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 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 02-Jul-2021 17:58:04 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A0C4DH29/2_msa/A0A0C4DH29_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A0C4DH29/3_mltree/A0A0C4DH29 --seed 2 --threads 2 --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 (2 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A0C4DH29/2_msa/A0A0C4DH29_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 97 sites WARNING: Sequences sp_P01756_HVM12_MOUSE_10090 and sp_P01757_HVM13_MOUSE_10090 are exactly identical! WARNING: Sequences tr_G1P3R4_G1P3R4_MYOLU_59463 and tr_G1PZN6_G1PZN6_MYOLU_59463 are exactly identical! WARNING: Sequences tr_G1QBP2_G1QBP2_MYOLU_59463 and tr_G1QG99_G1QG99_MYOLU_59463 are exactly identical! WARNING: Sequences tr_A0A2I2ZCN6_A0A2I2ZCN6_GORGO_9595 and sp_P01743_HV146_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RCM2_A0A2I3RCM2_PANTR_9598 and tr_A0A2R8ZPX9_A0A2R8ZPX9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3RT04_A0A2I3RT04_PANTR_9598 and tr_A0A2R9BGQ2_A0A2R9BGQ2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3S4I1_A0A2I3S4I1_PANTR_9598 and sp_A0A0C4DH38_HV551_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3S4I1_A0A2I3S4I1_PANTR_9598 and tr_A0A2R8ZFN9_A0A2R8ZFN9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SB50_A0A2I3SB50_PANTR_9598 and tr_A0A2R8ZJ75_A0A2R8ZJ75_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SLP9_A0A2I3SLP9_PANTR_9598 and tr_A0A2R8ZD36_A0A2R8ZD36_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3SUC8_A0A2I3SUC8_PANTR_9598 and tr_A0A2R8ZB84_A0A2R8ZB84_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3T0N2_A0A2I3T0N2_PANTR_9598 and tr_A0A2R9APQ7_A0A2R9APQ7_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3TM71_A0A2I3TM71_PANTR_9598 and tr_A0A2R8ZQ55_A0A2R8ZQ55_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2RIL7_H2RIL7_PANTR_9598 and tr_A0A2R8ZD60_A0A2R8ZD60_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6UMB3_F6UMB3_ORNAN_9258 and tr_F6UMB9_F6UMB9_ORNAN_9258 are exactly identical! WARNING: Sequences tr_F6UMB3_F6UMB3_ORNAN_9258 and tr_F6WX17_F6WX17_ORNAN_9258 are exactly identical! WARNING: Sequences tr_F7B7J7_F7B7J7_ORNAN_9258 and tr_F7E071_F7E071_ORNAN_9258 are exactly identical! WARNING: Sequences tr_A0A0G2JT95_A0A0G2JT95_RAT_10116 and tr_M0R8Q9_M0R8Q9_RAT_10116 are exactly identical! WARNING: Sequences sp_P01768_HV330_HUMAN_9606 and sp_P0DP03_HV335_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A1D5Q6L6_A0A1D5Q6L6_MACMU_9544 and tr_G7P8Z6_G7P8Z6_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5RE67_A0A1D5RE67_MACMU_9544 and tr_A0A0D9R9D0_A0A0D9R9D0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5RE67_A0A1D5RE67_MACMU_9544 and tr_A0A2K5NSS8_A0A2K5NSS8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5RHL0_A0A1D5RHL0_MACMU_9544 and tr_A0A2I3LGI1_A0A2I3LGI1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5RHL0_A0A1D5RHL0_MACMU_9544 and tr_A0A2K6D0G6_A0A2K6D0G6_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5RHL0_A0A1D5RHL0_MACMU_9544 and tr_A0A2K5XSZ2_A0A2K5XSZ2_MANLE_9568 are exactly identical! WARNING: Sequences tr_H9H2S9_H9H2S9_MACMU_9544 and tr_G7P8Z3_G7P8Z3_MACFA_9541 are exactly identical! WARNING: Sequences tr_H9H495_H9H495_MACMU_9544 and tr_G8F4H4_G8F4H4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1B8Y637_A0A1B8Y637_XENTR_8364 and tr_F7DCM9_F7DCM9_XENTR_8364 are exactly identical! WARNING: Sequences tr_A0A1B8Y645_A0A1B8Y645_XENTR_8364 and tr_F7AA19_F7AA19_XENTR_8364 are exactly identical! WARNING: Sequences tr_A0A1B8Y667_A0A1B8Y667_XENTR_8364 and tr_F7CX19_F7CX19_XENTR_8364 are exactly identical! WARNING: Sequences tr_A0A286ZIM4_A0A286ZIM4_PIG_9823 and tr_A0A287B2M5_A0A287B2M5_PIG_9823 are exactly identical! WARNING: Sequences tr_A0A287A195_A0A287A195_PIG_9823 and tr_A0A287A6T3_A0A287A6T3_PIG_9823 are exactly identical! WARNING: Sequences tr_G8F6A1_G8F6A1_MACFA_9541 and tr_A0A2K6CXC3_A0A2K6CXC3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3M2H8_A0A2I3M2H8_PAPAN_9555 and tr_A0A2K5XS06_A0A2K5XS06_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A091D7S3_A0A091D7S3_FUKDA_885580 and tr_A0A091DV01_A0A091DV01_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A091DVJ1_A0A091DVJ1_FUKDA_885580 and tr_A0A091EFX3_A0A091EFX3_FUKDA_885580 are exactly identical! WARNING: Sequences tr_A0A2K5NS22_A0A2K5NS22_CERAT_9531 and tr_A0A2K5XFH2_A0A2K5XFH2_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 37 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A0C4DH29/3_mltree/A0A0C4DH29.raxml.reduced.phy Alignment comprises 1 partitions and 97 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 97 / 97 Gaps: 0.62 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A0C4DH29/3_mltree/A0A0C4DH29.raxml.rba Parallelization scheme autoconfig: 2 worker(s) x 1 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 / 97 / 7760 [00:00:00] Data distribution: max. searches per worker: 10 Starting ML tree search with 20 distinct starting trees [00:00:00 -125126.340147] Initial branch length optimization [00:00:02 -108057.636907] Model parameter optimization (eps = 10.000000) [00:00:26 -107371.654317] AUTODETECT spr round 1 (radius: 