1s autopkgtest [18:00:09]: starting date and time: 2024-07-12 18:00:09+0000 1s autopkgtest [18:00:09]: git checkout: fd3bed09 nova: allow more retries for quota issues 1s autopkgtest [18:00:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.axpfhp1d/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade paml --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-91.secgroup --name adt-oracular-amd64-paml-20240712-174257-juju-7f2275-prod-proposed-migration-environment-2-fac69f6e-da4e-49cf-aca0-15ec9476fcb1 --image adt/ubuntu-oracular-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 127s autopkgtest [18:02:15]: testbed dpkg architecture: amd64 129s autopkgtest [18:02:17]: testbed apt version: 2.9.6 129s autopkgtest [18:02:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 134s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 134s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 134s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 134s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [334 kB] 134s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [46.6 kB] 134s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [70.9 kB] 134s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [98.2 kB] 134s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2104 B] 134s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B] 134s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB] 134s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 134s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [368 kB] 134s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [224 kB] 134s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9228 B] 134s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7644 B] 134s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B] 134s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B] 136s Fetched 1342 kB in 0s (5241 kB/s) 136s Reading package lists... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Calculating upgrade... 148s The following packages will be upgraded: 148s libc-bin libc-dev-bin libc-devtools libc6 libc6-dev locales 148s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 10.3 MB of archives. 148s After this operation, 34.8 kB of additional disk space will be used. 148s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-devtools amd64 2.39-3.1ubuntu3 [29.3 kB] 148s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-3.1ubuntu3 [2120 kB] 148s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-3.1ubuntu3 [20.4 kB] 148s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-3.1ubuntu3 [3262 kB] 148s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-3.1ubuntu3 [680 kB] 148s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 locales all 2.39-3.1ubuntu3 [4220 kB] 148s Preconfiguring packages ... 148s Fetched 10.3 MB in 0s (81.9 MB/s) 148s (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 ... 74486 files and directories currently installed.) 148s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_amd64.deb ... 148s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 148s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_amd64.deb ... 148s Unpacking libc6-dev:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 149s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_amd64.deb ... 149s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 149s Preparing to unpack .../libc6_2.39-3.1ubuntu3_amd64.deb ... 149s Unpacking libc6:amd64 (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 149s Setting up libc6:amd64 (2.39-3.1ubuntu3) ... 149s Error: Could not restart systemd, systemd binary not working 149s (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 ... 74486 files and directories currently installed.) 149s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_amd64.deb ... 149s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 149s Setting up libc-bin (2.39-3.1ubuntu3) ... 149s (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 ... 74486 files and directories currently installed.) 149s Preparing to unpack .../locales_2.39-3.1ubuntu3_all.deb ... 149s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 150s Setting up locales (2.39-3.1ubuntu3) ... 150s Generating locales (this might take a while)... 152s en_US.UTF-8... done 152s Generation complete. 152s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 152s Setting up libc-devtools (2.39-3.1ubuntu3) ... 152s Setting up libc6-dev:amd64 (2.39-3.1ubuntu3) ... 152s Processing triggers for man-db (2.12.1-2) ... 153s Processing triggers for systemd (256-1ubuntu1) ... 154s Reading package lists... 155s Building dependency tree... 155s Reading state information... 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 156s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 156s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 156s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 157s Reading package lists... 157s Reading package lists... 157s Building dependency tree... 157s Reading state information... 158s Calculating upgrade... 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Reading package lists... 158s Building dependency tree... 158s Reading state information... 159s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 174s autopkgtest [18:03:02]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 174s autopkgtest [18:03:02]: @@@@@@@@@@@@@@@@@@@@ apt-source paml 178s Get:1 http://ftpmaster.internal/ubuntu oracular/universe paml 4.9j+dfsg-4 (dsc) [2204 B] 178s Get:2 http://ftpmaster.internal/ubuntu oracular/universe paml 4.9j+dfsg-4 (tar) [1375 kB] 178s Get:3 http://ftpmaster.internal/ubuntu oracular/universe paml 4.9j+dfsg-4 (diff) [7128 B] 179s gpgv: Signature made Sat Dec 24 15:02:32 2022 UTC 179s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 179s gpgv: issuer "emollier@debian.org" 179s gpgv: Can't check signature: No public key 179s dpkg-source: warning: cannot verify inline signature for ./paml_4.9j+dfsg-4.dsc: no acceptable signature found 179s autopkgtest [18:03:07]: testing package paml version 4.9j+dfsg-4 180s autopkgtest [18:03:08]: build not needed 195s autopkgtest [18:03:23]: test run-unit-test: preparing testbed 196s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Starting pkgProblemResolver with broken count: 0 197s Starting 2 pkgProblemResolver with broken count: 0 197s Done 198s The following additional packages will be installed: 198s paml paml-doc 198s The following NEW packages will be installed: 198s autopkgtest-satdep paml paml-doc 198s 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. 198s Need to get 1644 kB/1645 kB of archives. 198s After this operation, 8286 kB of additional disk space will be used. 198s Get:1 /tmp/autopkgtest.KcBMR0/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [708 B] 198s Get:2 http://ftpmaster.internal/ubuntu oracular/universe amd64 paml amd64 4.9j+dfsg-4 [641 kB] 198s Get:3 http://ftpmaster.internal/ubuntu oracular/universe amd64 paml-doc all 4.9j+dfsg-4 [1003 kB] 198s Fetched 1644 kB in 0s (22.2 MB/s) 198s Selecting previously unselected package paml. 198s (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 ... 74486 files and directories currently installed.) 198s Preparing to unpack .../paml_4.9j+dfsg-4_amd64.deb ... 198s Unpacking paml (4.9j+dfsg-4) ... 198s Selecting previously unselected package paml-doc. 198s Preparing to unpack .../paml-doc_4.9j+dfsg-4_all.deb ... 198s Unpacking paml-doc (4.9j+dfsg-4) ... 198s Selecting previously unselected package autopkgtest-satdep. 198s Preparing to unpack .../1-autopkgtest-satdep.deb ... 198s Unpacking autopkgtest-satdep (0) ... 198s Setting up paml-doc (4.9j+dfsg-4) ... 198s Setting up paml (4.9j+dfsg-4) ... 198s Setting up autopkgtest-satdep (0) ... 210s (Reading database ... 74701 files and directories currently installed.) 210s Removing autopkgtest-satdep (0) ... 213s autopkgtest [18:03:41]: test run-unit-test: [----------------------- 214s Test 1 216s 216s CODONML in paml version 4.9j, October 2019 216s 216s ---------------------------------------------- 216s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 216s TTC | TCC | TAC | TGC 216s Leu L TTA | TCA | *** * TAA | *** * TGA 216s TTG | TCG | TAG | Trp W TGG 216s ---------------------------------------------- 216s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 216s CTC | CCC | CAC | CGC 216s CTA | CCA | Gln Q CAA | CGA 216s CTG | CCG | CAG | CGG 216s ---------------------------------------------- 216s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 216s ATC | ACC | AAC | AGC 216s ATA | ACA | Lys K AAA | Arg R AGA 216s Met M ATG | ACG | AAG | AGG 216s ---------------------------------------------- 216s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 216s GTC | GCC | GAC | GGC 216s GTA | GCA | Glu E GAA | GGA 216s GTG | GCG | GAG | GGG 216s ---------------------------------------------- 216s Nice code, uuh? 216s NSsites batch run (ncatG as in YNGP2000): 0 1 2 216s ns = 13 ls = 273 216s Reading sequences, sequential format.. 216s Reading seq # 1: U68496 Reading seq # 2: U68497 Reading seq # 3: U68498 Reading seq # 4: U68499 Reading seq # 5: U68500 Reading seq # 6: U68501 Reading seq # 7: U68502 Reading seq # 8: U68503 Reading seq # 9: U68504 Reading seq #10: U68505 Reading seq #11: U68506 Reading seq #12: U68507 Reading seq #13: U68508 216s Sequences read.. 216s Counting site patterns.. 0:00 216s Compressing, 79 patterns at 91 / 91 sites (100.0%), 0:00 216s Collecting fpatt[] & pose[], 79 patterns at 91 / 91 sites (100.0%), 0:00 216s Counting codons.. 216s 216s 624 bytes for distance 216s 77104 bytes for conP 216s 6952 bytes for fhK 216s 5000000 bytes for space 216s 216s 216s Model 0: one-ratio 216s 216s TREE # 1 216s (1, 2, ((3, (4, 5)), (6, (7, (8, ((((9, 11), 10), 12), 13)))))); MP score: 136 216s 424072 bytes for conP, adjusted 216s 216s 0.071831 0.089025 0.013728 0.066302 0.066586 0.075598 0.031583 0.018772 0.016656 0.021574 0.020717 0.035124 0.102376 0.024845 0.108261 0.023731 0.020699 0.058793 0.105878 0.018762 0.070512 0.011546 0.086050 0.300000 1.300000 216s 216s ntime & nrate & np: 23 2 25 216s 216s Bounds (np=25): 216s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 216s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 216s 216s np = 25 216s lnL0 = -1289.344778 216s 216s Iterating by ming2 216s Initial: fx= 1289.344778 216s x= 0.07183 0.08903 0.01373 0.06630 0.06659 0.07560 0.03158 0.01877 0.01666 0.02157 0.02072 0.03512 0.10238 0.02484 0.10826 0.02373 0.02070 0.05879 0.10588 0.01876 0.07051 0.01155 0.08605 0.30000 1.30000 216s 216s 1 h-m-p 0.0000 0.0016 1074.8514 ++YCYCCC 1210.775425 5 0.0003 40 | 0/25 216s 2 h-m-p 0.0002 0.0012 205.4628 +YYCYCCC 1182.808016 6 0.0010 78 | 0/25 216s 3 h-m-p 0.0001 0.0003 322.6390 +CYYCCC 1176.394055 5 0.0003 115 | 0/25 216s 4 h-m-p 0.0000 0.0002 1646.9023 +YCCCC 1169.031860 4 0.0001 151 | 0/25 216s 5 h-m-p 0.0006 0.0031 190.1173 YYCCC 1162.689996 4 0.0009 185 | 0/25 216s 6 h-m-p 0.0011 0.0053 83.4734 YCCC 1159.456414 3 0.0016 218 | 0/25 216s 7 h-m-p 0.0017 0.0084 38.5206 CCCC 1158.442341 3 0.0018 252 | 0/25 216s 8 h-m-p 0.0012 0.0058 17.4432 YYC 1158.312244 2 0.0010 282 | 0/25 216s 9 h-m-p 0.0017 0.0374 10.3792 CCC 1158.218581 2 0.0022 314 | 0/25 216s 10 h-m-p 0.0014 0.0172 16.5674 YC 1158.033361 1 0.0030 343 | 0/25 216s 11 h-m-p 0.0015 0.0176 33.2994 +YCCCCC 1157.220399 5 0.0065 381 | 0/25 221s 12 h-m-p 0.0010 0.0051 192.0222 YYYCCCC 1156.495524 6 0.0010 418 | 0/25 221s 13 h-m-p 0.0011 0.0057 71.6134 YYC 1156.249602 2 0.0010 448 | 0/25 221s 14 h-m-p 0.0094 0.0471 6.0239 YCC 1156.216375 2 0.0017 479 | 0/25 221s 15 h-m-p 0.0046 0.0983 2.2398 YC 1156.085854 1 0.0091 508 | 0/25 221s 16 h-m-p 0.0038 0.0666 5.4454 +CCCCC 1154.516746 4 0.0184 545 | 0/25 221s 17 h-m-p 0.0017 0.0087 44.9970 YCCCC 1151.166841 4 0.0040 580 | 0/25 221s 18 h-m-p 0.0011 0.0055 82.3239 +YCCCC 1145.592554 4 0.0031 616 | 0/25 221s 19 h-m-p 0.0007 0.0033 69.3617 YCCCC 1144.174644 4 0.0012 651 | 0/25 221s 20 h-m-p 0.0008 0.0039 30.0464 CCC 1143.893096 2 0.0009 683 | 0/25 221s 21 h-m-p 0.0013 0.0067 17.1754 YCC 1143.838244 2 0.0006 714 | 0/25 221s 22 h-m-p 0.0013 0.0143 7.4082 YC 1143.816635 1 0.0009 743 | 0/25 221s 23 h-m-p 0.0042 0.0730 1.5326 C 1143.793205 0 0.0042 771 | 0/25 221s 24 h-m-p 0.0028 0.0646 2.2939 +CCCC 1143.461035 3 0.0135 806 | 0/25 221s 25 h-m-p 0.0008 0.0106 37.1187 +YCCCCC 1141.545399 5 0.0038 844 | 0/25 221s 26 h-m-p 0.0004 0.0019 73.9632 YCCCC 1140.767154 4 0.0008 879 | 0/25 221s 27 h-m-p 0.0012 0.0062 10.8681 CYC 1140.702918 2 0.0012 910 | 0/25 221s 28 h-m-p 0.0672 4.2681 0.1871 ++CCC 1139.492646 2 1.0011 944 | 0/25 221s 29 h-m-p 1.0151 7.2622 0.1845 CYC 1138.572287 2 1.2212 1000 | 0/25 221s 30 h-m-p 1.5486 7.9864 0.1455 CCC 1138.063806 2 1.3451 1057 | 0/25 221s 31 h-m-p 1.6000 8.0000 0.0870 CCC 1137.823738 2 1.4227 1114 | 0/25 221s 32 h-m-p 1.6000 8.0000 0.0451 CCC 1137.739536 2 1.4611 1171 | 0/25 221s 33 h-m-p 1.6000 8.0000 0.0142 CCC 1137.701790 2 1.3987 1228 | 0/25 221s 34 h-m-p 1.6000 8.0000 0.0106 CC 1137.691915 1 1.4349 1283 | 0/25 221s 35 h-m-p 1.6000 8.0000 0.0081 YC 1137.689901 1 1.0946 1337 | 0/25 221s 36 h-m-p 1.6000 8.0000 0.0025 CC 1137.689126 1 1.9759 1392 | 0/25 221s 37 h-m-p 1.6000 8.0000 0.0005 CC 1137.688439 1 2.1920 1447 | 0/25 221s 38 h-m-p 0.4992 8.0000 0.0023 +YC 1137.688199 1 1.4239 1502 | 0/25 221s 39 h-m-p 1.6000 8.0000 0.0002 Y 1137.688191 0 1.1168 1555 | 0/25 221s 40 h-m-p 1.6000 8.0000 0.0001 Y 1137.688190 0 0.9975 1608 | 0/25 221s 41 h-m-p 1.6000 8.0000 0.0000 Y 1137.688190 0 0.9797 1661 | 0/25 221s 42 h-m-p 1.6000 8.0000 0.0000 Y 1137.688190 0 1.0797 1714 | 0/25 221s 43 h-m-p 1.6000 8.0000 0.0000 C 1137.688190 0 1.2886 1767 | 0/25 221s 44 h-m-p 1.6000 8.0000 0.0000 C 1137.688190 0 1.6000 1820 | 0/25 221s 45 h-m-p 1.6000 8.0000 0.0000 Y 1137.688190 0 1.6000 1873 | 0/25 221s 46 h-m-p 1.6000 8.0000 0.0000 N 1137.688190 0 0.2000 1926 221s Out.. 221s lnL = -1137.688190 221s 1927 lfun, 1927 eigenQcodon, 44321 P(t) 221s 221s Time used: 0:07 221s 221s 221s Model 1: NearlyNeutral 221s 221s TREE # 1 221s (1, 2, ((3, (4, 5)), (6, (7, (8, ((((9, 11), 10), 12), 13)))))); MP score: 136 221s 0.105120 0.083566 0.049344 0.078191 0.082361 0.018194 0.027476 0.089270 0.028497 0.108008 0.047205 0.028636 0.099656 0.032775 0.032128 0.091725 0.076504 0.053630 0.072412 0.032345 0.043396 0.029850 0.060330 2.471747 0.572887 0.355846 221s 221s ntime & nrate & np: 23 2 26 221s 221s Bounds (np=26): 221s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000010 0.000001 221s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 0.999990 1.000000 221s Qfactor_NS = 4.405207 221s 221s np = 26 221s lnL0 = -1180.075908 221s 221s Iterating by ming2 221s Initial: fx= 1180.075908 234s x= 0.10512 0.08357 0.04934 0.07819 0.08236 0.01819 0.02748 0.08927 0.02850 0.10801 0.04721 0.02864 0.09966 0.03277 0.03213 0.09173 0.07650 0.05363 0.07241 0.03234 0.04340 0.02985 0.06033 2.47175 0.57289 0.35585 234s 234s 1 h-m-p 0.0000 0.0012 608.4570 +++CCCCC 1129.249552 4 0.0006 42 | 0/26 234s 2 h-m-p 0.0002 0.0010 108.7622 +YYCCCCC 1122.990935 6 0.0008 82 | 0/26 234s 3 h-m-p 0.0001 0.0003 232.0198 +YCYCC 1120.992366 4 0.0002 118 | 0/26 234s 4 h-m-p 0.0002 0.0012 110.2603 +CYC 1117.782807 2 0.0010 151 | 0/26 234s 5 h-m-p 0.0004 0.0020 108.5732 CYCCC 1115.695378 4 0.0008 187 | 0/26 234s 6 h-m-p 0.0006 0.0029 21.6145 YCCC 1115.475098 3 0.0011 221 | 0/26 234s 7 h-m-p 0.0011 0.0071 22.4734 YCC 1115.250434 2 0.0017 253 | 0/26 234s 8 h-m-p 0.0013 0.0065 27.7783 CC 1115.068318 1 0.0013 284 | 0/26 234s 9 h-m-p 0.0020 0.0244 17.6685 YCC 1114.987901 2 0.0012 316 | 0/26 234s 10 h-m-p 0.0022 0.0128 9.8599 YC 1114.963832 1 0.0009 346 | 0/26 234s 11 h-m-p 0.0030 0.0540 3.1342 YC 1114.956494 1 0.0018 376 | 0/26 234s 12 h-m-p 0.0021 0.0437 2.6540 YC 1114.953047 1 0.0014 406 | 0/26 234s 13 h-m-p 0.0019 0.1083 2.0377 C 1114.950449 0 0.0018 435 | 0/26 234s 14 h-m-p 0.0016 0.1441 2.3521 +YC 1114.944112 1 0.0041 466 | 0/26 234s 15 h-m-p 0.0016 0.0679 6.0333 YC 1114.929678 1 0.0036 496 | 0/26 234s 16 h-m-p 0.0010 0.0330 22.2821 YC 1114.894646 1 0.0024 526 | 0/26 234s 17 h-m-p 0.0016 0.0198 33.4531 YC 1114.838035 1 0.0026 556 | 0/26 234s 18 h-m-p 0.0035 0.0398 25.1009 YC 1114.814850 1 0.0014 586 | 0/26 234s 19 h-m-p 0.0195 0.0975 1.3665 -C 1114.813794 0 0.0013 616 | 0/26 234s 20 h-m-p 0.0032 0.7570 0.5622 CC 1114.811896 1 0.0050 647 | 0/26 234s 21 h-m-p 0.0037 0.2589 0.7433 YC 1114.806110 1 0.0077 703 | 0/26 234s 22 h-m-p 0.0017 0.1858 3.3040 +CC 1114.771486 1 0.0091 761 | 0/26 234s 23 h-m-p 0.0021 0.0584 14.2981 YC 1114.711240 1 0.0037 791 | 0/26 234s 24 h-m-p 0.0081 0.0662 6.4293 -YC 1114.705849 1 0.0009 822 | 0/26 234s 25 h-m-p 0.0080 0.2347 0.7095 CC 1114.705260 1 0.0023 853 | 0/26 234s 26 h-m-p 0.0036 0.6833 0.4641 C 1114.704822 0 0.0039 908 | 0/26 234s 27 h-m-p 0.0441 2.3536 0.0414 CC 1114.702253 1 0.0634 965 | 0/26 234s 28 h-m-p 0.0043 0.2058 0.6063 +YC 1114.676666 1 0.0146 1022 | 0/26 234s 29 h-m-p 1.6000 8.0000 0.0039 YC 1114.650330 1 3.6729 1078 | 0/26 234s 30 h-m-p 1.6000 8.0000 0.0043 C 1114.642899 0 1.6010 1133 | 0/26 234s 31 h-m-p 1.6000 8.0000 0.0011 CC 1114.641824 1 1.4401 1190 | 0/26 234s 32 h-m-p 1.6000 8.0000 0.0004 Y 1114.641738 0 1.2632 1245 | 0/26 234s 33 h-m-p 1.6000 8.0000 0.0002 Y 1114.641736 0 0.9989 1300 | 0/26 234s 34 h-m-p 1.6000 8.0000 0.0000 Y 1114.641736 0 1.0618 1355 | 0/26 234s 35 h-m-p 1.6000 8.0000 0.0000 Y 1114.641736 0 1.0946 1410 | 0/26 234s 36 h-m-p 1.6000 8.0000 0.0000 Y 1114.641736 0 1.1327 1465 | 0/26 234s 37 h-m-p 1.6000 8.0000 0.0000 Y 1114.641736 0 0.8971 1520 | 0/26 234s 38 h-m-p 1.6000 8.0000 0.0000 C 1114.641736 0 0.4519 1575 234s Out.. 234s lnL = -1114.641736 234s 1576 lfun, 4728 eigenQcodon, 72496 P(t) 234s 234s Time used: 0:20 234s 234s 234s Model 2: PositiveSelection 234s 234s TREE # 1 234s (1, 2, ((3, (4, 5)), (6, (7, (8, ((((9, 11), 10), 12), 13)))))); MP score: 136 234s initial w for M2:NSpselection reset. 