RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 24-Jun-2021 05:23:48 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/2_msa/P47989_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/3_mltree/P47989 --seed 2 --threads 8 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (8 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/2_msa/P47989_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 1616 sites WARNING: Sequences tr_G7X818_G7X818_ASPKW_1033177 and tr_A0A146FJ84_A0A146FJ84_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XJ24_G7XJ24_ASPKW_1033177 and tr_A0A146FB69_A0A146FB69_9EURO_1069201 are exactly identical! WARNING: Sequences tr_F4P2N0_F4P2N0_BATDJ_684364 and tr_A0A177WLK3_A0A177WLK3_BATDE_403673 are exactly identical! WARNING: Sequences tr_I1PCH6_I1PCH6_ORYGL_4538 and tr_A0A0D3FK37_A0A0D3FK37_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_G3Y9C6_G3Y9C6_ASPNA_380704 and tr_A0A319AGP3_A0A319AGP3_9EURO_1450533 are exactly identical! WARNING: Sequences tr_N4UBK7_N4UBK7_FUSC1_1229664 and tr_A0A2H3SYL7_A0A2H3SYL7_FUSOX_5507 are exactly identical! WARNING: Sequences tr_A0A067F1T2_A0A067F1T2_CITSI_2711 and tr_A0A2H5P453_A0A2H5P453_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A1S3X7W9_A0A1S3X7W9_TOBAC_4097 and tr_A0A1U7W5N1_A0A1U7W5N1_NICSY_4096 are exactly identical! WARNING: Duplicate sequences found: 8 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/3_mltree/P47989.raxml.reduced.phy Alignment comprises 1 partitions and 1614 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 1616 / 1614 Gaps: 17.26 % Invariant sites: 0.56 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/3_mltree/P47989.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 8 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 202 / 16160 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -2190009.041738] Initial branch length optimization [00:00:07 -1886152.946012] Model parameter optimization (eps = 10.000000) [00:00:59 -1880967.155994] AUTODETECT spr round 1 (radius: 5) [00:04:26 -1352031.876381] AUTODETECT spr round 2 (radius: 10) [00:08:57 -965456.352028] AUTODETECT spr round 3 (radius: 15) [00:13:01 -817942.764847] AUTODETECT spr round 4 (radius: 20) [00:17:34 -783795.104154] AUTODETECT spr round 5 (radius: 25) [00:23:12 -771911.797338] SPR radius for FAST iterations: 25 (autodetect) [00:23:12 -771911.797338] Model parameter optimization (eps = 3.000000) [00:23:35 -771721.606519] FAST spr round 1 (radius: 25) [00:27:57 -680888.881714] FAST spr round 2 (radius: 25) [00:31:06 -677954.891125] FAST spr round 3 (radius: 25) [00:33:58 -677768.718697] FAST spr round 4 (radius: 25) [00:36:23 -677717.787312] FAST spr round 5 (radius: 25) [00:38:40 -677704.998363] FAST spr round 6 (radius: 25) [00:40:55 -677692.854411] FAST spr round 7 (radius: 25) [00:43:07 -677690.923094] FAST spr round 8 (radius: 25) [00:45:18 -677690.391659] FAST spr round 9 (radius: 25) [00:47:26 -677688.283172] FAST spr round 10 (radius: 25) [00:49:40 -677688.215409] Model parameter optimization (eps = 1.000000) [00:50:03 -677683.163201] SLOW spr round 1 (radius: 5) [00:53:39 -677555.537502] SLOW spr round 2 (radius: 5) [00:56:56 -677539.105486] SLOW spr round 3 (radius: 5) [01:00:03 -677539.105348] SLOW spr round 4 (radius: 10) [01:03:19 -677539.105348] SLOW spr round 5 (radius: 15) [01:09:02 -677539.105348] SLOW spr round 6 (radius: 20) [01:17:01 -677539.105348] SLOW spr round 7 (radius: 25) [01:27:02 -677539.105348] Model parameter optimization (eps = 0.100000) [01:27:20] ML tree search #1, logLikelihood: -677538.873589 [01:27:20 -2178616.997257] Initial branch length optimization [01:27:28 -1880884.881065] Model parameter optimization (eps = 10.000000) [01:28:21 -1875501.568428] AUTODETECT spr round 1 (radius: 5) [01:31:51 -1367925.994001] AUTODETECT spr round 2 (radius: 10) [01:35:57 -1026500.733215] AUTODETECT spr round 3 (radius: 15) [01:39:53 -914646.903303] AUTODETECT spr round 4 (radius: 20) [01:44:25 -811400.892977] AUTODETECT spr round 5 (radius: 25) [01:50:53 -796423.610759] SPR radius for FAST iterations: 25 (autodetect) [01:50:53 -796423.610759] Model parameter optimization (eps = 3.000000) [01:51:04 -796406.091057] FAST spr round 1 (radius: 25) [01:55:59 -681491.678102] FAST spr round 2 (radius: 25) [01:59:11 -678082.297257] FAST spr round 3 (radius: 25) [02:02:01 -677938.172279] FAST spr round 4 (radius: 25) [02:04:25 -677870.158060] FAST spr round 5 (radius: 25) [02:06:45 -677869.806884] FAST spr round 6 (radius: 25) [02:09:03 -677864.792145] FAST spr round 7 (radius: 25) [02:11:20 -677864.769430] Model parameter optimization (eps = 1.000000) [02:11:41 -677708.018395] SLOW spr round 1 (radius: 5) [02:15:21 -677540.627258] SLOW spr round 2 (radius: 5) [02:18:39 -677532.564167] SLOW spr round 3 (radius: 5) [02:21:49 -677532.564166] SLOW spr round 4 (radius: 10) [02:25:05 -677532.564166] SLOW spr round 5 (radius: 15) [02:30:50 -677532.564166] SLOW spr round 6 (radius: 