5) [00:02:06 -81775.983500] AUTODETECT spr round 2 (radius: 10) [00:03:55 -65323.465608] AUTODETECT spr round 3 (radius: 15) [00:05:55 -56070.418896] AUTODETECT spr round 4 (radius: 20) [00:08:25 -50793.437437] AUTODETECT spr round 5 (radius: 25) [00:11:07 -49401.174665] SPR radius for FAST iterations: 25 (autodetect) [00:11:07 -49401.174665] Model parameter optimization (eps = 3.000000) [00:11:24 -49307.343289] FAST spr round 1 (radius: 25) [00:13:49 -42716.874093] FAST spr round 2 (radius: 25) [00:15:41 -42258.434976] FAST spr round 3 (radius: 25) [00:17:19 -42231.767834] FAST spr round 4 (radius: 25) [00:18:41 -42230.653350] FAST spr round 5 (radius: 25) [00:20:04 -42230.653283] Model parameter optimization (eps = 1.000000) [00:20:24 -42228.908349] SLOW spr round 1 (radius: 5) [00:22:12 -42217.885861] SLOW spr round 2 (radius: 5) [00:23:56 -42217.282343] SLOW spr round 3 (radius: 5) [00:25:37 -42217.282261] SLOW spr round 4 (radius: 10) [00:27:19 -42213.853259] SLOW spr round 5 (radius: 5) [00:29:20 -42213.853202] SLOW spr round 6 (radius: 10) [00:31:15 -42213.157693] SLOW spr round 7 (radius: 5) [00:33:17 -42207.547026] SLOW spr round 8 (radius: 5) [00:35:08 -42207.547025] SLOW spr round 9 (radius: 10) [00:36:54 -42207.023246] SLOW spr round 10 (radius: 5) [00:38:53 -42207.022588] SLOW spr round 11 (radius: 10) [00:40:41 -42206.536638] SLOW spr round 12 (radius: 5) [00:42:38 -42200.954016] SLOW spr round 13 (radius: 5) [00:44:21 -42198.942645] SLOW spr round 14 (radius: 5) [00:45:57 -42198.782385] SLOW spr round 15 (radius: 5) [00:47:34 -42198.782293] SLOW spr round 16 (radius: 10) [00:49:20 -42198.782293] SLOW spr round 17 (radius: 15) [00:52:35 -42196.129923] SLOW spr round 18 (radius: 5) [00:54:41 -42193.535331] SLOW spr round 19 (radius: 5) [00:56:28 -42193.535284] SLOW spr round 20 (radius: 10) [00:58:11 -42193.535284] SLOW spr round 21 (radius: 15) [01:01:11 -42192.158423] SLOW spr round 22 (radius: 5) [01:03:09 -42192.158409] SLOW spr round 23 (radius: 10) [01:05:01 -42192.158409] SLOW spr round 24 (radius: 15) [01:07:40 -42192.158409] SLOW spr round 25 (radius: 20) [01:11:26 -42189.112132] SLOW spr round 26 (radius: 5) [01:13:29 -42184.813419] SLOW spr round 27 (radius: 5) [01:15:15 -42184.812555] SLOW spr round 28 (radius: 10) [01:16:55 -42184.812552] SLOW spr round 29 (radius: 15) [01:19:40 -42184.812552] SLOW spr round 30 (radius: 20) [01:23:15 -42184.812552] SLOW spr round 31 (radius: 25) [01:27:32 -42184.812552] Model parameter optimization (eps = 0.100000) [01:27:36] [worker #0] ML tree search #1, logLikelihood: -42184.744529 [01:27:37 -125430.977886] Initial branch length optimization [01:27:38 -107951.726971] Model parameter optimization (eps = 10.000000) [01:28:00 -107328.479013] AUTODETECT spr round 1 (radius: 5) [01:29:37 -82681.538856] AUTODETECT spr round 2 (radius: 10) [01:31:25 -63602.227381] AUTODETECT spr round 3 (radius: 15) [01:33:28 -55920.494474] AUTODETECT spr round 4 (radius: 20) [01:36:03 -50502.714851] AUTODETECT spr round 5 (radius: 25) [01:38:32 -48807.658118] SPR radius for FAST iterations: 25 (autodetect) [01:38:32 -48807.658118] Model parameter optimization (eps = 3.000000) [01:38:48 -48723.463118] FAST spr round 1 (radius: 25) [01:41:04 -42701.242235] FAST spr round 2 (radius: 25) [01:42:53 -42364.120745] FAST spr round 3 (radius: 25) [01:44:26 -42266.039254] FAST spr round 4 (radius: 25) [01:45:53 -42256.764898] FAST spr round 5 (radius: 25) [01:47:15 -42238.995294] FAST spr round 6 (radius: 25) [01:47:47] [worker #1] ML tree search #2, logLikelihood: -42134.544313 [01:48:32 -42237.772322] FAST spr round 7 (radius: 25) [01:49:47 -42236.986391] FAST spr round 8 (radius: 25) [01:51:01 -42235.470483] FAST spr round 9 (radius: 25) [01:52:16 -42235.182784] FAST spr round 10 (radius: 25) [01:53:29 -42235.182783] Model parameter optimization (eps = 1.000000) [01:53:40 -42226.280336] SLOW spr round 1 (radius: 5) [01:55:23 -42205.753602] SLOW spr round 2 (radius: 5) [01:57:02 -42200.372299] SLOW spr round 3 (radius: 5) [01:58:38 -42200.333184] SLOW spr round 4 (radius: 10) [02:00:24 -42195.864745] SLOW spr round 5 (radius: 5) [02:02:32 -42191.210918] SLOW spr round 6 (radius: 5) [02:04:23 -42191.097755] SLOW spr round 7 (radius: 5) [02:06:06 -42191.097223] SLOW spr round 8 (radius: 10) [02:07:49 -42188.834773] SLOW spr round 9 (radius: 5) [02:09:56 -42188.833959] SLOW spr round 10 (radius: 10) [02:11:54 -42187.179771] SLOW spr round 11 (radius: 5) [02:13:52 -42187.013657] SLOW spr round 12 (radius: 5) [02:15:38 -42187.013657] SLOW spr round 13 (radius: 10) [02:17:25 -42186.043374] SLOW spr round 14 (radius: 5) [02:19:32 -42182.604901] SLOW spr round 15 (radius: 5) [02:21:32 -42181.200555] SLOW spr round 16 (radius: 5) [02:23:12 -42180.597659] SLOW spr round 17 (radius: 5) [02:24:49 -42180.597659] SLOW spr round 18 (radius: 10) [02:26:27 -42180.541911] SLOW spr round 19 (radius: 15) [02:29:39 -42178.133751] SLOW spr round 20 (radius: 5) [02:31:42 -42178.132880] SLOW spr round 21 (radius: 10) [02:33:41 -42178.093229] SLOW spr round 22 (radius: 15) [02:36:42 -42177.584322] SLOW spr round 23 (radius: 5) [02:38:50 -42175.232602] SLOW spr round 24 (radius: 5) [02:40:45 -42175.224703] SLOW spr round 25 (radius: 10) [02:42:33 -42175.224685] SLOW spr round 26 (radius: 15) [02:45:47 -42175.224673] SLOW spr round 27 (radius: 20) [02:50:11 -42174.011048] SLOW spr round 28 (radius: 5) [02:52:14 -42174.011041] SLOW spr round 29 (radius: 10) [02:54:14 -42174.011037] SLOW spr round 30 (radius: 15) [02:57:03 -42174.011035] SLOW spr round 31 (radius: 20) [03:01:25 -42174.011032] SLOW spr round 32 (radius: 25) [03:06:18 -42174.011031] Model parameter optimization (eps = 0.100000) [03:06:23] [worker #0] ML tree search #3, logLikelihood: -42173.987681 [03:06:23 -124603.814670] Initial branch length optimization [03:06:25 -107640.404907] Model parameter optimization (eps = 10.000000) [03:06:51 -107009.964011] AUTODETECT spr round 1 (radius: 5) [03:08:27 -82604.263313] AUTODETECT spr round 2 (radius: 10) [03:10:15 -68048.446635] AUTODETECT spr round 3 (radius: 15) [03:12:17 -60535.910541] AUTODETECT spr round 4 (radius: 20) [03:14:45 -55470.365542] AUTODETECT spr round 5 (radius: 25) [03:17:51 -49574.454390] SPR radius for FAST iterations: 25 (autodetect) [03:17:51 -49574.454390] Model parameter optimization (eps = 3.000000) [03:18:06 -49509.380184] FAST spr round 1 (radius: 25) [03:20:30 -42695.571785] FAST spr round 2 (radius: 25) [03:22:13 -42288.212710] FAST spr round 3 (radius: 25) [03:23:45 -42232.962409] FAST spr round 4 (radius: 25) [03:25:09 -42219.844173] FAST spr round 5 (radius: 25) [03:26:26 -42218.475040] FAST spr round 6 (radius: 25) [03:27:43 -42218.475040] Model parameter optimization (eps = 1.000000) [03:27:53 -42211.826528] SLOW spr round 1 (radius: 5) [03:29:40 -42202.227682] SLOW spr round 2 (radius: 5) [03:31:16 -42199.485219] SLOW spr round 3 (radius: 5) [03:32:50 -42199.485173] SLOW spr round 4 (radius: 10) [03:34:23 -42198.960299] SLOW spr round 5 (radius: 5) [03:36:12 -42197.506877] SLOW spr round 6 (radius: 5) [03:37:51 -42197.506877] SLOW spr round 7 (radius: 10) [03:39:26 -42196.652441] SLOW spr round 8 (radius: 5) [03:41:14 -42196.652435] SLOW spr round 9 (radius: 10) [03:42:57 -42196.179253] SLOW spr round 10 (radius: 5) [03:44:55 -42196.005235] SLOW spr round 11 (radius: 5) [03:45:40] [worker #1] ML tree search #4, logLikelihood: -42148.717452 [03:46:38 -42196.004503] SLOW spr round 12 (radius: 10) [03:48:15 -42195.827572] SLOW spr round 13 (radius: 5) [03:50:07 -42194.962059] SLOW spr round 14 (radius: 5) [03:51:48 -42194.962059] SLOW spr round 15 (radius: 10) [03:53:26 -42193.503689] SLOW spr round 16 (radius: 5) [03:55:16 -42191.601290] SLOW spr round 17 (radius: 5) [03:56:56 -42191.601218] SLOW spr round 18 (radius: 10) [03:58:30 -42191.601218] SLOW spr round 19 (radius: 15) [04:01:12 -42191.387297] SLOW spr round 20 (radius: 5) [04:03:06 -42191.387297] SLOW spr round 21 (radius: 10) [04:04:55 -42191.387297] SLOW spr round 22 (radius: 15) [04:07:24 -42191.387297] SLOW spr round 23 (radius: 20) [04:10:50 -42190.142044] SLOW spr round 24 (radius: 5) [04:12:45 -42188.262041] SLOW spr round 25 (radius: 5) [04:14:26 -42188.261892] SLOW spr round 26 (radius: 10) [04:16:03 -42188.261891] SLOW spr round 27 (radius: 15) [04:18:42 -42188.261891] SLOW spr round 28 (radius: 20) [04:22:10 -42188.261891] SLOW spr round 29 (radius: 25) [04:26:03 -42181.643658] SLOW spr round 30 (radius: 5) [04:28:04 -42181.643597] SLOW spr round 31 (radius: 10) [04:29:58 -42181.643597] SLOW spr round 32 (radius: 15) [04:32:26 -42181.643597] SLOW spr round 33 (radius: 20) [04:36:03 -42181.643597] SLOW spr round 34 (radius: 25) [04:40:03 -42181.643597] Model parameter optimization (eps = 0.100000) [04:40:07] [worker #0] ML tree search #5, logLikelihood: -42181.595649 [04:40:07 -125087.348878] Initial branch length optimization [04:40:09 -108198.350461] Model parameter optimization (eps = 10.000000) [04:40:39 -107538.785229] AUTODETECT spr round 1 (radius: 5) [04:42:15 -82327.549185] AUTODETECT spr round 2 (radius: 10) [04:43:59 -66128.648026] AUTODETECT spr round 3 (radius: 15) [04:46:06 -53376.913180] AUTODETECT spr round 4 (radius: 20) [04:48:40 -49047.410155] AUTODETECT spr round 5 (radius: 25) [04:51:35 -48699.404733] SPR radius for FAST iterations: 25 (autodetect) [04:51:35 -48699.404733] Model parameter optimization (eps = 3.000000) [04:51:54 -48626.906199] FAST spr round 1 (radius: 25) [04:54:18 -42575.566807] FAST spr round 2 (radius: 25) [04:56:03 -42291.077009] FAST spr round 3 (radius: 25) [04:57:34 -42251.331080] FAST spr round 4 (radius: 25) [04:58:59 -42244.143851] FAST spr round 5 (radius: 25) [05:00:18 -42244.143443] Model parameter optimization (eps = 1.000000) [05:00:28 -42243.404836] SLOW spr round 1 (radius: 5) [05:02:12 -42228.480257] SLOW spr round 2 (radius: 5) [05:03:55 -42226.574039] SLOW spr round 3 (radius: 5) [05:05:28 -42226.285627] SLOW spr round 4 (radius: 5) [05:07:00 -42226.285624] SLOW spr round 5 (radius: 10) [05:08:34 -42223.714561] SLOW spr round 6 (radius: 5) [05:10:24 -42219.677768] SLOW spr round 7 (radius: 5) [05:12:04 -42219.677344] SLOW spr round 8 (radius: 10) [05:13:40 -42219.031381] SLOW spr round 9 (radius: 5) [05:15:32 -42218.307131] SLOW spr round 10 (radius: 5) [05:15:52] [worker #1] ML tree search #6, logLikelihood: -42188.426332 [05:17:16 -42217.885756] SLOW spr round 11 (radius: 5) [05:18:49 -42217.885756] SLOW spr round 12 (radius: 