234s 234s 0.109350 0.015551 0.019494 0.069530 0.060093 0.073611 0.074846 0.029967 0.084615 0.086002 0.014959 0.095131 0.034837 0.055324 0.097984 0.065617 0.019357 0.103930 0.046706 0.070081 0.070416 0.049506 0.072098 2.594607 1.496434 0.113539 0.204100 2.324971 234s 234s ntime & nrate & np: 23 3 28 234s 234s Bounds (np=28): 234s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 -99.000000 -99.000000 0.000001 1.000000 257s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 99.000000 99.000000 1.000000 999.000000 257s Qfactor_NS = 4.130742 257s 257s np = 28 257s lnL0 = -1158.334366 257s 257s Iterating by ming2 257s Initial: fx= 1158.334366 257s x= 0.10935 0.01555 0.01949 0.06953 0.06009 0.07361 0.07485 0.02997 0.08461 0.08600 0.01496 0.09513 0.03484 0.05532 0.09798 0.06562 0.01936 0.10393 0.04671 0.07008 0.07042 0.04951 0.07210 2.59461 1.49643 0.11354 0.20410 2.32497 257s 257s 1 h-m-p 0.0000 0.0008 571.3598 +++YCCCC 1122.117000 4 0.0005 43 | 0/28 257s 2 h-m-p 0.0003 0.0014 124.7479 +YYCCC 1113.766881 4 0.0010 81 | 0/28 257s 3 h-m-p 0.0001 0.0005 103.1135 +CYCC 1112.036539 3 0.0004 118 | 0/28 257s 4 h-m-p 0.0002 0.0009 101.9966 YCCC 1110.984509 3 0.0004 154 | 0/28 257s 5 h-m-p 0.0001 0.0006 78.7367 +YCCC 1110.521210 3 0.0004 191 | 0/28 257s 6 h-m-p 0.0008 0.0088 34.5695 CYC 1110.210195 2 0.0009 225 | 0/28 257s 7 h-m-p 0.0011 0.0056 11.4702 CCC 1110.129181 2 0.0015 260 | 0/28 257s 8 h-m-p 0.0003 0.0016 15.3231 ++ 1110.030705 m 0.0016 291 | 0/28 257s 9 h-m-p -0.0000 -0.0000 24.6036 257s h-m-p: -4.57682566e-20 -2.28841283e-19 2.46036472e+01 1110.030705 257s .. | 0/28 257s 10 h-m-p 0.0000 0.0042 28.1488 +++CCC 1109.699856 2 0.0008 357 | 0/28 257s 11 h-m-p 0.0005 0.0023 36.6895 CCCC 1109.418190 3 0.0007 394 | 0/28 257s 12 h-m-p 0.0001 0.0005 29.6844 ++ 1109.304608 m 0.0005 425 | 0/28 257s 13 h-m-p 0.0008 0.0074 19.2642 CCC 1109.212958 2 0.0009 460 | 0/28 257s 14 h-m-p 0.0012 0.0186 15.0897 CCC 1109.157991 2 0.0010 495 | 0/28 257s 15 h-m-p 0.0007 0.0034 13.2947 YC 1109.103205 1 0.0015 527 | 0/28 257s 16 h-m-p 0.0003 0.0014 29.8818 ++ 1108.952324 m 0.0014 558 | 0/28 257s 17 h-m-p 0.0007 0.0099 60.9975 YCC 1108.747968 2 0.0014 592 | 0/28 257s 18 h-m-p 0.0010 0.0174 87.5889 YCCC 1108.369882 3 0.0020 628 | 0/28 257s 19 h-m-p 0.0014 0.0075 123.1960 CCC 1107.878990 2 0.0018 663 | 0/28 257s 20 h-m-p 0.0011 0.0055 99.2811 YCCC 1107.493820 3 0.0018 699 | 0/28 257s 21 h-m-p 0.0011 0.0055 85.0998 CCC 1107.279820 2 0.0011 734 | 0/28 257s 22 h-m-p 0.0008 0.0038 42.4184 YCC 1107.155997 2 0.0014 768 | 0/28 257s 23 h-m-p 0.0012 0.0059 13.2809 CC 1107.118098 1 0.0016 801 | 0/28 257s 24 h-m-p 0.0010 0.0049 4.0922 YC 1107.107312 1 0.0023 833 | 0/28 257s 25 h-m-p 0.0008 0.0039 5.0230 +CC 1107.092280 1 0.0032 867 | 0/28 257s 26 h-m-p 0.0037 0.0948 4.3728 CC 1107.074932 1 0.0053 900 | 0/28 257s 27 h-m-p 0.0002 0.0011 16.5506 ++ 1107.048620 m 0.0011 931 | 1/28 257s 28 h-m-p 0.0003 0.0111 65.4014 +CCC 1106.961294 2 0.0018 967 | 1/28 257s 29 h-m-p 0.0029 0.0428 41.2754 CCC 1106.881727 2 0.0027 1002 | 1/28 257s 30 h-m-p 0.0076 0.0399 14.9207 CC 1106.859538 1 0.0023 1035 | 1/28 257s 31 h-m-p 0.0079 0.0494 4.2337 YC 1106.855842 1 0.0016 1067 | 1/28 257s 32 h-m-p 0.0063 0.7429 1.0606 +CC 1106.838933 1 0.0347 1101 | 1/28 257s 33 h-m-p 0.0027 0.1626 13.8406 +CYC 1106.773721 2 0.0101 1136 | 1/28 257s 34 h-m-p 0.0041 0.0658 33.7047 +YYC 1106.541903 2 0.0143 1170 | 1/28 257s 35 h-m-p 0.0027 0.0135 36.4468 YC 1106.513837 1 0.0016 1202 | 1/28 257s 36 h-m-p 0.0729 0.3644 0.4913 -C 1106.513010 0 0.0041 1234 | 1/28 257s 37 h-m-p 0.0145 7.2477 0.5028 ++CCC 1106.473821 2 0.2584 1298 | 1/28 257s 38 h-m-p 0.9540 8.0000 0.1362 YC 1106.450842 1 0.5762 1357 | 1/28 257s 39 h-m-p 1.1339 8.0000 0.0692 CC 1106.445640 1 1.0457 1417 | 0/28 257s 40 h-m-p 0.0211 0.1550 3.4283 -YC 1106.445436 1 0.0009 1477 | 0/28 257s 41 h-m-p 0.2522 8.0000 0.0117 +C 1106.445046 0 1.1676 1509 | 0/28 257s 42 h-m-p 1.6000 8.0000 0.0037 C 1106.445005 0 1.5375 1568 | 0/28 257s 43 h-m-p 1.6000 8.0000 0.0006 Y 1106.445004 0 1.1719 1627 | 0/28 257s 44 h-m-p 1.6000 8.0000 0.0001 Y 1106.445004 0 1.1078 1686 | 0/28 257s 45 h-m-p 1.6000 8.0000 0.0000 Y 1106.445004 0 1.0580 1745 | 0/28 257s 46 h-m-p 1.6000 8.0000 0.0000 C 1106.445004 0 1.4769 1804 | 0/28 257s 47 h-m-p 1.6000 8.0000 0.0000 -------Y 1106.445004 0 0.0000 1870 257s Out.. 257s lnL = -1106.445004 257s 1871 lfun, 7484 eigenQcodon, 129099 P(t) 257s 257s BEBing (dim = 4). This may take several minutes. 257s Calculating f(x_h|w): 10 categories 21 w sets. 257s Calculating f(X), the marginal likelihood. 257s log(fX) = -1112.401420 S = -1023.138908 -111.908274 257s Calculating f(w|X), posterior probabilities of site classes. 257s did 10 / 79 patterns 0:43 did 20 / 79 patterns 0:43 did 30 / 79 patterns 0:43 did 40 / 79 patterns 0:43 did 50 / 79 patterns 0:43 did 60 / 79 patterns 0:43 did 70 / 79 patterns 0:43 did 79 / 79 patterns 0:43 257s Time used: 0:43 257s Passed 257s 257s Test 2 257s 257s 15 verbose | verbose 1.00 257s 7 runmode | runmode 0.00 257s 4 seqtype | seqtype 1.00 257s 13 CodonFreq | CodonFreq 2.00 257s 9 clock | clock 0.00 257s 16 model | model 0.00 257s 20 NSsites | NSsites 2.00 257s 22 icode | icode 0.00 257s 24 fix_kappa | fix_kappa 0.00 257s 25 kappa | kappa 1.60 257s 26 fix_omega | fix_omega 0.00 257s 27 omega | omega 0.80 257s 31 ncatG | ncatG 10.00 257s 11 getSE | getSE 0.00 257s 12 RateAncestor | RateAncestor 0.00 257s 36 Small_Diff | Small_Diff 0.00 257s 6 cleandata | cleandata 0.00 257s 8 method | method 0.00 257s CODONML in paml version 4.9j, October 2019 257s 257s ---------------------------------------------- 257s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 257s TTC | TCC | TAC | TGC 257s Leu L TTA | TCA | *** * TAA | *** * TGA 257s TTG | TCG | TAG | Trp W TGG 257s ---------------------------------------------- 257s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 257s CTC | CCC | CAC | CGC 257s CTA | CCA | Gln Q CAA | CGA 257s CTG | CCG | CAG | CGG 257s ---------------------------------------------- 257s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 257s ATC | ACC | AAC | AGC 257s ATA | ACA | Lys K AAA | Arg R AGA 257s Met M ATG | ACG | AAG | AGG 257s ---------------------------------------------- 257s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 257s GTC | GCC | GAC | GGC 257s GTA | GCA | Glu E GAA | GGA 257s GTG | GCG | GAG | GGG 257s ---------------------------------------------- 257s Nice code, uuh? 257s 257s 257s Ambiguity character definition table: 257s 257s T (1): T 257s C (1): C 257s A (1): A 257s G (1): G 257s U (1): T 257s Y (2): T C 257s R (2): A G 257s M (2): C A 257s K (2): T G 257s S (2): C G 257s W (2): T A 257s H (3): T C A 257s B (3): T C G 257s V (3): C A G 257s D (3): T A G 257s - (4): T C A G 257s N (4): T C A G 257s ? (4): T C A G 257s ns = 25 ls = 405 257s Reading sequences, sequential format.. 257s Reading seq # 1: __1_H._rufescens 257s Reading seq # 2: __2_H._sorenseni 257s Reading seq # 3: __3_H._walallensis 257s Reading seq # 4: __4_H._kamtschatkana 257s Reading seq # 5: __5_H._sieboldii 257s Reading seq # 6: __6_H._discus_hannai 257s Reading seq # 7: __7_H._gigantea 257s Reading seq # 8: __8_H._corrugata 257s Reading seq # 9: __9_H._cracherodii 257s Reading seq #10: _10_H._fulgens 257s Reading seq #11: _11_H._roei 257s Reading seq #12: _12_H._scalaris 257s Reading seq #13: _13_H._laevigata 257s Reading seq #14: _14_H._cyclobates 257s Reading seq #15: _15_H._rubra 257s Reading seq #16: _16_H._conicopora 257s Reading seq #17: _17_H._pustulata 257s Reading seq #18: _18_H._midae 257s Reading seq #19: _19_H._ovina 257s Reading seq #20: _20_H._diversicolor 257s Reading seq #21: _21_H._varia 257s Reading seq #22: _22_H._australis 257s Reading seq #23: _23_H._t.tuberculata 257s Reading seq #24: _24_H._t.coccinea 257s Reading seq #25: _25_H._iris 257s 257s Sequences read.. 257s Counting site patterns.. 0:00 257s Compressing, 132 patterns at 135 / 135 sites (100.0%), 0:00 257s Collecting fpatt[] & pose[], 132 patterns at 135 / 135 sites (100.0%), 0:00 257s 1 ambiguous codons are seen in the data: 257s --- 257s Counting codons.. 257s 257s 2400 bytes for distance 257s 128832 bytes for conP 257s 3168 bytes for fhK 257s 5000000 bytes for space 257s 257s TREE # 1 257s ((10, (((4, (1, (2, 3))), (5, (6, 7))), (8, 9))), 25, ((17, (24, 23)), (22, ((18, ((11, (12, 13)), (14, (15, 16)))), ((19, 21), 20))))); MP score: -1 257s 1481568 bytes for conP, adjusted 257s 257s initial w for M2:NSpselection reset. 257s 307s 0.066745 0.096428 0.010759 0.041161 0.081511 0.088665 0.028375 0.021268 0.053736 0.025716 0.096816 0.030752 0.024848 0.023580 0.051515 0.086084 0.030203 0.032178 0.052711 0.039300 0.041396 0.093505 0.023027 0.102708 0.034631 0.019987 0.104073 0.052391 0.089864 0.054001 0.024289 0.108968 0.100394 0.044479 0.045202 0.069030 0.047583 0.051540 0.028294 0.035703 0.070410 0.065087 0.039654 0.071763 0.034529 0.098310 0.084619 1.600000 1.437561 0.452661 0.428079 2.305419 307s 307s ntime & nrate & np: 47 3 52 307s 307s Bounds (np=52): 307s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 -99.000000 -99.000000 0.000001 1.000000 307s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 99.000000 99.000000 1.000000 999.000000 307s Qfactor_NS = 6.182002 307s 307s np = 52 307s lnL0 = -5095.267883 307s 307s Iterating by ming2 307s Initial: fx= 5095.267883 307s x= 0.06674 0.09643 0.01076 0.04116 0.08151 0.08867 0.02837 0.02127 0.05374 0.02572 0.09682 0.03075 0.02485 0.02358 0.05151 0.08608 0.03020 0.03218 0.05271 0.03930 0.04140 0.09351 0.02303 0.10271 0.03463 0.01999 0.10407 0.05239 0.08986 0.05400 0.02429 0.10897 0.10039 0.04448 0.04520 0.06903 0.04758 0.05154 0.02829 0.03570 0.07041 0.06509 0.03965 0.07176 0.03453 0.09831 0.08462 1.60000 1.43756 0.45266 0.42808 2.30542 307s 307s 1 h-m-p 0.0000 0.0003 3059.1724 +++ 4554.803802 m 0.0003 58 | 0/52 307s 2 h-m-p 0.0000 0.0001 766.9436 ++ 4550.179966 m 0.0001 113 | 0/52 307s 3 h-m-p 0.0000 0.0001 365.8311 ++ 4537.893067 m 0.0001 168 | 1/52 307s 4 h-m-p 0.0000 0.0000 1505.5293 ++ 4531.944810 m 0.0000 223 | 1/52 307s 5 h-m-p -0.0000 -0.0000 569.8360 307s h-m-p: -1.18375595e-21 -5.91877977e-21 5.69835961e+02 4531.944810 307s .. | 1/52 307s 6 h-m-p 0.0000 0.0003 419.8676 +YCYC 4529.531537 3 0.0001 335 | 1/52 307s 7 h-m-p 0.0000 0.0002 329.0757 +YYYCYYCCC 4519.176849 8 0.0002 402 | 0/52 307s 8 h-m-p 0.0000 0.0002 883.5308 ++ 4502.209666 m 0.0002 457 | 0/52 307s 9 h-m-p 0.0000 0.0000 2273.6961 ++ 4499.011773 m 0.0000 512 | 0/52 307s 10 h-m-p 0.0000 0.0002 268.6193 ++ 4494.649148 m 0.0002 567 | 1/52 307s 11 h-m-p 0.0003 0.0014 146.6006 +YCCCC 4489.136848 4 0.0008 630 | 1/52 307s 12 h-m-p 0.0002 0.0009 186.9189 +YCCCC 4485.488630 4 0.0005 693 | 1/52 307s 13 h-m-p 0.0002 0.0009 147.6050 +YCCC 4483.372241 3 0.0005 754 | 1/52 307s 14 h-m-p 0.0008 0.0047 92.3446 CYC 4482.006653 2 0.0008 812 | 1/52 307s 15 h-m-p 0.0004 0.0020 97.1003 YCCCC 4480.308973 4 0.0009 874 | 1/52 307s 16 h-m-p 0.0004 0.0018 149.3689 YCC 4479.195991 2 0.0006 932 | 1/52 307s 17 h-m-p 0.0003 0.0025 273.3209 +YC 4476.288039 1 0.0008 989 | 1/52 307s 18 h-m-p 0.0006 0.0029 135.0295 YCCC 4474.586507 3 0.0010 1049 | 1/52 307s 19 h-m-p 0.0003 0.0015 145.9823 +YCCC 4473.250691 3 0.0008 1110 | 1/52 307s 20 h-m-p 0.0008 0.0039 131.5202 YCCC 4471.549485 3 0.0013 1170 | 1/52 307s 21 h-m-p 0.0013 0.0063 55.5725 CCC 4470.753235 2 0.0016 1229 | 1/52 307s 22 h-m-p 0.0009 0.0047 91.0992 CCC 4470.234776 2 0.0007 1288 | 1/52 307s 23 h-m-p 0.0013 0.0132 52.4184 CCC 4469.597077 2 0.0017 1347 | 1/52 307s 24 h-m-p 0.0031 0.0156 22.2305 YCC 4469.341411 2 0.0022 1405 | 1/52 433s 25 h-m-p 0.0019 0.0173 25.8297 CC 4469.067772 1 0.0025 1462 | 1/52 433s 26 h-m-p 0.0026 0.0247 24.3081 CCC 4468.848998 2 0.0024 1521 | 1/52 433s 27 h-m-p 0.0033 0.0677 17.7216 CCC 4468.693441 2 0.0029 1580 | 1/52 433s 28 h-m-p 0.0031 0.0221 16.2949 YCC 4468.580712 2 0.0026 1638 | 1/52 433s 29 h-m-p 0.0035 0.0532 11.9391 CC 4468.459941 1 0.0043 1695 | 1/52 433s 30 h-m-p 0.0028 0.0555 18.6995 CC 4468.328229 1 0.0032 1752 | 1/52 433s 31 h-m-p 0.0066 0.0759 9.1882 YC 4468.262612 1 0.0036 1808 | 1/52 433s 32 h-m-p 0.0042 0.1050 7.8641 YC 4468.213144 1 0.0032 1864 | 1/52 433s 33 h-m-p 0.0046 0.0500 5.4854 CC 4468.167838 1 0.0040 1921 | 1/52 433s 34 h-m-p 0.0043 0.1339 5.1105 YC 4468.059533 1 0.0083 1977 | 1/52 433s 35 h-m-p 0.0036 0.0636 11.8585 CC 4467.887856 1 0.0049 2034 | 1/52 433s 36 h-m-p 0.0043 0.0644 13.5025 CCC 4467.573695 2 0.0067 2093 | 1/52 433s 37 h-m-p 0.0057 0.0324 15.8699 CCC 4467.117055 2 0.0073 2152 | 1/52 433s 38 h-m-p 0.0034 0.0209 34.5819 YCC 4466.165063 2 0.0067 2210 | 1/52 433s 39 h-m-p 0.0023 0.0115 24.5639 CCC 4465.812555 2 0.0035 2269 | 1/52 433s 40 h-m-p 0.0060 0.0299 8.4723 YC 4465.693540 1 0.0035 2325 | 1/52 433s 41 h-m-p 0.0059 0.0845 4.9662 CC 4465.577820 1 0.0065 2382 | 1/52 433s 42 h-m-p 0.0036 0.0392 9.0162 YC 4465.395114 1 0.0061 2438 | 1/52 433s 43 h-m-p 0.0033 0.0221 16.7115 YC 4464.978274 1 0.0081 2494 | 1/52 433s 44 h-m-p 0.0012 0.0060 34.4479 +YC 4464.669702 1 0.0031 2551 | 1/52 433s 45 h-m-p 0.0027 0.0135 10.2066 YC 4464.621700 1 0.0021 2607 | 1/52 433s 46 h-m-p 0.0061 0.0719 3.5236 YC 4464.608116 1 0.0031 2663 | 1/52 433s 47 h-m-p 0.0072 0.2738 1.5217 YC 4464.605250 1 0.0030 2719 | 1/52 433s 48 h-m-p 0.0043 0.4854 1.0577 CC 4464.603699 1 0.0035 2776 | 1/52 433s 49 h-m-p 0.0051 0.9512 0.7234 CC 4464.601851 1 0.0071 2833 | 1/52 433s 50 h-m-p 0.0061 0.9076 0.8412 C 4464.599605 0 0.0070 2939 | 1/52 433s 51 h-m-p 0.0079 0.8566 0.7468 CC 4464.597247 1 0.0065 3047 | 1/52 433s 52 h-m-p 0.0118 1.3283 0.4141 YC 4464.588275 1 0.0208 3154 | 1/52 433s 53 h-m-p 0.0067 0.3564 1.2926 CC 4464.569355 1 0.0085 3262 | 1/52 433s 54 h-m-p 0.0062 1.3355 1.7793 YC 4464.531680 1 0.0108 3318 | 1/52 433s 55 h-m-p 0.0097 0.2189 1.9791 CC 4464.524763 1 0.0036 3375 | 1/52 433s 56 h-m-p 0.0075 0.2901 0.9573 YC 4464.523518 1 0.0032 3431 | 1/52 433s 57 h-m-p 0.0112 3.1607 0.2705 Y 4464.523321 0 0.0052 3537 | 1/52 433s 58 h-m-p 0.0220 2.8036 0.0634 C 4464.523177 0 0.0197 3643 | 1/52 433s 59 h-m-p 0.0175 0.8998 0.0714 ++CC 4464.517521 1 0.2485 3753 | 1/52 433s 60 h-m-p 0.0957 1.0687 0.1852 -C 4464.517407 0 0.0063 3860 | 1/52 433s 61 h-m-p 0.3052 8.0000 0.0039 +YC 4464.515512 1 0.9203 3968 | 1/52 433s 62 h-m-p 1.2616 8.0000 0.0028 YC 4464.514304 1 2.6250 4075 | 1/52 433s 63 h-m-p 1.6000 8.0000 0.0008 +YC 4464.512208 1 5.1851 4183 | 1/52 433s 64 h-m-p 1.6000 8.0000 0.0023 C 4464.511428 0 1.9032 4289 | 1/52 433s 65 h-m-p 1.6000 8.0000 0.0006 C 4464.511379 0 1.3279 4395 | 1/52 433s 66 h-m-p 1.6000 8.0000 0.0001 C 4464.511376 0 1.3311 4501 | 1/52 433s 67 h-m-p 1.6000 8.0000 0.0001 C 4464.511376 0 1.3800 4607 | 1/52 433s 68 h-m-p 1.6000 8.0000 0.0000 C 4464.511376 0 1.2920 4713 | 1/52 433s 69 h-m-p 1.6000 8.0000 0.0000 C 4464.511376 0 1.3676 4819 | 1/52 433s 70 h-m-p 1.6000 8.0000 0.0000 C 4464.511376 0 1.6000 4925 | 1/52 433s 71 h-m-p 1.6000 8.0000 0.0000 ---Y 4464.511376 0 0.0063 5034 433s Out.. 433s lnL = -4464.511376 433s 5035 lfun, 20140 eigenQcodon, 709935 P(t) 433s 433s Collecting RasMol commands for coloring structure into RasMol.txt 433s Choose color scheme (0: 5 colors, 1: white->red, 2: rainbow) darkblue [2,2,120] mean_w < 0.62619 433s lightblue [133,57,240] mean_w < 1.25239 433s purple [186,60,200] mean_w < 1.87858 433s pinkred [200,60,160] mean_w < 2.50477 433s red [250,5,5] mean_w < 3.13097 433s 433s BEBing (dim = 4). This may take several minutes. 433s Calculating f(x_h|w): 10 categories 21 w sets. 433s S10 w log{f(x|w)}: 0.0500 -46.233224 433s S10 w log{f(x|w)}: 0.1500 -39.238122 433s S10 w log{f(x|w)}: 0.2500 -36.352917 433s S10 w log{f(x|w)}: 0.3500 -34.683527 433s S10 w log{f(x|w)}: 0.4500 -33.605538 433s S10 w log{f(x|w)}: 0.5500 -32.877304 433s S10 w log{f(x|w)}: 0.6500 -32.379593 433s S10 w log{f(x|w)}: 0.7500 -32.044719 433s S10 w log{f(x|w)}: 0.8500 -31.830535 433s S10 w log{f(x|w)}: 0.9500 -31.709001 433s S10 w log{f(x|w)}: 1.0000 -31.676619 433s S10 w log{f(x|w)}: 1.5000 -32.036251 433s S10 w log{f(x|w)}: 2.5000 -34.474325 433s S10 w log{f(x|w)}: 3.5000 -37.625640 433s S10 w log{f(x|w)}: 4.5000 -40.887847 433s S10 w log{f(x|w)}: 5.5000 -44.050748 433s S10 w log{f(x|w)}: 6.5000 -47.027386 433s S10 w log{f(x|w)}: 7.5000 -49.782035 433s S10 w log{f(x|w)}: 8.5000 -52.305216 433s S10 w log{f(x|w)}: 9.5000 -54.602287 433s S10 w log{f(x|w)}: 10.5000 -56.686716 433s Calculating f(X), the marginal likelihood. 433s log(fX) = -4474.552012 S = -4283.950698 -226.824089 433s Calculating f(w|X), posterior probabilities of site classes. 433s did 10 / 132 patterns 2:56 did 20 / 132 patterns 2:56 did 30 / 132 patterns 2:56 did 40 / 132 patterns 2:56 did 50 / 132 patterns 2:56 did 60 / 132 patterns 2:56 did 70 / 132 patterns 2:56 did 80 / 132 patterns 2:56 did 90 / 132 patterns 2:56 did 100 / 132 patterns 2:56 did 110 / 132 patterns 2:56 did 120 / 132 patterns 2:56 did 130 / 132 patterns 2:56 did 132 / 132 patterns 2:56 433s Time used: 2:56 433s Passed 433s 433s Test 3 433s 433s CODONML in paml version 4.9j, October 2019 433s 433s ---------------------------------------------- 433s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 433s TTC | TCC | TAC | TGC 433s Leu L TTA | TCA | *** * TAA | *** * TGA 433s TTG | TCG | TAG | Trp W TGG 433s ---------------------------------------------- 433s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 433s CTC | CCC | CAC | CGC 433s CTA | CCA | Gln Q CAA | CGA 433s CTG | CCG | CAG | CGG 433s ---------------------------------------------- 433s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 433s ATC | ACC | AAC | AGC 433s ATA | ACA | Lys K AAA | Arg R AGA 433s Met M ATG | ACG | AAG | AGG 433s ---------------------------------------------- 433s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 433s GTC | GCC | GAC | GGC 433s GTA | GCA | Glu E GAA | GGA 433s GTG | GCG | GAG | GGG 433s ---------------------------------------------- 433s Nice code, uuh? 433s ns = 25 ls = 402 433s Reading sequences, sequential format.. 