20) [02:38:38 -677532.564166] SLOW spr round 7 (radius: 25) [02:48:25 -677532.564166] Model parameter optimization (eps = 0.100000) [02:48:43] ML tree search #2, logLikelihood: -677532.321498 [02:48:43 -2177334.968661] Initial branch length optimization [02:48:54 -1877469.460708] Model parameter optimization (eps = 10.000000) [02:49:51 -1872193.719921] AUTODETECT spr round 1 (radius: 5) [02:53:21 -1342949.274901] AUTODETECT spr round 2 (radius: 10) [02:57:57 -1008998.506702] AUTODETECT spr round 3 (radius: 15) [03:02:37 -861748.975908] AUTODETECT spr round 4 (radius: 20) [03:07:30 -792099.691979] AUTODETECT spr round 5 (radius: 25) [03:14:18 -790470.770173] SPR radius for FAST iterations: 25 (autodetect) [03:14:18 -790470.770173] Model parameter optimization (eps = 3.000000) [03:14:31 -790453.566309] FAST spr round 1 (radius: 25) [03:19:43 -681908.156437] FAST spr round 2 (radius: 25) [03:23:04 -678134.698729] FAST spr round 3 (radius: 25) [03:25:59 -677886.767434] FAST spr round 4 (radius: 25) [03:28:37 -677833.146890] FAST spr round 5 (radius: 25) [03:30:59 -677829.390162] FAST spr round 6 (radius: 25) [03:33:18 -677826.686655] FAST spr round 7 (radius: 25) [03:35:35 -677824.323325] FAST spr round 8 (radius: 25) [03:37:52 -677824.127723] FAST spr round 9 (radius: 25) [03:40:07 -677823.512413] FAST spr round 10 (radius: 25) [03:42:24 -677817.358317] FAST spr round 11 (radius: 25) [03:44:40 -677817.358316] Model parameter optimization (eps = 1.000000) [03:44:47 -677816.948721] SLOW spr round 1 (radius: 5) [03:48:18 -677731.168585] SLOW spr round 2 (radius: 5) [03:51:28 -677710.628727] SLOW spr round 3 (radius: 5) [03:54:33 -677708.144022] SLOW spr round 4 (radius: 5) [03:57:37 -677708.143993] SLOW spr round 5 (radius: 10) [04:00:48 -677708.143993] SLOW spr round 6 (radius: 15) [04:06:36 -677708.143993] SLOW spr round 7 (radius: 20) [04:14:40 -677708.143993] SLOW spr round 8 (radius: 25) [04:24:43 -677708.143993] Model parameter optimization (eps = 0.100000) [04:25:00] ML tree search #3, logLikelihood: -677554.981986 [04:25:01 -2190322.212727] Initial branch length optimization [04:25:08 -1886110.052780] Model parameter optimization (eps = 10.000000) [04:26:13 -1880684.106410] AUTODETECT spr round 1 (radius: 5) [04:29:38 -1365657.946037] AUTODETECT spr round 2 (radius: 10) [04:34:05 -1030006.478004] AUTODETECT spr round 3 (radius: 15) [04:38:46 -841324.197716] AUTODETECT spr round 4 (radius: 20) [04:43:57 -779113.059366] AUTODETECT spr round 5 (radius: 25) [04:50:26 -763139.116437] SPR radius for FAST iterations: 25 (autodetect) [04:50:26 -763139.116437] Model parameter optimization (eps = 3.000000) [04:50:55 -762932.149629] FAST spr round 1 (radius: 25) [04:55:37 -679935.828051] FAST spr round 2 (radius: 25) [04:58:57 -677781.579996] FAST spr round 3 (radius: 25) [05:01:55 -677676.141021] FAST spr round 4 (radius: 25) [05:04:23 -677670.204594] FAST spr round 5 (radius: 25) [05:06:45 -677668.238105] FAST spr round 6 (radius: 25) [05:09:06 -677667.260145] FAST spr round 7 (radius: 25) [05:11:27 -677664.768466] FAST spr round 8 (radius: 25) [05:13:45 -677663.870638] FAST spr round 9 (radius: 25) [05:16:03 -677663.222145] FAST spr round 10 (radius: 25) [05:18:21 -677661.152549] FAST spr round 11 (radius: 25) [05:20:37 -677651.444986] FAST spr round 12 (radius: 25) [05:22:54 -677651.444946] Model parameter optimization (eps = 1.000000) [05:23:18 -677644.200388] SLOW spr round 1 (radius: 5) [05:26:54 -677557.195773] SLOW spr round 2 (radius: 5) [05:30:12 -677544.195786] SLOW spr round 3 (radius: 5) [05:33:19 -677544.195585] SLOW spr round 4 (radius: 10) [05:36:34 -677544.195585] SLOW spr round 5 (radius: 15) [05:42:13 -677544.195585] SLOW spr round 6 (radius: 20) [05:50:03 -677544.195585] SLOW spr round 7 (radius: 25) [05:59:58 -677544.195585] Model parameter optimization (eps = 0.100000) [06:00:11] ML tree search #4, logLikelihood: -677543.631459 [06:00:11 -2185210.889916] Initial branch length optimization [06:00:19 -1881785.171285] Model parameter optimization (eps = 10.000000) [06:01:09 -1876611.993046] AUTODETECT spr round 1 (radius: 5) [06:04:36 -1359577.260561] AUTODETECT spr round 2 (radius: 10) [06:09:24 -970749.427562] AUTODETECT spr round 3 (radius: 15) [06:13:26 -867147.144892] AUTODETECT spr round 4 (radius: 20) [06:18:02 -835079.161521] AUTODETECT spr round 5 (radius: 25) [06:23:32 -810567.008214] SPR radius for FAST iterations: 25 (autodetect) [06:23:33 -810567.008214] Model parameter optimization (eps = 3.000000) [06:23:43 -810554.144205] FAST spr round 1 (radius: 25) [06:28:35 -703996.428019] FAST spr round 2 (radius: 25) [06:32:04 -680481.550674] FAST spr round 3 (radius: 25) [06:35:03 -678015.965685] FAST spr round 4 (radius: 25) RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 25-Jun-2021 03:33:21 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/2_msa/P47989_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/3_mltree/P47989 --seed 2 --threads 8 