10) [05:20:22 -42215.991238] SLOW spr round 13 (radius: 5) [05:22:11 -42215.869500] SLOW spr round 14 (radius: 5) [05:23:49 -42215.868995] SLOW spr round 15 (radius: 10) [05:25:24 -42214.322270] SLOW spr round 16 (radius: 5) [05:27:13 -42214.322253] SLOW spr round 17 (radius: 10) [05:28:57 -42214.187651] SLOW spr round 18 (radius: 5) [05:30:52 -42214.104444] SLOW spr round 19 (radius: 10) [05:32:35 -42214.068561] SLOW spr round 20 (radius: 15) [05:35:18 -42211.063825] SLOW spr round 21 (radius: 5) [05:37:15 -42209.759972] SLOW spr round 22 (radius: 5) [05:39:01 -42209.759852] SLOW spr round 23 (radius: 10) [05:40:38 -42209.112449] SLOW spr round 24 (radius: 5) [05:42:30 -42209.103137] SLOW spr round 25 (radius: 10) [05:44:13 -42209.102159] SLOW spr round 26 (radius: 15) [05:46:50 -42209.102056] SLOW spr round 27 (radius: 20) [05:50:51 -42208.868813] SLOW spr round 28 (radius: 5) [05:52:46 -42208.868777] SLOW spr round 29 (radius: 10) [05:54:36 -42206.797987] SLOW spr round 30 (radius: 5) [05:56:22 -42206.797939] SLOW spr round 31 (radius: 10) [05:58:04 -42206.797938] SLOW spr round 32 (radius: 15) [06:00:38 -42206.797938] SLOW spr round 33 (radius: 20) [06:04:34 -42206.797938] SLOW spr round 34 (radius: 25) [06:08:48 -42206.797938] Model parameter optimization (eps = 0.100000) [06:08:53] [worker #0] ML tree search #7, logLikelihood: -42206.776527 [06:08:53 -123810.817932] Initial branch length optimization [06:08:55 -107226.334484] Model parameter optimization (eps = 10.000000) [06:09:20 -106680.040854] AUTODETECT spr round 1 (radius: 5) [06:10:57 -83138.003879] AUTODETECT spr round 2 (radius: 10) [06:12:43 -66567.787430] AUTODETECT spr round 3 (radius: 15) [06:14:46 -56578.826181] AUTODETECT spr round 4 (radius: 20) [06:17:11 -53618.395536] AUTODETECT spr round 5 (radius: 25) [06:20:06 -50099.007606] SPR radius for FAST iterations: 25 (autodetect) [06:20:06 -50099.007606] Model parameter optimization (eps = 3.000000) [06:20:22 -49979.045403] FAST spr round 1 (radius: 25) [06:22:53 -42663.055372] FAST spr round 2 (radius: 25) [06:24:41 -42290.838476] FAST spr round 3 (radius: 25) [06:26:19 -42224.997178] FAST spr round 4 (radius: 25) [06:27:45 -42215.859236] FAST spr round 5 (radius: 25) [06:29:02 -42215.858807] Model parameter optimization (eps = 1.000000) [06:29:12 -42203.927088] SLOW spr round 1 (radius: 5) [06:30:55 -42191.379226] SLOW spr round 2 (radius: 5) [06:32:32 -42189.819658] SLOW spr round 3 (radius: 5) [06:34:06 -42189.819604] SLOW spr round 4 (radius: 10) [06:35:40 -42188.226090] SLOW spr round 5 (radius: 5) [06:37:35 -42187.190052] SLOW spr round 6 (radius: 5) [06:39:18 -42187.190044] SLOW spr round 7 (radius: 10) [06:41:01 -42187.061530] SLOW spr round 8 (radius: 5) [06:42:58 -42187.061503] SLOW spr round 9 (radius: 10) [06:44:46 -42186.912381] SLOW spr round 10 (radius: 5) [06:46:40 -42186.906753] SLOW spr round 11 (radius: 10) [06:48:26 -42186.903869] SLOW spr round 12 (radius: 15) [06:51:10 -42186.288071] SLOW spr round 13 (radius: 5) [06:51:29] [worker #1] ML tree search #8, logLikelihood: -42136.092295 [06:53:08 -42186.094934] SLOW spr round 14 (radius: 5) [06:54:52 -42186.094869] SLOW spr round 15 (radius: 10) [06:56:31 -42186.094869] SLOW spr round 16 (radius: 15) [06:59:20 -42185.412745] SLOW spr round 17 (radius: 5) [07:01:20 -42185.021106] SLOW spr round 18 (radius: 5) [07:03:07 -42185.021106] SLOW spr round 19 (radius: 10) [07:04:47 -42185.021106] SLOW spr round 20 (radius: 15) [07:07:32 -42184.439100] SLOW spr round 21 (radius: 5) [07:09:29 -42175.171557] SLOW spr round 22 (radius: 5) [07:11:12 -42175.171557] SLOW spr round 23 (radius: 10) [07:12:51 -42174.744980] SLOW spr round 24 (radius: 5) [07:14:44 -42174.744969] SLOW spr round 25 (radius: 10) [07:16:32 -42174.744969] SLOW spr round 26 (radius: 15) [07:19:14 -42174.098166] SLOW spr round 27 (radius: 5) [07:21:15 -42170.747117] SLOW spr round 28 (radius: 5) [07:23:01 -42170.746933] SLOW spr round 29 (radius: 10) [07:24:43 -42170.448471] SLOW spr round 30 (radius: 5) [07:26:41 -42167.795616] SLOW spr round 31 (radius: 5) [07:28:24 -42167.722539] SLOW spr round 32 (radius: 10) [07:30:01 -42167.239400] SLOW spr round 33 (radius: 5) [07:31:55 -42167.239398] SLOW spr round 34 (radius: 10) [07:33:41 -42167.239398] SLOW spr round 35 (radius: 15) [07:36:22 -42166.754214] SLOW spr round 36 (radius: 5) [07:38:23 -42166.752825] SLOW spr round 37 (radius: 10) [07:40:14 -42166.752823] SLOW spr round 38 (radius: 15) [07:42:49 -42166.213954] SLOW spr round 39 (radius: 5) [07:44:45 -42166.213954] SLOW spr round 40 (radius: 10) [07:46:33 -42166.213954] SLOW spr round 41 (radius: 15) [07:49:08 -42165.892165] SLOW spr round 42 (radius: 5) [07:51:06 -42165.892165] SLOW spr round 43 (radius: 10) [07:53:01 -42165.892165] SLOW spr round 44 (radius: 15) [07:55:38 -42165.892165] SLOW spr round 45 (radius: 20) [07:59:28 -42165.588448] SLOW spr round 46 (radius: 5) [08:01:37 -42150.105850] SLOW spr round 47 (radius: 5) [08:03:29 -42146.633070] SLOW spr round 48 (radius: 5) [08:05:07 -42146.633016] SLOW spr round 49 (radius: 10) [08:06:43 -42146.157820] SLOW spr round 50 (radius: 5) [08:08:38 -42146.156933] SLOW spr round 51 (radius: 10) [08:10:26 -42146.156879] SLOW spr round 52 (radius: 15) [08:13:15 -42146.156875] SLOW spr round 53 (radius: 20) [08:16:57 -42146.156874] SLOW spr round 54 (radius: 25) [08:20:50 -42142.321069] SLOW spr round 55 (radius: 5) [08:22:50 -42140.990089] SLOW spr round 56 (radius: 5) [08:24:36 -42140.989957] SLOW spr round 57 (radius: 10) [08:26:18 -42140.989950] SLOW spr round 58 (radius: 15) [08:29:16 -42140.989949] SLOW spr round 59 (radius: 20) [08:32:58 -42140.581078] SLOW spr round 60 (radius: 5) [08:35:04 -42140.509827] SLOW spr round 61 (radius: 10) [08:37:10 -42140.087439] SLOW spr round 62 (radius: 5) [08:39:11 -42139.380453] SLOW spr round 63 (radius: 5) [08:40:55 -42139.380419] SLOW spr round 64 (radius: 10) [08:42:32 -42139.380419] SLOW spr round 65 (radius: 15) [08:42:54] [worker #1] ML tree search #10, logLikelihood: -42108.824399 [08:45:16 -42139.380419] SLOW spr round 66 (radius: 20) [08:48:49 -42139.380419] SLOW spr round 67 (radius: 25) [08:52:43 -42139.380419] Model parameter optimization (eps = 0.100000) [08:52:46] [worker #0] ML tree search #9, logLikelihood: -42139.340722 [08:52:46 -125256.461558] Initial branch length optimization [08:52:48 -108458.624615] Model parameter optimization (eps = 10.000000) [08:53:12 -107677.370587] AUTODETECT spr round 1 (radius: 5) [08:54:46 -81558.993712] AUTODETECT spr round 2 (radius: 10) [08:56:28 -65650.246499] AUTODETECT spr round 3 (radius: 15) [08:58:22 -56210.101320] AUTODETECT spr round 4 (radius: 20) [09:00:33 -53513.632304] AUTODETECT spr round 5 (radius: 25) [09:03:00 -51661.600424] SPR radius for FAST iterations: 25 (autodetect) [09:03:00 -51661.600424] Model parameter optimization (eps = 3.000000) [09:03:14 -51581.969264] FAST spr round 1 (radius: 25) [09:05:45 -42871.838566] FAST spr round 2 (radius: 25) [09:07:34 -42264.468306] FAST spr round 3 (radius: 25) [09:09:08 -42218.846719] FAST spr round 4 (radius: 25) [09:10:33 -42211.540894] FAST spr round 5 (radius: 25) [09:11:53 -42211.540856] Model parameter optimization (eps = 1.000000) [09:12:02 -42209.871275] SLOW spr round 1 (radius: 5) [09:13:49 -42195.623423] SLOW spr round 2 (radius: 5) [09:15:33 -42188.481518] SLOW spr round 3 (radius: 5) [09:17:13 -42188.481328] SLOW spr round 4 (radius: 10) [09:18:53 -42185.627197] SLOW spr round 5 (radius: 5) [09:20:50 -42185.597731] SLOW spr round 6 (radius: 10) [09:22:39 -42184.402708] SLOW spr round 7 (radius: 5) [09:24:38 -42180.885598] SLOW spr round 8 (radius: 5) [09:26:23 -42180.885596] SLOW spr round 9 (radius: 10) [09:28:04 -42179.927760] SLOW spr round 10 (radius: 5) [09:30:01 -42177.784583] SLOW spr round 11 (radius: 5) [09:31:43 -42177.784402] SLOW spr round 12 (radius: 10) [09:33:18 -42177.130091] SLOW spr round 13 (radius: 5) [09:35:13 -42175.269883] SLOW spr round 14 (radius: 5) [09:36:55 -42175.269861] SLOW spr round 15 (radius: 10) [09:38:33 -42174.286334] SLOW spr round 16 (radius: 5) [09:40:29 -42172.194014] SLOW spr round 17 (radius: 5) [09:42:15 -42172.194006] SLOW spr round 18 (radius: 10) [09:43:54 -42172.194006] SLOW spr round 19 (radius: 15) [09:46:36 -42170.795552] SLOW spr round 20 (radius: 5) [09:48:36 -42170.724544] SLOW spr round 21 (radius: 10) [09:50:29 -42170.724543] SLOW spr round 22 (radius: 15) [09:52:56 -42170.724543] SLOW spr round 23 (radius: 20) [09:56:27 -42169.604680] SLOW spr round 24 (radius: 5) [09:58:30 -42169.604674] SLOW spr round 25 (radius: 10) [10:00:25 -42169.466736] SLOW spr round 26 (radius: 5) [10:02:22 -42169.466667] SLOW spr round 27 (radius: 10) [10:04:07 -42169.466667] SLOW spr round 28 (radius: 15) [10:06:37 -42169.466667] SLOW spr round 29 (radius: 20) [10:10:07 -42169.466667] SLOW spr round 30 (radius: 25) [10:14:07 -42167.181458] SLOW spr round 31 (radius: 5) [10:16:16 -42165.334395] SLOW spr round 32 (radius: 5) [10:16:53] [worker #1] ML tree search #12, logLikelihood: -42211.408330 [10:18:10 -42165.102401] SLOW spr round 33 (radius: 5) [10:19:51 -42165.102341] SLOW spr round 34 (radius: 10) [10:21:29 -42165.102341] SLOW spr round 35 (radius: 15) [10:24:12 -42165.102341] SLOW spr round 36 (radius: 20) [10:27:46 -42165.102341] SLOW spr round 37 (radius: 25) [10:31:43 -42165.102341] Model parameter optimization (eps = 0.100000) [10:31:51] [worker #0] ML tree search #11, logLikelihood: -42164.925691 [10:31:52 -123553.988708] Initial branch length optimization [10:31:54 -106756.495748] Model parameter optimization (eps = 10.000000) [10:32:24 -106204.669033] AUTODETECT spr round 1 (radius: 5) [10:34:01 -82498.655570] AUTODETECT spr round 2 (radius: 10) [10:35:46 -66034.314158] AUTODETECT spr round 3 (radius: 15) [10:37:50 -54190.498823] AUTODETECT spr round 4 (radius: 20) [10:40:11 -51125.840805] AUTODETECT spr round 5 (radius: 25) [10:42:37 -49996.392539] SPR radius for FAST iterations: 25 (autodetect) [10:42:37 -49996.392539] Model parameter optimization (eps = 3.000000) [10:42:54 -49881.475998] FAST spr round 1 (radius: 25) [10:45:18 -42759.344838] FAST spr round 2 (radius: 25) [10:47:01 -42297.443748] FAST spr round 3 (radius: 25) [10:48:32 -42240.536628] FAST spr round 4 (radius: 25) [10:49:58 -42230.294066] FAST spr round 5 (radius: 25) [10:51:23 -42211.987228] FAST spr round 6 (radius: 25) [10:52:45 -42203.579693] FAST spr round 7 (radius: 25) [10:54:04 -42199.570334] FAST spr round 8 (radius: 