2900     -473.9767        0.010         663 
+3000     -473.9767        0.010         663 
+3100     -473.9765        0.010         663 
+3200     -473.9765        0.010         663 
 Reached termination condition!
-last topological improvement at gen 265
-Improvement over last 500 gen = 0.00098
-Current score = -473.9855
+last topological improvement at gen 663
+Improvement over last 500 gen = 0.00073
+Current score = -473.9765
 Performing final optimizations...
-pass 1 : -473.9855   (branch= 0.0000  subset rates= 0.0000)
-pass 2 : -473.9635   (branch= 0.0206  subset rates= 0.0015)
-pass 3 : -473.9534   (branch= 0.0076  subset rates= 0.0025)
-pass 4 : -473.9534   (branch= 0.0000  subset rates= 0.0000)
-pass 5 : -473.9530   (branch= 0.0004  subset rates= 0.0000)
+pass 1 : -473.9764   (branch= 0.0001  subset rates= 0.0000)
+pass 2 : -473.9596   (branch= 0.0153  subset rates= 0.0015)
+pass 3 : -473.9548   (branch= 0.0024  subset rates= 0.0024)
+pass 4 : -473.9540   (branch= 0.0008  subset rates= 0.0000)
+pass 5 : -473.9529   (branch= 0.0012  subset rates= 0.0000)
 pass 6 : -473.9522   (branch= 0.0007  subset rates= 0.0000)
-pass 7 : -473.9515   (branch= 0.0007  subset rates= 0.0000)
-pass 8 : -473.9514   (branch= 0.0001  subset rates= 0.0000)
-pass 9 : -473.9512   (branch= 0.0003  subset rates= 0.0000)
-pass 10: -473.9510   (branch= 0.0001  subset rates= 0.0000)
-pass 11: -473.9510   (branch= 0.0001  subset rates= 0.0000)
-pass 12: -473.9510   (branch= 0.0000  subset rates= 0.0000)
-pass 13: -473.9510   (branch= 0.0000  subset rates= 0.0000)
+pass 7 : -473.9518   (branch= 0.0004  subset rates= 0.0000)
+pass 8 : -473.9513   (branch= 0.0005  subset rates= 0.0000)
+pass 9 : -473.9509   (branch= 0.0002  subset rates= 0.0001)
+pass 10: -473.9508   (branch= 0.0001  subset rates= 0.0000)
+pass 11: -473.9508   (branch= 0.0000  subset rates= 0.0000)
+pass 12: -473.9508   (branch= 0.0000  subset rates= 0.0000)
+pass 13: -473.9508   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
-Final score = -473.9510
+Final score = -473.9508
 Time used so far = 0 hours, 0 minutes and 7 seconds
 
 MODEL REPORT - Parameter values are FINAL
@@ -23053,13 +19344,13 @@
     no rate heterogeneity
 
 Subset rate multipliers:
-    0.59  2.07  2.81
+    0.59  2.07  2.80
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
     8 branches were collapsed.
 
->>>Completed Search rep 3 (of 5)<<<
+>>>Completed Search rep 1 (of 5)<<<
 
->>>Search rep 4 (of 5)<<<
+>>>Search rep 2 (of 5)<<<
 Obtained starting tree 1 from Nexus
 MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
 Model 1
@@ -23088,79 +19379,60 @@
 
 Subset rate multipliers:
     1.00  1.00  1.00
-Starting with seed=857892252
+Starting with seed=2102612689
 