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (8 threads), thread pinning: OFF WARNING: The model you specified on the command line (LG4X) will be ignored since the binary MSA file already contains a model definition. If you want to change the model, please re-run RAxML-NG with the original PHYLIP/FASTA alignment and --redo option. [00:00:00] Loading binary alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/3_mltree/P47989.raxml.rba [00:00:00] Alignment comprises 1001 taxa, 1 partitions and 1614 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 1616 / 1614 Gaps: 17.26 % Invariant sites: 0.56 % Parallelization scheme autoconfig: 1 worker(s) x 8 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] NOTE: Resuming execution from checkpoint (logLH: -678015.97, ML trees: 4, bootstraps: 0) [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 202 / 16160 [00:00:00] Data distribution: max. searches per worker: 16 Starting ML tree search with 20 distinct starting trees [00:00:00 -678015.965685] SPR radius for FAST iterations: 25 (autodetect) [00:00:00 -678015.965685] FAST spr round 4 (radius: 25) [00:02:42 -677862.120406] FAST spr round 5 (radius: 25) [00:04:55 -677856.731104] FAST spr round 6 (radius: 25) [00:07:04 -677855.752329] FAST spr round 7 (radius: 25) [00:09:12 -677854.793882] FAST spr round 8 (radius: 25) [00:11:19 -677854.793882] Model parameter optimization (eps = 1.000000) [00:11:38 -677704.883276] SLOW spr round 1 (radius: 5) [00:15:06 -677555.496305] SLOW spr round 2 (radius: 5) [00:18:17 -677538.142031] SLOW spr round 3 (radius: 5) [00:21:15 -677538.142023] SLOW spr round 4 (radius: 10) [00:24:23 -677538.142023] SLOW spr round 5 (radius: 15) [00:29:56 -677538.142023] SLOW spr round 6 (radius: 20) [00:37:30 -677538.142023] SLOW spr round 7 (radius: 25) [00:47:03 -677538.142023] Model parameter optimization (eps = 0.100000) [00:47:12] ML tree search #5, logLikelihood: -677538.128771 [00:47:13 -2178422.752265] Initial branch length optimization [00:47:23 -1882255.452294] Model parameter optimization (eps = 10.000000) [00:48:13 -1876675.702265] AUTODETECT spr round 1 (radius: 5) [00:51:36 -1349057.294453] AUTODETECT spr round 2 (radius: 10) [00:56:04 -967866.839407] AUTODETECT spr round 3 (radius: 15) [01:00:20 -798845.884292] AUTODETECT spr round 4 (radius: 20) [01:05:25 -761924.426795] AUTODETECT spr round 5 (radius: 25) [01:11:04 -758318.690106] SPR radius for FAST iterations: 25 (autodetect) [01:11:04 -758318.690106] Model parameter optimization (eps = 3.000000) [01:11:13 -758303.202572] FAST spr round 1 (radius: 25) [01:15:41 -680755.338009] FAST spr round 2 (radius: 25) [01:18:52 -677995.944714] FAST spr round 3 (radius: 25) [01:21:37 -677844.958120] FAST spr round 4 (radius: 25) [01:23:52 -677833.874143] FAST spr round 5 (radius: 25) [01:26:02 -677832.443689] FAST spr round 6 (radius: 25) [01:28:10 -677828.885030] FAST spr round 7 (radius: 25) [01:30:18 -677823.235879] FAST spr round 8 (radius: 25) [01:32:26 -677822.893356] FAST spr round 9 (radius: 25) [01:34:33 -677817.331003] FAST spr round 10 (radius: 25) [01:36:39 -677813.708123] FAST spr round 11 (radius: 25) [01:38:45 -677813.708107] Model parameter optimization (eps = 1.000000) [01:39:08 -677667.088435] SLOW spr round 1 (radius: 5) [01:42:34 -677558.321951] SLOW spr round 2 (radius: 5) [01:45:39 -677542.374322] SLOW spr round 3 (radius: 5) [01:48:37 -677542.374298] SLOW spr round 4 (radius: 10) [01:51:42 -677542.374297] SLOW spr round 5 (radius: 15) [01:57:15 -677542.374297] SLOW spr round 6 (radius: 20) [02:04:56 -677542.374297] SLOW spr round 7 (radius: 25) [02:14:51 -677542.374297] Model parameter optimization (eps = 0.100000) [02:15:00] ML tree search #6, logLikelihood: -677542.078596 [02:15:01 -2190157.504456] Initial branch length optimization [02:15:09 -1885602.865857] Model parameter optimization (eps = 10.000000) [02:16:01 -1880458.520477] AUTODETECT spr round 1 (radius: 5) [02:19:22 -1371551.713364] AUTODETECT spr round 2 (radius: 10) [02:23:24 -993873.727630] AUTODETECT spr round 3 (radius: 15) [02:27:35 -853101.268914] AUTODETECT spr round 4 (radius: 20) [02:32:05 -785792.240353] AUTODETECT spr round 5 (radius: 25) [02:37:42 -778489.867831] SPR radius for FAST iterations: 25 (autodetect) [02:37:42 -778489.867831] Model parameter optimization (eps = 3.000000) [02:38:06 -778264.696248] FAST spr round 1 (radius: 25) [02:42:45 -681230.965935] FAST spr round 2 (radius: 25) [02:46:00 -677948.884509] FAST spr round 3 (radius: 25) [02:48:51 -677744.868976] FAST spr round 4 (radius: 25) [02:51:12 -677739.723400] FAST spr round 5 (radius: 25) [02:53:33 -677735.481108] FAST spr round 6 (radius: 25) [02:55:52 -677733.599992] FAST spr round 7 (radius: 25) [02:58:11 -677718.062176] FAST spr round 8 (radius: 25) [03:00:29 -677716.169873] FAST spr round 9 (radius: 25) [03:02:44 -677711.045097] FAST spr round 10 (radius: 25) [03:04:56 -677710.534619] FAST spr round 11 (radius: 25) [03:07:07 -677708.189069] FAST spr round 12 (radius: 25) [03:09:16 -677707.249975] FAST spr round 13 (radius: 25) [03:11:24 -677704.349886] FAST spr round 14 (radius: 25) [03:13:31 -677704.349882] Model parameter optimization (eps = 1.000000) [03:13:42 -677701.664253] SLOW spr round 1 (radius: 5) [03:17:11 -677564.186932] SLOW spr round 2 (radius: 5) [03:20:23 -677548.860869] SLOW spr round 3 (radius: 5) [03:23:23 -677548.860849] SLOW spr round 4 (radius: 10) [03:26:31 -677548.860849] SLOW spr round 5 (radius: 15) [03:32:09 -677548.860849] SLOW spr round 6 (radius: 20) [03:40:00 -677548.860849] SLOW spr round 7 (radius: 25) [03:50:10 -677548.860849] Model parameter optimization (eps = 0.100000) [03:50:25] ML tree search #7, logLikelihood: -677548.504018 [03:50:25 -2182997.269450] Initial branch length optimization [03:50:32 -1882075.748316] Model parameter optimization (eps = 10.000000) [03:51:31 -1876637.140523] AUTODETECT spr round 1 (radius: 5) [03:54:56 -1345432.756532] AUTODETECT spr round 2 (radius: 10) [03:59:21 -1008734.307821] AUTODETECT spr round 3 (radius: 15) [04:03:46 -871536.032670] AUTODETECT spr round 4 (radius: 20) [04:08:41 -788600.187278] AUTODETECT spr round 5 (radius: 25) [04:14:19 -775101.311457] SPR radius for FAST iterations: 25 (autodetect) [04:14:19 -775101.311457] Model parameter optimization (eps = 3.000000) [04:14:29 -775081.368570] FAST spr round 1 (radius: 25) [04:18:51 -680701.094432] FAST spr round 2 (radius: 25) [04:22:03 -678035.411809] FAST spr round 3 (radius: 25) [04:24:47 -677886.689348] FAST spr round 4 (radius: 25) [04:27:12 -677857.972693] FAST spr round 5 (radius: 25) [04:29:25 -677842.623129] FAST spr round 6 (radius: 25) [04:31:35 -677835.970776] FAST spr round 7 (radius: 25) [04:33:44 -677832.232728] FAST spr round 8 (radius: 25) [04:35:51 -677830.216320] FAST spr round 9 (radius: 25) [04:37:59 -677824.391143] FAST spr round 10 (radius: 25) [04:40:06 -677821.983030] FAST spr round 11 (radius: 25) [04:42:14 -677821.983026] Model parameter optimization (eps = 1.000000) [04:42:20 -677821.719994] SLOW spr round 1 (radius: 5) [04:45:51 -677716.239307] SLOW spr round 2 (radius: 5) [04:49:00 -677702.999298] SLOW spr round 3 (radius: 5) [04:52:01 -677702.999253] SLOW spr round 4 (radius: 10) [04:55:12 -677702.999252] SLOW spr round 5 (radius: 15) [05:00:52 -677702.999252] SLOW spr round 6 (radius: 20) [05:08:38 -677702.999252] SLOW spr round 7 (radius: 25) [05:18:26 -677702.999252] Model parameter optimization (eps = 0.100000) [05:18:34] ML tree search #8, logLikelihood: -677702.996717 [05:18:34 -2176902.840357] Initial branch length optimization [05:18:42 -1877319.322172] Model parameter optimization (eps = 10.000000) [05:19:40 -1872188.434225] AUTODETECT spr round 1 (radius: 5) [05:23:00 -1335000.025016] AUTODETECT spr round 2 (radius: 10) [05:27:42 -933556.553420] AUTODETECT spr round 3 (radius: 15) [05:31:48 -815562.629195] AUTODETECT spr round 4 (radius: 20) [05:37:12 -771273.126634] AUTODETECT spr round 5 (radius: 25) [05:43:09 -765040.695269] SPR radius for FAST iterations: 25 (autodetect) [05:43:09 -765040.695269] Model parameter optimization (eps = 3.000000) [05:43:33 -764856.553765] FAST spr round 1 (radius: 25) [05:47:54 -679784.729321] FAST spr round 2 (radius: 25) [05:51:06 -677860.743869] FAST spr round 3 (radius: 25) [05:53:57 -677726.144711] FAST spr round 4 (radius: 25) [05:56:20 -677699.743349] FAST spr round 5 (radius: 25) [05:58:32 -677695.046098] FAST spr round 6 (radius: 25) [06:00:43 -677693.114948] FAST spr round 7 (radius: 25) [06:02:52 -677690.619616] FAST spr round 8 (radius: 25) [06:05:01 -677687.663784] FAST spr round 9 (radius: 25) [06:07:09 -677687.126678] FAST spr round 10 (radius: 25) [06:09:17 -677687.126676] Model parameter optimization (eps = 1.000000) [06:09:32 -677684.049977] SLOW spr round 1 (radius: 5) [06:13:05 -677581.481783] SLOW spr round 2 (radius: 5) [06:16:17 -677561.287901] SLOW spr round 3 (radius: 5) [06:19:18 -677561.020543] SLOW spr round 4 (radius: 5) [06:22:17 -677561.020527] SLOW spr round 5 (radius: 10) [06:25:28 -677549.942759] SLOW spr round 6 (radius: 5) [06:29:30 -677539.182198] SLOW spr round 7 (radius: 5) [06:32:57 -677538.370290] SLOW spr round 8 (radius: 5) [06:36:07 -677538.370248] SLOW spr round 9 (radius: 10) [06:39:16 -677538.370248] SLOW spr round 10 (radius: 15) [06:44:47 -677538.370248] SLOW spr round 11 (radius: 20) [06:52:30 -677538.370248] SLOW spr round 12 (radius: 25) [07:02:15 -677538.370248] Model parameter optimization (eps = 0.100000) [07:02:21] ML tree search #9, logLikelihood: -677538.307391 [07:02:21 -2181841.753826] Initial branch length optimization [07:02:30 -1878766.030174] Model parameter optimization (eps = 10.000000) [07:03:19 -1873498.309016] AUTODETECT spr round 1 (radius: 5) [07:06:40 -1368459.313940] AUTODETECT spr round 2 (radius: 10) [07:11:07 -989726.958889] AUTODETECT spr round 3 (radius: 15) [07:15:19 -811477.432526] AUTODETECT spr round 4 (radius: 20) [07:20:05 -776025.717887] AUTODETECT spr round 5 (radius: 25) [07:25:38 -773806.315103] SPR radius for FAST iterations: 25 (autodetect) [07:25:38 -773806.315103] Model parameter optimization (eps = 3.000000) [07:26:05 -773595.501716] FAST spr round 1 (radius: 25) [07:31:02 -681845.349333] FAST spr round 2 (radius: 25) [07:34:16 -677875.880324] FAST spr round 3 (radius: 25) [07:37:03 -677719.824416] FAST spr round 4 (radius: 25) [07:39:20 -677711.659307] FAST spr round 5 (radius: 25) [07:41:34 -677710.690916] FAST spr round 6 (radius: 25) [07:43:45 -677710.038873] FAST spr round 7 (radius: 25) [07:45:54 -677709.420334] FAST spr round 8 (radius: 25) [07:48:02 -677709.349314] Model parameter optimization (eps = 1.000000) [07:48:08 -677709.147225] SLOW spr round 1 (radius: 5) [07:51:39 -677582.740887] SLOW spr round 2 (radius: 5) [07:54:51 -677574.968803] SLOW spr round 3 (radius: 5) [07:57:57 -677561.951151] SLOW spr round 4 (radius: 5) [08:00:57 -677561.581642] SLOW spr round 5 (radius: 5) [08:03:54 -677561.581610] SLOW spr round 6 (radius: 10) [08:07:02 -677561.581610] SLOW spr round 7 (radius: 15) [08:12:39 -677561.581610] SLOW spr round 8 (radius: 20) [08:20:27 -677561.581610] SLOW spr round 9 (radius: 25) [08:30:13 -677561.581610] Model parameter optimization (eps = 0.100000) [08:30:18] ML tree search #10, logLikelihood: -677561.573948 [08:30:18 -2173895.630625] Initial branch length optimization [08:30:25 -1875159.456047] Model parameter optimization (eps = 10.000000) [08:31:18 -1870076.914173] AUTODETECT spr round 1 (radius: 5) [08:34:42 -1348182.089481] AUTODETECT spr round 2 (radius: 10) [08:39:00 -970881.273477] AUTODETECT spr round 3 (radius: 15) [08:43:19 -803104.628492] AUTODETECT spr round 4 (radius: 20) [08:48:35 -776300.328772] AUTODETECT spr round 5 (radius: 25) [08:54:53 -767684.210834] SPR radius for FAST iterations: 25 (autodetect) [08:54:53 -767684.210834] Model parameter optimization (eps = 3.000000) [08:55:11 -767415.846705] FAST spr round 1 (radius: 25) [08:59:54 -680728.211946] FAST spr round 2 (radius: 25) [09:03:08 -677968.396290] FAST spr round 3 (radius: 25) [09:06:00 -677783.932952] FAST spr round 4 (radius: 25) [09:08:31 -677684.897771] FAST spr round 5 (radius: 25) [09:10:42 -677681.810849] FAST spr round 6 (radius: 25) [09:12:52 -677671.255271] FAST spr round 7 (radius: 25) [09:15:01 -677670.306205] FAST spr round 8 (radius: 25) [09:17:08 -677670.306204] Model parameter optimization (eps = 1.000000) [09:17:19 -677669.681382] SLOW spr round 1 (radius: 5) [09:20:52 -677571.128987] SLOW spr round 2 (radius: 5) [09:23:58 -677568.923720] SLOW spr round 3 (radius: 5) [09:26:58 -677568.923689] SLOW spr round 4 (radius: 10) [09:30:07 -677568.923689] SLOW spr round 5 (radius: 15) [09:35:43 -677568.923689] SLOW spr round 6 (radius: 20) [09:43:31 -677568.923689] SLOW spr round 7 (radius: 25) [09:53:18 -677568.923689] Model parameter optimization (eps = 0.100000) [09:53:31] ML tree search #11, logLikelihood: -677568.735242 [09:53:31 -2178255.674957] Initial branch length optimization [09:53:40 -1878272.115929] Model parameter optimization (eps = 10.000000) [09:54:43 -1872652.821404] AUTODETECT spr round 1 (radius: 5) [09:58:06 -1337267.546716] AUTODETECT spr round 2 (radius: 10) [10:02:30 -975546.018665] AUTODETECT spr round 3 (radius: 15) [10:06:35 -862270.542340] AUTODETECT spr round 4 (radius: 20) [10:11:01 -788853.218122] AUTODETECT spr round 5 (radius: 25) [10:16:33 -782470.283451] SPR radius for FAST iterations: 25 (autodetect) [10:16:33 -782470.283451] Model parameter optimization (eps = 3.000000) [10:17:00 -782254.853195] FAST spr round 1 (radius: 25) [10:21:55 -681016.357431] FAST spr round 2 (radius: 25) [10:25:05 -677883.681539] FAST spr round 3 (radius: 25) [10:27:46 -677741.121366] FAST spr round 4 (radius: 25) [10:30:03 -677737.892352] FAST spr round 5 (radius: 25) [10:32:15 -677736.364460] FAST spr round 6 (radius: 25) [10:34:27 -677715.619129] FAST spr round 7 (radius: 25) [10:36:41 -677701.206871] FAST spr round 8 (radius: 25) [10:38:50 -677701.206817] Model parameter optimization (eps = 1.000000) [10:39:09 -677698.970738] SLOW spr round 1 (radius: 5) [10:42:35 -677555.434115] SLOW spr round 2 (radius: 5) [10:45:46 -677542.021812] SLOW spr round 3 (radius: 5) [10:48:47 -677542.021807] SLOW spr round 4 (radius: 10) [10:51:54 -677542.021807] SLOW spr round 5 (radius: 15) [10:57:26 -677542.021807] SLOW spr round 6 (radius: 20) [11:04:59 -677542.021807] SLOW spr round 7 (radius: 25) [11:14:45 -677542.021807] Model parameter optimization (eps = 0.100000) [11:14:55] ML tree search #12, logLikelihood: -677541.980332 [11:14:55 -2189578.620933] Initial branch length optimization [11:15:03 -1887528.962050] Model parameter optimization (eps = 10.000000) [11:16:00 -1882196.788084] AUTODETECT spr round 1 (radius: 5) [11:19:21 -1378666.686247] AUTODETECT spr round 2 (radius: 10) [11:23:32 -1000948.921390] AUTODETECT spr round 3 (radius: 15) [11:28:00 -774676.817642] AUTODETECT spr round 4 (radius: 20) [11:32:57 -755068.446413] AUTODETECT spr round 5 (radius: 25) [11:38:25 -754591.323460] SPR radius for FAST iterations: 25 (autodetect) [11:38:25 -754591.323460] Model parameter optimization (eps = 3.000000) [11:38:34 -754571.789893] FAST spr round 1 (radius: 25) [11:42:47 -680556.197004] FAST spr round 2 (radius: 25) [11:45:59 -678100.904281] FAST spr round 3 (radius: 25) [11:48:44 -677941.226433] FAST spr round 4 (radius: 25) [11:51:11 -677900.957346] FAST spr round 5 (radius: 25) [11:53:23 -677895.046949] FAST spr round 6 (radius: 25) [11:55:34 -677887.098923] FAST spr round 7 (radius: 25) [11:57:51 -677869.510801] FAST spr round 8 (radius: 25) [11:59:59 -677868.695141] FAST spr round 9 (radius: 25) [12:02:09 -677864.756630] FAST spr round 10 (radius: 25) [12:04:17 -677864.756629] Model parameter optimization (eps = 1.000000) [12:04:36 -677702.678019] SLOW spr round 1 (radius: 5) [12:08:04 -677566.788308] SLOW spr round 2 (radius: 5) [12:11:19 -677550.590800] SLOW spr round 3 (radius: 5) [12:14:28 -677538.844670] SLOW spr round 4 (radius: 5) [12:17:28 -677538.510216] SLOW spr round 5 (radius: 5) [12:20:28 -677538.510192] SLOW spr round 6 (radius: 10) [12:23:35 -677538.510192] SLOW spr round 7 (radius: 15) [12:29:11 -677538.510192] SLOW spr round 8 (radius: 20) [12:36:55 -677538.510192] SLOW spr round 9 (radius: 25) [12:46:42 -677538.510192] Model parameter optimization (eps = 0.100000) [12:46:55] ML tree search #13, logLikelihood: -677537.526707 [12:46:55 -2182411.480305] Initial branch length optimization [12:47:03 -1875356.188753] Model parameter optimization (eps = 10.000000) [12:48:09 -1870112.420655] AUTODETECT spr round 1 (radius: 5) [12:51:32 -1335899.832038] AUTODETECT spr round 2 (radius: 10) [12:55:53 -964776.476567] AUTODETECT spr round 3 (radius: 15) [12:59:56 -842702.854866] AUTODETECT spr round 4 (radius: 20) [13:04:50 -779014.450102] AUTODETECT spr round 5 (radius: 25) [13:11:01 -768636.135395] SPR radius for FAST iterations: 25 (autodetect) [13:11:01 -768636.135395] Model parameter optimization (eps = 3.000000) [13:11:29 -768407.995692] FAST spr round 1 (radius: 25) [13:16:28 -680316.540111] FAST spr round 2 (radius: 25) [13:19:43 -677868.080573] FAST spr round 3 (radius: 25) [13:22:28 -677776.876912] FAST spr round 4 (radius: 25) [13:24:50 -677760.660812] FAST spr round 5 (radius: 25) [13:27:03 -677757.733270] FAST spr round 6 (radius: 25) [13:29:13 -677757.733270] Model parameter optimization (eps = 1.000000) [13:29:31 -677756.638908] SLOW spr round 1 (radius: 5) [13:33:07 -677594.580201] SLOW spr round 2 (radius: 5) [13:36:28 -677548.790594] SLOW spr round 3 (radius: 5) [13:39:32 -677542.509049] SLOW spr round 4 (radius: 5) [13:42:31 -677542.508980] SLOW spr round 5 (radius: 10) [13:45:38 -677542.508980] SLOW spr round 6 (radius: 15) [13:51:17 -677542.508980] SLOW spr round 7 (radius: 20) [13:59:06 -677542.508980] SLOW spr round 8 (radius: 25) [14:09:06 -677542.508980] Model parameter optimization (eps = 0.100000) [14:09:11] ML tree search #14, logLikelihood: -677542.501092 [14:09:11 -2180624.406547] Initial branch length optimization [14:09:19 -1877433.043876] Model parameter optimization (eps = 10.000000) [14:10:18 -1871959.849194] AUTODETECT spr round 1 (radius: 5) [14:13:41 -1350655.035271] AUTODETECT spr round 2 (radius: 10) [14:18:13 -1040198.998315] AUTODETECT spr round 3 (radius: 15) [14:22:40 -883616.475409] AUTODETECT spr round 4 (radius: 20) [14:27:19 -797554.359893] AUTODETECT spr round 5 (radius: 25) [14:33:01 -784102.098757] SPR radius for FAST iterations: 25 (autodetect) [14:33:01 -784102.098757] Model parameter optimization (eps = 3.000000) [14:33:11 -784083.970785] FAST spr round 1 (radius: 25) [14:37:55 -681354.259304] FAST spr round 2 (radius: 25) [14:41:09 -678002.849657] FAST spr round 3 (radius: 25) [14:43:53 -677884.155305] FAST spr round 4 (radius: 25) [14:46:17 -677868.865090] FAST spr round 5 (radius: 25) [14:48:29 -677866.074799] FAST spr round 6 (radius: 25) [14:50:39 -677864.039620] FAST spr round 7 (radius: 25) [14:52:48 -677860.097808] FAST spr round 8 (radius: 25) [14:54:58 -677850.679011] FAST spr round 9 (radius: 25) [14:57:06 -677845.196393] FAST spr round 10 (radius: 25) [14:59:18 -677824.927360] FAST spr round 11 (radius: 25) [15:01:30 -677812.942623] FAST spr round 12 (radius: 25) [15:03:38 -677812.215858] FAST spr round 13 (radius: 25) [15:05:45 -677812.215858] Model parameter optimization (eps = 1.000000) [15:05:51 -677811.928928] SLOW spr round 1 (radius: 5) [15:09:20 -677721.288270] SLOW spr round 2 (radius: 5) [15:12:28 -677717.008686] SLOW spr round 3 (radius: 5) [15:15:31 -677713.816233] SLOW spr round 4 (radius: 5) [15:18:31 -677713.816217] SLOW spr round 5 (radius: 10) [15:21:41 -677713.816217] SLOW spr round 6 (radius: 15) [15:27:25 -677713.816217] SLOW spr round 7 (radius: 20) [15:35:22 -677713.816217] SLOW spr round 8 (radius: 25) [15:45:23 -677713.816217] Model