25) [10:55:19 -42199.570076] Model parameter optimization (eps = 1.000000) [10:55:31 -42186.128301] SLOW spr round 1 (radius: 5) [10:57:15 -42165.051889] SLOW spr round 2 (radius: 5) [10:58:55 -42159.490517] SLOW spr round 3 (radius: 5) [11:00:31 -42159.486703] SLOW spr round 4 (radius: 10) [11:02:12 -42157.520076] SLOW spr round 5 (radius: 5) [11:04:12 -42156.908059] SLOW spr round 6 (radius: 5) [11:05:56 -42156.908045] SLOW spr round 7 (radius: 10) [11:07:34 -42156.316933] SLOW spr round 8 (radius: 5) [11:09:33 -42156.316845] SLOW spr round 9 (radius: 10) [11:11:20 -42155.627552] SLOW spr round 10 (radius: 5) [11:13:17 -42153.795088] SLOW spr round 11 (radius: 5) [11:14:57 -42153.795049] SLOW spr round 12 (radius: 10) [11:16:34 -42152.379793] SLOW spr round 13 (radius: 5) [11:18:25 -42151.740752] SLOW spr round 14 (radius: 5) [11:20:05 -42151.740752] SLOW spr round 15 (radius: 10) [11:21:42 -42151.258834] SLOW spr round 16 (radius: 5) [11:23:32 -42151.258832] SLOW spr round 17 (radius: 10) [11:25:17 -42150.954618] SLOW spr round 18 (radius: 5) [11:27:13 -42150.954588] SLOW spr round 19 (radius: 10) [11:29:05 -42148.834285] SLOW spr round 20 (radius: 5) [11:31:02 -42148.834211] SLOW spr round 21 (radius: 10) [11:32:49 -42148.834211] SLOW spr round 22 (radius: 15) [11:35:34 -42140.952276] SLOW spr round 23 (radius: 5) [11:37:32 -42139.908450] SLOW spr round 24 (radius: 5) [11:39:16 -42139.908447] SLOW spr round 25 (radius: 10) [11:40:53 -42139.908447] SLOW spr round 26 (radius: 15) [11:43:35 -42139.908447] SLOW spr round 27 (radius: 20) [11:44:50] [worker #1] ML tree search #14, logLikelihood: -42201.903953 [11:47:19 -42139.908447] SLOW spr round 28 (radius: 25) [11:51:31 -42139.908447] Model parameter optimization (eps = 0.100000) [11:51:35] [worker #0] ML tree search #13, logLikelihood: -42139.898679 [11:51:35 -125097.655111] Initial branch length optimization [11:51:36 -107920.981775] Model parameter optimization (eps = 10.000000) [11:52:02 -107270.176142] AUTODETECT spr round 1 (radius: 5) [11:53:36 -82464.116919] AUTODETECT spr round 2 (radius: 10) [11:55:20 -64961.787060] AUTODETECT spr round 3 (radius: 15) [11:57:20 -56635.670422] AUTODETECT spr round 4 (radius: 20) [11:59:47 -51314.945226] AUTODETECT spr round 5 (radius: 25) [12:02:24 -49478.507802] SPR radius for FAST iterations: 25 (autodetect) [12:02:24 -49478.507802] Model parameter optimization (eps = 3.000000) [12:02:40 -49417.583011] FAST spr round 1 (radius: 25) [12:05:02 -42735.547310] FAST spr round 2 (radius: 25) [12:06:45 -42425.731310] FAST spr round 3 (radius: 25) [12:08:18 -42247.054797] FAST spr round 4 (radius: 25) [12:09:44 -42217.592868] FAST spr round 5 (radius: 25) [12:11:04 -42209.393298] FAST spr round 6 (radius: 25) [12:12:23 -42208.720709] FAST spr round 7 (radius: 25) [12:13:39 -42208.720661] Model parameter optimization (eps = 1.000000) [12:13:53 -42202.602126] SLOW spr round 1 (radius: 5) [12:15:42 -42184.940403] SLOW spr round 2 (radius: 5) [12:17:22 -42184.164344] SLOW spr round 3 (radius: 5) [12:18:59 -42184.164342] SLOW spr round 4 (radius: 10) [12:20:39 -42181.043752] SLOW spr round 5 (radius: 5) [12:22:44 -42177.243940] SLOW spr round 6 (radius: 5) [12:24:34 -42177.243874] SLOW spr round 7 (radius: 10) [12:26:17 -42174.828503] SLOW spr round 8 (radius: 5) [12:28:17 -42166.842846] SLOW spr round 9 (radius: 5) [12:30:02 -42165.457168] SLOW spr round 10 (radius: 5) [12:31:39 -42165.457106] SLOW spr round 11 (radius: 10) [12:33:15 -42163.758696] SLOW spr round 12 (radius: 5) [12:35:12 -42162.338960] SLOW spr round 13 (radius: 5) [12:36:56 -42162.338947] SLOW spr round 14 (radius: 10) [12:38:36 -42160.899962] SLOW spr round 15 (radius: 5) [12:40:39 -42157.152340] SLOW spr round 16 (radius: 5) [12:42:29 -42157.152329] SLOW spr round 17 (radius: 10) [12:44:10 -42155.365443] SLOW spr round 18 (radius: 5) [12:46:08 -42153.498375] SLOW spr round 19 (radius: 5) [12:47:54 -42153.497501] SLOW spr round 20 (radius: 10) [12:49:36 -42153.307447] SLOW spr round 21 (radius: 5) [12:51:38 -42153.307404] SLOW spr round 22 (radius: 10) [12:53:25 -42153.259488] SLOW spr round 23 (radius: 15) [12:56:08 -42148.582721] SLOW spr round 24 (radius: 5) [12:58:11 -42147.191431] SLOW spr round 25 (radius: 5) [13:00:01 -42147.041256] SLOW spr round 26 (radius: 5) [13:01:43 -42147.041255] SLOW spr round 27 (radius: 10) [13:03:23 -42145.872856] SLOW spr round 28 (radius: 5) [13:05:18 -42145.774389] SLOW spr round 29 (radius: 10) [13:05:25] [worker #1] ML tree search #16, logLikelihood: -42177.240857 [13:07:04 -42145.513099] SLOW spr round 30 (radius: 5) [13:08:58 -42144.572186] SLOW spr round 31 (radius: 5) [13:10:40 -42144.571991] SLOW spr round 32 (radius: 10) [13:12:18 -42144.571896] SLOW spr round 33 (radius: 15) [13:15:13 -42141.148399] SLOW spr round 34 (radius: 5) [13:17:16 -42140.496269] SLOW spr round 35 (radius: 5) [13:19:05 -42140.496260] SLOW spr round 36 (radius: 10) [13:20:46 -42140.496257] SLOW spr round 37 (radius: 15) [13:23:36 -42139.222194] SLOW spr round 38 (radius: 5) [13:25:42 -42138.079661] SLOW spr round 39 (radius: 5) [13:27:32 -42138.079646] SLOW spr round 40 (radius: 10) [13:29:11 -42138.079646] SLOW spr round 41 (radius: 15) [13:31:59 -42137.430071] SLOW spr round 42 (radius: 