433s Reading seq # 1: __1_H._rufescens Reading seq # 2: __2_H._sorenseni Reading seq # 3: __3_H._walallensis Reading seq # 4: __4_H._kamtschatkana Reading seq # 5: __5_H._sieboldii Reading seq # 6: __6_H._discus_hannai Reading seq # 7: __7_H._gigantea Reading seq # 8: __8_H._corrugata Reading seq # 9: __9_H._cracherodii Reading seq #10: _10_H._fulgens Reading seq #11: _11_H._roei Reading seq #12: _12_H._scalaris Reading seq #13: _13_H._laevigata Reading seq #14: _14_H._cyclobates Reading seq #15: _15_H._rubra Reading seq #16: _16_H._conicopora Reading seq #17: _17_H._pustulata Reading seq #18: _18_H._midae Reading seq #19: _19_H._ovina Reading seq #20: _20_H._diversicolor Reading seq #21: _21_H._varia Reading seq #22: _22_H._australis Reading seq #23: _23_H._t.tuberculata Reading seq #24: _24_H._t.coccinea Reading seq #25: _25_H._iris 433s Sequences read.. 433s Counting site patterns.. 0:00 433s 433s Compressing, 132 patterns at 134 / 134 sites (100.0%), 0:00 433s 433s Collecting fpatt[] & pose[], 132 patterns at 134 / 134 sites (100.0%), 0:00 433s 1 ambiguous codons are seen in the data: 433s --- 433s Counting codons.. 433s 433s 2400 bytes for distance 433s 128832 bytes for conP 433s 539438413402754048 bytes for fhK 433s 5000000 bytes for space 433s 433s TREE # 1 433s ((10, (((4, (1, (2, 3))), (5, (6, 7))), (8, 9))), 25, ((17, (24, 23)), (22, ((18, ((11, (12, 13)), (14, (15, 16)))), ((19, 21), 20))))); MP score: -1 433s 1481568 bytes for conP, adjusted 433s 433s 0.100642 0.092427 0.085672 0.102960 0.078869 0.098763 0.096545 0.077837 0.037678 0.109938 0.039829 0.084825 0.063703 0.053649 0.077826 0.074673 0.104940 0.027500 0.037345 0.084139 0.048206 0.064188 0.088678 0.048971 0.085176 0.029388 0.106118 0.108194 0.071676 0.013308 0.102202 0.098153 0.059930 0.051822 0.102877 0.109730 0.058441 0.088132 0.105772 0.057185 0.049195 0.060900 0.038759 0.082059 0.066880 0.079778 0.011000 1.000000 1.600000 0.800000 433s 433s ntime & nrate & np: 47 2 50 433s 433s Bounds (np=50): 433s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.010000 0.000100 0.000100 467s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 99.000000 999.000000 999.000000 467s 467s np = 50 467s lnL0 = -5173.656252 467s 467s Iterating by ming2 467s Initial: fx= 5173.656252 467s x= 0.10064 0.09243 0.08567 0.10296 0.07887 0.09876 0.09654 0.07784 0.03768 0.10994 0.03983 0.08482 0.06370 0.05365 0.07783 0.07467 0.10494 0.02750 0.03734 0.08414 0.04821 0.06419 0.08868 0.04897 0.08518 0.02939 0.10612 0.10819 0.07168 0.01331 0.10220 0.09815 0.05993 0.05182 0.10288 0.10973 0.05844 0.08813 0.10577 0.05719 0.04919 0.06090 0.03876 0.08206 0.06688 0.07978 0.01100 1.00000 1.60000 0.80000 467s 467s 1 h-m-p 0.0000 0.0005 3232.9952 +++ 4722.809153 m 0.0005 56 | 0/50 467s 2 h-m-p 0.0000 0.0000 275971.6975 YCYC 4719.791808 3 0.0000 113 | 0/50 467s 3 h-m-p 0.0000 0.0001 489.3799 ++ 4714.822236 m 0.0001 166 | 1/50 467s 4 h-m-p 0.0001 0.0004 329.1256 +CYCCC 4695.707207 4 0.0004 227 | 0/50 467s 5 h-m-p 0.0000 0.0000 3390.2031 +CYCC 4693.261340 3 0.0000 286 | 0/50 467s 6 h-m-p 0.0000 0.0001 1085.8493 +YYCCC 4688.706424 4 0.0000 346 | 0/50 467s 7 h-m-p 0.0000 0.0000 2059.9282 ++ 4684.671668 m 0.0000 399 | 0/50 467s 8 h-m-p -0.0000 -0.0000 1132.6104 467s h-m-p: -7.45405690e-22 -3.72702845e-21 1.13261037e+03 4684.671668 467s .. | 0/50 467s 9 h-m-p 0.0000 0.0000 1102.9119 +YCCCC 4680.232307 4 0.0000 510 | 0/50 467s 10 h-m-p 0.0000 0.0000 277.3412 ++ 4679.252196 m 0.0000 563 | 1/50 467s 11 h-m-p 0.0000 0.0001 410.3415 ++ 4670.867562 m 0.0001 616 | 2/50 467s 12 h-m-p 0.0000 0.0001 1431.4966 ++ 4662.016255 m 0.0001 669 | 2/50 467s 13 h-m-p 0.0000 0.0001 656.1071 +YCCC 4657.273441 3 0.0001 728 | 2/50 467s 14 h-m-p 0.0001 0.0004 442.6851 +YYCCC 4650.507861 4 0.0003 788 | 1/50 467s 15 h-m-p 0.0000 0.0001 2656.0950 YCC 4648.498822 2 0.0000 844 | 1/50 467s 16 h-m-p 0.0000 0.0001 677.6907 ++ 4644.869832 m 0.0001 897 | 1/50 467s 17 h-m-p 0.0000 0.0000 636.8790 ++ 4643.723790 m 0.0000 950 | 2/50 467s 18 h-m-p 0.0000 0.0001 719.1145 ++ 4640.450366 m 0.0001 1003 | 2/50 467s 19 h-m-p 0.0000 0.0001 1088.5867 +YYYYCYCCC 4633.067835 8 0.0001 1068 | 1/50 467s 20 h-m-p 0.0000 0.0000 5081.2569 +YYYCC 4631.500632 4 0.0000 1127 | 1/50 467s 21 h-m-p 0.0000 0.0001 4230.7601 +CYCCC 4620.303871 4 0.0001 1189 | 1/50 467s 22 h-m-p 0.0000 0.0000 7053.9351 +CYC 4607.824907 2 0.0000 1246 | 1/50 467s 23 h-m-p 0.0000 0.0000 2340.3285 ++ 4601.612033 m 0.0000 1299 | 1/50 467s 24 h-m-p 0.0001 0.0003 1199.5088 CCCC 4597.612266 3 0.0001 1358 | 1/50 467s 25 h-m-p 0.0000 0.0002 638.8726 YC 4594.753289 1 0.0001 1412 | 1/50 467s 26 h-m-p 0.0002 0.0008 224.7686 YCCCC 4592.002157 4 0.0003 1472 | 1/50 467s 27 h-m-p 0.0004 0.0019 60.7438 YCCC 4590.567854 3 0.0007 1530 | 1/50 467s 28 h-m-p 0.0007 0.0045 58.6271 CCCC 4588.653710 3 0.0011 1589 | 1/50 467s 29 h-m-p 0.0003 0.0015 69.2770 YCCCC 4587.559707 4 0.0007 1649 | 1/50 467s 30 h-m-p 0.0003 0.0017 88.0814 CCCC 4586.921552 3 0.0004 1708 | 1/50 467s 31 h-m-p 0.0008 0.0039 43.9520 YCC 4586.678691 2 0.0005 1764 | 1/50 467s 32 h-m-p 0.0011 0.0076 19.1131 YC 4586.570456 1 0.0007 1818 | 1/50 467s 33 h-m-p 0.0009 0.0092 14.1579 YC 4586.492634 1 0.0007 1872 | 1/50 467s 34 h-m-p 0.0007 0.0132 14.0599 +YCC 4586.170738 2 0.0020 1929 | 1/50 467s 35 h-m-p 0.0006 0.0079 47.4873 YC 4585.447557 1 0.0011 1983 | 1/50 467s 36 h-m-p 0.0007 0.0105 80.5628 YCCC 4583.809573 3 0.0014 2041 | 1/50 467s 37 h-m-p 0.0014 0.0070 57.0667 YYC 4582.595815 2 0.0012 2096 | 1/50 467s 38 h-m-p 0.0011 0.0061 58.9834 CYC 4581.267296 2 0.0011 2152 | 1/50 467s 39 h-m-p 0.0010 0.0074 62.2564 CCC 4579.336906 2 0.0013 2209 | 1/50 467s 40 h-m-p 0.0011 0.0057 57.7413 YYC 4577.871936 2 0.0009 2264 | 1/50 467s 41 h-m-p 0.0011 0.0082 49.1775 YCC 4574.981616 2 0.0020 2320 | 1/50 533s 42 h-m-p 0.0013 0.0064 62.0377 CCCC 4572.733734 3 0.0014 2379 | 1/50 533s 43 h-m-p 0.0010 0.0048 89.3698 CCCC 4570.155261 3 0.0012 2438 | 1/50 533s 44 h-m-p 0.0005 0.0027 81.0261 YCCC 4568.593970 3 0.0010 2496 | 1/50 533s 45 h-m-p 0.0009 0.0051 89.7480 CCCC 4566.894843 3 0.0011 2555 | 1/50 533s 46 h-m-p 0.0016 0.0080 48.6697 YCC 4566.213952 2 0.0010 2611 | 0/50 533s 47 h-m-p 0.0006 0.0068 88.3922 -CYC 4566.188496 2 0.0000 2668 | 0/50 533s 48 h-m-p 0.0001 0.0071 42.4437 ++CCC 4565.761227 2 0.0010 2727 | 0/50 533s 49 h-m-p 0.0013 0.0312 32.3656 YC 4564.893894 1 0.0028 2781 | 0/50 533s 50 h-m-p 0.0012 0.0111 78.5153 CCCC 4563.721533 3 0.0016 2840 | 0/50 533s 51 h-m-p 0.0033 0.0175 38.4788 CCC 4563.406395 2 0.0009 2897 | 0/50 533s 52 h-m-p 0.0024 0.0207 14.8039 YCC 4563.180874 2 0.0016 2953 | 0/50 533s 53 h-m-p 0.0024 0.0426 9.6156 CC 4562.681880 1 0.0034 3008 | 0/50 533s 54 h-m-p 0.0019 0.0164 17.2362 YCCC 4561.319331 3 0.0035 3066 | 0/50 533s 55 h-m-p 0.0013 0.0064 42.1094 CCC 4560.133762 2 0.0014 3123 | 0/50 533s 56 h-m-p 0.0016 0.0097 37.9837 CCCC 4558.928216 3 0.0023 3182 | 0/50 533s 57 h-m-p 0.0012 0.0059 34.7080 YCCC 4558.678742 3 0.0007 3240 | 0/50 533s 58 h-m-p 0.0020 0.0466 12.8834 YC 4558.615043 1 0.0009 3294 | 0/50 533s 59 h-m-p 0.0027 0.0785 4.1829 CC 4558.547406 1 0.0030 3349 | 0/50 533s 60 h-m-p 0.0038 0.0388 3.3100 +CCC 4557.757654 2 0.0186 3407 | 0/50 533s 61 h-m-p 0.0006 0.0032 16.4816 YC 4557.472543 1 0.0015 3461 | 0/50 533s 62 h-m-p 0.0012 0.0060 9.8199 YC 4557.426407 1 0.0009 3515 | 0/50 533s 63 h-m-p 0.0060 0.1108 1.5077 CC 4557.401097 1 0.0051 3570 | 0/50 533s 64 h-m-p 0.0047 0.4349 1.6202 ++CCCC 4555.292892 3 0.1265 3631 | 0/50 533s 65 h-m-p 0.0847 0.4237 0.1450 +CC 4554.369125 1 0.3216 3687 | 0/50 533s 66 h-m-p 0.2294 1.1470 0.1598 +CYC 4553.095579 2 0.8644 3794 | 0/50 533s 67 h-m-p 0.0925 0.4626 0.1090 ++ 4552.632480 m 0.4626 3897 | 1/50 533s 68 h-m-p 0.4437 5.5594 0.1136 YCC 4552.141330 2 0.9273 4003 | 1/50 533s 69 h-m-p 1.6000 8.0000 0.0276 YC 4551.961529 1 0.8997 4106 | 1/50 533s 70 h-m-p 1.3985 8.0000 0.0178 CCC 4551.587213 2 2.0181 4212 | 1/50 533s 71 h-m-p 1.6000 8.0000 0.0189 CCC 4551.242352 2 1.3360 4318 | 1/50 533s 72 h-m-p 0.6118 3.0591 0.0398 +YCC 4550.787483 2 2.0115 4424 | 1/50 533s 73 h-m-p 1.6000 8.0000 0.0305 CCC 4550.489785 2 1.3189 4530 | 1/50 533s 74 h-m-p 1.6000 8.0000 0.0068 CC 4550.318052 1 1.9410 4634 | 1/50 533s 75 h-m-p 1.3733 8.0000 0.0097 CC 4550.248924 1 1.3226 4738 | 1/50 533s 76 h-m-p 1.6000 8.0000 0.0061 CC 4550.195366 1 2.4509 4842 | 1/50 533s 77 h-m-p 1.6000 8.0000 0.0088 CC 4550.128728 1 2.2356 4946 | 1/50 533s 78 h-m-p 1.6000 8.0000 0.0113 CY 4550.065001 1 1.5567 5050 | 1/50 533s 79 h-m-p 1.6000 8.0000 0.0047 CC 4550.035591 1 1.4150 5154 | 1/50 533s 80 h-m-p 1.3570 7.9228 0.0049 CC 4550.018555 1 1.5957 5258 | 1/50 533s 81 h-m-p 1.1729 8.0000 0.0066 CC 4550.003086 1 1.7381 5362 | 1/50 533s 82 h-m-p 1.5275 8.0000 0.0075 CC 4549.996146 1 1.2350 5466 | 1/50 533s 83 h-m-p 1.6000 8.0000 0.0037 YC 4549.995021 1 1.1360 5569 | 1/50 533s 84 h-m-p 1.6000 8.0000 0.0013 YC 4549.994774 1 1.1148 5672 | 1/50 533s 85 h-m-p 1.6000 8.0000 0.0004 Y 4549.994732 0 0.9789 5774 | 1/50 533s 86 h-m-p 1.6000 8.0000 0.0001 Y 4549.994728 0 0.9215 5876 | 1/50 533s 87 h-m-p 1.6000 8.0000 0.0000 Y 4549.994728 0 0.7580 5978 | 1/50 533s 88 h-m-p 1.6000 8.0000 0.0000 Y 4549.994728 0 0.7445 6080 | 1/50 533s 89 h-m-p 1.6000 8.0000 0.0000 Y 4549.994728 0 0.9241 6182 | 1/50 533s 90 h-m-p 1.6000 8.0000 0.0000 C 4549.994728 0 1.8714 6284 | 1/50 533s 91 h-m-p 1.6000 8.0000 0.0000 ----------------.. | 1/50 533s 92 h-m-p 0.0160 8.0000 0.0015 --------C 4549.994728 0 0.0000 6510 | 1/50 533s 93 h-m-p 0.0130 6.5092 0.0012 ------------C 4549.994728 0 0.0000 6624 | 1/50 533s 94 h-m-p 0.0007 0.3676 0.0272 -----------.. | 1/50 533s 95 h-m-p 0.0160 8.0000 0.0015 ----------Y 4549.994728 0 0.0000 6847 | 1/50 542s 96 h-m-p 0.0160 8.0000 0.0020 -------------.. | 1/50 542s 97 h-m-p 0.0160 8.0000 0.0015 ---------Y 4549.994728 0 0.0000 7071 | 1/50 542s 98 h-m-p 0.0160 8.0000 0.0013 -----------C 4549.994728 0 0.0000 7184 | 1/50 542s 99 h-m-p 0.0004 0.1916 0.2992 ----------.. | 1/50 542s 100 h-m-p 0.0160 8.0000 0.0015 ------------- | 1/50 542s 101 h-m-p 0.0160 8.0000 0.0015 ------------- 542s Out.. 542s lnL = -4549.994728 542s 7521 lfun, 7521 eigenQcodon, 706974 P(t) 542s 542s Time used: 1:49 542s Passed 542s 542s Test 4 543s 543s CODONML in paml version 4.9j, October 2019 543s 543s ---------------------------------------------- 543s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 543s TTC | TCC | TAC | TGC 543s Leu L TTA | TCA | *** * TAA | *** * TGA 543s TTG | TCG | TAG | Trp W TGG 543s ---------------------------------------------- 543s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 543s CTC | CCC | CAC | CGC 543s CTA | CCA | Gln Q CAA | CGA 543s CTG | CCG | CAG | CGG 543s ---------------------------------------------- 543s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 543s ATC | ACC | AAC | AGC 543s ATA | ACA | Lys K AAA | Arg R AGA 543s Met M ATG | ACG | AAG | AGG 543s ---------------------------------------------- 543s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 543s GTC | GCC | GAC | GGC 543s GTA | GCA | Glu E GAA | GGA 543s GTG | GCG | GAG | GGG 543s ---------------------------------------------- 543s Nice code, uuh? 543s ns = 7 ls = 390 543s Reading sequences, sequential format.. 543s Reading seq # 1: Hsa_Human Reading seq # 2: Hla_gibbon Reading seq # 3: Cgu/Can_colobus Reading seq # 4: Pne_langur Reading seq # 5: Mmu_rhesus Reading seq # 6: Ssc_squirrelM Reading seq # 7: Cja_marmoset 543s Sequences read.. 543s Counting site patterns.. 0:00 543s Compressing, 81 patterns at 130 / 130 sites (100.0%), 0:00 543s Collecting fpatt[] & pose[], 81 patterns at 130 / 130 sites (100.0%), 0:00 543s Counting codons.. 543s 543s 168 bytes for distance 543s 79056 bytes for conP 543s 15552162532423707392 bytes for fhK 543s 5000000 bytes for space 543s 543s 2 branch types are in tree. Stop if wrong. 543s TREE # 1 543s ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 543s 197640 bytes for conP, adjusted 543s 543s 0.028026 0.071632 0.055956 0.076933 0.098389 0.068349 0.092183 0.103113 0.043061 0.033688 0.092273 1.149485 0.957063 0.981150 543s 543s ntime & nrate & np: 11 3 14 543s 543s Bounds (np=14): 543s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 0.000100 543s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 999.000000 543s 543s np = 14 543s lnL0 = -943.459833 543s 543s Iterating by ming2 543s Initial: fx= 943.459833 543s x= 0.02803 0.07163 0.05596 0.07693 0.09839 0.06835 0.09218 0.10311 0.04306 0.03369 0.09227 1.14948 0.95706 0.98115 543s 543s 1 h-m-p 0.0000 0.0010 297.6864 +++YYCCC 924.997071 4 0.0006 28 | 0/14 543s 2 h-m-p 0.0001 0.0007 121.8601 YCYCCC 922.130460 5 0.0004 53 | 0/14 543s 3 h-m-p 0.0002 0.0011 41.1881 CCCC 921.898100 3 0.0003 76 | 0/14 543s 4 h-m-p 0.0003 0.0053 36.9789 +YYYC 921.370003 3 0.0012 97 | 0/14 543s 5 h-m-p 0.0003 0.0043 133.1177 +CYCCC 918.907417 4 0.0018 122 | 0/14 543s 6 h-m-p 0.0007 0.0033 328.0667 YCCCC 914.098764 4 0.0015 146 | 0/14 543s 7 h-m-p 0.0002 0.0010 659.5852 YC 911.033177 1 0.0005 164 | 0/14 543s 8 h-m-p 0.0002 0.0010 465.0418 CCC 909.772417 2 0.0003 185 | 0/14 543s 9 h-m-p 0.0007 0.0033 50.7098 YC 909.603507 1 0.0004 203 | 0/14 543s 10 h-m-p 0.0017 0.0323 12.4084 CCC 909.473982 2 0.0024 224 | 0/14 543s 11 h-m-p 0.0006 0.0124 48.8433 +CYC 909.031602 2 0.0023 245 | 0/14 543s 12 h-m-p 0.0012 0.0062 98.5259 CCCC 908.547507 3 0.0012 268 | 0/14 543s 13 h-m-p 0.0080 0.0400 2.2407 -YC 908.544382 1 0.0010 287 | 0/14 543s 14 h-m-p 0.0057 2.8469 4.3875 +++YCY 904.901627 2 0.8771 310 | 0/14 543s 15 h-m-p 1.1392 5.6960 0.5588 CCC 904.064164 2 1.2788 331 | 0/14 543s 16 h-m-p 1.0060 5.0302 0.5926 CCCCC 903.735134 4 1.2665 370 | 0/14 543s 17 h-m-p 1.4024 8.0000 0.5351 CCCC 903.508235 3 2.0871 407 | 0/14 543s 18 h-m-p 1.6000 8.0000 0.4335 CCC 903.425987 2 1.8970 442 | 0/14 543s 19 h-m-p 1.6000 8.0000 0.1986 CCC 903.410874 2 1.3619 477 | 0/14 543s 20 h-m-p 1.6000 8.0000 0.0974 YC 903.402815 1 3.8263 509 | 0/14 546s 21 h-m-p 1.6000 8.0000 0.1917 ++ 903.357224 m 8.0000 540 | 0/14 546s 22 h-m-p 0.8749 8.0000 1.7528 +CYC 903.272512 2 4.0331 575 | 0/14 546s 23 h-m-p 1.6000 8.0000 2.3365 CCC 903.201556 2 2.3233 596 | 0/14 546s 24 h-m-p 1.6000 8.0000 2.9900 YC 903.163984 1 3.7989 614 | 0/14 546s 25 h-m-p 1.6000 8.0000 4.0774 YCC 903.137662 2 3.1502 634 | 0/14 546s 26 h-m-p 1.6000 8.0000 6.9776 YCC 903.116591 2 3.3945 654 | 0/14 546s 27 h-m-p 1.6000 8.0000 10.0397 YC 903.103247 1 3.0992 672 | 0/14 546s 28 h-m-p 1.6000 8.0000 14.7194 YCC 903.093888 2 3.2664 692 | 0/14 546s 29 h-m-p 1.6000 8.0000 22.7053 YC 903.087363 1 3.1319 710 | 0/14 546s 30 h-m-p 1.6000 8.0000 32.2258 YC 903.083075 1 3.1907 728 | 0/14 546s 31 h-m-p 1.6000 8.0000 47.6762 YC 903.080066 1 3.1909 746 | 0/14 546s 32 h-m-p 1.4955 7.4775 69.9675 YC 903.078039 1 3.2659 764 | 0/14 546s 33 h-m-p 0.5720 2.8601 103.0286 ++ 903.076668 m 2.8601 781 | 1/14 546s 34 h-m-p 1.6000 8.0000 0.0090 YC 903.076552 1 0.9966 799 | 1/14 546s 35 h-m-p 1.6000 8.0000 0.0000 C 903.076551 0 1.3850 829 | 1/14 546s 36 h-m-p 1.5123 8.0000 0.0000 Y 903.076551 0 0.9841 859 | 1/14 546s 37 h-m-p 1.6000 8.0000 0.0000 C 903.076551 0 1.9325 889 546s Out.. 546s lnL = -903.076551 546s 890 lfun, 1780 eigenQcodon, 9790 P(t) 546s 546s 2 branch types are in tree. Stop if wrong. 