parameter optimization (eps = 0.100000) [15:45:28] ML tree search #15, logLikelihood: -677713.810176 [15:45:28 -2172100.676018] Initial branch length optimization [15:45:35 -1874169.873158] Model parameter optimization (eps = 10.000000) [15:46:30 -1868809.104656] AUTODETECT spr round 1 (radius: 5) [15:49:52 -1377474.572818] AUTODETECT spr round 2 (radius: 10) [15:54:09 -963118.556545] AUTODETECT spr round 3 (radius: 15) [15:58:09 -795325.294784] AUTODETECT spr round 4 (radius: 20) [16:02:58 -771410.224499] AUTODETECT spr round 5 (radius: 25) [16:08:09 -771261.291037] SPR radius for FAST iterations: 25 (autodetect) [16:08:09 -771261.291037] Model parameter optimization (eps = 3.000000) [16:08:31 -771042.001391] FAST spr round 1 (radius: 25) [16:13:06 -680333.014385] FAST spr round 2 (radius: 25) [16:16:17 -677909.746110] FAST spr round 3 (radius: 25) [16:19:03 -677795.045002] FAST spr round 4 (radius: 25) [16:21:23 -677748.643778] FAST spr round 5 (radius: 25) [16:23:36 -677740.575775] FAST spr round 6 (radius: 25) [16:25:45 -677730.431379] FAST spr round 7 (radius: 25) [16:27:53 -677729.301578] FAST spr round 8 (radius: 25) [16:30:01 -677727.559869] FAST spr round 9 (radius: 25) [16:32:08 -677726.613720] FAST spr round 10 (radius: 25) [16:34:15 -677726.613715] Model parameter optimization (eps = 1.000000) [16:34:32 -677723.368157] SLOW spr round 1 (radius: 5) [16:37:59 -677575.637908] SLOW spr round 2 (radius: 5) [16:41:05 -677572.992592] SLOW spr round 3 (radius: 5) [16:44:04 -677572.992583] SLOW spr round 4 (radius: 10) [16:47:11 -677572.992583] SLOW spr round 5 (radius: 15) [16:52:46 -677572.992583] SLOW spr round 6 (radius: 20) [17:00:27 -677572.992583] SLOW spr round 7 (radius: 25) [17:10:04 -677572.992583] Model parameter optimization (eps = 0.100000) [17:10:16] ML tree search #16, logLikelihood: -677572.457525 [17:10:16 -2197144.435134] Initial branch length optimization [17:10:25 -1890450.268451] Model parameter optimization (eps = 10.000000) [17:11:25 -1884937.333553] AUTODETECT spr round 1 (radius: 5) [17:14:47 -1336919.013599] AUTODETECT spr round 2 (radius: 10) [17:19:23 -970035.751391] AUTODETECT spr round 3 (radius: 15) [17:23:33 -831283.289691] AUTODETECT spr round 4 (radius: 20) [17:27:51 -799237.803290] AUTODETECT spr round 5 (radius: 25) [17:33:49 -785004.389458] SPR radius for FAST iterations: 25 (autodetect) [17:33:49 -785004.389458] Model parameter optimization (eps = 3.000000) [17:34:11 -784816.118067] FAST spr round 1 (radius: 25) [17:39:11 -685398.980184] FAST spr round 2 (radius: 25) [17:42:20 -678228.767516] FAST spr round 3 (radius: 25) [17:45:07 -677782.138589] FAST spr round 4 (radius: 25) [17:47:32 -677725.232756] FAST spr round 5 (radius: 25) [17:49:46 -677714.789571] FAST spr round 6 (radius: 25) [17:51:56 -677714.230976] FAST spr round 7 (radius: 25) [17:54:05 -677711.835701] FAST spr round 8 (radius: 25) [17:56:13 -677701.521185] FAST spr round 9 (radius: 25) [17:58:20 -677699.296215] FAST spr round 10 (radius: 25) [18:00:27 -677697.886751] FAST spr round 11 (radius: 25) [18:02:34 -677697.825746] Model parameter optimization (eps = 1.000000) [18:02:52 -677694.754037] SLOW spr round 1 (radius: 5) [18:06:18 -677581.633782] SLOW spr round 2 (radius: 5) [18:09:28 -677561.877915] SLOW spr round 3 (radius: 5) [18:12:26 -677561.877901] SLOW spr round 4 (radius: 10) [18:15:32 -677561.877901] SLOW spr round 5 (radius: 15) [18:21:09 -677561.877901] SLOW spr round 6 (radius: 20) [18:29:04 -677561.877901] SLOW spr round 7 (radius: 25) [18:39:15 -677561.877901] Model parameter optimization (eps = 0.100000) [18:39:30] ML tree search #17, logLikelihood: -677561.335289 [18:39:30 -2179008.916968] Initial branch length optimization [18:39:37 -1883365.759203] Model parameter optimization (eps = 10.000000) [18:40:38 -1878096.751835] AUTODETECT spr round 1 (radius: 5) [18:43:58 -1352683.328187] AUTODETECT spr round 2 (radius: 10) [18:48:38 -966853.752975] AUTODETECT spr round 3 (radius: 15) [18:52:35 -827824.894885] AUTODETECT spr round 4 (radius: 20) [18:57:05 -779172.809620] AUTODETECT spr round 5 (radius: 25) [19:01:46 -774414.094408] SPR radius for FAST iterations: 25 (autodetect) [19:01:46 -774414.094408] Model parameter optimization (eps = 3.000000) [19:01:55 -774395.613403] FAST spr round 1 (radius: 25) [19:06:18 -681664.557684] FAST spr round 2 (radius: 25) [19:09:29 -678192.047244] FAST spr round 3 (radius: 25) [19:12:16 -677945.573265] FAST spr round 4 (radius: 25) [19:14:38 -677905.378791] FAST spr round 5 (radius: 25) [19:16:54 -677890.324721] FAST spr round 6 (radius: 25) [19:19:02 -677889.068820] FAST spr round 7 (radius: 25) [19:21:09 -677887.324844] FAST spr round 8 (radius: 25) [19:23:16 -677886.358488] FAST spr round 9 (radius: 25) [19:25:22 -677884.692159] FAST spr round 10 (radius: 25) [19:27:28 -677883.939684] FAST spr round 11 (radius: 25) [19:29:34 -677883.939680] Model parameter optimization (eps = 1.000000) [19:29:40 -677883.312186] SLOW