-Initial ln Likelihood: -608.4729
+Initial ln Likelihood: -621.4204
 optimizing: starting branch lengths, subset rates...
-pass 1:+  116.991 (branch= 106.63 scale=  0.44 subset rates=  9.93)
-pass 2:+   11.607 (branch=   7.05 scale=  0.00 subset rates=  4.55)
-pass 3:+    3.796 (branch=   2.20 scale=  0.00 subset rates=  1.60)
-pass 4:+    0.991 (branch=   0.41 scale=  0.01 subset rates=  0.57)
-pass 5:+    0.196 (branch=   0.16 scale=  0.00 subset rates=  0.03)
-pass 6:+    0.033 (branch=   0.03 scale=  0.00 subset rates=  0.00)
+pass 1:+  126.879 (branch= 115.75 scale=  0.84 subset rates= 10.29)
+pass 2:+   14.864 (branch=   9.78 scale=  0.00 subset rates=  5.08)
+pass 3:+    3.762 (branch=   2.04 scale=  0.00 subset rates=  1.72)
+pass 4:+    0.945 (branch=   0.32 scale=  0.02 subset rates=  0.61)
+pass 5:+    0.062 (branch=   0.04 scale=  0.00 subset rates=  0.02)
+pass 6:+    0.038 (branch=   0.04 scale=  0.00 subset rates=  0.00)
 pass 7:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
-lnL after optimization: -474.8588
+lnL after optimization: -474.8703
 gen      current_lnL    precision  last_tree_imp  
-0        -474.8588        0.010           0 
-100      -474.8216        0.010           0 
-200      -474.8017        0.010           0 
-300      -474.7061        0.010         233 
-400      -474.6864        0.010         233 
-500      -474.6826        0.010         233 
-600      -474.6722        0.010         233 
-700      -474.6104        0.010         661 
-800      -474.0404        0.010         767 
-900      -474.0225        0.010         767 
-1000     -474.0065        0.010         767 
-1100     -474.0018        0.010         767 
-1200     -473.9925        0.010         767 
-1300     -473.9879        0.010         767 
-1400     -473.9850        0.010         767 
-1500     -473.9813        0.010         767 
-1600     -473.9799        0.010         767 
-1700     -473.9794        0.010         767 
-1800     -473.9784        0.010         767 
-1900     -473.9778        0.010         767 
-2000     -473.9772        0.010         767 
-2100     -473.9764        0.010         767 
-2200     -473.9758        0.010         767 
-2300     -473.9757        0.010         767 
-2400     -473.9748        0.010         767 
-2500     -473.9742        0.010         767 
-2600     -473.9740        0.010         767 
-2700     -473.9737        0.010         767 
-2800     -473.9726        0.010         767 
-2900     -473.9724        0.010         767 
-3000     -473.9722        0.010         767 
-3100     -473.9721        0.010         767 
-3200     -473.9718        0.010         767 
-3300     -473.9713        0.010         767 
-3400     -473.9713        0.010         767 
-3500     -473.9713        0.010         767 
-Reached termination condition!
-last topological improvement at gen 767
-Improvement over last 500 gen = 0.00090
-Current score = -473.9713
+0        -474.8703        0.010           0 
+100      -474.8246        0.010           0 
+200      -474.8160        0.010           0 
+300      -474.7392        0.010         224 
+400      -474.7245        0.010         224 
+500      -474.5290        0.010         429 
+600      -474.4732        0.010         502 
+700      -474.4649        0.010         502 
+800      -474.4584        0.010         502 
+900      -474.4515        0.010         502 
+1000     -474.4453        0.010         502 
+1100     -474.4357        0.010         502 
+1200     -474.4236        0.010         502 
+1300     -474.4207        0.010         502 
+1400     -474.4150        0.010         502 
+1500     -474.4128        0.010         502 
+1600     -474.4091        0.010         502 
+1700     -474.4058        0.010         502 
+1800     -474.4028        0.010         502 
+1900     -474.4021        0.010         502 
+2000     -474.4005        0.010         502 
+NOTE: ****Specified time limit (5 seconds) reached...
+Current score = -474.3986
 Performing final optimizations...
-pass 1 : -473.9695   (branch= 0.0000  subset rates= 0.0018)
-pass 2 : -473.9579   (branch= 0.0094  subset rates= 0.0022)
-pass 3 : -473.9531   (branch= 0.0048  subset rates= 0.0000)
-pass 4 : -473.9531   (branch= 0.0000  subset rates= 0.0000)
-pass 5 : -473.9523   (branch= 0.0008  subset rates= 0.0000)
-pass 6 : -473.9523   (branch= 0.0000  subset rates= 0.0000)
-pass 7 : -473.9517   (branch= 0.0006  subset rates= 0.0000)
-pass 8 : -473.9510   (branch= 0.0006  subset rates= 0.0001)
-pass 9 : -473.9509   (branch= 0.0001  subset rates= 0.0000)
-pass 10: -473.9508   (branch= 0.0000  subset rates= 0.0000)
-pass 11: -473.9508   (branch= 0.0001  subset rates= 0.0000)
-pass 12: -473.9508   (branch= 0.0000  subset rates= 0.0000)
-pass 13: -473.9508   (branch= 0.0000  subset rates= 0.0000)
-pass 14: -473.9507   (branch= 0.0000  subset rates= 0.0000)
+pass 1 : -474.3726   (branch= 0.0231  subset rates= 0.0030)
+pass 2 : -474.3550   (branch= 0.0157  subset rates= 0.0019)
+pass 3 : -474.3471   (branch= 0.0079  subset rates= 0.0000)
+pass 4 : -474.3379   (branch= 0.0080  subset rates= 0.0011)
+pass 5 : -474.3352   (branch= 0.0027  subset rates= 0.0000)
+pass 6 : -474.3334   (branch= 0.0017  subset rates= 0.0000)
+pass 7 : -474.3326   (branch= 0.0007  subset rates= 0.0002)
+pass 8 : -474.3321   (branch= 0.0004  subset rates= 0.0000)
+pass 9 : -474.3318   (branch= 0.0004  subset rates= 0.0000)
+pass 10: -474.3317   (branch= 0.0001  subset rates= 0.0000)
+pass 11: -474.3317   (branch= 0.0000  subset rates= 0.0000)
+pass 12: -474.3317   (branch= 0.0000  subset rates= 0.0000)
 Looking for minimum length branches...
-Final score = -473.9507
-Time used so far = 0 hours, 0 minutes and 8 seconds
+Final score = -474.3317
+Time used so far = 0 hours, 0 minutes and 12 seconds
 