546s TREE # 2 546s ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 546s 0.069480 0.103440 0.051153 0.092497 0.062865 0.015509 0.013023 0.097705 0.102499 0.043447 0.080809 1.185314 0.853600 0.931131 546s 546s ntime & nrate & np: 11 3 14 546s 546s Bounds (np=14): 546s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 0.000100 546s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 999.000000 546s 546s np = 14 546s lnL0 = -941.357529 546s 546s Iterating by ming2 546s Initial: fx= 941.357529 546s x= 0.06948 0.10344 0.05115 0.09250 0.06286 0.01551 0.01302 0.09770 0.10250 0.04345 0.08081 1.18531 0.85360 0.93113 546s 546s 1 h-m-p 0.0000 0.0010 476.7869 ++YYYCCC 930.848252 5 0.0002 28 | 0/14 546s 2 h-m-p 0.0002 0.0008 168.2903 +YYCCCC 921.380196 5 0.0006 54 | 0/14 546s 3 h-m-p 0.0001 0.0006 96.7986 CYCCC 920.539607 4 0.0002 78 | 0/14 546s 4 h-m-p 0.0008 0.0057 28.3088 CCCC 920.146115 3 0.0011 101 | 0/14 546s 5 h-m-p 0.0005 0.0035 68.2539 YCCC 919.396430 3 0.0010 123 | 0/14 546s 6 h-m-p 0.0004 0.0030 199.2245 +CCCCC 916.415981 4 0.0015 149 | 0/14 546s 7 h-m-p 0.0004 0.0021 688.4993 CYCCCC 911.045143 5 0.0008 175 | 0/14 546s 8 h-m-p 0.0002 0.0012 329.2282 CCCC 909.833185 3 0.0004 198 | 0/14 546s 9 h-m-p 0.0004 0.0020 124.6552 CCCC 909.249657 3 0.0005 221 | 0/14 546s 10 h-m-p 0.0015 0.0074 37.6056 YYCC 908.971589 3 0.0010 242 | 0/14 546s 11 h-m-p 0.0012 0.0067 33.4830 YYC 908.768046 2 0.0010 261 | 0/14 546s 12 h-m-p 0.0008 0.0194 42.7447 +YCCC 907.632042 3 0.0056 284 | 0/14 546s 13 h-m-p 0.0012 0.0058 65.1698 YCY 907.442123 2 0.0006 304 | 0/14 546s 14 h-m-p 0.0167 2.9830 2.5116 +++CCCC 903.900712 3 1.3203 330 | 0/14 546s 15 h-m-p 0.9090 4.5452 0.6484 CCCCC 902.530318 4 1.2916 355 | 0/14 546s 16 h-m-p 1.3126 6.5629 0.5966 YCCC 902.015736 3 0.8726 391 | 0/14 546s 17 h-m-p 0.9151 4.5755 0.4369 CCCC 901.791986 3 1.3142 428 | 0/14 546s 18 h-m-p 1.6000 8.0000 0.1747 CCC 901.693096 2 2.1852 463 | 0/14 546s 19 h-m-p 1.6000 8.0000 0.1898 CYC 901.641951 2 1.7612 497 | 0/14 546s 20 h-m-p 1.6000 8.0000 0.0843 YC 901.634405 1 1.0970 529 | 0/14 546s 21 h-m-p 1.6000 8.0000 0.0199 C 901.633921 0 1.4608 560 | 0/14 546s 22 h-m-p 1.6000 8.0000 0.0160 +CC 901.633408 1 5.5691 594 | 0/14 546s 23 h-m-p 1.3548 8.0000 0.0656 +C 901.631626 0 5.2006 626 | 0/14 546s 24 h-m-p 1.6000 8.0000 0.0778 CC 901.631004 1 1.8865 659 | 0/14 546s 25 h-m-p 1.6000 8.0000 0.0300 C 901.630895 0 1.4146 690 | 0/14 547s 26 h-m-p 1.6000 8.0000 0.0010 C 901.630891 0 1.2840 721 | 0/14 547s 27 h-m-p 1.6000 8.0000 0.0007 C 901.630891 0 1.3830 752 | 0/14 547s 28 h-m-p 1.6000 8.0000 0.0002 Y 901.630891 0 1.1849 783 | 0/14 547s 29 h-m-p 1.6000 8.0000 0.0000 Y 901.630891 0 0.9320 814 | 0/14 547s 30 h-m-p 1.6000 8.0000 0.0000 C 901.630891 0 1.8552 845 | 0/14 547s 31 h-m-p 1.6000 8.0000 0.0000 Y 901.630891 0 0.1739 876 | 0/14 547s 32 h-m-p 0.2115 8.0000 0.0000 C 901.630891 0 0.1944 907 | 0/14 547s 33 h-m-p 0.2405 8.0000 0.0000 Y 901.630891 0 0.2405 938 | 0/14 547s 34 h-m-p 0.3014 8.0000 0.0000 Y 901.630891 0 0.0753 969 | 0/14 547s 35 h-m-p 0.1042 8.0000 0.0000 Y 901.630891 0 0.0260 1000 547s Out.. 547s lnL = -901.630891 547s 1001 lfun, 2002 eigenQcodon, 11011 P(t) 547s 547s Tree comparisons (Kishino & Hasegawa 1989; Shimodaira & Hasegawa 1999) 547s Reading lnf for tree # 1 Reading lnf for tree # 2, done. 547s Calculating SEs by sitewise comparison, 0:05 547s RELL Bootstrapping.. replicate: 100 / 10000 0:05 RELL Bootstrapping.. replicate: 200 / 10000 0:05 RELL Bootstrapping.. replicate: 300 / 10000 0:05 RELL Bootstrapping.. replicate: 400 / 10000 0:05 RELL Bootstrapping.. replicate: 500 / 10000 0:05 RELL Bootstrapping.. replicate: 600 / 10000 0:05 RELL Bootstrapping.. replicate: 700 / 10000 0:05 RELL Bootstrapping.. replicate: 800 / 10000 0:05 RELL Bootstrapping.. replicate: 900 / 10000 0:05 RELL Bootstrapping.. replicate: 1000 / 10000 0:05 RELL Bootstrapping.. replicate: 1100 / 10000 0:05 RELL Bootstrapping.. replicate: 1200 / 10000 0:05 RELL Bootstrapping.. replicate: 1300 / 10000 0:05 RELL Bootstrapping.. replicate: 1400 / 10000 0:05 RELL Bootstrapping.. replicate: 1500 / 10000 0:05 RELL Bootstrapping.. replicate: 1600 / 10000 0:05 RELL Bootstrapping.. replicate: 1700 / 10000 0:05 RELL Bootstrapping.. replicate: 1800 / 10000 0:05 RELL Bootstrapping.. replicate: 1900 / 10000 0:05 RELL Bootstrapping.. replicate: 2000 / 10000 0:05 RELL Bootstrapping.. replicate: 2100 / 10000 0:05 RELL Bootstrapping.. replicate: 2200 / 10000 0:05 RELL Bootstrapping.. replicate: 2300 / 10000 0:05 RELL Bootstrapping.. replicate: 2400 / 10000 0:05 RELL Bootstrapping.. replicate: 2500 / 10000 0:05 RELL Bootstrapping.. replicate: 2600 / 10000 0:05 RELL Bootstrapping.. replicate: 2700 / 10000 0:05 RELL Bootstrapping.. replicate: 2800 / 10000 0:05 RELL Bootstrapping.. replicate: 2900 / 10000 0:05 RELL Bootstrapping.. replicate: 3000 / 10000 0:05 RELL Bootstrapping.. replicate: 3100 / 10000 0:05 RELL Bootstrapping.. replicate: 3200 / 10000 0:05 RELL Bootstrapping.. replicate: 3300 / 10000 0:05 RELL Bootstrapping.. replicate: 3400 / 10000 0:05 RELL Bootstrapping.. replicate: 3500 / 10000 0:05 RELL Bootstrapping.. replicate: 3600 / 10000 0:05 RELL Bootstrapping.. replicate: 3700 / 10000 0:05 RELL Bootstrapping.. replicate: 3800 / 10000 0:05 RELL Bootstrapping.. replicate: 3900 / 10000 0:05 RELL Bootstrapping.. replicate: 4000 / 10000 0:05 RELL Bootstrapping.. replicate: 4100 / 10000 0:05 RELL Bootstrapping.. replicate: 4200 / 10000 0:05 RELL Bootstrapping.. replicate: 4300 / 10000 0:05 RELL Bootstrapping.. replicate: 4400 / 10000 0:05 RELL Bootstrapping.. replicate: 4500 / 10000 0:05 RELL Bootstrapping.. replicate: 4600 / 10000 0:05 RELL Bootstrapping.. replicate: 4700 / 10000 0:05 RELL Bootstrapping.. replicate: 4800 / 10000 0:05 RELL Bootstrapping.. replicate: 4900 / 10000 0:05 RELL Bootstrapping.. replicate: 5000 / 10000 0:05 RELL Bootstrapping.. replicate: 5100 / 10000 0:05 RELL Bootstrapping.. replicate: 5200 / 10000 0:05 RELL Bootstrapping.. replicate: 5300 / 10000 0:05 RELL Bootstrapping.. replicate: 5400 / 10000 0:05 RELL Bootstrapping.. replicate: 5500 / 10000 0:05 RELL Bootstrapping.. replicate: 5600 / 10000 0:05 RELL Bootstrapping.. replicate: 5700 / 10000 0:05 RELL Bootstrapping.. replicate: 5800 / 10000 0:05 RELL Bootstrapping.. replicate: 5900 / 10000 0:05 RELL Bootstrapping.. replicate: 6000 / 10000 0:05 RELL Bootstrapping.. replicate: 6100 / 10000 0:05 RELL Bootstrapping.. replicate: 6200 / 10000 0:05 RELL Bootstrapping.. replicate: 6300 / 10000 0:05 RELL Bootstrapping.. replicate: 6400 / 10000 0:05 RELL Bootstrapping.. replicate: 6500 / 10000 0:05 RELL Bootstrapping.. replicate: 6600 / 10000 0:05 RELL Bootstrapping.. replicate: 6700 / 10000 0:05 RELL Bootstrapping.. replicate: 6800 / 10000 0:05 RELL Bootstrapping.. replicate: 6900 / 10000 0:05 RELL Bootstrapping.. replicate: 7000 / 10000 0:05 RELL Bootstrapping.. replicate: 7100 / 10000 0:05 RELL Bootstrapping.. replicate: 7200 / 10000 0:05 RELL Bootstrapping.. replicate: 7300 / 10000 0:05 RELL Bootstrapping.. replicate: 7400 / 10000 0:05 RELL Bootstrapping.. replicate: 7500 / 10000 0:05 RELL Bootstrapping.. replicate: 7600 / 10000 0:05 RELL Bootstrapping.. replicate: 7700 / 10000 0:05 RELL Bootstrapping.. replicate: 7800 / 10000 0:05 RELL Bootstrapping.. replicate: 7900 / 10000 0:05 RELL Bootstrapping.. replicate: 8000 / 10000 0:05 RELL Bootstrapping.. replicate: 8100 / 10000 0:05 RELL Bootstrapping.. replicate: 8200 / 10000 0:05 RELL Bootstrapping.. replicate: 8300 / 10000 0:05 RELL Bootstrapping.. replicate: 8400 / 10000 0:05 RELL Bootstrapping.. replicate: 8500 / 10000 0:05 RELL Bootstrapping.. replicate: 8600 / 10000 0:05 RELL Bootstrapping.. replicate: 8700 / 10000 0:05 RELL Bootstrapping.. replicate: 8800 / 10000 0:05 RELL Bootstrapping.. replicate: 8900 / 10000 0:05 RELL Bootstrapping.. replicate: 9000 / 10000 0:05 RELL Bootstrapping.. replicate: 9100 / 10000 0:05 RELL Bootstrapping.. replicate: 9200 / 10000 0:05 RELL Bootstrapping.. replicate: 9300 / 10000 0:05 RELL Bootstrapping.. replicate: 9400 / 10000 0:05 RELL Bootstrapping.. replicate: 9500 / 10000 0:05 RELL Bootstrapping.. replicate: 9600 / 10000 0:05 RELL Bootstrapping.. replicate: 9700 / 10000 0:05 RELL Bootstrapping.. replicate: 9800 / 10000 0:05 RELL Bootstrapping.. replicate: 9900 / 10000 0:05 RELL Bootstrapping.. replicate: 10000 / 10000 0:05 547s now doing S-H test 547s 547s Time used: 0:05 547s Passed 547s 547s Test 5 547s 547s 15 verbose | verbose 1.00 547s 7 runmode | runmode 0.00 547s 4 seqtype | seqtype 1.00 547s 13 CodonFreq | CodonFreq 2.00 547s 9 clock | clock 0.00 547s 16 model | model 2.00 547s 20 NSsites | NSsites 0.00 547s 22 icode | icode 0.00 547s 24 fix_kappa | fix_kappa 0.00 547s 25 kappa | kappa 2.00 547s 26 fix_omega | fix_omega 0.00 547s 27 omega | omega 2.00 547s 28 fix_alpha | fix_alpha 1.00 547s 29 alpha | alpha 0.00 547s 30 Malpha | Malpha 0.00 547s 31 ncatG | ncatG 4.00 547s 11 getSE | getSE 0.00 547s 12 RateAncestor | RateAncestor 0.00 547s 8 method | method 0.00 547s 37 fix_blength | fix_blength 0.00 547s CODONML in paml version 4.9j, October 2019 547s 547s ---------------------------------------------- 547s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 547s TTC | TCC | TAC | TGC 547s Leu L TTA | TCA | *** * TAA | *** * TGA 547s TTG | TCG | TAG | Trp W TGG 547s ---------------------------------------------- 547s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 547s CTC | CCC | CAC | CGC 547s CTA | CCA | Gln Q CAA | CGA 547s CTG | CCG | CAG | CGG 547s ---------------------------------------------- 547s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 547s ATC | ACC | AAC | AGC 547s ATA | ACA | Lys K AAA | Arg R AGA 547s Met M ATG | ACG | AAG | AGG 547s ---------------------------------------------- 547s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 547s GTC | GCC | GAC | GGC 547s GTA | GCA | Glu E GAA | GGA 547s GTG | GCG | GAG | GGG 547s ---------------------------------------------- 547s Nice code, uuh? 547s 547s 547s Ambiguity character definition table: 547s 547s T (1): T 547s C (1): C 547s A (1): A 547s G (1): G 547s U (1): T 547s Y (2): T C 547s R (2): A G 547s M (2): C A 547s K (2): T G 547s S (2): C G 547s W (2): T A 547s H (3): T C A 547s B (3): T C G 547s V (3): C A G 547s D (3): T A G 547s - (4): T C A G 547s N (4): T C A G 547s ? (4): T C A G 547s ns = 7 ls = 390 547s Reading sequences, sequential format.. 547s Reading seq # 1: Hsa_Human 547s Reading seq # 2: Hla_gibbon 547s Reading seq # 3: Cgu/Can_colobus 547s Reading seq # 4: Pne_langur 547s Reading seq # 5: Mmu_rhesus 547s Reading seq # 6: Ssc_squirrelM 547s Reading seq # 7: Cja_marmoset 547s 547s Sequences read.. 547s Counting site patterns.. 0:00 547s Compressing, 81 patterns at 130 / 130 sites (100.0%), 0:00 547s Collecting fpatt[] & pose[], 81 patterns at 130 / 130 sites (100.0%), 0:00 547s Counting codons.. 547s 547s 168 bytes for distance 547s 79056 bytes for conP 547s 16918333343455671296 bytes for fhK 547s 5000000 bytes for space 547s 547s 2 branch types are in tree. Stop if wrong. 547s TREE # 1 547s ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 547s 197640 bytes for conP, adjusted 547s 547s 0.031100 0.057329 0.011198 0.050062 0.079492 0.075071 0.072188 0.041102 0.084577 0.046572 0.095144 1.692190 1.879076 1.929417 547s 547s ntime & nrate & np: 11 3 14 547s 547s Bounds (np=14): 547s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 0.000100 547s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 999.000000 547s 547s np = 14 547s lnL0 = -931.683823 547s 547s Iterating by ming2 547s Initial: fx= 931.683823 547s x= 0.03110 0.05733 0.01120 0.05006 0.07949 0.07507 0.07219 0.04110 0.08458 0.04657 0.09514 1.69219 1.87908 1.92942 547s 547s 1 h-m-p 0.0000 0.0010 300.6316 ++YYCCCC 925.257275 5 0.0003 29 | 0/14 547s 2 h-m-p 0.0001 0.0007 136.7386 +YCYCCC 921.377813 5 0.0004 55 | 0/14 547s 3 h-m-p 0.0001 0.0005 81.8581 CYCCC 920.885940 4 0.0002 79 | 0/14 549s 4 h-m-p 0.0007 0.0088 21.5537 CYC 920.713128 2 0.0009 99 | 0/14 549s 5 h-m-p 0.0006 0.0061 30.3754 CCC 920.538343 2 0.0008 120 | 0/14 549s 6 h-m-p 0.0004 0.0038 67.4815 +YCCC 920.112623 3 0.0010 143 | 0/14 549s 7 h-m-p 0.0003 0.0080 205.8714 ++YCCCC 915.490084 4 0.0038 169 | 0/14 549s 8 h-m-p 0.0007 0.0036 646.3998 YCYCCCC 907.361445 6 0.0018 196 | 0/14 549s 9 h-m-p 0.0005 0.0025 541.6273 CCCC 905.764015 3 0.0005 219 | 0/14 549s 10 h-m-p 0.0008 0.0040 74.1007 YCC 905.608060 2 0.0004 239 | 0/14 549s 11 h-m-p 0.0056 0.0372 5.0808 YC 905.599464 1 0.0007 257 | 0/14 549s 12 h-m-p 0.0011 0.0760 3.3198 +YC 905.582546 1 0.0037 276 | 0/14 549s 13 h-m-p 0.0004 0.0745 28.0680 +YCCC 905.462695 3 0.0033 299 | 0/14 549s 14 h-m-p 0.1328 3.9271 0.7039 +YCCC 904.373434 3 1.3083 322 | 0/14 549s 15 h-m-p 1.2153 6.0766 0.6252 CCCC 903.884885 3 1.3165 359 | 0/14 549s 16 h-m-p 1.6000 8.0000 0.2684 CCC 903.766850 2 1.3530 394 | 0/14 549s 17 h-m-p 0.8342 8.0000 0.4353 +YC 903.654224 1 2.1508 427 | 0/14 549s 18 h-m-p 1.5066 8.0000 0.6214 CC 903.572223 1 1.4956 460 | 0/14 549s 19 h-m-p 1.6000 8.0000 0.4803 CC 903.517114 1 2.2768 493 | 0/14 549s 20 h-m-p 1.6000 8.0000 0.4061 +CCC 903.444862 2 5.3716 529 | 0/14 549s 21 h-m-p 1.6000 8.0000 0.9955 +YC 903.289535 1 4.6218 562 | 0/14 549s 22 h-m-p 1.6000 8.0000 1.8465 CCC 903.235969 2 2.3967 597 | 0/14 549s 23 h-m-p 1.6000 8.0000 2.3830 +YCCC 903.179711 3 4.5149 620 | 0/14 549s 24 h-m-p 1.6000 8.0000 4.1346 YCC 903.147119 2 2.7062 640 | 0/14 549s 25 h-m-p 1.6000 8.0000 5.9078 YC 903.122453 1 3.9033 658 | 0/14 549s 26 h-m-p 1.6000 8.0000 8.9175 YC 903.107457 1 2.7293 676 | 0/14 549s 27 h-m-p 1.6000 8.0000 12.7899 YC 903.095980 1 3.9851 694 | 0/14 549s 28 h-m-p 1.6000 8.0000 19.8452 YC 903.089171 1 2.6668 712 | 0/14 549s 29 h-m-p 1.6000 8.0000 27.8232 +YC 903.083848 1 4.0986 731 | 0/14 549s 30 h-m-p 1.6000 8.0000 43.7461 YC 903.080771 1 2.6181 749 | 0/14 549s 31 h-m-p 1.6000 8.0000 60.7310 +YC 903.078314 1 4.2439 768 | 0/14 549s 32 h-m-p 0.6636 3.3179 96.8472 +C 903.076932 0 2.5500 786 | 0/14 549s 33 h-m-p 0.1114 0.5571 133.4917 ++ 903.076635 m 0.5571 803 | 1/14 549s 34 h-m-p 0.4520 8.0000 0.0008 YC 903.076551 1 1.0068 821 | 1/14 549s 35 h-m-p 1.6000 8.0000 0.0000 Y 903.076551 0 1.1285 851 | 1/14 549s 36 h-m-p 1.6000 8.0000 0.0000 Y 903.076551 0 1.1420 881 549s Out.. 549s lnL = -903.076551 549s 882 lfun, 1764 eigenQcodon, 9702 P(t) 549s 549s d123[*] = 0.03093 0.03339 0.00627 average 0.02353 549s [B] = 0.00003 0.00003 0.00003 average 0.00003 549s accept =982.57114999.00000191.44798 549s 549s w =999.00000 dN = 0.03251 dS = 0.00003 d4 = 0.00003 (55.6 four-fold sites) 549s dN*= 0.03053 dS*= 0.00004 S* = 89.52 N* = 300.48 549s 549s d123[*] = 0.00729 0.00768 0.01045 average 0.00848 549s [B] = 0.01072 0.01138 0.01114 average 0.01108 549s accept = 0.68069 0.67535 0.93805 549s 549s w = 0.67535 dN = 0.00748 dS = 0.01108 d4 = 0.00940 (55.6 four-fold sites) 549s dN*= 0.00702 dS*= 0.01335 S* = 89.52 N* = 300.48 549s 549s d123[*] = 0.01118 0.01178 0.01602 average 0.01300 549s [B] = 0.01643 0.01744 0.01708 average 0.01699 549s accept = 0.68069 0.67535 0.93805 549s 549s w = 0.67535 dN = 0.01147 dS = 0.01699 d4 = 0.01442 (55.6 four-fold sites) 549s dN*= 0.01077 dS*= 0.02047 S* = 89.52 N* = 300.48 549s 549s d123[*] = 0.01222 0.01288 0.01751 average 0.01420 549s [B] = 0.01796 0.01907 0.01867 average 0.01856 549s accept = 0.68069 0.67535 0.93805 549s 549s w = 0.67535 dN = 0.01254 dS = 0.01856 d4 = 0.01576 (55.6 four-fold sites) 549s dN*= 0.01177 dS*= 0.02237 S* = 89.52 N* = 300.48 549s 549s d123[*] = 0.02257 0.02378 0.03234 average 0.02623 549s [B] = 0.03316 0.03521 0.03447 average 0.03428 549s accept = 0.68069 0.67535 0.93805 549s 549s w = 0.67535 dN = 0.02315 dS = 0.03428 d4 = 0.02910 (55.6 four-fold sites) 549s dN*= 0.02174 dS*= 0.04130 S* = 89.52 N* = 300.48 549s 549s d123[*] = 0.01258 0.01326 0.01803 average 0.01462 551s [B] = 0.01849 0.01963 0.01922 average 0.01911 551s accept = 0.68069 0.67535 0.93805 551s 551s w = 0.67535 dN = 0.01291 dS = 0.01911 d4 = 0.01622 (55.6 four-fold sites) 551s dN*= 0.01212 dS*= 0.02303 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.01506 0.01587 0.02158 average 0.01750 551s [B] = 0.02213 0.02350 0.02301 average 0.02288 551s accept = 0.68069 0.67535 0.93805 551s 551s w = 0.67535 dN = 0.01545 dS = 0.02288 d4 = 0.01942 (55.6 four-fold sites) 551s dN*= 0.01451 dS*= 0.02756 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.00561 0.00591 0.00803 average 0.00652 551s [B] = 0.00824 0.00875 0.00856 average 0.00852 551s accept = 0.68069 0.67535 0.93805 551s 551s w = 0.67535 dN = 0.00575 dS = 0.00852 d4 = 0.00723 (55.6 four-fold sites) 551s dN*= 0.00540 dS*= 0.01026 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.03473 0.03658 0.04976 average 0.04036 551s [B] = 0.05102 0.05417 0.05304 average 0.05274 551s accept = 0.68069 0.67535 0.93805 551s 551s w = 0.67535 dN = 0.03562 dS = 0.05274 d4 = 0.04477 (55.6 four-fold sites) 551s dN*= 0.03345 dS*= 0.06355 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.01191 0.01254 0.01706 average 0.01384 551s [B] = 0.01749 0.01857 0.01819 average 0.01808 551s accept = 0.68069 0.67535 0.93805 551s 551s w = 0.67535 dN = 0.01221 dS = 0.01808 d4 = 0.01535 (55.6 four-fold sites) 551s dN*= 0.01147 dS*= 0.02179 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.00669 0.00705 0.00958 average 0.00777 551s [B] = 0.00983 0.01043 0.01022 average 0.01016 551s accept = 0.68069 0.67535 0.93805 551s 551s w = 0.67535 dN = 0.00686 dS = 0.01016 d4 = 0.00862 (55.6 four-fold sites) 551s dN*= 0.00644 dS*= 0.01224 S* = 89.52 N* = 300.48 551s 551s 2 branch types are in tree. Stop if wrong. 