spr round 1 (radius: 5) [19:33:10 -677764.672685] SLOW spr round 2 (radius: 5) [19:36:16 -677751.245256] SLOW spr round 3 (radius: 5) [19:39:17 -677748.042138] SLOW spr round 4 (radius: 5) [19:42:16 -677745.855666] SLOW spr round 5 (radius: 5) [19:45:14 -677745.855646] SLOW spr round 6 (radius: 10) [19:48:23 -677745.855646] SLOW spr round 7 (radius: 15) [19:54:03 -677745.855646] SLOW spr round 8 (radius: 20) [20:01:54 -677745.855646] SLOW spr round 9 (radius: 25) [20:12:09 -677745.855646] Model parameter optimization (eps = 0.100000) [20:12:11] ML tree search #18, logLikelihood: -677745.855268 [20:12:12 -2194008.504334] Initial branch length optimization [20:12:23 -1890838.991853] Model parameter optimization (eps = 10.000000) [20:13:30 -1885586.881653] AUTODETECT spr round 1 (radius: 5) [20:16:57 -1333830.076937] AUTODETECT spr round 2 (radius: 10) [20:21:23 -944778.228386] AUTODETECT spr round 3 (radius: 15) [20:25:12 -820634.275322] AUTODETECT spr round 4 (radius: 20) [20:29:24 -771195.829789] AUTODETECT spr round 5 (radius: 25) [20:34:40 -765041.009330] SPR radius for FAST iterations: 25 (autodetect) [20:34:40 -765041.009330] Model parameter optimization (eps = 3.000000) [20:35:02 -764786.432795] FAST spr round 1 (radius: 25) [20:39:35 -680343.130829] FAST spr round 2 (radius: 25) [20:42:45 -677966.051166] FAST spr round 3 (radius: 25) [20:45:30 -677711.607114] FAST spr round 4 (radius: 25) [20:47:47 -677705.129793] FAST spr round 5 (radius: 25) [20:49:57 -677703.898799] FAST spr round 6 (radius: 25) [20:52:06 -677703.898774] Model parameter optimization (eps = 1.000000) [20:52:20 -677700.802033] SLOW spr round 1 (radius: 5) [20:55:54 -677567.984098] SLOW spr round 2 (radius: 5) [20:59:02 -677549.252857] SLOW spr round 3 (radius: 5) [21:02:01 -677549.252855] SLOW spr round 4 (radius: 10) [21:05:09 -677549.252855] SLOW spr round 5 (radius: 15) [21:10:44 -677549.252855] SLOW spr round 6 (radius: 20) [21:18:30 -677549.252855] SLOW spr round 7 (radius: 25) [21:28:34 -677549.252855] Model parameter optimization (eps = 0.100000) [21:28:45] ML tree search #19, logLikelihood: -677549.048579 [21:28:45 -2182683.420941] Initial branch length optimization [21:28:52 -1879555.959067] Model parameter optimization (eps = 10.000000) [21:30:19 -1874107.790293] AUTODETECT spr round 1 (radius: 5) [21:33:41 -1361636.084674] AUTODETECT spr round 2 (radius: 10) [21:38:09 -995119.462955] AUTODETECT spr round 3 (radius: 15) [21:42:17 -814243.077590] AUTODETECT spr round 4 (radius: 20) [21:46:39 -783516.878163] AUTODETECT spr round 5 (radius: 25) [21:52:22 -778243.080588] SPR radius for FAST iterations: 25 (autodetect) [21:52:22 -778243.080588] Model parameter optimization (eps = 3.000000) [21:52:48 -778014.478097] FAST spr round 1 (radius: 25) [21:57:30 -681827.541329] FAST spr round 2 (radius: 25) [22:00:38 -677990.080339] FAST spr round 3 (radius: 25) [22:03:20 -677773.256405] FAST spr round 4 (radius: 25) [22:05:41 -677763.943993] FAST spr round 5 (radius: 25) [22:07:55 -677756.479895] FAST spr round 6 (radius: 25) [22:10:04 -677750.956685] FAST spr round 7 (radius: 25) [22:12:13 -677747.736530] FAST spr round 8 (radius: 25) [22:14:22 -677744.927176] FAST spr round 9 (radius: 25) [22:16:29 -677743.117457] FAST spr round 10 (radius: 25) [22:18:37 -677742.562811] FAST spr round 11 (radius: 25) [22:20:51 -677724.275724] FAST spr round 12 (radius: 25) [22:22:58 -677724.275722] Model parameter optimization (eps = 1.000000) [22:23:03 -677724.057590] SLOW spr round 1 (radius: 5) [22:26:26 -677598.404881] SLOW spr round 2 (radius: 5) [22:29:33 -677583.944607] SLOW spr round 3 (radius: 5) [22:32:35 -677581.215520] SLOW spr round 4 (radius: 5) [22:35:34 -677581.215515] SLOW spr round 5 (radius: 10) [22:38:43 -677581.215515] SLOW spr round 6 (radius: 15) [22:44:18 -677581.215515] SLOW spr round 7 (radius: 20) [22:51:59 -677581.215515] SLOW spr round 8 (radius: 25) [23:01:46 -677581.215515] Model parameter optimization (eps = 0.100000) [23:01:50] ML tree search #20, logLikelihood: -677581.211452 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.195814,0.288748) (0.264992,0.420669) (0.262605,0.934083) (0.276590,2.121156) Base frequencies (model): M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 Substitution rates (model): M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 Final LogLikelihood: -677532.321498 AIC score: 1359074.642997 / AICc score: 9403134.642997 / BIC score: 1369877.000021 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=1616). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/3_mltree/P47989.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/3_mltree/P47989.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/3_mltree/P47989.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/P47989/3_mltree/P47989.raxml.log Analysis started: 25-Jun-2021 03:33:21 / finished: 26-Jun-2021 02:35:12 Elapsed time: 82911.174 seconds (this run) / 106614.243 seconds (total with restarts)