-MODEL REPORT - Parameter values are FINAL
+MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT
 Model 1
   Number of states = 2 (ordered standard data)
   Character change matrix:
@@ -23186,158 +19458,25 @@
     no rate heterogeneity
 
 Subset rate multipliers:
-    0.59  2.07  2.80
+    0.62  1.94  2.83
 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    8 branches were collapsed.
-
->>>Completed Search rep 4 (of 5)<<<
-
->>>Search rep 5 (of 5)<<<
-Obtained starting tree 1 from Nexus
-MODEL REPORT - Parameters are at their INITIAL values (not yet optimized)
-Model 1
-  Number of states = 2 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 3
-  Number of states = 4 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Subset rate multipliers:
-    1.00  1.00  1.00
-Starting with seed=785239318
-
-Initial ln Likelihood: -693.0632
-optimizing: starting branch lengths, subset rates...
-pass 1:+  187.310 (branch= 174.63 scale=  2.41 subset rates= 10.27)
-pass 2:+   23.438 (branch=  18.48 scale=  0.04 subset rates=  4.93)
-pass 3:+    6.277 (branch=   4.46 scale=  0.00 subset rates=  1.82)
-pass 4:+    1.024 (branch=   0.43 scale=  0.01 subset rates=  0.58)
-pass 5:+    0.102 (branch=   0.07 scale=  0.00 subset rates=  0.03)
-pass 6:+    0.054 (branch=   0.05 scale=  0.00 subset rates=  0.00)
-pass 7:+    0.013 (branch=   0.01 scale=  0.00 subset rates=  0.00)
-pass 8:+    0.000 (branch=   0.00 scale=  0.00 subset rates=  0.00)
-lnL after optimization: -474.8449
-gen      current_lnL    precision  last_tree_imp  
-0        -474.8449        0.010           0 
-100      -474.7608        0.010          89 
-200      -474.7414        0.010          89 
-300      -474.1207        0.010         281 
-400      -474.1028        0.010         281 
-500      -474.0346        0.010         434 
-600      -474.0250        0.010         434 
-700      -474.0160        0.010         434 
-800      -474.0099        0.010         434 
-900      -474.0043        0.010         434 
-1000     -474.0023        0.010         434 
-1100     -474.0002        0.010         434 
-1200     -473.9991        0.010         434 
-1300     -473.9968        0.010         434 
-1400     -473.9941        0.010         434 
-1500     -473.9920        0.010         434 
-1600     -473.9890        0.010         434 
-1700     -473.9860        0.010         434 
-1800     -473.9855        0.010         434 
-1900     -473.9854        0.010         434 
-2000     -473.9849        0.010         434 
-2100     -473.9838        0.010         434 
-2200     -473.9835        0.010         434 
-2300     -473.9824        0.010         434 
-2400     -473.9823        0.010         434 
-2500     -473.9822        0.010         434 
-2600     -473.9820        0.010         434 
-2700     -473.9814        0.010         434 
-2800     -473.9804        0.010         434 
-2900     -473.9803        0.010         434 
-3000     -473.9801        0.010         434 
-3100     -473.9793        0.010         434 
-3200     -473.9787        0.010         434 
-3300     -473.9786        0.010         434 
-3400     -473.9786        0.010         434 
-3500     -473.9786        0.010         434 
-3600     -473.9785        0.010         434 
-Reached termination condition!
-last topological improvement at gen 434
-Improvement over last 500 gen = 0.00080
-Current score = -473.9785
-Performing final optimizations...
-pass 1 : -473.9785   (branch= 0.0000  subset rates= 0.0000)
-pass 2 : -473.9647   (branch= 0.0129  subset rates= 0.0009)
-pass 3 : -473.9576   (branch= 0.0056  subset rates= 0.0015)
-pass 4 : -473.9551   (branch= 0.0025  subset rates= 0.0000)
-pass 5 : -473.9543   (branch= 0.0008  subset rates= 0.0000)
-pass 6 : -473.9534   (branch= 0.0009  subset rates= 0.0000)
-pass 7 : -473.9518   (branch= 0.0010  subset rates= 0.0007)
-pass 8 : -473.9513   (branch= 0.0004  subset rates= 0.0000)
-pass 9 : -473.9510   (branch= 0.0004  subset rates= 0.0000)
-pass 10: -473.9509   (branch= 0.0001  subset rates= 0.0000)
-pass 11: -473.9508   (branch= 0.0000  subset rates= 0.0000)
-pass 12: -473.9508   (branch= 0.0000  subset rates= 0.0000)
-pass 13: -473.9508   (branch= 0.0000  subset rates= 0.0000)
-Looking for minimum length branches...
-Final score = -473.9508
-Time used = 0 hours, 0 minutes and 11 seconds
-
-MODEL REPORT - Parameter values are FINAL
-Model 1
-  Number of states = 2 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.50, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
-
-Model 2
-  Number of states = 3 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.33, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
+    7 branches were collapsed.
 