551s TREE # 2 551s ((1, 2), ((3, 4), 5), (6, 7)); MP score: 65 551s 0.075051 0.023585 0.036207 0.100850 0.027850 0.097622 0.079728 0.055988 0.062040 0.076055 0.080764 2.242868 2.280825 2.330915 551s 551s ntime & nrate & np: 11 3 14 551s 551s Bounds (np=14): 551s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 0.000100 551s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 999.000000 551s 551s np = 14 551s lnL0 = -934.236267 551s 551s Iterating by ming2 551s Initial: fx= 934.236267 551s x= 0.07505 0.02359 0.03621 0.10085 0.02785 0.09762 0.07973 0.05599 0.06204 0.07606 0.08076 2.24287 2.28083 2.33091 551s 551s 1 h-m-p 0.0000 0.0009 242.0431 +++YYCCC 920.086738 4 0.0006 28 | 0/14 551s 2 h-m-p 0.0002 0.0009 84.2925 YCCCCC 918.794539 5 0.0004 54 | 0/14 551s 3 h-m-p 0.0003 0.0017 43.6718 YYC 918.573130 2 0.0003 73 | 0/14 551s 4 h-m-p 0.0008 0.0091 16.3112 CC 918.489744 1 0.0007 92 | 0/14 551s 5 h-m-p 0.0004 0.0091 27.1366 YC 918.338818 1 0.0011 110 | 0/14 551s 6 h-m-p 0.0008 0.0038 35.5064 YYC 918.225558 2 0.0007 129 | 0/14 551s 7 h-m-p 0.0004 0.0103 65.7945 +CCCC 917.594189 3 0.0022 153 | 0/14 551s 8 h-m-p 0.0004 0.0055 386.9779 +CYYCCC 910.939207 5 0.0034 180 | 0/14 551s 9 h-m-p 0.0001 0.0003 5683.8021 YCYCCC 905.165235 5 0.0002 206 | 0/14 551s 10 h-m-p 0.0008 0.0039 68.3196 CCC 905.092860 2 0.0003 227 | 0/14 551s 11 h-m-p 0.0026 0.0172 7.0219 CC 905.071973 1 0.0010 246 | 0/14 551s 12 h-m-p 0.0004 0.0298 15.9364 +YCC 904.942424 2 0.0031 267 | 0/14 551s 13 h-m-p 0.0004 0.0266 113.5656 ++YCCC 903.674550 3 0.0048 291 | 0/14 551s 14 h-m-p 0.7357 3.8427 0.7440 CYCCC 902.233609 4 1.0283 315 | 0/14 551s 15 h-m-p 1.6000 8.0000 0.3870 CYC 901.954210 2 1.3960 349 | 0/14 551s 16 h-m-p 1.3072 8.0000 0.4133 CCC 901.781760 2 1.8687 384 | 0/14 551s 17 h-m-p 1.6000 8.0000 0.3830 CYC 901.702197 2 1.6745 418 | 0/14 551s 18 h-m-p 1.6000 8.0000 0.2197 C 901.680873 0 1.6000 449 | 0/14 551s 19 h-m-p 1.6000 8.0000 0.1180 YC 901.665823 1 2.5453 481 | 0/14 551s 20 h-m-p 1.4323 8.0000 0.2097 CC 901.649018 1 2.1607 514 | 0/14 551s 21 h-m-p 1.5398 8.0000 0.2943 CCC 901.635308 2 2.0716 549 | 0/14 551s 22 h-m-p 1.6000 8.0000 0.2422 C 901.631164 0 1.7361 580 | 0/14 551s 23 h-m-p 1.6000 8.0000 0.0765 CC 901.630900 1 1.3353 613 | 0/14 551s 24 h-m-p 1.6000 8.0000 0.0190 Y 901.630891 0 1.2528 644 | 0/14 551s 25 h-m-p 1.6000 8.0000 0.0011 C 901.630891 0 1.2895 675 | 0/14 551s 26 h-m-p 1.6000 8.0000 0.0001 Y 901.630891 0 1.1249 706 | 0/14 551s 27 h-m-p 1.6000 8.0000 0.0000 C 901.630891 0 1.9166 737 | 0/14 551s 28 h-m-p 1.6000 8.0000 0.0000 ---C 901.630891 0 0.0063 771 551s Out.. 551s lnL = -901.630891 551s 772 lfun, 1544 eigenQcodon, 8492 P(t) 551s 551s d123[*] = 0.03023 0.03255 0.00961 average 0.02413 551s [B] = 0.00422 0.00448 0.00439 average 0.00436 551s accept = 7.16053 7.26348 2.18931 551s 551s w = 7.26348 dN = 0.03170 dS = 0.00436 d4 = 0.00370 (55.6 four-fold sites) 551s dN*= 0.02975 dS*= 0.00526 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.00673 0.00705 0.01167 average 0.00848 551s [B] = 0.01230 0.01306 0.01279 average 0.01272 551s accept = 0.54721 0.53964 0.91259 551s 551s w = 0.53964 dN = 0.00686 dS = 0.01272 d4 = 0.01079 (55.6 four-fold sites) 551s dN*= 0.00644 dS*= 0.01534 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.01033 0.01081 0.01791 average 0.01302 551s [B] = 0.01888 0.02004 0.01962 average 0.01951 551s accept = 0.54721 0.53964 0.91259 551s 551s w = 0.53964 dN = 0.01053 dS = 0.01951 d4 = 0.01656 (55.6 four-fold sites) 551s dN*= 0.00988 dS*= 0.02353 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.01145 0.01199 0.01985 average 0.01443 551s [B] = 0.02093 0.02221 0.02175 average 0.02163 551s accept = 0.54721 0.53964 0.91259 551s 551s w = 0.53964 dN = 0.01167 dS = 0.02163 d4 = 0.01835 (55.6 four-fold sites) 551s dN*= 0.01096 dS*= 0.02608 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.03422 0.03684 0.01087 average 0.02731 551s [B] = 0.00478 0.00507 0.00497 average 0.00494 551s accept = 7.16053 7.26348 2.18931 551s 551s w = 7.26348 dN = 0.03588 dS = 0.00494 d4 = 0.00419 (55.6 four-fold sites) 551s dN*= 0.03367 dS*= 0.00596 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.01165 0.01220 0.02020 average 0.01468 551s [B] = 0.02130 0.02261 0.02213 average 0.02201 551s accept = 0.54721 0.53964 0.91259 551s 551s w = 0.53964 dN = 0.01188 dS = 0.02201 d4 = 0.01868 (55.6 four-fold sites) 551s dN*= 0.01115 dS*= 0.02655 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.01377 0.01441 0.02386 average 0.01735 551s [B] = 0.02516 0.02671 0.02615 average 0.02601 551s accept = 0.54721 0.53964 0.91259 551s 551s w = 0.53964 dN = 0.01403 dS = 0.02601 d4 = 0.02207 (55.6 four-fold sites) 551s dN*= 0.01317 dS*= 0.03136 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.00457 0.00478 0.00792 average 0.00576 551s [B] = 0.00835 0.00886 0.00868 average 0.00863 551s accept = 0.54721 0.53964 0.91259 551s 551s w = 0.53964 dN = 0.00466 dS = 0.00863 d4 = 0.00732 (55.6 four-fold sites) 551s dN*= 0.00437 dS*= 0.01041 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.03179 0.03327 0.05509 average 0.04005 551s [B] = 0.05809 0.06166 0.06037 average 0.06004 551s accept = 0.54721 0.53964 0.91259 551s 551s w = 0.53964 dN = 0.03240 dS = 0.06004 d4 = 0.05095 (55.6 four-fold sites) 551s dN*= 0.03041 dS*= 0.07241 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.01108 0.01160 0.01920 average 0.01396 551s [B] = 0.02025 0.02149 0.02104 average 0.02093 551s accept = 0.54721 0.53964 0.91259 551s 551s w = 0.53964 dN = 0.01129 dS = 0.02093 d4 = 0.01776 (55.6 four-fold sites) 551s dN*= 0.01060 dS*= 0.02524 S* = 89.52 N* = 300.48 551s 551s d123[*] = 0.00611 0.00639 0.01059 average 0.00770 551s [B] = 0.01116 0.01185 0.01160 average 0.01154 551s accept = 0.54721 0.53964 0.91259 551s 551s w = 0.53964 dN = 0.00623 dS = 0.01154 d4 = 0.00979 (55.6 four-fold sites) 551s dN*= 0.00584 dS*= 0.01392 S* = 89.52 N* = 300.48 551s 551s Tree comparisons (Kishino & Hasegawa 1989; Shimodaira & Hasegawa 1999) 551s Reading lnf for tree # 1 Reading lnf for tree # 2, done. 551s Calculating SEs by sitewise comparison, 0:04 551s RELL Bootstrapping.. replicate: 100 / 10000 0:04 RELL Bootstrapping.. replicate: 200 / 10000 0:04 RELL Bootstrapping.. replicate: 300 / 10000 0:04 RELL Bootstrapping.. replicate: 400 / 10000 0:04 RELL Bootstrapping.. replicate: 500 / 10000 0:04 RELL Bootstrapping.. replicate: 600 / 10000 0:04 RELL Bootstrapping.. replicate: 700 / 10000 0:04 RELL Bootstrapping.. replicate: 800 / 10000 0:04 RELL Bootstrapping.. replicate: 900 / 10000 0:04 RELL Bootstrapping.. replicate: 1000 / 10000 0:04 RELL Bootstrapping.. replicate: 1100 / 10000 0:04 RELL Bootstrapping.. replicate: 1200 / 10000 0:04 RELL Bootstrapping.. replicate: 1300 / 10000 0:04 RELL Bootstrapping.. replicate: 1400 / 10000 0:04 RELL Bootstrapping.. replicate: 1500 / 10000 0:04 RELL Bootstrapping.. replicate: 1600 / 10000 0:04 RELL Bootstrapping.. replicate: 1700 / 10000 0:04 RELL Bootstrapping.. replicate: 1800 / 10000 0:04 RELL Bootstrapping.. replicate: 1900 / 10000 0:04 RELL Bootstrapping.. replicate: 2000 / 10000 0:04 RELL Bootstrapping.. replicate: 2100 / 10000 0:04 RELL Bootstrapping.. replicate: 2200 / 10000 0:04 RELL Bootstrapping.. replicate: 2300 / 10000 0:04 RELL Bootstrapping.. replicate: 2400 / 10000 0:04 RELL Bootstrapping.. replicate: 2500 / 10000 0:04 RELL Bootstrapping.. replicate: 2600 / 10000 0:04 RELL Bootstrapping.. replicate: 2700 / 10000 0:04 RELL Bootstrapping.. replicate: 2800 / 10000 0:04 RELL Bootstrapping.. replicate: 2900 / 10000 0:04 RELL Bootstrapping.. replicate: 3000 / 10000 0:04 RELL Bootstrapping.. replicate: 3100 / 10000 0:04 RELL Bootstrapping.. replicate: 3200 / 10000 0:04 RELL Bootstrapping.. replicate: 3300 / 10000 0:04 RELL Bootstrapping.. replicate: 3400 / 10000 0:04 RELL Bootstrapping.. replicate: 3500 / 10000 0:04 RELL Bootstrapping.. replicate: 3600 / 10000 0:04 RELL Bootstrapping.. replicate: 3700 / 10000 0:04 RELL Bootstrapping.. replicate: 3800 / 10000 0:04 RELL Bootstrapping.. replicate: 3900 / 10000 0:04 RELL Bootstrapping.. replicate: 4000 / 10000 0:04 RELL Bootstrapping.. replicate: 4100 / 10000 0:04 RELL Bootstrapping.. replicate: 4200 / 10000 0:04 RELL Bootstrapping.. replicate: 4300 / 10000 0:04 RELL Bootstrapping.. replicate: 4400 / 10000 0:04 RELL Bootstrapping.. replicate: 4500 / 10000 0:04 RELL Bootstrapping.. replicate: 4600 / 10000 0:04 RELL Bootstrapping.. replicate: 4700 / 10000 0:04 RELL Bootstrapping.. replicate: 4800 / 10000 0:04 RELL Bootstrapping.. replicate: 4900 / 10000 0:04 RELL Bootstrapping.. replicate: 5000 / 10000 0:04 RELL Bootstrapping.. replicate: 5100 / 10000 0:04 RELL Bootstrapping.. replicate: 5200 / 10000 0:04 RELL Bootstrapping.. replicate: 5300 / 10000 0:04 RELL Bootstrapping.. replicate: 5400 / 10000 0:04 RELL Bootstrapping.. replicate: 5500 / 10000 0:04 RELL Bootstrapping.. replicate: 5600 / 10000 0:04 RELL Bootstrapping.. replicate: 5700 / 10000 0:04 RELL Bootstrapping.. replicate: 5800 / 10000 0:04 RELL Bootstrapping.. replicate: 5900 / 10000 0:04 RELL Bootstrapping.. replicate: 6000 / 10000 0:04 RELL Bootstrapping.. replicate: 6100 / 10000 0:04 RELL Bootstrapping.. replicate: 6200 / 10000 0:04 RELL Bootstrapping.. replicate: 6300 / 10000 0:04 RELL Bootstrapping.. replicate: 6400 / 10000 0:04 RELL Bootstrapping.. replicate: 6500 / 10000 0:04 RELL Bootstrapping.. replicate: 6600 / 10000 0:04 RELL Bootstrapping.. replicate: 6700 / 10000 0:04 RELL Bootstrapping.. replicate: 6800 / 10000 0:04 RELL Bootstrapping.. replicate: 6900 / 10000 0:04 RELL Bootstrapping.. replicate: 7000 / 10000 0:04 RELL Bootstrapping.. replicate: 7100 / 10000 0:04 RELL Bootstrapping.. replicate: 7200 / 10000 0:04 RELL Bootstrapping.. replicate: 7300 / 10000 0:04 RELL Bootstrapping.. replicate: 7400 / 10000 0:04 RELL Bootstrapping.. replicate: 7500 / 10000 0:04 RELL Bootstrapping.. replicate: 7600 / 10000 0:04 RELL Bootstrapping.. replicate: 7700 / 10000 0:04 RELL Bootstrapping.. replicate: 7800 / 10000 0:04 RELL Bootstrapping.. replicate: 7900 / 10000 0:04 RELL Bootstrapping.. replicate: 8000 / 10000 0:04 RELL Bootstrapping.. replicate: 8100 / 10000 0:04 RELL Bootstrapping.. replicate: 8200 / 10000 0:04 RELL Bootstrapping.. replicate: 8300 / 10000 0:04 RELL Bootstrapping.. replicate: 8400 / 10000 0:04 RELL Bootstrapping.. replicate: 8500 / 10000 0:04 RELL Bootstrapping.. replicate: 8600 / 10000 0:04 RELL Bootstrapping.. replicate: 8700 / 10000 0:04 RELL Bootstrapping.. replicate: 8800 / 10000 0:04 RELL Bootstrapping.. replicate: 8900 / 10000 0:04 RELL Bootstrapping.. replicate: 9000 / 10000 0:04 RELL Bootstrapping.. replicate: 9100 / 10000 0:04 RELL Bootstrapping.. replicate: 9200 / 10000 0:04 RELL Bootstrapping.. replicate: 9300 / 10000 0:04 RELL Bootstrapping.. replicate: 9400 / 10000 0:04 RELL Bootstrapping.. replicate: 9500 / 10000 0:04 RELL Bootstrapping.. replicate: 9600 / 10000 0:04 RELL Bootstrapping.. replicate: 9700 / 10000 0:04 RELL Bootstrapping.. replicate: 9800 / 10000 0:04 RELL Bootstrapping.. replicate: 9900 / 10000 0:04 RELL Bootstrapping.. replicate: 10000 / 10000 0:04 551s now doing S-H test 551s 551s Time used: 0:04 551s Passed 551s 551s Test 6 551s 551s CODONML in paml version 4.9j, October 2019 551s 551s ---------------------------------------------- 551s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 551s TTC | TCC | TAC | TGC 551s Leu L TTA | TCA | *** * TAA | *** * TGA 551s TTG | TCG | TAG | Trp W TGG 551s ---------------------------------------------- 551s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 551s CTC | CCC | CAC | CGC 551s CTA | CCA | Gln Q CAA | CGA 551s CTG | CCG | CAG | CGG 551s ---------------------------------------------- 551s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 551s ATC | ACC | AAC | AGC 551s ATA | ACA | Lys K AAA | Arg R AGA 551s Met M ATG | ACG | AAG | AGG 551s ---------------------------------------------- 551s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 551s GTC | GCC | GAC | GGC 551s GTA | GCA | Glu E GAA | GGA 551s GTG | GCG | GAG | GGG 551s ---------------------------------------------- 551s Nice code, uuh? 551s ns = 19 ls = 390 551s Reading sequences, sequential format.. 551s Reading seq # 1: 1.human Reading seq # 2: 2.chimp_bonobo_gorilla Reading seq # 3: 3.orangutan_Ppy Reading seq # 4: 4.gibbon_Ggo Reading seq # 5: 5.colobus_Cgu&Can Reading seq # 6: 6.langur_Sen&Sve Reading seq # 7: 7.langur_Tob&Tfr Reading seq # 8: 8.Douc_langur_Pne Reading seq # 9: 9.probiscis_Nla Reading seq #10: 10.baboon_Pcy Reading seq #11: 11.mangabey_Cat Reading seq #12: 12.rhesus_Mmu Reading seq #13: 13.Allen_Ani Reading seq #14: 14.talapoin_Mta Reading seq #15: 15.patas_Epa Reading seq #16: 16.vervet_Cae Reading seq #17: 17.squirrel_m Reading seq #18: 18.tamarin_Soe Reading seq #19: 19.Marmoset_Cja 551s Sequences read.. 551s Counting site patterns.. 0:00 551s Compressing, 86 patterns at 130 / 130 sites (100.0%), 0:00 551s Collecting fpatt[] & pose[], 86 patterns at 130 / 130 sites (100.0%), 0:00 551s Counting codons.. 551s 551s 1368 bytes for distance 551s 83936 bytes for conP 551s 2752 bytes for fhK 551s 5000000 bytes for space 551s 551s 2 branch types are in tree. Stop if wrong. 551s TREE # 1 551s (((((6, 7, 8), 9), 5), (((10, 11), 12), 13, (14, (15, 16)))), (((1, 2), 3), 4), (17, (18, 19))); MP score: 83 551s 629520 bytes for conP, adjusted 551s 551s 0.107588 0.104516 0.059098 0.067502 0.014536 0.075737 0.098872 0.089463 0.021946 0.038354 0.087666 0.104872 0.018475 0.076220 0.050663 0.037886 0.059464 0.057443 0.063080 0.060305 0.100313 0.023249 0.096378 0.050501 0.094199 0.044711 0.053048 0.085066 0.071347 0.070793 0.094653 0.024104 0.092023 3.000000 1.280671 0.065654 0.216121 2.304522 551s 551s ntime & nrate & np: 33 3 38 551s 551s Bounds (np=38): 551s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 -99.000000 -99.000000 0.000001 1.000000 551s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 99.000000 99.000000 1.000000 999.000000 551s branch=0 freq=0.771186 w0 = 0.216121 551s branch=0 freq=0.228814 w1 = 1.000000 551s Qfactor for branch 0 = 6.469097 551s branch=1 freq=0.635100 w0 = 0.216121 551s branch=1 freq=0.188437 w1 = 1.000000 551s branch=1 freq=0.176463 w2 = 2.304522 551s Qfactor for branch 1 = 4.458889 551s w[0] = 0.216121 551s w[1] = 1.000000 551s w[2] = 2.304522 551s 551s np = 38 551s lnL0 = -1170.510371 551s 551s Iterating by ming2 586s Initial: fx= 1170.510371 586s x= 0.10759 0.10452 0.05910 0.06750 0.01454 0.07574 0.09887 0.08946 0.02195 0.03835 0.08767 0.10487 0.01848 0.07622 0.05066 0.03789 0.05946 0.05744 0.06308 0.06030 0.10031 0.02325 0.09638 0.05050 0.09420 0.04471 0.05305 0.08507 0.07135 0.07079 0.09465 0.02410 0.09202 3.00000 1.28067 0.06565 0.21612 2.30452 586s 586s 1 h-m-p 0.0000 0.0003 483.9952 +++ 1109.235496 m 0.0003 44 | 0/38 586s 2 h-m-p 0.0000 0.0000 12700.9024 ++ 1093.582500 m 0.0000 85 | 1/38 586s 3 h-m-p 0.0000 0.0000 116509.2020 ++ 1080.652428 m 0.0000 126 | 2/38 586s 4 h-m-p 0.0000 0.0001 918.3404 ++ 1059.696792 m 0.0001 167 | 3/38 586s 5 h-m-p 0.0000 0.0000 1805.2631 ++ 1057.546562 m 0.0000 208 | 4/38 586s 6 h-m-p 0.0000 0.0000 3553.7472 ++ 1050.131735 m 0.0000 249 | 5/38 586s 7 h-m-p 0.0000 0.0000 886.6789 ++ 1045.317249 m 0.0000 290 | 6/38 586s 8 h-m-p 0.0000 0.0000 499.6069 ++ 1043.750998 m 0.0000 331 | 7/38 586s 9 h-m-p 0.0001 0.0004 113.1480 YCCC 1042.889279 3 0.0002 377 | 7/38 586s 10 h-m-p 0.0001 0.0006 96.8046 CCCC 1042.340426 3 0.0002 424 | 7/38 586s 11 h-m-p 0.0003 0.0016 39.7204 YCY 1042.202423 2 0.0002 468 | 7/38 586s 12 h-m-p 0.0002 0.0023 41.3693 +YYCC 1041.787740 3 0.0006 514 | 7/38 586s 13 h-m-p 0.0001 0.0006 82.4843 CCCC 1041.598598 3 0.0002 561 | 7/38 586s 14 h-m-p 0.0002 0.0014 70.4745 CCCC 1041.316276 3 0.0003 608 | 7/38 586s 15 h-m-p 0.0002 0.0008 51.6667 CCC 1041.220945 2 0.0002 653 | 7/38 586s 16 h-m-p 0.0003 0.0031 37.8296 YCCC 1041.046441 3 0.0005 699 | 7/38 586s 17 h-m-p 0.0005 0.0033 44.2837 CC 1040.891360 1 0.0004 742 | 7/38 586s 18 h-m-p 0.0006 0.0048 34.0336 CY 1040.738241 1 0.0006 785 | 7/38 586s 19 h-m-p 0.0003 0.0021 59.1637 CCC 1040.554051 2 0.0004 830 | 7/38 586s 20 h-m-p 0.0005 0.0033 48.6562 CCCC 1040.269208 3 0.0008 877 | 7/38 586s 21 h-m-p 0.0002 0.0009 120.9858 YCCC 1039.998654 3 0.0003 923 | 7/38 586s 22 h-m-p 0.0003 0.0016 133.7742 CCCC 1039.730344 3 0.0003 970 | 7/38 586s 23 h-m-p 0.0002 0.0012 81.4156 CCCC 1039.554109 3 0.0003 1017 | 7/38 586s 24 h-m-p 0.0003 0.0013 74.1735 YCC 1039.495918 2 0.0001 1061 | 7/38 586s 25 h-m-p 0.0003 0.0057 34.5426 CC 1039.422332 1 0.0005 1104 | 7/38 586s 26 h-m-p 0.0008 0.0087 19.9024 CC 1039.363979 1 0.0008 1147 | 7/38 586s 27 h-m-p 0.0006 0.0110 29.9034 CC 1039.285519 1 0.0008 1190 | 7/38 586s 28 h-m-p 0.0009 0.0204 26.1512 ++CC 1038.176316 1 0.0141 1235 | 7/38 586s 29 h-m-p 0.0003 0.0014 116.8597 CCC 1038.053767 2 0.0003 1280 | 7/38 586s 30 h-m-p 0.0069 0.0344 2.5570 YC 1038.050443 1 0.0009 1322 | 7/38 586s 31 h-m-p 0.0004 0.0672 5.2609 ++++ 1037.359865 m 0.0672 1365 | 8/38 586s 32 h-m-p 0.1937 1.8802 1.8226 CCC 1036.885904 2 0.2683 1410 | 7/38 586s 33 h-m-p 0.1089 0.8439 4.4911 -CCC 1036.875845 2 0.0090 1456 | 7/38 586s 34 h-m-p 0.0424 0.5146 0.9492 ++ 1036.426754 m 0.5146 1497 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 2 r = 1 fhK = -8.95194e-08 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 4 r = 1 fhK = -6.65338e-08 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 9 r = 1 fhK = -3.22585e-08 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 15 r = 1 fhK = -5.90097e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 20 r = 1 fhK = -1.45262e-08 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 29 r = 1 fhK = -7.67590e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 30 r = 1 fhK = -1.10491e-08 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 33 r = 1 fhK = -5.25955e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 36 r = 1 fhK = -3.55746e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 41 r = 1 fhK = -6.70628e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 42 r = 1 fhK = -1.47886e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 48 r = 1 fhK = -6.16625e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 49 r = 1 fhK = -1.38724e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 54 r = 1 fhK = -3.43244e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 55 r = 1 fhK = -4.37246e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 56 r = 1 fhK = -2.93415e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 64 r = 1 fhK = -6.64706e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 65 r = 1 fhK = -8.55258e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 82 r = 1 fhK = -3.14614e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 2 r = 3 fhK = -7.42300e-08 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 4 r = 3 fhK = -5.59665e-08 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 9 r = 3 fhK = -2.87212e-08 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 15 r = 3 fhK = -4.94396e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 29 r = 3 fhK = -7.14773e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 30 r = 3 fhK = -9.43929e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 33 r = 3 fhK = -4.85220e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 34 r = 3 fhK = -3.49360e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 36 r = 3 fhK = -3.06030e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 39 r = 3 fhK = -1.39697e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 41 r = 3 fhK = -5.32335e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 42 r = 3 fhK = -1.32768e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 49 r = 3 fhK = -1.09583e-09 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 54 r = 3 fhK = -3.14206e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 55 r = 3 fhK = -3.76390e-10 586s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 586s 586s fx_r: h = 56 r = 3 fhK = -2.74436e-10 626s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 626s 626s fx_r: h = 64 r = 3 fhK = -5.98636e-10 626s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 626s 626s fx_r: h = 65 r = 3 fhK = -7.80351e-09 626s 0.042769 0.076010 0.026312 0.008871 0.001964 0.000004 0.023112 0.007332 0.037717 0.023169 0.000004 0.000004 0.008208 0.000004 0.008175 0.015682 0.007310 0.015945 0.006387 0.016301 0.008285 0.067912 0.006698 0.008575 0.015484 0.000004 0.000004 0.034001 0.134329 0.026470 0.000004 0.031988 0.040982 4.225249 0.373416 0.123531 -0.000059 2.781207 626s 626s fx_r: h = 82 r = 3 fhK = -2.71612e-09 | 8/38 626s 35 h-m-p 0.3131 1.6021 1.5598 YCCC 1036.292545 3 0.1651 1574 | 8/38 626s 36 h-m-p 0.3218 2.8441 0.8002 +YCCC 1036.042346 3 0.9016 1621 | 8/38 626s 37 h-m-p 1.0684 8.0000 0.6753 YCCC 1035.906377 3 0.7703 1697 | 8/38 626s 38 h-m-p 1.5879 8.0000 0.3276 CCC 1035.799958 2 1.5009 1772 | 8/38 626s 39 h-m-p 1.6000 8.0000 0.2183 CCC 1035.719168 2 2.1292 1847 | 8/38 626s 40 h-m-p 1.6000 8.0000 0.1077 CCC 1035.656176 2 2.3696 1922 | 8/38 626s 41 h-m-p 1.6000 8.0000 0.1237 CC 1035.624931 1 1.3507 1995 | 8/38 626s 42 h-m-p 1.6000 8.0000 0.0786 YC 1035.590772 1 3.5864 2067 | 8/38 626s 43 h-m-p 1.6000 8.0000 0.1230 CC 1035.563795 1 2.3946 2140 | 8/38 626s 44 h-m-p 1.6000 8.0000 0.1407 CC 1035.545518 1 1.9393 2213 | 8/38 626s 45 h-m-p 1.6000 8.0000 0.1171 C 1035.534789 0 1.5602 2284 | 8/38 626s 46 h-m-p 1.6000 8.0000 0.0299 YC 1035.534003 1 1.1610 2356 | 8/38 626s 47 h-m-p 1.6000 8.0000 0.0094 Y 1035.533954 0 1.1094 2427 | 8/38 626s 48 h-m-p 1.6000 8.0000 0.0017 Y 1035.533948 0 1.1879 2498 | 8/38 626s 49 h-m-p 1.2040 8.0000 0.0017 C 1035.533946 0 1.4880 2569 | 8/38 626s 50 h-m-p 1.5919 8.0000 0.0016 +Y 1035.533940 0 6.9192 2641 | 8/38 626s 51 h-m-p 1.2102 8.0000 0.0089 +C 1035.533919 0 4.7971 2713 | 8/38 626s 52 h-m-p 1.6000 8.0000 0.0053 Y 1035.533916 0 1.1722 2784 | 8/38 626s 53 h-m-p 1.6000 8.0000 0.0006 Y 1035.533916 0 1.0610 2855 | 8/38 626s 54 h-m-p 1.6000 8.0000 0.0001 C 1035.533916 0 1.6268 2926 | 8/38 626s 55 h-m-p 1.6000 8.0000 0.0000 Y 1035.533916 0 1.2702 2997 | 8/38 626s 56 h-m-p 1.6000 8.0000 0.0000 Y 1035.533916 0 3.8565 3068 | 8/38 626s 57 h-m-p 1.3464 8.0000 0.0000 -C 1035.533916 0 0.0841 3140 | 8/38 626s 58 h-m-p 0.0913 8.0000 0.0000 Y 1035.533916 0 0.0130 3211 | 8/38 626s 59 h-m-p 0.0160 8.0000 0.0000 Y 1035.533916 0 0.0160 3282 | 8/38 626s 60 h-m-p 0.0175 8.0000 0.0000 ------------N 1035.533916 0 0.0000 3365 626s Out.. 626s lnL = -1035.533916 626s 3366 lfun, 16830 eigenQcodon, 444312 P(t) 626s 626s BEBing (dim = 4). This may take many minutes. 626s Trying to get 0.6M memory in lfunNSsites_ACD 626s 626s Calculating f(x_h|w) for 121 w's 627s 10 / 121 sets. w for branches: 0.9500 0.9500 lnfX = -1058.2048 20 / 121 sets. w for branches: 0.0500 9.5000 lnfX = -1109.1659 30 / 121 sets. w for branches: 0.1500 9.5000 lnfX = -1072.3725 40 / 121 sets. w for branches: 0.2500 9.5000 lnfX = -1060.2342 50 / 121 sets. w for branches: 0.3500 9.5000 lnfX = -1055.3913 60 / 121 sets. w for branches: 0.4500 9.5000 lnfX = -1054.1055 70 / 121 sets. w for branches: 0.5500 9.5000 lnfX = -1054.9336 80 / 121 sets. w for branches: 0.6500 9.5000 lnfX = -1057.1652 90 / 121 sets. w for branches: 0.7500 9.5000 lnfX = -1060.3966 100 / 121 sets. w for branches: 0.8500 9.5000 lnfX = -1064.3759 110 / 121 sets. w for branches: 0.9500 9.5000 lnfX = -1068.9350 120 / 121 sets. w for branches: 1.0000 9.5000 lnfX = -1071.3936 121 / 121 sets. w for branches: 1.0000 10.5000 lnfX = -1073.7801 627s Time: 1:16 627s Calculating the marginal likelihood f(X). 627s 1000 / 10000 grid points, 1:16 2000 / 10000 grid points, 1:16 3000 / 10000 grid points, 1:16 4000 / 10000 grid points, 1:16 5000 / 10000 grid points, 1:16 6000 / 10000 grid points, 1:16 7000 / 10000 grid points, 1:16 8000 / 10000 grid points, 1:16 9000 / 10000 grid points, 1:16 10000 / 10000 grid points, 1:16 log(fX) = -1040.172967 S = -972.039038 -64.399163 627s Calculating f(w_k|X), posterior for site classes for each site. Slow! 627s did 10 / 86 site patterns 1:16 did 20 / 86 site patterns 1:16 did 30 / 86 site patterns 1:16 did 40 / 86 site patterns 1:16 did 50 / 86 site patterns 1:16 did 60 / 86 site patterns 1:16 did 70 / 86 site patterns 1:16 did 80 / 86 site patterns 1:16 did 86 / 86 site patterns 1:16 627s Time used: 1:16 627s Passed 627s 627s Test 7 627s BASEML in paml version 4.9j, October 2019 627s ns = 35 ls = 1812 627s Reading sequences, sequential format.. 627s Reading seq # 1: Equus Reading seq # 2: Rhinoceros Reading seq # 3: Balaenoptera Reading seq # 4: Physeter Reading seq # 5: Hippopotamus Reading seq # 6: Bos Reading seq # 7: Canis Reading seq # 8: Ursus Reading seq # 9: Felis Reading seq #10: Homo Reading seq #11: Pan Reading seq #12: Gorilla Reading seq #13: Pongo Reading seq #14: Macaca Reading seq #15: Callithrix Reading seq #16: Galago Reading seq #17: Loris Reading seq #18: Daubentonia Reading seq #19: Lepilemur Reading seq #20: Propithecus Reading seq #21: Varecia Reading seq #22: Hapalemur Reading seq #23: Lemur Reading seq #24: Eulemur Reading seq #25: Cheirogaleus Reading seq #26: Mirza Reading seq #27: M.ravelobensis Reading seq #28: M.sambiranensis Reading seq #29: M.myoxinus Reading seq #30: M.tavaratra Reading seq #31: M.griseorufus Reading seq #32: M.berthae Reading seq #33: M.murinus Reading seq #34: M.rufus1 Reading seq #35: M.rufus2 627s Sequences read.. 627s Counting site patterns.. 0:00 627s 627s 627s Compressing, 1023 patterns at 1812 / 1812 sites (100.0%), 0:00 627s 627s 627s Collecting fpatt[] & pose[], 1023 patterns at 1812 / 1812 sites (100.0%), 0:00 627s Counting frequencies.. 627s 627s 7140 bytes for distance 627s 1113024 bytes for conP 627s 40920 bytes for fhK 627s 8000000 bytes for space 627s 627s 3 branch types are in tree. Stop if wrong. 627s TREE # 1: (((((((((((27, (28, (35, (30, (34, (32, 29)))))), (31, 33)), 26), 25), 19), 20), (((22, 23), 24), 21)), 18), (16, 17)), (15, (14, (13, (12, (11, 10)))))), ((9, (7, 8)), ((((4, 3), 5), 6), (2, 1)))); MP score: -1.00 627s 627s found 3 branch rates in tree. 627s 0 0 0 0 0 0 0 0 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 627s 627s ntime & nrate & np: 40 1 44 627s 36..37 37..38 38..39 39..40 40..41 41..42 42..43 43..44 44..45 45..46 46..27 46..47 47..28 47..48 48..35 48..49 49..30 49..50 50..34 50..51 51..32 51..29 45..52 52..31 52..33 44..26 43..25 42..19 41..20 40..53 53..54 54..55 55..22 55..23 54..24 53..21 39..18 38..56 56..16 56..17 37..57 57..15 57..58 58..14 58..59 59..13 59..60 60..12 60..61 61..11 61..10 36..62 62..63 63..9 63..64 64..7 64..8 62..65 65..66 66..67 67..68 68..4 68..3 67..5 66..6 65..69 69..2 69..1 627s 627s 0.583224 0.694184 0.401973 0.653832 0.802078 0.543981 0.528051 0.764791 0.681511 0.554771 0.806569 0.690580 0.475835 0.780937 0.862043 0.751017 0.786437 0.749927 0.537336 0.549336 0.894333 0.504706 0.869330 0.540760 0.528574 0.868373 0.484040 0.459957 0.581424 0.673135 0.559596 0.537080 0.856256 0.570822 0.146107 0.131411 0.131820 0.053427 0.146365 0.108367 1.000000 1.000000 2.264374 0.499362 627s 627s lnL0 = -31855.322140 627s 627s Bounds (np=44): 627s 0.000004 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000001 0.000100 0.000100 0.000100 0.000100 0.000100 0.000100 0.000100 0.000100 0.000010 0.005000 635s 50.000000 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 0.999999 99.000000 99.000000 99.000000 99.000000 99.000000 99.000000 999.000000 999.000000 999.000000 999.000000 635s 635s Iterating by ming2 635s Initial: fx= 31855.322140 635s x= 0.58322 0.69418 0.40197 0.65383 0.80208 0.54398 0.52805 0.76479 0.68151 0.55477 0.80657 0.69058 0.47584 0.78094 0.86204 0.75102 0.78644 0.74993 0.53734 0.54934 0.89433 0.50471 0.86933 0.54076 0.52857 0.86837 0.48404 0.45996 0.58142 0.67313 0.55960 0.53708 0.85626 0.57082 0.14611 0.13141 0.13182 0.05343 0.14637 0.10837 1.00000 1.00000 2.26437 0.49936 635s 635s 1 h-m-p 0.0000 0.0001 11315.7018 ++ 27633.030273 m 0.0001 49 | 0/44 635s 2 h-m-p 0.0001 0.0004 2068.9556 +YCC 27059.270028 2 0.0003 100 | 0/44 635s 3 h-m-p 0.0000 0.0001 1243.6593 ++ 26937.923977 m 0.0001 147 | 1/44 635s 4 h-m-p 0.0001 0.0004 1649.8065 ++ 26682.086192 m 0.0004 194 | 1/44 635s 5 h-m-p 0.0001 0.0006 1676.3426 CCCCC 26608.562861 4 0.0002 249 | 1/44 635s 6 h-m-p 0.0002 0.0010 632.6721 +YYCCCC 26510.938077 5 0.0007 305 | 1/44 635s 7 h-m-p 0.0001 0.0005 639.8078 CYCCC 26490.273758 4 0.0002 359 | 1/44 635s 8 h-m-p 0.0002 0.0010 496.9103 +YYCCC 26438.538013 4 0.0007 413 | 1/44 635s 9 h-m-p 0.0002 0.0009 516.2083 YCCC 26415.345453 3 0.0004 465 | 1/44 635s 10 h-m-p 0.0004 0.0022 236.8693 YCCC 26398.544713 3 0.0009 517 | 1/44 635s 11 h-m-p 0.0005 0.0023 350.6088 YCC 26380.871474 2 0.0008 567 | 1/44 635s 12 h-m-p 0.0005 0.0024 210.8499 ++ 26360.070195 m 0.0024 614 | 1/44 635s 13 h-m-p 0.0002 0.0009 332.7472 ++ 26348.637228 m 0.0009 661 | 1/44 635s 14 h-m-p 0.0009 0.0046 260.2828 CC 26337.973519 1 0.0012 710 | 1/44 635s 15 h-m-p 0.0004 0.0020 165.9025 YC 26333.202295 1 0.0010 758 | 1/44 635s 16 h-m-p 0.0008 0.0040 98.7352 CC 26330.557128 1 0.0012 807 | 1/44 635s 17 h-m-p 0.0021 0.0103 36.2967 CC 26329.678854 1 0.0017 856 | 1/44 635s 18 h-m-p 0.0039 0.0473 15.9137 CC 26328.905545 1 0.0044 905 | 1/44 635s 19 h-m-p 0.0030 0.0324 23.3695 YC 26327.476498 1 0.0048 953 | 1/44 635s 20 h-m-p 0.0033 0.0310 34.4092 CC 26325.076060 1 0.0045 1002 | 1/44 635s 21 h-m-p 0.0035 0.0270 43.5955 CC 26322.382850 1 0.0032 1051 | 1/44 635s 22 h-m-p 0.0029 0.0144 35.7675 CCC 26319.283554 2 0.0031 1102 | 1/44 635s 23 h-m-p 0.0038 0.0203 29.3104 YC 26306.825757 1 0.0080 1150 | 1/44 635s 24 h-m-p 0.0012 0.0059 58.8988 +YC 26280.764307 1 0.0050 1199 | 1/44 635s 25 h-m-p 0.0013 0.0066 80.4501 +YCC 26245.899157 2 0.0046 1250 | 1/44 635s 26 h-m-p 0.0017 0.0084 145.3062 YCC 26215.311720 2 0.0033 1300 | 1/44 635s 27 h-m-p 0.0009 0.0043 125.6307 YCCC 26204.149335 3 0.0020 1352 | 1/44 635s 28 h-m-p 0.0007 0.0037 51.8106 YCC 26202.147753 2 0.0017 1402 | 1/44 635s 29 h-m-p 0.0033 0.0163 20.9098 YC 26201.626987 1 0.0019 1450 | 1/44 635s 30 h-m-p 0.0033 0.0405 12.3027 YC 26200.649076 1 0.0055 1498 | 1/44 635s 31 h-m-p 0.0049 0.0438 13.6301 YC 26196.717701 1 0.0102 1546 | 1/44 635s 32 h-m-p 0.0030 0.0152 28.6766 YC 26185.172058 1 0.0075 1594 | 1/44 635s 33 h-m-p 0.0034 0.0170 55.6300 CCC 26171.481141 2 0.0047 1645 | 1/44 635s 34 h-m-p 0.0009 0.0043 70.2658 +YCC 26165.529759 2 0.0025 1696 | 1/44 635s 35 h-m-p 0.0044 0.0220 17.7459 YC 26165.064014 1 0.0027 1744 | 1/44 635s 36 h-m-p 0.0078 0.0655 6.1159 C 26164.740831 0 0.0075 1791 | 1/44 635s 37 h-m-p 0.0086 0.1673 5.3385 YC 26163.276233 1 0.0183 1839 | 1/44 635s 38 h-m-p 0.0079 0.0826 12.4616 YC 26155.484994 1 0.0178 1887 | 1/44 635s 39 h-m-p 0.0011 0.0054 61.8999 ++ 26137.785050 m 0.0054 1934 | 1/44 635s 40 h-m-p 0.0000 0.0000 55.2695 635s h-m-p: 0.00000000e+00 0.00000000e+00 5.52694767e+01 26137.785050 635s .. | 1/44 635s 41 h-m-p 0.0000 0.0012 300.4149 ++CCC 26129.150390 2 0.0002 2031 | 1/44 635s 42 h-m-p 0.0001 0.0004 387.7963 YC 26120.781986 1 0.0002 2079 | 1/44 635s 43 h-m-p 0.0002 0.0009 183.4664 YC 26116.172661 1 0.0004 2127 | 1/44 635s 44 h-m-p 0.0002 0.0041 316.8027 CC 26111.365304 1 0.0003 2176 | 1/44 645s 45 h-m-p 0.0003 0.0023 354.3868 +YC 26098.531641 1 0.0009 2225 | 1/44 645s 46 h-m-p 0.0005 0.0025 466.0860 CCC 26086.176039 2 0.0007 2276 | 1/44 645s 47 h-m-p 0.0007 0.0036 246.8948 YC 26074.416577 1 0.0015 2324 | 1/44 645s 48 h-m-p 0.0003 0.0013 393.4042 +YCC 26064.467836 2 0.0008 2375 | 1/44 645s 49 h-m-p 0.0006 0.0029 180.6978 +YC 26057.016239 1 0.0016 2424 | 1/44 645s 50 h-m-p 0.0012 0.0070 233.9825 YCCC 26053.873668 3 0.0006 2476 | 1/44 645s 51 h-m-p 0.0005 0.0025 126.3141 YC 26051.392889 1 0.0010 2524 | 1/44 645s 52 h-m-p 0.0003 0.0016 122.2019 YC 26049.972454 1 0.0007 2572 | 1/44 645s 53 h-m-p 0.0009 0.0057 97.1243 CC 26048.566477 1 0.0010 2621 | 1/44 645s 54 h-m-p 0.0016 0.0151 63.0459 CC 26047.016431 1 0.0021 2670 | 1/44 645s 55 h-m-p 0.0025 0.0174 52.9521 YC 26046.115673 1 0.0018 2718 | 1/44 645s 56 h-m-p 0.0016 0.0169 61.3835 CC 26045.147437 1 0.0019 2767 | 1/44 645s 57 h-m-p 0.0026 0.0137 43.3263 YC 26044.577370 1 0.0018 2815 | 1/44 645s 58 h-m-p 0.0029 0.0148 27.0949 CY 26044.119139 1 0.0027 2864 | 1/44 645s 59 h-m-p 0.0033 0.0301 22.0580 C 26043.709353 0 0.0031 2911 | 1/44 645s 60 h-m-p 0.0031 0.0443 22.3928 CC 26043.183258 1 0.0040 2960 | 1/44 645s 61 h-m-p 0.0040 0.0506 22.4606 CC 26042.719954 1 0.0033 3009 | 1/44 645s 62 h-m-p 0.0046 0.0255 16.0728 C 26042.143297 0 0.0046 3056 | 1/44 645s 63 h-m-p 0.0030 0.0866 24.7251 +YC 26040.251525 1 0.0077 3105 | 1/44 645s 64 h-m-p 0.0033 0.0256 58.4611 CC 26037.146875 1 0.0048 3154 | 1/44 645s 65 h-m-p 0.0043 0.0217 30.7653 CC 26035.527431 1 0.0040 3203 | 1/44 645s 66 h-m-p 0.0049 0.0264 25.3540 CC 26032.630235 1 0.0073 3252 | 1/44 645s 67 h-m-p 0.0024 0.0271 79.0667 YC 26027.236139 1 0.0042 3300 | 1/44 645s 68 h-m-p 0.0022 0.0110 48.5132 CC 26024.825177 1 0.0030 3349 | 1/44 645s 69 h-m-p 0.0027 0.0381 53.4911 +CYC 26016.018450 2 0.0104 3400 | 1/44 645s 70 h-m-p 0.0031 0.0159 182.6684 CCCC 26000.450717 3 0.0053 3453 | 1/44 645s 71 h-m-p 0.0018 0.0089 152.6195 CCC 25996.254994 2 0.0019 3504 | 1/44 645s 72 h-m-p 0.0026 0.0131 26.8764 YC 25995.733187 1 0.0021 3552 | 1/44 645s 73 h-m-p 0.0043 0.0493 13.2068 YC 25995.486226 1 0.0032 3600 | 1/44 645s 74 h-m-p 0.0059 0.0671 7.1945 CC 25995.178364 1 0.0082 3649 | 1/44 645s 75 h-m-p 0.0034 0.0923 17.2859 YC 25994.435359 1 0.0077 3697 | 1/44 645s 76 h-m-p 0.0045 0.0271 29.8057 CC 25993.717223 1 0.0040 3746 | 1/44 645s 77 h-m-p 0.0062 0.0308 13.4179 YC 25993.247569 1 0.0046 3794 | 1/44 645s 78 h-m-p 0.0046 0.1935 13.4154 ++CC 25983.890390 1 0.0662 3845 | 1/44 645s 79 h-m-p 0.0023 0.0113 232.8538 YC 25972.612124 1 0.0047 3893 | 1/44 645s 80 h-m-p 0.0011 0.0055 71.4651 YC 25970.947713 1 0.0025 3941 | 1/44 645s 81 h-m-p 0.0093 0.0464 11.2314 CC 25970.799598 1 0.0028 3990 | 1/44 645s 82 h-m-p 0.0100 0.0790 3.1644 C 25970.687372 0 0.0091 4037 | 1/44 645s 83 h-m-p 0.0034 0.0531 8.4276 ++ 25967.933208 m 0.0531 4084 | 1/44 645s 84 h-m-p 0.0020 0.0114 226.3428 YCCC 25963.942163 3 0.0034 4136 | 1/44 645s 85 h-m-p 0.0072 0.0362 34.2094 YC 25963.483199 1 0.0029 4184 | 1/44 645s 86 h-m-p 0.0277 0.1749 3.5989 CC 25963.351560 1 0.0094 4233 | 1/44 645s 87 h-m-p 0.0054 1.0418 6.2523 +++YC 25955.292183 1 0.2207 4284 | 1/44 645s 88 h-m-p 1.2211 8.0000 1.1301 CCC 25950.445422 2 1.5055 4335 | 1/44 645s 89 h-m-p 1.6000 8.0000 0.8587 YCC 25948.694802 2 1.2409 4385 | 1/44 645s 90 h-m-p 1.6000 8.0000 0.5425 CYC 25947.617667 2 1.9720 4478 | 1/44 645s 91 h-m-p 1.6000 8.0000 0.4837 C 25947.060645 0 1.6144 4568 | 1/44 645s 92 h-m-p 1.6000 8.0000 0.2190 YC 25945.946499 1 3.2112 4659 | 1/44 645s 93 h-m-p 1.6000 8.0000 0.2297 CC 25944.693768 1 2.1332 4751 | 1/44 645s 94 h-m-p 1.6000 8.0000 0.2275 C 25944.272411 0 1.6539 4841 | 1/44 645s 95 h-m-p 1.6000 8.0000 0.1897 YC 25943.463001 1 3.2671 4932 | 1/44 645s 96 h-m-p 1.6000 8.0000 0.2729 YC 25942.629767 1 2.5072 5023 | 1/44 645s 97 h-m-p 1.2894 8.0000 0.5307 YC 25942.173853 1 2.2556 5114 | 1/44 645s 98 h-m-p 1.6000 8.0000 0.2398 C 25941.900897 0 1.6790 5204 | 1/44 651s 99 h-m-p 0.9370 8.0000 0.4297 YC 25941.520527 1 2.2758 5295 | 1/44 651s 100 h-m-p 1.6000 8.0000 0.2203 CC 25941.104717 1 2.3025 5387 | 1/44 651s 101 h-m-p 1.6000 8.0000 0.0491 C 25941.040998 0 1.3290 5477 | 1/44 651s 102 h-m-p 0.6432 8.0000 0.1015 +Y 25941.024808 0 2.0872 5568 | 1/44 651s 103 h-m-p 1.6000 8.0000 0.0193 Y 25941.016787 0 2.6088 5658 | 1/44 651s 104 h-m-p 1.5305 8.0000 0.0329 C 25941.012960 0 2.1056 5748 | 1/44 651s 105 h-m-p 1.6000 8.0000 0.0105 Y 25941.010875 0 3.0249 5838 | 1/44 651s 106 h-m-p 1.6000 8.0000 0.0139 C 25941.009847 0 2.3915 5928 | 1/44 651s 107 h-m-p 1.6000 8.0000 0.0089 C 25941.009291 0 2.1731 6018 | 1/44 651s 108 h-m-p 1.6000 8.0000 0.0078 C 25941.009113 0 1.9696 6108 | 1/44 651s 109 h-m-p 1.6000 8.0000 0.0048 C 25941.009094 0 1.2913 6198 | 1/44 651s 110 h-m-p 1.6000 8.0000 0.0003 C 25941.009093 0 2.1815 6288 | 1/44 651s 111 h-m-p 1.6000 8.0000 0.0001 Y 25941.009092 0 2.5960 6378 | 1/44 651s 112 h-m-p 1.6000 8.0000 0.0000 C 25941.009092 0 1.6000 6468 | 1/44 651s 113 h-m-p 1.6000 8.0000 0.0000 Y 25941.009092 0 1.1481 6558 | 1/44 651s 114 h-m-p 1.6000 8.0000 0.0000 C 25941.009092 0 1.6198 6648 | 1/44 651s 115 h-m-p 1.6000 8.0000 0.0000 C 25941.009092 0 0.4659 6738 651s Out... 651s lnL = -25941.009092 651s Calculating SE's 651s 651s Time used: 0:24 651s Passed 651s 651s Test 8 654s 654s AAML in paml version 4.9j, October 2019 654s 654s ---------------------------------------------- 654s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 654s TTC | TCC | TAC | TGC 654s Leu L TTA | TCA | *** * TAA | Trp W TGA 654s TTG | TCG | TAG | TGG 654s ---------------------------------------------- 654s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 654s CTC | CCC | CAC | CGC 654s CTA | CCA | Gln Q CAA | CGA 654s CTG | CCG | CAG | CGG 654s ---------------------------------------------- 654s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 654s ATC | ACC | AAC | AGC 654s Met M ATA | ACA | Lys K AAA | *** * AGA 654s ATG | ACG | AAG | AGG 654s ---------------------------------------------- 654s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 654s GTC | GCC | GAC | GGC 654s GTA | GCA | Glu E GAA | GGA 654s GTG | GCG | GAG | GGG 654s ---------------------------------------------- 654s Nice code, uuh? 654s ns = 7 ls = 3331 654s Reading sequences, sequential format.. 