5) [13:34:00 -42137.429441] SLOW spr round 43 (radius: 10) [13:35:53 -42137.429123] SLOW spr round 44 (radius: 15) [13:38:33 -42137.428966] SLOW spr round 45 (radius: 20) [13:42:28 -42137.428889] SLOW spr round 46 (radius: 25) [13:46:46 -42136.003354] SLOW spr round 47 (radius: 5) [13:48:50 -42136.003303] SLOW spr round 48 (radius: 10) [13:50:45 -42136.003295] SLOW spr round 49 (radius: 15) [13:53:27 -42136.003291] SLOW spr round 50 (radius: 20) [13:57:29 -42136.003289] SLOW spr round 51 (radius: 25) [14:02:04 -42136.003288] Model parameter optimization (eps = 0.100000) [14:02:11] [worker #0] ML tree search #15, logLikelihood: -42135.977791 [14:02:11 -125154.357444] Initial branch length optimization [14:02:13 -108125.378586] Model parameter optimization (eps = 10.000000) [14:02:48 -107465.441373] AUTODETECT spr round 1 (radius: 5) [14:04:25 -81859.520205] AUTODETECT spr round 2 (radius: 10) [14:06:10 -65792.933633] AUTODETECT spr round 3 (radius: 15) [14:08:21 -54412.177237] AUTODETECT spr round 4 (radius: 20) [14:11:04 -49786.198294] AUTODETECT spr round 5 (radius: 25) [14:14:02 -48894.360169] SPR radius for FAST iterations: 25 (autodetect) [14:14:02 -48894.360169] Model parameter optimization (eps = 3.000000) [14:14:17 -48833.425894] FAST spr round 1 (radius: 25) [14:16:35 -42885.014477] FAST spr round 2 (radius: 25) [14:18:16 -42505.397579] FAST spr round 3 (radius: 25) [14:19:48 -42461.907686] FAST spr round 4 (radius: 25) [14:21:09 -42452.831700] FAST spr round 5 (radius: 25) [14:22:27 -42448.882157] FAST spr round 6 (radius: 25) [14:23:42 -42448.881286] Model parameter optimization (eps = 1.000000) [14:23:53 -42446.170470] SLOW spr round 1 (radius: 5) [14:25:34 -42428.800415] SLOW spr round 2 (radius: 5) [14:27:17 -42428.453175] SLOW spr round 3 (radius: 5) [14:28:50 -42428.453161] SLOW spr round 4 (radius: 10) [14:30:23 -42425.402799] SLOW spr round 5 (radius: 5) [14:32:21 -42422.784148] SLOW spr round 6 (radius: 5) [14:34:05 -42421.577342] SLOW spr round 7 (radius: 5) [14:35:43 -42421.577299] SLOW spr round 8 (radius: 10) [14:37:20 -42418.414762] SLOW spr round 9 (radius: 5) [14:39:10 -42418.365252] SLOW spr round 10 (radius: 10) [14:40:52 -42416.895484] SLOW spr round 11 (radius: 5) [14:42:40 -42416.010417] SLOW spr round 12 (radius: 5) [14:44:20 -42416.010353] SLOW spr round 13 (radius: 10) [14:45:56 -42415.942766] SLOW spr round 14 (radius: 15) [14:48:33 -42413.471445] SLOW spr round 15 (radius: 5) [14:50:26 -42410.702070] SLOW spr round 16 (radius: 5) [14:52:08] [worker #1] ML tree search #18, logLikelihood: -42141.238798 [14:52:08 -42409.505223] SLOW spr round 17 (radius: 5) [14:53:44 -42409.505215] SLOW spr round 18 (radius: 10) [14:55:16 -42407.180058] SLOW spr round 19 (radius: 5) [14:57:08 -42403.044612] SLOW spr round 20 (radius: 5) [14:58:49 -42403.044553] SLOW spr round 21 (radius: 10) [15:00:27 -42398.290703] SLOW spr round 22 (radius: 5) [15:02:23 -42398.138727] SLOW spr round 23 (radius: 5) [15:04:05 -42398.138727] SLOW spr round 24 (radius: 10) [15:05:42 -42398.105922] SLOW spr round 25 (radius: 15) [15:08:19 -42396.862699] SLOW spr round 26 (radius: 5) [15:10:19 -42384.077614] SLOW spr round 27 (radius: 5) [15:12:08 -42334.293835] SLOW spr round 28 (radius: 5) [15:13:47 -42322.505842] SLOW spr round 29 (radius: 5) [15:15:19 -42322.505598] SLOW spr round 30 (radius: 10) [15:16:52 -42321.818316] SLOW spr round 31 (radius: 5) [15:18:50 -42321.727849] SLOW spr round 32 (radius: 10) [15:20:41 -42321.727812] SLOW spr round 33 (radius: 15) [15:23:15 -42321.584475] SLOW spr round 34 (radius: 5) [15:25:08 -42321.236426] SLOW spr round 35 (radius: 5) [15:26:49 -42321.236417] SLOW spr round 36 (radius: 10) [15:28:25 -42319.479292] SLOW spr round 37 (radius: 5) [15:30:14 -42319.411309] SLOW spr round 38 (radius: 10) [15:31:54 -42319.411181] SLOW spr round 39 (radius: 15) [15:34:21 -42317.746229] SLOW spr round 40 (radius: 5) [15:36:20 -42317.746048] SLOW spr round 41 (radius: 10) [15:38:12 -42315.345009] SLOW spr round 42 (radius: 5) [15:40:10 -42313.244025] SLOW spr round 43 (radius: 5) [15:41:56 -42313.244022] SLOW spr round 44 (radius: 10) [15:43:39 -42313.244022] SLOW spr round 45 (radius: 15) [15:46:19 -42313.051831] SLOW spr round 46 (radius: 5) [15:48:14 -42313.051831] SLOW spr round 47 (radius: 10) [15:49:58 -42313.051831] SLOW spr round 48 (radius: 15) [15:52:23 -42312.992193] SLOW spr round 49 (radius: 20) [15:56:05 -42264.463711] SLOW spr round 50 (radius: 5) [15:58:05 -42171.017045] SLOW spr round 51 (radius: 5) [15:59:51 -42165.513499] SLOW spr round 52 (radius: 5) [16:01:28 -42165.112941] SLOW spr round 53 (radius: 5) [16:03:01 -42165.112935] SLOW spr round 54 (radius: 10) [16:04:33 -42165.112932] SLOW spr round 55 (radius: 15) [16:07:12 -42165.112930] SLOW spr round 56 (radius: 20) [16:08:35] [worker #1] ML tree search #20, logLikelihood: -42132.882519 [16:10:49 -42165.090677] SLOW spr round 57 (radius: 25) [16:15:01 -42164.543406] SLOW spr round 58 (radius: 5) [16:17:06 -42152.487793] SLOW spr round 59 (radius: 5) [16:18:56 -42146.961327] SLOW spr round 60 (radius: 5) [16:20:37 -42145.374471] SLOW spr round 61 (radius: 5) [16:22:11 -42145.374233] SLOW spr round 62 (radius: 10) [16:23:43 -42144.004809] SLOW spr round 63 (radius: 5) [16:25:34 -42144.004796] SLOW spr round 64 (radius: 10) [16:27:16 -42144.004796] SLOW spr round 65 (radius: 15) [16:29:45 -42144.004795] SLOW spr round 66 (radius: 20) [16:33:29 -42144.004795] SLOW spr round 67 (radius: 25) [16:37:42 -42144.004795] Model parameter optimization (eps = 0.100000) [16:37:51] [worker #0] ML tree search #17, logLikelihood: -42143.420341 [16:37:51 -125104.230039] Initial branch length optimization [16:37:53 -107636.195800] Model parameter optimization (eps = 10.000000) [16:38:18 -106942.473816] AUTODETECT spr round 1 (radius: 5) [16:39:52 -82190.426516] AUTODETECT spr round 2 (radius: 10) [16:41:34 -66751.550518] AUTODETECT spr round 3 (radius: 15) [16:43:37 -57674.636662] AUTODETECT spr round 4 (radius: 20) [16:46:20 -52861.263650] AUTODETECT spr round 5 (radius: 25) [16:48:52 -49607.231842] SPR radius for FAST iterations: 25 (autodetect) [16:48:52 -49607.231842] Model parameter optimization (eps = 3.000000) [16:49:10 -49542.996205] FAST spr round 1 (radius: 25) [16:51:25 -42718.872166] FAST spr round 2 (radius: 25) [16:53:03 -42338.337958] FAST spr round 3 (radius: 25) [16:54:33 -42295.408729] FAST spr round 4 (radius: 25) [16:56:00 -42266.733112] FAST spr round 5 (radius: 25) [16:57:18 -42264.799755] FAST spr round 6 (radius: 25) [16:58:34 -42263.612273] FAST spr round 7 (radius: 25) [16:59:48 -42263.612272] Model parameter optimization (eps = 1.000000) [16:59:56 -42262.723504] SLOW spr round 1 (radius: 5) [17:01:36 -42247.378978] SLOW spr round 2 (radius: 5) [17:03:15 -42235.076643] SLOW spr round 3 (radius: 5) [17:04:51 -42235.076505] SLOW spr round 4 (radius: 10) [17:06:31 -42231.134090] SLOW spr round 5 (radius: 5) [17:08:29 -42230.193648] SLOW spr round 6 (radius: 5) [17:10:12 -42230.193644] SLOW spr round 7 (radius: 10) [17:11:48 -42229.926501] SLOW spr round 8 (radius: 5) [17:13:39 -42229.814861] SLOW spr round 9 (radius: 5) [17:15:20 -42229.813517] SLOW spr round 10 (radius: 10) [17:16:56 -42229.553116] SLOW spr round 11 (radius: 5) [17:18:51 -42223.557734] SLOW spr round 12 (radius: 5) [17:20:33 -42223.163767] SLOW spr round 13 (radius: 5) [17:22:13 -42223.163634] SLOW spr round 14 (radius: 10) [17:23:54 -42220.734813] SLOW spr round 15 (radius: 5) [17:25:52 -42219.553132] SLOW spr round 16 (radius: 5) [17:27:35 -42219.553049] SLOW spr round 17 (radius: 10) [17:29:17 -42219.486748] SLOW spr round 18 (radius: 15) [17:32:07 -42218.073297] SLOW spr round 19 (radius: 5) [17:34:03 -42208.791349] SLOW spr round 20 (radius: 5) [17:35:44 -42208.791338] SLOW spr round 21 (radius: 10) [17:37:20 -42208.749457] SLOW spr round 22 (radius: 15) [17:39:58 -42207.982820] SLOW spr round 23 (radius: 5) [17:41:54 -42207.755412] SLOW spr round 24 (radius: 5) [17:43:38 -42207.755410] SLOW spr round 25 (radius: 10) [17:45:17 -42207.286042] SLOW spr round 26 (radius: 5) [17:47:05 -42207.286040] SLOW spr round 27 (radius: 10) [17:48:47 -42207.206457] SLOW spr round 28 (radius: 15) [17:51:18 -42207.206423] SLOW spr round 29 (radius: 20) [17:54:49 -42191.228405] SLOW spr round 30 (radius: 5) [17:56:47 -42188.252901] SLOW spr round 31 (radius: 5) [17:58:37 -42188.252811] SLOW spr round 32 (radius: 10) [18:00:17 -42188.188157] SLOW spr round 33 (radius: 15) [18:02:59 -42187.975925] SLOW spr round 34 (radius: 5) [18:04:53 -42187.975884] SLOW spr round 35 (radius: 10) [18:06:44 -42187.975884] SLOW spr round 36 (radius: 15) [18:09:23 -42187.810270] SLOW spr round 37 (radius: 5) [18:11:16 -42185.404683] SLOW spr round 38 (radius: 5) [18:12:57 -42185.404669] SLOW spr round 39 (radius: 10) [18:14:35 -42185.404669] SLOW spr round 40 (radius: 15) [18:17:22 -42185.404669] SLOW spr round 41 (radius: 20) [18:20:56 -42185.053650] SLOW spr round 42 (radius: 5) [18:22:50 -42185.053606] SLOW spr round 43 (radius: 10) [18:24:40 -42185.053606] SLOW spr round 44 (radius: 15) [18:27:11 -42185.053606] SLOW spr round 45 (radius: 20) [18:30:53 -42184.970028] SLOW spr round 46 (radius: 25) [18:34:50 -42180.535328] SLOW spr round 47 (radius: 5) [18:36:50 -42180.535284] SLOW spr round 48 (radius: 10) [18:38:44 -42180.535283] SLOW spr round 49 (radius: 15) [18:41:18 -42180.535283] SLOW spr round 50 (radius: 20) [18:44:56 -42180.535283] SLOW spr round 51 (radius: 25) [18:48:32 -42180.535283] Model parameter optimization (eps = 0.100000) [18:48:42] [worker #0] ML tree search #19, logLikelihood: -42178.162244 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.215167,0.286819) (0.167951,0.734935) (0.493157,0.828188) (0.123725,3.284923) 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: -42108.824399 AIC score: 88227.648797 / AICc score: 8132287.648797 / BIC score: 93389.944309 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=97). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A0C4DH29/3_mltree/A0A0C4DH29.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A0C4DH29/3_mltree/A0A0C4DH29.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A0C4DH29/3_mltree/A0A0C4DH29.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/A0A0C4DH29/3_mltree/A0A0C4DH29.raxml.log Analysis started: 02-Jul-2021 17:58:04 / finished: 03-Jul-2021 12:46:47 Elapsed time: 67723.142 seconds Consumed energy: 4598.327 Wh (= 23 km in an electric car, or 115 km with an e-scooter!)