-Model 3
-  Number of states = 4 (ordered standard data)
-  Character change matrix:
-    One rate (ordered symmetric one rate Mkv model)
-  Equilibrium State Frequencies: equal (0.25, fixed)
-  Rate Heterogeneity Model:
-    no rate heterogeneity
+>>>Terminated Search rep 2 (of 5)<<<
 
-Subset rate multipliers:
-    0.59  2.06  2.81
-NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1)
-    8 branches were collapsed.
+NOTE: ***Search was terminated before full auto-termination condition was reached!
+Likelihood scores, topologies and model estimates obtained may not be fully optimal!***
 
->>>Completed Search rep 5 (of 5)<<<
 
 #######################################################
 
-Completed 5 replicate search(es) (of 5).
+Completed 2 replicate search(es) (of 5).
 
 NOTE: Unless the following output indicates that search replicates found the
 	same topology, you should assume that they found different topologies.
 Results:
-Replicate 1 : -473.9508       
-Replicate 2 : -474.3317       
-Replicate 3 : -473.9510        (same topology as 1)
-Replicate 4 : -473.9507 (best) (same topology as 1)
-Replicate 5 : -473.9508        (same topology as 1)
+Replicate 1 : -473.9508 (best)
+Replicate 2 : -474.3317        (TERMINATED PREMATURELY) 
 
 Parameter estimates across search replicates:
 
@@ -23353,14 +19492,9 @@
 Treelengths and subset rate multipliers:
           TL   R(1)  R(2)  R(3)
 rep 1:  4.349 0.588 2.067 2.800
-rep 2:  4.369 0.619 1.942 2.819
-rep 3:  4.352 0.586 2.071 2.809
-rep 4:  4.350 0.588 2.067 2.803
-rep 5:  4.349 0.589 2.063 2.806
+rep 2:  4.370 0.619 1.937 2.830
 
-Saving final trees from all search reps to ch.p.mkvO.ssr.best.all.tre
-
-Saving final tree from best search rep (#4) to ch.p.mkvO.ssr.best.tre
+Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre
 #######################################################
 TREEFILES PASS
 ALL TESTS COMPLETED SUCCESSFULLY
@@ -23433,11 +19567,11 @@
    dh_gencontrol
    dh_md5sums
    dh_builddeb
-dpkg-deb: building package 'garli' in '../garli_2.1-9_arm64.deb'.
-dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_arm64.deb'.
+dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_arm64.deb'.
 dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-9_arm64.deb'.
+dpkg-deb: building package 'garli' in '../garli_2.1-9_arm64.deb'.
 dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-9_all.deb'.
-dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-9_arm64.deb'.
+dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-9_arm64.deb'.
  dpkg-genbuildinfo --build=binary -O../garli_2.1-9_arm64.buildinfo
  dpkg-genchanges --build=binary -O../garli_2.1-9_arm64.changes
 dpkg-genchanges: info: binary-only upload (no source code included)
@@ -23445,12 +19579,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: not including original source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/3746721/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/3746721/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/3475926 and its subdirectories
-I: Current time: Thu Oct 30 00:36:12 -12 2025
-I: pbuilder-time-stamp: 1761827772
+I: removing directory /srv/workspace/pbuilder/3746721 and its subdirectories
+I: Current time: Fri Oct 31 02:46:47 +14 2025
+I: pbuilder-time-stamp: 1761828407