654s Reading seq # 1: human Reading seq # 2: chimpanzee Reading seq # 3: bonobo Reading seq # 4: gorilla Reading seq # 5: orangutan Reading seq # 6: Sumatran Reading seq # 7: gibbon 654s Sequences read.. 654s Counting site patterns.. 0:00 654s Compressing, 469 patterns at 3331 / 3331 sites (100.0%), 0:00 654s Collecting fpatt[] & pose[], 469 patterns at 3331 / 3331 sites (100.0%), 0:00 654s Counting frequencies.. 654s 654s 168 bytes for distance 654s 450240 bytes for conP 654s 12519973076356386560 bytes for fhK 654s 5000000 bytes for space 654s 654s TREE # 1 654s (((1, (2, 3)), 4), (5, 6), 7); MP score: -1 654s 1125600 bytes for conP, adjusted 654s 654s 0.016944 0.108889 0.069301 0.039449 0.094089 0.066592 0.077789 0.026022 0.026714 0.108734 0.036189 3.000000 1.500000 654s 654s ntime & nrate & np: 11 2 13 654s 654s Bounds (np=13): 654s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 654s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 654s 654s np = 13 654s lnL0 = -15489.430316 654s 654s Iterating by ming2 654s Initial: fx= 15489.430316 654s x= 0.01694 0.10889 0.06930 0.03945 0.09409 0.06659 0.07779 0.02602 0.02671 0.10873 0.03619 3.00000 1.50000 654s 654s 1 h-m-p 0.0000 0.0000 7373.9525 +CCCCC 15034.237939 4 0.0000 27 | 0/13 654s 2 h-m-p 0.0000 0.0000 4510.7380 +YYYCCC 14934.991717 5 0.0000 51 | 0/13 654s 3 h-m-p 0.0000 0.0000 5261.9910 +YCYCCC 14898.224114 5 0.0000 76 | 0/13 654s 4 h-m-p 0.0000 0.0000 2350.2438 YCYCCC 14882.666118 5 0.0000 100 | 0/13 654s 5 h-m-p 0.0000 0.0001 757.8082 YYC 14880.438783 2 0.0000 118 | 0/13 654s 6 h-m-p 0.0000 0.0002 365.1236 CC 14879.584035 1 0.0000 136 | 0/13 654s 7 h-m-p 0.0000 0.0002 357.9243 CCC 14878.902578 2 0.0000 156 | 0/13 654s 8 h-m-p 0.0000 0.0006 199.0428 CCC 14878.286769 2 0.0001 176 | 0/13 654s 9 h-m-p 0.0000 0.0011 362.4963 +CCC 14876.478447 2 0.0001 197 | 0/13 654s 10 h-m-p 0.0000 0.0003 1348.7753 CCC 14873.823317 2 0.0000 217 | 0/13 654s 11 h-m-p 0.0000 0.0006 1207.8283 +YYCCCCC 14861.606897 6 0.0002 244 | 0/13 654s 12 h-m-p 0.0000 0.0001 17796.8151 +YYYYCYCYCC 14777.046312 10 0.0001 274 | 0/13 654s 13 h-m-p 0.0166 0.0979 81.7377 CCCCC 14752.944640 4 0.0163 298 | 0/13 654s 14 h-m-p 1.5840 8.0000 0.8391 CYCCC 14718.838493 4 2.9704 321 | 0/13 654s 15 h-m-p 1.6000 8.0000 0.1552 YCCC 14717.740799 3 3.0477 355 | 0/13 654s 16 h-m-p 1.6000 8.0000 0.2246 CC 14717.271796 1 1.5010 386 | 0/13 654s 17 h-m-p 1.6000 8.0000 0.0612 YC 14717.200228 1 0.9436 416 | 0/13 654s 18 h-m-p 0.8299 8.0000 0.0695 YC 14717.118709 1 1.6969 446 | 0/13 654s 19 h-m-p 1.6000 8.0000 0.0110 ++ 14716.821343 m 8.0000 475 | 0/13 654s 20 h-m-p 0.7155 5.9395 0.1235 YYYCCCC 14716.565770 6 0.7747 513 | 0/13 654s 21 h-m-p 0.3771 8.0000 0.2538 +YYCCCCC 14715.942701 6 1.9341 553 | 0/13 665s 22 h-m-p 1.5425 7.7126 0.1815 CCCC 14715.753391 3 0.5794 588 | 0/13 665s 23 h-m-p 0.0979 8.0000 1.0743 +CYC 14715.111552 2 0.4970 621 | 0/13 665s 24 h-m-p 1.6000 8.0000 0.0935 YCCC 14714.889639 3 0.8818 642 | 0/13 665s 25 h-m-p 0.3104 8.0000 0.2656 +CYCCC 14714.363536 4 1.8165 679 | 0/13 665s 26 h-m-p 1.6000 8.0000 0.0199 CC 14714.212299 1 0.5167 710 | 0/13 665s 27 h-m-p 0.0476 8.0000 0.2160 ++CYCCC 14713.698593 4 1.4756 748 | 0/13 665s 28 h-m-p 1.6000 8.0000 0.0792 YCYCCC 14713.136109 5 3.8554 785 | 0/13 665s 29 h-m-p 1.6000 8.0000 0.0386 YC 14713.017454 1 0.2129 815 | 0/13 665s 30 h-m-p 0.0319 8.0000 0.2578 ++YCYC 14712.572340 3 1.3100 850 | 0/13 665s 31 h-m-p 1.6000 8.0000 0.0922 +YCYC 14712.127172 3 4.3675 884 | 0/13 665s 32 h-m-p 1.5293 8.0000 0.2632 YYC 14711.652678 2 2.0388 915 | 0/13 665s 33 h-m-p 0.2050 1.0252 2.3808 CYCCC 14711.442941 4 0.0750 951 | 0/13 665s 34 h-m-p 1.6000 8.0000 0.0909 YCYC 14711.269321 3 0.9522 971 | 0/13 665s 35 h-m-p 0.2672 8.0000 0.3240 +CC 14710.912402 1 1.5192 1003 | 0/13 665s 36 h-m-p 1.6000 8.0000 0.1200 YCCCCC 14710.584713 5 2.0196 1041 | 0/13 665s 37 h-m-p 0.4414 8.0000 0.5489 CYC 14710.312783 2 0.4931 1073 | 0/13 665s 38 h-m-p 1.6000 8.0000 0.0715 YCYC 14710.099966 3 1.0110 1106 | 0/13 665s 39 h-m-p 0.4391 8.0000 0.1646 +CCCC 14709.877178 3 2.0405 1142 | 0/13 665s 40 h-m-p 1.6000 8.0000 0.0505 YC 14709.816630 1 0.6993 1172 | 0/13 665s 41 h-m-p 0.1642 8.0000 0.2152 +CYCC 14709.673778 3 1.1473 1207 | 0/13 665s 42 h-m-p 1.6000 8.0000 0.0315 CYCCC 14709.526559 4 3.2049 1243 | 0/13 665s 43 h-m-p 0.8471 8.0000 0.1191 CCY 14709.348652 2 0.8810 1276 | 0/13 665s 44 h-m-p 0.7036 6.6008 0.1491 YYYC 14709.191438 3 0.6167 1308 | 0/13 665s 45 h-m-p 0.9632 8.0000 0.0955 CCCC 14709.090169 3 1.2852 1343 | 0/13 665s 46 h-m-p 0.4288 8.0000 0.2861 +YCC 14708.797991 2 1.1595 1376 | 0/13 665s 47 h-m-p 1.6000 8.0000 0.1464 YCCC 14708.608307 3 0.8240 1410 | 0/13 665s 48 h-m-p 0.4331 8.0000 0.2785 +YC 14708.421934 1 1.2754 1441 | 0/13 665s 49 h-m-p 1.6000 8.0000 0.0935 CCC 14708.345681 2 1.7260 1474 | 0/13 665s 50 h-m-p 1.0819 8.0000 0.1492 YC 14708.312305 1 0.4725 1504 | 0/13 665s 51 h-m-p 1.6000 8.0000 0.0360 CCC 14708.290112 2 2.0661 1537 | 0/13 665s 52 h-m-p 1.6000 8.0000 0.0058 ++ 14708.249341 m 8.0000 1566 | 0/13 665s 53 h-m-p 0.7576 8.0000 0.0613 +YCYC 14708.130492 3 2.0850 1600 | 0/13 665s 54 h-m-p 1.6000 8.0000 0.0525 YC 14707.921249 1 2.9105 1630 | 0/13 665s 55 h-m-p 1.4341 8.0000 0.1066 CCC 14707.901228 2 0.2799 1663 | 0/13 665s 56 h-m-p 0.3317 8.0000 0.0900 +C 14707.886274 0 1.2339 1693 | 0/13 665s 57 h-m-p 1.6000 8.0000 0.0164 +YC 14707.871674 1 4.7506 1724 | 0/13 665s 58 h-m-p 1.6000 8.0000 0.0136 C 14707.864019 0 1.5927 1753 | 0/13 665s 59 h-m-p 0.9756 8.0000 0.0222 +YY 14707.852994 1 3.1099 1784 | 0/13 665s 60 h-m-p 1.6000 8.0000 0.0202 ++ 14707.778568 m 8.0000 1813 | 0/13 665s 61 h-m-p 1.6000 8.0000 0.0613 YCC 14707.734934 2 0.9133 1845 | 0/13 665s 62 h-m-p 0.1835 7.5366 0.3049 CYC 14707.703185 2 0.3503 1877 | 0/13 665s 63 h-m-p 1.6000 8.0000 0.0166 C 14707.699632 0 1.4821 1906 | 0/13 665s 64 h-m-p 1.6000 8.0000 0.0067 +Y 14707.698514 0 4.7869 1936 | 0/13 665s 65 h-m-p 1.6000 8.0000 0.0058 ++ 14707.692742 m 8.0000 1965 | 0/13 665s 66 h-m-p 1.6000 8.0000 0.0087 +YC 14707.689584 1 4.2564 1996 | 0/13 665s 67 h-m-p 1.6000 8.0000 0.0050 YC 14707.682964 1 2.7489 2026 | 0/13 665s 68 h-m-p 0.3257 8.0000 0.0425 +CYC 14707.671901 2 2.1468 2059 | 0/13 665s 69 h-m-p 1.6000 8.0000 0.0227 C 14707.666375 0 1.6000 2088 | 0/13 665s 70 h-m-p 1.2929 8.0000 0.0281 YC 14707.665945 1 0.7250 2118 | 0/13 665s 71 h-m-p 1.6000 8.0000 0.0078 C 14707.665615 0 1.5287 2147 | 0/13 665s 72 h-m-p 1.6000 8.0000 0.0069 C 14707.665516 0 1.6000 2176 | 0/13 665s 73 h-m-p 1.6000 8.0000 0.0004 +Y 14707.665449 0 5.0343 2206 | 0/13 665s 74 h-m-p 1.4836 8.0000 0.0012 ++ 14707.664837 m 8.0000 2235 | 0/13 665s 75 h-m-p 0.8407 8.0000 0.0115 YC 14707.664021 1 1.5458 2265 | 0/13 674s 76 h-m-p 1.6000 8.0000 0.0094 C 14707.663939 0 1.2884 2294 | 0/13 674s 77 h-m-p 1.6000 8.0000 0.0001 C 14707.663936 0 1.3672 2323 | 0/13 674s 78 h-m-p 0.3476 8.0000 0.0003 +++ 14707.663926 m 8.0000 2353 | 0/13 674s 79 h-m-p 1.0381 8.0000 0.0024 +Y 14707.663877 0 3.3627 2383 | 0/13 674s 80 h-m-p 1.6000 8.0000 0.0020 Y 14707.663790 0 3.5504 2412 | 0/13 674s 81 h-m-p 1.6000 8.0000 0.0001 Y 14707.663788 0 1.0454 2441 | 0/13 674s 82 h-m-p 1.6000 8.0000 0.0000 ++ 14707.663788 m 8.0000 2470 | 0/13 674s 83 h-m-p 0.6789 8.0000 0.0005 +C 14707.663785 0 2.5823 2500 | 0/13 674s 84 h-m-p 1.6000 8.0000 0.0003 Y 14707.663780 0 3.7912 2529 | 0/13 674s 85 h-m-p 1.6000 8.0000 0.0000 +C 14707.663780 0 5.8325 2559 | 0/13 674s 86 h-m-p 1.6000 8.0000 0.0000 ++ 14707.663780 m 8.0000 2588 | 0/13 674s 87 h-m-p 0.2969 8.0000 0.0001 +C 14707.663779 0 1.0303 2618 | 0/13 674s 88 h-m-p 1.6000 8.0000 0.0000 C 14707.663779 0 1.6000 2647 | 0/13 674s 89 h-m-p 1.6000 8.0000 0.0000 +C 14707.663779 0 5.9888 2677 | 0/13 674s 90 h-m-p 1.6000 8.0000 0.0000 ++ 14707.663779 m 8.0000 2706 | 0/13 674s 91 h-m-p 1.0152 8.0000 0.0000 C 14707.663779 0 1.0152 2735 | 0/13 674s 92 h-m-p 1.6000 8.0000 0.0000 Y 14707.663779 0 1.6000 2764 | 0/13 674s 93 h-m-p 1.6000 8.0000 0.0000 ++ 14707.663779 m 8.0000 2793 | 0/13 674s 94 h-m-p 0.1009 8.0000 0.0000 ++Y 14707.663779 0 1.1973 2824 | 0/13 674s 95 h-m-p 1.4855 8.0000 0.0000 C 14707.663779 0 1.4855 2853 | 0/13 674s 96 h-m-p 1.6000 8.0000 0.0000 C 14707.663779 0 2.0192 2882 | 0/13 674s 97 h-m-p 1.6000 8.0000 0.0000 -C 14707.663779 0 0.1000 2912 | 0/13 674s 98 h-m-p 0.0160 8.0000 0.0005 --C 14707.663779 0 0.0003 2943 | 0/13 674s 99 h-m-p 0.0575 8.0000 0.0000 --------------.. | 0/13 674s 100 h-m-p 0.0160 8.0000 0.0010 ------------- | 0/13 674s 101 h-m-p 0.0160 8.0000 0.0010 ------------- 674s Out.. 674s lnL = -14707.663779 674s 3065 lfun, 3065 eigenQcodon, 33715 P(t) 674s Calculating SE's 674s 674s Reconstructed ancestral states go into file rst. 674s 674s lnL = -14707.663779 from ProbSitePattern. 674s Marginal reconstruction. 674s Node 8: lnL = -14707.663779 674s Node 9: lnL = -14707.663779 674s Node 10: lnL = -14707.663779 674s Node 11: lnL = -14707.663779 674s Node 12: lnL = -14707.663779 674s 674s lnL = -14707.663779 from ProbSitePattern. 674s Joint reconstruction. 674s 674s 4502400 bytes for conP, adjusted 674s 674s Time used: 0:23 674s Passed 674s 674s Test 9 674s 674s CODONML in paml version 4.9j, October 2019 674s 674s ---------------------------------------------- 674s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 674s TTC | TCC | TAC | TGC 674s Leu L TTA | TCA | *** * TAA | Trp W TGA 674s TTG | TCG | TAG | TGG 674s ---------------------------------------------- 674s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 674s CTC | CCC | CAC | CGC 674s CTA | CCA | Gln Q CAA | CGA 674s CTG | CCG | CAG | CGG 674s ---------------------------------------------- 674s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 674s ATC | ACC | AAC | AGC 674s Met M ATA | ACA | Lys K AAA | *** * AGA 674s ATG | ACG | AAG | AGG 674s ---------------------------------------------- 674s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 674s GTC | GCC | GAC | GGC 674s GTA | GCA | Glu E GAA | GGA 674s GTG | GCG | GAG | GGG 674s ---------------------------------------------- 674s Nice code, uuh? 674s 674s 674s 70 one-step aa pairs. 674s Reading omega class from OmegaAA.dat. 674s 2 dN/dS ratios estimated from data. 674s 674s Class #1: RH RK DE AG AP AS AT AV NI NS NT NY CG CF CS CW CY QL QP GS GW GV IL IM IF IS IT IV LM LF LP LS LW LV MT MV FS FY FV PS PT ST SW SY 674s 674s 674s pair 1: |RH| |HR ( 8, 1)| in class 1 674s pair 2: |RK| |KR (11, 1)| 674s This pair cannot change in one step and is ignored! 674s 674s pair 3: |DE| |ED ( 6, 3)| in class 1 674s pair 4: |AG| |GA ( 7, 0)| in class 1 674s pair 5: |AP| |PA (14, 0)| in class 1 674s pair 6: |AS| |SA (15, 0)| in class 1 674s pair 7: |AT| |TA (16, 0)| in class 1 674s pair 8: |AV| |VA (19, 0)| in class 1 674s pair 9: |NI| |IN ( 9, 2)| in class 1 674s pair 10: |NS| |SN (15, 2)| in class 1 674s pair 11: |NT| |TN (16, 2)| in class 1 674s pair 12: |NY| |YN (18, 2)| in class 1 674s pair 13: |CG| |GC ( 7, 4)| in class 1 674s pair 14: |CF| |FC (13, 4)| in class 1 674s pair 15: |CS| |SC (15, 4)| in class 1 674s pair 16: |CW| |WC (17, 4)| in class 1 674s pair 17: |CY| |YC (18, 4)| in class 1 674s pair 18: |QL| |LQ (10, 5)| in class 1 674s pair 19: |QP| |PQ (14, 5)| in class 1 674s pair 20: |GS| |SG (15, 7)| in class 1 674s pair 21: |GW| |WG (17, 7)| in class 1 674s pair 22: |GV| |VG (19, 7)| in class 1 674s pair 23: |IL| |LI (10, 9)| in class 1 674s pair 24: |IM| |MI (12, 9)| in class 1 674s pair 25: |IF| |FI (13, 9)| in class 1 674s pair 26: |IS| |SI (15, 9)| in class 1 674s pair 27: |IT| |TI (16, 9)| in class 1 674s pair 28: |IV| |VI (19, 9)| in class 1 674s pair 29: |LM| |ML (12,10)| in class 1 674s pair 30: |LF| |FL (13,10)| in class 1 674s pair 31: |LP| |PL (14,10)| in class 1 674s pair 32: |LS| |SL (15,10)| in class 1 674s pair 33: |LW| |WL (17,10)| in class 1 674s pair 34: |LV| |VL (19,10)| in class 1 674s pair 35: |MT| |TM (16,12)| in class 1 674s pair 36: |MV| |VM (19,12)| in class 1 674s pair 37: |FS| |SF (15,13)| in class 1 674s pair 38: |FY| |YF (18,13)| in class 1 674s pair 39: |FV| |VF (19,13)| in class 1 674s pair 40: |PS| |SP (15,14)| in class 1 674s pair 41: |PT| |TP (16,14)| in class 1 674s pair 42: |ST| |TS (16,15)| in class 1 674s pair 43: |SW| |WS (17,15)| in class 1 674s pair 44: |SY| |YS (18,15)| in class 1 ns = 6 ls = 10707 674s Reading sequences, sequential format.. 674s Reading seq # 1: 1.Human_Horai Reading seq # 2: 2.Human_Arnason Reading seq # 3: 3.Chimp_Horai Reading seq # 4: 4.Chimp_Arnason Reading seq # 5: 5.Gorilla_Horai Reading seq # 6: 6.Gorilla_Arnason 674s Sequences read.. 674s Counting site patterns.. 0:00 674s Compressing, 607 patterns at 3569 / 3569 sites (100.0%), 0:00 674s Collecting fpatt[] & pose[], 607 patterns at 3569 / 3569 sites (100.0%), 0:00 674s Counting codons.. 674s 674s 120 bytes for distance 674s 582720 bytes for conP 674s 2855178673434517504 bytes for fhK 674s 5000000 bytes for space 674s 674s 2 branch types are in tree. Stop if wrong. 674s TREE # 1 674s ((1, 2), (3, 4), (5, 6)); MP score: 1801 674s 1165440 bytes for conP, adjusted 674s 674s 0.106251 0.060982 0.088080 0.044992 0.091541 0.070461 0.079723 0.091510 0.028368 1.463747 1.391455 1.350465 1.583630 1.212626 674s 674s ntime & nrate & np: 9 5 14 674s 674s Bounds (np=14): 680s 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000004 0.000100 0.000100 0.000100 0.000100 0.000100 680s 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 50.000000 999.000000 999.000000 999.000000 999.000000 999.000000 680s 680s np = 14 680s lnL0 = -25119.790103 680s 680s Iterating by ming2 680s Initial: fx= 25119.790103 680s x= 0.10625 0.06098 0.08808 0.04499 0.09154 0.07046 0.07972 0.09151 0.02837 1.46375 1.39146 1.35046 1.58363 1.21263 680s 680s 1 h-m-p 0.0000 0.0000 12212.8402 ++ 24121.527441 m 0.0000 19 | 0/14 680s 2 h-m-p 0.0000 0.0000 59162.3541 ++ 23636.016213 m 0.0000 36 | 0/14 680s 3 h-m-p 0.0000 0.0000 56169.3489 ++ 23619.371154 m 0.0000 53 | 1/14 680s 4 h-m-p 0.0000 0.0000 5558.9869 +YYYCYCCC 23518.952693 7 0.0000 81 | 0/14 680s 5 h-m-p 0.0000 0.0000 46470.1762 C 23517.150651 0 0.0000 98 | 0/14 680s 6 h-m-p 0.0000 0.0000 1820.8549 YCCCC 23513.623806 4 0.0000 122 | 0/14 680s 7 h-m-p 0.0000 0.0001 3042.5619 +CYCCC 23399.059655 4 0.0001 147 | 0/14 680s 8 h-m-p 0.0000 0.0000 18762.0264 +YCCC 23378.041999 3 0.0000 170 | 0/14 680s 9 h-m-p 0.0000 0.0003 3070.0935 +++ 22293.414319 m 0.0003 188 | 0/14 680s 10 h-m-p 0.0000 0.0001 7615.5619 +YYCYCCC 22091.052988 6 0.0000 215 | 0/14 680s 11 h-m-p 0.0000 0.0001 2818.7895 +CCC 22009.520428 2 0.0001 237 | 0/14 680s 12 h-m-p 0.0001 0.0006 1177.9360 ++ 21590.842811 m 0.0006 254 | 0/14 680s 13 h-m-p 0.0000 0.0000 1747.7899 680s h-m-p: 2.23572920e-21 1.11786460e-20 1.74778993e+03 21590.842811 680s .. | 0/14 680s 14 h-m-p 0.0000 0.0000 142044.1406 YCCYC 21534.162399 4 0.0000 292 | 0/14 680s 15 h-m-p 0.0000 0.0000 4439.2260 +YYCCCCC 21473.124377 6 0.0000 320 | 0/14 680s 16 h-m-p 0.0000 0.0000 9505.0705 +YYCCC 21457.582950 4 0.0000 344 | 0/14 680s 17 h-m-p 0.0000 0.0000 16869.4634 +YCYCC 21439.417764 4 0.0000 368 | 0/14 680s 18 h-m-p 0.0000 0.0000 14662.1917 ++ 21416.378880 m 0.0000 385 | 0/14 680s 19 h-m-p 0.0000 0.0000 219290.0156 -CYCCC 21401.733323 4 0.0000 410 | 0/14 680s 20 h-m-p 0.0000 0.0000 1400.9599 +YCYCCC 21392.810874 5 0.0000 436 | 0/14 680s 21 h-m-p 0.0000 0.0000 3674.6452 CYCCC 21363.604739 4 0.0000 460 | 0/14 680s 22 h-m-p 0.0000 0.0005 1390.1644 ++ 21142.317759 m 0.0005 477 | 0/14 680s 23 h-m-p 0.0001 0.0007 273.6412 -YCCC 21140.940276 3 0.0000 500 | 0/14 680s 24 h-m-p 0.0000 0.0033 954.7616 +++YCCCC 20829.531681 4 0.0014 527 | 0/14 680s 25 h-m-p 0.0002 0.0011 349.6405 CCCCC 20816.773590 4 0.0003 552 | 0/14 680s 26 h-m-p 0.0009 0.0403 102.6884 ++CYYYCCC 20638.667430 6 0.0338 581 | 0/14 680s 27 h-m-p 0.0059 0.0294 155.4331 YCYCC 20610.134406 4 0.0125 604 | 0/14 680s 28 h-m-p 0.0127 0.0637 8.4332 +YYYYCC 20605.219699 5 0.0482 628 | 0/14 680s 29 h-m-p 0.3112 1.5559 0.9191 CYCC 20583.315928 3 0.4051 650 | 0/14 680s 30 h-m-p 0.2091 1.5783 1.7810 +CCCYC 20545.281938 4 1.2057 690 | 0/14 680s 31 h-m-p 0.2576 1.2878 2.4076 +YYCCC 20521.026302 4 0.8130 714 | 0/14 680s 32 h-m-p 0.3358 1.6792 2.8216 CYCCC 20517.342547 4 0.2278 738 | 0/14 680s 33 h-m-p 0.6285 8.0000 1.0228 YCCC 20506.220705 3 1.5002 760 | 0/14 680s 34 h-m-p 0.6167 3.0836 1.3100 CYCCC 20499.842003 4 1.1707 784 | 0/14 680s 35 h-m-p 0.7598 5.9052 2.0184 YYCC 20492.447325 3 1.1446 805 | 0/14 680s 36 h-m-p 1.2878 6.4392 1.2984 CCCC 20487.430168 3 1.7509 828 | 0/14 680s 37 h-m-p 1.6000 8.0000 0.6558 CCC 20485.094774 2 2.2561 849 | 0/14 680s 38 h-m-p 1.6000 8.0000 0.4078 YC 20483.578230 1 3.6439 881 | 0/14 680s 39 h-m-p 1.6000 8.0000 0.1109 YC 20482.195817 1 2.9568 913 | 0/14 680s 40 h-m-p 0.8322 8.0000 0.3942 +CCC 20480.052584 2 3.7349 949 | 0/14 680s 41 h-m-p 1.6000 8.0000 0.2864 +YC 20476.706707 1 4.3427 982 | 0/14 680s 42 h-m-p 1.6000 8.0000 0.7334 YCCC 20473.021632 3 3.5263 1018 | 0/14 680s 43 h-m-p 1.6000 8.0000 0.0736 +YCC 20469.021945 2 5.0493 1053 | 0/14 680s 44 h-m-p 1.6000 8.0000 0.1031 +YCCC 20463.633088 3 4.3782 1090 | 0/14 680s 45 h-m-p 0.1877 8.0000 2.4042 ++YYYC 20455.897916 3 2.8287 1126 | 0/14 684s 46 h-m-p 1.6000 8.0000 0.0741 YCCC 20451.970608 3 2.9069 1148 | 0/14 684s 47 h-m-p 0.7913 3.9564 0.0845 YCYC 20449.818940 3 1.9537 1183 | 0/14 684s 48 h-m-p 0.6248 8.0000 0.2643 +C 20449.206446 0 2.4741 1215 | 0/14 684s 49 h-m-p 1.0397 8.0000 0.6289 YC 20448.590412 1 1.9742 1247 | 0/14 684s 50 h-m-p 1.6000 8.0000 0.2502 +YC 20447.758001 1 4.8805 1280 | 0/14 684s 51 h-m-p 0.5537 2.7684 0.3321 +YCYC 20446.894892 3 1.5086 1316 | 0/14 684s 52 h-m-p 1.6000 8.0000 0.1445 CC 20446.374771 1 1.5691 1349 | 0/14 684s 53 h-m-p 1.6000 8.0000 0.1282 +YCCC 20445.759463 3 4.6819 1386 | 0/14 684s 54 h-m-p 1.6000 8.0000 0.2002 CYC 20445.015893 2 1.2762 1420 | 0/14 684s 55 h-m-p 0.5331 8.0000 0.4792 +CCC 20443.563817 2 2.6194 1456 | 0/14 684s 56 h-m-p 1.6000 8.0000 0.2823 YCCC 20441.697958 3 3.9146 1492 | 0/14 684s 57 h-m-p 0.8436 4.2181 0.1785 CCCC 20440.763113 3 1.4522 1529 | 0/14 684s 58 h-m-p 0.9997 8.0000 0.2593 CYC 20440.487906 2 1.3414 1563 | 0/14 684s 59 h-m-p 1.6000 8.0000 0.0981 C 20440.397714 0 1.6000 1594 | 0/14 684s 60 h-m-p 1.6000 8.0000 0.0039 CC 20440.385439 1 1.2774 1627 | 0/14 684s 61 h-m-p 0.6177 8.0000 0.0080 YC 20440.383281 1 1.5069 1659 | 0/14 684s 62 h-m-p 1.6000 8.0000 0.0010 C 20440.382822 0 1.4442 1690 | 0/14 684s 63 h-m-p 0.5922 8.0000 0.0024 +Y 20440.382781 0 1.7688 1722 | 0/14 684s 64 h-m-p 1.6000 8.0000 0.0012 C 20440.382775 0 1.4045 1753 | 0/14 684s 65 h-m-p 1.6000 8.0000 0.0002 C 20440.382774 0 1.8765 1784 | 0/14 684s 66 h-m-p 1.6000 8.0000 0.0001 Y 20440.382774 0 0.2866 1815 | 0/14 684s 67 h-m-p 0.3581 8.0000 0.0001 -C 20440.382774 0 0.0224 1847 | 0/14 684s 68 h-m-p 0.0160 8.0000 0.0002 -----Y 20440.382774 0 0.0000 1883 684s Out.. 684s lnL = -20440.382774 684s 1884 lfun, 3768 eigenQcodon, 16956 P(t) 684s 684s Time used: 0:10 684s Passed 684s 684s Test 10 684s 684s CODONML in paml version 4.9j, October 2019 684s 684s ---------------------------------------------- 684s Phe F TTT | Ser S TCT | Tyr Y TAT | Cys C TGT 684s TTC | TCC | TAC | TGC 684s Leu L TTA | TCA | *** * TAA | Trp W TGA 684s TTG | TCG | TAG | TGG 684s ---------------------------------------------- 684s Leu L CTT | Pro P CCT | His H CAT | Arg R CGT 684s CTC | CCC | CAC | CGC 684s CTA | CCA | Gln Q CAA | CGA 684s CTG | CCG | CAG | CGG 684s ---------------------------------------------- 684s Ile I ATT | Thr T ACT | Asn N AAT | Ser S AGT 684s ATC | ACC | AAC | AGC 684s Met M ATA | ACA | Lys K AAA | *** * AGA 684s ATG | ACG | AAG | AGG 684s ---------------------------------------------- 684s Val V GTT | Ala A GCT | Asp D GAT | Gly G GGT 684s GTC | GCC | GAC | GGC 684s GTA | GCA | Glu E GAA | GGA 684s GTG | GCG | GAG | GGG 684s ---------------------------------------------- 684s Nice code, uuh? 684s ns = 2 ls = 10707 684s Reading sequences, sequential format.. 684s Reading seq # 1: Human_Horai Reading seq # 2: Chimp_Horai 684s Sequences read.. 684s Counting site patterns.. 0:00 684s Compressing, 243 patterns at 3569 / 3569 sites (100.0%), 0:00 684s Collecting fpatt[] & pose[], 243 patterns at 3569 / 3569 sites (100.0%), 0:00 684s Counting codons.. 684s 684s 8 bytes for distance 684s 233280 bytes for conP 684s 1769524631699768576 bytes for fhK 684s 5000000 bytes for space 684s 684s TREE # 1 684s (1, 2); MP score: 1008 684s 0.362723 1.234567 2.155230 2.615968 2.217444 1.267874 1.909031 1.418367 -0.452955 0.493048 1.819293 1.462056 -0.412657 0.659213 1.573559 -1.129266 -0.017806 1.665763 -0.631450 1.120298 2.005956 2.571619 0.725866 0.842480 1.750757 1.113351 -0.896469 -0.039582 1.530051 1.660100 -0.699407 -0.814473 0.273249 0.535931 -1.632839 1.860965 2.108652 2.105368 0.391166 0.923906 2.208115 1.915317 -0.509645 0.927954 1.922278 1.552842 -0.781847 -0.324850 0.833696 0.440017 0.924628 1.092319 -0.689793 0.718292 2.030454 1.384480 -0.752419 -0.270995 1.097503 1.401785 -0.007293 0.124175 1.635340 1.112568 1.414000 684s 684s ntime & nrate & np: 1 64 65 684s 684s Bounds (np=65): 684s 0.000004 0.000100 0.000100 0.000100 0.000100 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 -29.000000 0.000100 684s 50.000000 999.000000 999.000000 999.000000 999.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 29.000000 999.000000 684s 684s np = 65 684s lnL0 = -18631.307087 684s 684s Iterating by ming2 684s Initial: fx= 18631.307087 687s x= 0.36272 1.23457 2.15523 2.61597 2.21744 1.26787 1.90903 1.41837 -0.45296 0.49305 1.81929 1.46206 -0.41266 0.65921 1.57356 -1.12927 -0.01781 1.66576 -0.63145 1.12030 2.00596 2.57162 0.72587 0.84248 1.75076 1.11335 -0.89647 -0.03958 1.53005 1.66010 -0.69941 -0.81447 0.27325 0.53593 -1.63284 1.86096 2.10865 2.10537 0.39117 0.92391 2.20812 1.91532 -0.50965 0.92795 1.92228 1.55284 -0.78185 -0.32485 0.83370 0.44002 0.92463 1.09232 -0.68979 0.71829 2.03045 1.38448 -0.75242 -0.27099 1.09750 1.40179 -0.00729 0.12418 1.63534 1.11257 1.41400 687s 687s 1 h-m-p 0.0000 0.0001 3480.1821 +YYCYCYCCC 18138.788707 8 0.0001 83 | 0/65 687s 2 h-m-p 0.0003 0.0027 774.4061 +YCYYCYYCCC 16657.334045 9 0.0026 167 | 0/65 687s 3 h-m-p 0.0003 0.0013 409.5261 YCYCCC 16608.154532 5 0.0006 243 | 0/65 687s 4 h-m-p 0.0000 0.0004 9292.1497 +YYYYC 16445.748404 4 0.0001 316 | 0/65 687s 5 h-m-p 0.0049 0.0245 141.7290 YYCCCCC 16395.235505 6 0.0052 394 | 0/65 687s 6 h-m-p 0.0023 0.0117 193.5971 CCCC 16388.539904 3 0.0007 468 | 0/65 687s 7 h-m-p 0.0021 0.1457 66.8334 +CCC 16370.348560 2 0.0108 541 | 0/65 687s 8 h-m-p 0.0133 0.0966 54.4081 YCCC 16361.286482 3 0.0090 614 | 0/65 687s 9 h-m-p 0.0101 0.1273 48.5976 CYC 16354.099948 2 0.0099 685 | 0/65 687s 10 h-m-p 0.0126 1.5171 38.3146 CC 16345.492855 1 0.0170 755 | 0/65 687s 11 h-m-p 0.0215 2.4145 30.2960 CCC 16336.844049 2 0.0214 827 | 0/65 687s 12 h-m-p 0.0175 1.7567 37.0257 CYC 16327.929111 2 0.0164 898 | 0/65 687s 13 h-m-p 0.0194 1.7676 31.3390 CC 16314.605629 1 0.0262 968 | 0/65 687s 14 h-m-p 0.0164 0.3417 50.0844 CCC 16293.442379 2 0.0247 1040 | 0/65 687s 15 h-m-p 0.0228 0.1721 54.2653 YYC 16275.490870 2 0.0198 1110 | 0/65 687s 16 h-m-p 0.0229 0.2239 46.8717 YCCC 16264.440403 3 0.0157 1183 | 0/65 687s 17 h-m-p 0.0204 0.3485 36.1928 CCC 16255.068088 2 0.0209 1255 | 0/65 687s 18 h-m-p 0.0159 0.1954 47.7506 CCCC 16245.657788 3 0.0176 1329 | 0/65 687s 19 h-m-p 0.0264 0.9544 31.8001 YC 16240.144835 1 0.0174 1398 | 0/65 687s 20 h-m-p 0.0219 0.8382 25.2742 CCC 16234.903995 2 0.0238 1470 | 0/65 687s 21 h-m-p 0.0196 0.3314 30.6959 CYC 16230.208628 2 0.0191 1541 | 0/65 687s 22 h-m-p 0.0219 0.2989 26.7995 CCCC 16225.161708 3 0.0248 1615 | 0/65 687s 23 h-m-p 0.0198 0.3914 33.5532 CCC 16220.661518 2 0.0176 1687 | 0/65 687s 24 h-m-p 0.0184 0.9677 32.1121 CCC 16215.569895 2 0.0204 1759 | 0/65 687s 25 h-m-p 0.0223 1.4582 29.3196 CYC 16210.287561 2 0.0219 1830 | 0/65 687s 26 h-m-p 0.0320 0.9110 20.0481 YCC 16206.450351 2 0.0230 1901 | 0/65 687s 27 h-m-p 0.0255 4.9032 18.1052 CC 16201.973377 1 0.0287 1971 | 0/65 687s 28 h-m-p 0.0271 1.2664 19.2191 CC 16196.176262 1 0.0343 2041 | 0/65 687s 29 h-m-p 0.0338 1.9272 19.4873 CC 16190.603261 1 0.0345 2111 | 0/65 687s 30 h-m-p 0.0246 1.4991 27.3380 CCC 16184.071842 2 0.0313 2183 | 0/65 687s 31 h-m-p 0.0259 0.4371 33.0382 YC 16179.329140 1 0.0208 2252 | 0/65 687s 32 h-m-p 0.0295 0.6371 23.2962 YCC 16176.583880 2 0.0209 2323 | 0/65 687s 33 h-m-p 0.0389 1.1049 12.4922 CCC 16174.487228 2 0.0354 2395 | 0/65 687s 34 h-m-p 0.0278 1.3048 15.8921 CC 16172.340371 1 0.0314 2465 | 0/65 687s 35 h-m-p 0.0286 1.3135 17.4402 YC 16167.804002 1 0.0613 2534 | 0/65 687s 36 h-m-p 0.0413 1.5473 25.8868 CCC 16162.528283 2 0.0479 2606 | 0/65 687s 37 h-m-p 0.0367 0.6126 33.7511 CCC 16154.431194 2 0.0567 2678 | 0/65 687s 38 h-m-p 0.0307 0.3019 62.3790 CCCC 16145.594913 3 0.0339 2752 | 0/65 687s 39 h-m-p 0.0569 0.3556 37.2214 YCCC 16141.074110 3 0.0309 2825 | 0/65 687s 40 h-m-p 0.0328 3.2400 35.0228 YCC 16138.588707 2 0.0192 2896 | 0/65 687s 41 h-m-p 0.0240 0.7440 27.9344 CCC 16135.959137 2 0.0272 2968 | 0/65 687s 42 h-m-p 0.0685 1.8147 11.0935 YC 16134.445450 1 0.0413 3037 | 0/65 687s 43 h-m-p 0.0277 1.9322 16.5572 CC 16132.027814 1 0.0424 3107 | 0/65 687s 44 h-m-p 0.0326 0.9735 21.5786 CC 16128.944524 1 0.0397 3177 | 0/65 687s 45 h-m-p 0.0375 5.0824 22.8531 CYC 16125.805240 2 0.0382 3248 | 0/65 687s 46 h-m-p 0.0576 2.5345 15.1714 YCC 16123.644349 2 0.0431 3319 | 0/65 687s 47 h-m-p 0.0319 1.9267 20.4817 CC 16121.871721 1 0.0292 3389 | 0/65 687s 48 h-m-p 0.0556 2.0597 10.7741 CCC 16120.607539 2 0.0460 3461 | 0/65 690s 49 h-m-p 0.0397 2.4501 12.4875 YC 16118.586175 1 0.0648 3530 | 0/65 690s 50 h-m-p 0.0415 1.3806 19.4995 CC 16116.728158 1 0.0390 3600 | 0/65 690s 51 h-m-p 0.0283 0.8722 26.8879 CCC 16114.341348 2 0.0370 3672 | 0/65 690s 52 h-m-p 0.0423 0.7059 23.5318 CYC 16112.262121 2 0.0408 3743 | 0/65 690s 53 h-m-p 0.0545 1.2430 17.6043 YC 16111.072304 1 0.0365 3812 | 0/65 690s 54 h-m-p 0.0392 0.9007 16.4010 CCC 16110.095386 2 0.0358 3884 | 0/65 690s 55 h-m-p 0.0339 0.9332 17.3258 CCC 16108.590739 2 0.0545 3956 | 0/65 690s 56 h-m-p 0.0918 1.0566 10.2814 YCC 16107.978866 2 0.0393 4027 | 0/65 690s 57 h-m-p 0.0548 1.4068 7.3721 CCC 16107.121643 2 0.0677 4099 | 0/65 690s 58 h-m-p 0.0257 1.1630 19.4630 CC 16106.076604 1 0.0299 4169 | 0/65 690s 59 h-m-p 0.0720 2.0598 8.0800 CC 16105.011764 1 0.0626 4239 | 0/65 690s 60 h-m-p 0.0616 1.4321 8.2017 YC 16104.494556 1 0.0299 4308 | 0/65 690s 61 h-m-p 0.0395 6.4428 6.2169 YC 16103.724664 1 0.0650 4377 | 0/65 690s 62 h-m-p 0.1282 6.3011 3.1529 YC 16103.360036 1 0.0783 4446 | 0/65 690s 63 h-m-p 0.0318 5.3693 7.7714 YC 16102.653079 1 0.0659 4515 | 0/65 690s 64 h-m-p 0.0774 3.4904 6.6133 CC 16102.003842 1 0.0893 4585 | 0/65 690s 65 h-m-p 0.0402 1.4815 14.7005 C 16101.446856 0 0.0396 4653 | 0/65 690s 66 h-m-p 0.1015 2.6585 5.7379 CCC 16100.965713 2 0.1239 4725 | 0/65 690s 67 h-m-p 0.1422 3.2240 4.9979 YCCC 16100.236944 3 0.2533 4798 | 0/65 690s 68 h-m-p 0.2758 3.4573 4.5911 YC 16099.966993 1 0.1135 4867 | 0/65 690s 69 h-m-p 0.3098 8.0000 1.6823 CC 16099.327393 1 0.4594 4937 | 0/65 690s 70 h-m-p 0.1942 6.2832 3.9801 YC 16099.085252 1 0.1075 5006 | 0/65 690s 71 h-m-p 0.3079 8.0000 1.3901 YC 16098.996163 1 0.2406 5075 | 0/65 690s 72 h-m-p 0.1299 7.2677 2.5741 +YYC 16098.799756 2 0.3999 5146 | 0/65 690s 73 h-m-p 0.6755 8.0000 1.5237 YC 16098.765897 1 0.1311 5215 | 0/65 690s 74 h-m-p 0.3341 8.0000 0.5980 YC 16098.687674 1 0.7089 5284 | 0/65 690s 75 h-m-p 0.6537 8.0000 0.6485 YC 16098.657340 1 0.4820 5418 | 0/65 690s 76 h-m-p 0.4876 8.0000 0.6411 YC 16098.647130 1 0.2095 5552 | 0/65 690s 77 h-m-p 0.1884 8.0000 0.7132 +CC 16098.589853 1 0.9572 5688 | 0/65 690s 78 h-m-p 1.6000 8.0000 0.0966 +YC 16098.435214 1 4.4822 5823 | 0/65 690s 79 h-m-p 0.9791 8.0000 0.4424 YC 16098.126359 1 1.9759 5957 | 0/65 690s 80 h-m-p 0.9365 8.0000 0.9334 CYC 16097.950241 2 0.8514 6093 | 0/65 690s 81 h-m-p 1.6000 8.0000 0.3338 YC 16097.869235 1 1.2616 6227 | 0/65 690s 82 h-m-p 1.6000 8.0000 0.2146 YC 16097.774015 1 3.5460 6361 | 0/65 690s 83 h-m-p 1.6000 8.0000 0.1419 +CC 16097.478365 1 5.8997 6497 | 0/65 690s 84 h-m-p 0.6255 8.0000 1.3386 CYCCC 16097.184403 4 1.0681 6637 | 0/65 690s 85 h-m-p 1.6000 8.0000 0.8764 CCCC 16096.440037 3 1.6947 6711 | 0/65 690s 86 h-m-p 1.1200 8.0000 1.3261 YC 16096.153745 1 0.6505 6845 | 0/65 690s 87 h-m-p 0.5964 8.0000 1.4464 CCC 16095.824378 2 1.0094 6917 | 0/65 690s 88 h-m-p 1.6000 8.0000 0.3103 YC 16095.643272 1 3.1126 6986 | 0/65 690s 89 h-m-p 1.6000 8.0000 0.3252 CCC 16095.444842 2 2.2599 7123 | 0/65 690s 90 h-m-p 1.1565 8.0000 0.6356 CC 16095.335806 1 0.9314 7258 | 0/65 690s 91 h-m-p 0.9096 8.0000 0.6508 CCC 16095.230783 2 1.2364 7395 | 0/65 690s 92 h-m-p 1.6000 8.0000 0.4211 CC 16095.179061 1 0.6336 7530 | 0/65 690s 93 h-m-p 0.8760 8.0000 0.3046 +CCC 16095.041015 2 3.7091 7668 | 0/65 690s 94 h-m-p 1.6000 8.0000 0.2587 YCC 16094.847510 2 2.6814 7804 | 0/65 690s 95 h-m-p 0.2949 8.0000 2.3528 CCCC 16094.737992 3 0.3680 7943 | 0/65 690s 96 h-m-p 1.1631 8.0000 0.7443 CCCC 16094.564712 3 1.5204 8017 | 0/65 690s 97 h-m-p 1.6000 8.0000 0.4757 YC 16094.377726 1 0.9634 8151 | 0/65 690s 98 h-m-p 0.3984 8.0000 1.1503 +YYC 16094.154154 2 1.3150 8287 | 0/65 690s 99 h-m-p 1.6000 8.0000 0.4595 CC 16094.022730 1 1.6600 8357 | 0/65 690s 100 h-m-p 1.6000 8.0000 0.3804 YC 16093.990396 1 1.2569 8491 | 0/65 690s 101 h-m-p 1.6000 8.0000 0.0310 YC 16093.980764 1 1.1743 8625 | 0/65 690s 102 h-m-p 0.0877 8.0000 0.4152 +YC 16093.970036 1 0.8275 8760 | 0/65 694s 103 h-m-p 1.0787 8.0000 0.3185 +YC 16093.932658 1 2.8029 8895 | 0/65 694s 104 h-m-p 1.6000 8.0000 0.1911 YC 16093.843992 1 3.8907 9029 | 0/65 694s 105 h-m-p 0.4391 8.0000 1.6935 YYC 16093.813321 2 0.3665 9164 | 0/65 694s 106 h-m-p 1.5488 8.0000 0.4008 YC 16093.782658 1 0.9822 9233 | 0/65 694s 107 h-m-p 1.6000 8.0000 0.0524 C 16093.770022 0 1.7902 9366 | 0/65 694s 108 h-m-p 0.1548 8.0000 0.6067 +CCC 16093.758044 2 0.9185 9504 | 0/65 694s 109 h-m-p 1.5145 8.0000 0.3679 CCC 16093.742353 2 1.9222 9641 | 0/65 694s 110 h-m-p 1.6000 8.0000 0.1230 CC 16093.729615 1 1.2858 9776 | 0/65 694s 111 h-m-p 0.1813 8.0000 0.8728 +CCC 16093.712598 2 0.9132 9914 | 0/65 694s 112 h-m-p 1.6000 8.0000 0.3282 C 16093.705388 0 1.6000 10047 | 0/65 694s 113 h-m-p 1.6000 8.0000 0.1097 YC 16093.701075 1 0.8416 10181 | 0/65 694s 114 h-m-p 0.1825 8.0000 0.5056 +CYC 16093.692610 2 1.4148 10318 | 0/65 694s 115 h-m-p 1.6000 8.0000 0.2278 YC 16093.674521 1 3.9101 10452 | 0/65 694s 116 h-m-p 1.6000 8.0000 0.1382 CC 16093.667050 1 0.5380 10587 | 0/65 694s 117 h-m-p 0.0912 8.0000 0.8152 ++YC 16093.651514 1 0.9577 10723 | 0/65 694s 118 h-m-p 1.3496 8.0000 0.5785 Y 16093.644147 0 0.8334 10856 | 0/65 694s 119 h-m-p 1.3062 8.0000 0.3691 CY 16093.630904 1 1.4224 10991 | 0/65 694s 120 h-m-p 0.3646 8.0000 1.4401 CCC 16093.620071 2 0.4613 11128 | 0/65 694s 121 h-m-p 1.6000 8.0000 0.3054 CCC 16093.603966 2 1.8091 11200 | 0/65 694s 122 h-m-p 1.6000 8.0000 0.1446 YC 16093.594457 1 0.8906 11334 | 0/65 694s 123 h-m-p 0.1584 8.0000 0.8127 +CYC 16093.571080 2 1.2224 11471 | 0/65 694s 124 h-m-p 1.3474 8.0000 0.7373 YYC 16093.551558 2 1.0607 11606 | 0/65 694s 125 h-m-p 1.6000 8.0000 0.2147 YC 16093.530121 1 0.7142 11740 | 0/65 694s 126 h-m-p 0.2002 8.0000 0.7658 +CYC 16093.501409 2 1.3509 11877 | 0/65 694s 127 h-m-p 1.6000 8.0000 0.3995 C 16093.475157 0 1.6264 12010 | 0/65 694s 128 h-m-p 1.6000 8.0000 0.2726 C 16093.453650 0 1.6000 12143 | 0/65 694s 129 h-m-p 0.2685 8.0000 1.6244 C 16093.440848 0 0.2736 12276 | 0/65 694s 130 h-m-p 0.3273 8.0000 1.3580 CCC 16093.417304 2 0.4848 12348 | 0/65 694s 131 h-m-p 1.6000 8.0000 0.3472 CCC 16093.397486 2 2.0525 12420 | 0/65 694s 132 h-m-p 1.6000 8.0000 0.1619 CYC 16093.380119 2 1.1074 12556 | 0/65 694s 133 h-m-p 0.0851 8.0000 2.1053 +YYC 16093.363471 2 0.2774 12692 | 0/65 694s 134 h-m-p 1.5416 8.0000 0.3789 YYC 16093.357835 2 1.1230 12762 | 0/65 694s 135 h-m-p 1.6000 8.0000 0.0891 YC 16093.352352 1 0.9764 12896 | 0/65 694s 136 h-m-p 0.4485 8.0000 0.1940 +Y 16093.349431 0 1.3738 13030 | 0/65 694s 137 h-m-p 1.6000 8.0000 0.0563 C 16093.348684 0 1.6000 13163 | 0/65 694s 138 h-m-p 1.6000 8.0000 0.0510 C 16093.348210 0 2.4605 13296 | 0/65 694s 139 h-m-p 1.6000 8.0000 0.0155 +YC 16093.346729 1 4.5977 13431 | 0/65 694s 140 h-m-p 1.4492 8.0000 0.0490 +C 16093.339873 0 5.0788 13565 | 0/65 694s 141 h-m-p 1.6000 8.0000 0.1513 YC 16093.335117 1 1.1250 13699 | 0/65 694s 142 h-m-p 0.7740 8.0000 0.2199 CC 16093.331805 1 1.2949 13834 | 0/65 694s 143 h-m-p 1.6000 8.0000 0.0292 C 16093.330508 0 2.0796 13967 | 0/65 694s 144 h-m-p 1.0238 8.0000 0.0592 +C 16093.328143 0 4.0953 14101 | 0/65 694s 145 h-m-p 1.6000 8.0000 0.1057 YC 16093.322762 1 3.0420 14235 | 0/65 694s 146 h-m-p 1.2707 8.0000 0.2530 YCYC 16093.303510 3 2.9969 14372 | 0/65 694s 147 h-m-p 1.6000 8.0000 0.4543 YY 16093.280157 1 1.4254 14506 | 0/65 694s 148 h-m-p 1.6000 8.0000 0.1982 CC 16093.271114 1 0.6158 14641 | 0/65 694s 149 h-m-p 0.2184 8.0000 0.5588 +CYC 16093.256868 2 1.3518 14778 | 0/65 694s 150 h-m-p 1.6000 8.0000 0.3421 -YC 16093.254820 1 0.1750 14913 | 0/65 694s 151 h-m-p 0.1215 8.0000 0.4929 ++YC 16093.244620 1 1.2967 15049 | 0/65 694s 152 h-m-p 1.6000 8.0000 0.2655 CC 16093.238046 1 2.2415 15184 | 0/65 694s 153 h-m-p 1.3968 8.0000 0.4260 C 16093.236673 0 0.4175 15317 | 0/65 694s 154 h-m-p 0.5983 8.0000 0.2973 YC 16093.234657 1 0.4153 15451 | 0/65 694s 155 h-m-p 0.3451 8.0000 0.3578 YC 16093.233664 1 0.6161 15585 | 0/65 694s 156 h-m-p 1.0078 8.0000 0.2187 C 16093.232222 0 1.3566 15718 | 0/65 695s 157 h-m-p 1.6000 8.0000 0.0639 C 16093.231349 0 1.3037 15851 | 0/65 695s 158 h-m-p 0.3452 8.0000 0.2411 +Y 16093.230673 0 0.9035 15985 | 0/65 695s 159 h-m-p 1.6000 8.0000 0.0391 C 16093.230385 0 2.0877 16118 | 0/65 695s 160 h-m-p 1.6000 8.0000 0.0234 Y 16093.230317 0 0.9680 16251 | 0/65 695s 161 h-m-p 0.3058 8.0000 0.0741 +C 16093.230180 0 1.6325 16385 | 0/65 695s 162 h-m-p 1.6000 8.0000 0.0402 Y 16093.230153 0 1.1048 16518 | 0/65 695s 163 h-m-p 1.6000 8.0000 0.0030 Y 16093.230152 0 0.9315 16651 | 0/65 695s 164 h-m-p 1.6000 8.0000 0.0007 Y 16093.230152 0 1.2306 16784 | 0/65 695s 165 h-m-p 1.6000 8.0000 0.0001 Y 16093.230152 0 1.2621 16917 | 0/65 695s 166 h-m-p 1.6000 8.0000 0.0000 Y 16093.230152 0 0.2045 17050 | 0/65 695s 167 h-m-p 0.2002 8.0000 0.0000 +C 16093.230152 0 0.8007 17184 | 0/65 695s 168 h-m-p 1.4548 8.0000 0.0000 C 16093.230152 0 0.3637 17317 | 0/65 695s 169 h-m-p 1.1564 8.0000 0.0000 ---------C 16093.230152 0 0.0000 17459 695s Out.. 695s lnL = -16093.230152 695s 17460 lfun, 17460 eigenQcodon, 34920 P(t) 695s 695s Time used: 0:11 695s Passed 695s 696s autopkgtest [18:11:44]: test run-unit-test: -----------------------] 697s autopkgtest [18:11:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 697s run-unit-test PASS 697s autopkgtest [18:11:45]: @@@@@@@@@@@@@@@@@@@@ summary 697s run-unit-test PASS 766s nova [W] Skipping flock for amd64 766s Creating nova instance adt-oracular-amd64-paml-20240712-174257-juju-7f2275-prod-proposed-migration-environment-2-fac69f6e-da4e-49cf-aca0-15ec9476fcb1 from image adt/ubuntu-oracular-amd64-server-20240712.img (UUID 9132249a-6053-4497-bc26-981612ca03ad)...