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) CPU E5-2690 v4 @ 2.60GHz, 28 cores, 251 GB RAM RAxML-NG was called at 01-Jul-2021 12:32:43 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IVF6/2_msa/Q8IVF6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IVF6/3_mltree/Q8IVF6 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IVF6/2_msa/Q8IVF6_trimmed_msa.fasta [00:00:00] Loaded alignment with 985 taxa and 281 sites WARNING: Sequences tr_E1C2Z8_E1C2Z8_CHICK_9031 and tr_U3I471_U3I471_ANAPL_8839 are exactly identical! WARNING: Sequences tr_E1C2Z8_E1C2Z8_CHICK_9031 and tr_A0A091V5Y3_A0A091V5Y3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_E1C2Z8_E1C2Z8_CHICK_9031 and tr_A0A2I0MQP0_A0A2I0MQP0_COLLI_8932 are exactly identical! WARNING: Sequences tr_E1C2Z8_E1C2Z8_CHICK_9031 and tr_A0A1V4KC98_A0A1V4KC98_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0J9YUH2_A0A0J9YUH2_MOUSE_10090 and tr_A0A0J9YUZ3_A0A0J9YUZ3_MOUSE_10090 are exactly identical! WARNING: Sequences tr_D3Z1P8_D3Z1P8_MOUSE_10090 and tr_E9Q637_E9Q637_MOUSE_10090 are exactly identical! WARNING: Sequences tr_D3Z1P8_D3Z1P8_MOUSE_10090 and tr_Q8C646_Q8C646_MOUSE_10090 are exactly identical! WARNING: Sequences tr_B6QKG3_B6QKG3_TALMQ_441960 and tr_A0A093UUF7_A0A093UUF7_TALMA_1077442 are exactly identical! WARNING: Sequences tr_G3S4C5_G3S4C5_GORGO_9595 and tr_H2R3U2_H2R3U2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S4C5_G3S4C5_GORGO_9595 and tr_A0A2R8MG44_A0A2R8MG44_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3S4C5_G3S4C5_GORGO_9595 and tr_A0A2R9BUB3_A0A2R9BUB3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0R3NVX8_A0A0R3NVX8_DROPS_46245 and tr_B4H9M9_B4H9M9_DROPE_7234 are exactly identical! WARNING: Sequences tr_B8NHI2_B8NHI2_ASPFN_332952 and tr_A0A1S9E0Y6_A0A1S9E0Y6_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_H9GWQ7_H9GWQ7_CANLF_9615 and tr_L7N0G0_L7N0G0_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3SVD9_A0A2I3SVD9_PANTR_9598 and sp_Q92527_ANKR7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3SVD9_A0A2I3SVD9_PANTR_9598 and tr_A0A2R8ZJB4_A0A2R8ZJB4_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q1R5_H2Q1R5_PANTR_9598 and tr_A0A2R9CCJ6_A0A2R9CCJ6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QB11_H2QB11_PANTR_9598 and tr_A0A2R8ZAT3_A0A2R8ZAT3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R0V4_H2R0V4_PANTR_9598 and tr_A0A2R9BFU1_A0A2R9BFU1_PANPA_9597 are exactly identical! WARNING: Sequences sp_A0A0A6YYL3_POTEB_HUMAN_9606 and sp_H3BUK9_POTB2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_A5A3E0_POTEF_HUMAN_9606 and sp_Q6S8J3_POTEE_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P0CG38_POTEI_HUMAN_9606 and sp_P0CG39_POTEJ_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5SQ80_A20A2_HUMAN_9606 and sp_Q5VUR7_A20A3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_Q2UGY0_Q2UGY0_ASPOR_510516 and tr_A0A1S9DZ77_A0A1S9DZ77_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_A0A1D5RJR8_A0A1D5RJR8_MACMU_9544 and tr_G7PSM8_G7PSM8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6W8P2_F6W8P2_MACMU_9544 and tr_G7Q115_G7Q115_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7ERD4_F7ERD4_MACMU_9544 and tr_G7P245_G7P245_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7XBG0_G7XBG0_ASPKW_1033177 and tr_A0A146FD03_A0A146FD03_9EURO_1069201 are exactly identical! WARNING: Sequences tr_B8AK75_B8AK75_ORYSI_39946 and tr_Q9AUW0_Q9AUW0_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_H0YUA6_H0YUA6_TAEGU_59729 and tr_A0A218UPI7_A0A218UPI7_9PASE_299123 are exactly identical! WARNING: Sequences tr_B4MF25_B4MF25_DROVI_7244 and tr_D0Z7C6_D0Z7C6_DROVI_7244 are exactly identical! WARNING: Sequences tr_A0A096MVX0_A0A096MVX0_PAPAN_9555 and tr_A0A2K5KKK9_A0A2K5KKK9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MZ42_A0A2I3MZ42_PAPAN_9555 and tr_A0A2K5XZW8_A0A2K5XZW8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9RFY7_A0A0D9RFY7_CHLSB_60711 and tr_A0A2K6BC05_A0A2K6BC05_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0B4GGJ3_A0A0B4GGJ3_METMF_1276143 and tr_A0A0B4IJM0_A0A0B4IJM0_METMF_1276143 are exactly identical! WARNING: Sequences tr_A0A091ILE9_A0A091ILE9_EGRGA_188379 and tr_A0A087RGP9_A0A087RGP9_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1S4APP5_A0A1S4APP5_TOBAC_4097 and tr_A0A1U7VUI0_A0A1U7VUI0_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2U3WK18_A0A2U3WK18_ODORO_9708 and tr_A0A2U3YM41_A0A2U3YM41_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3WK18_A0A2U3WK18_ODORO_9708 and tr_A0A2Y9KGW3_A0A2Y9KGW3_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 39 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/Q8IVF6/3_mltree/Q8IVF6.raxml.reduced.phy Alignment comprises 1 partitions and 281 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 281 / 281 Gaps: 22.39 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IVF6/3_mltree/Q8IVF6.raxml.rba Parallelization scheme autoconfig: 6 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 985 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 281 / 22480 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -464615.132527] Initial branch length optimization [00:00:08 -401799.449911] Model parameter optimization (eps = 10.000000) [00:01:27 -400797.331416] AUTODETECT spr round 1 (radius: 5) [00:05:52 -317025.914926] AUTODETECT spr round 2 (radius: 10) [00:10:44 -254981.183283] AUTODETECT spr round 3 (radius: 15) [00:15:58 -234869.263304] AUTODETECT spr round 4 (radius: 20) [00:22:06 -222655.261137] AUTODETECT spr round 5 (radius: 25) [00:29:04 -217569.922486] SPR radius for FAST iterations: 25 (autodetect) [00:29:04 -217569.922486] Model parameter optimization (eps = 3.000000) [00:29:39 -217372.044084] FAST spr round 1 (radius: 25) [00:38:14 -202561.951663] FAST spr round 2 (radius: 25) [00:44:17 -201885.063947] FAST spr round 3 (radius: 25) [00:49:19 -201799.278790] FAST spr round 4 (radius: 25) [00:53:49 -201755.521622] FAST spr round 5 (radius: 25) [00:58:09 -201260.178725] FAST spr round 6 (radius: 25) [01:01:59 -201257.405515] FAST spr round 7 (radius: 25) [01:05:36 -201257.404344] Model parameter optimization (eps = 1.000000) [01:05:51 -201256.619771] SLOW spr round 1 (radius: 5) [01:10:36 -201209.181277] SLOW spr round 2 (radius: 5) [01:15:13 -201202.035649] SLOW spr round 3 (radius: 5) [01:19:40 -201202.033554] SLOW spr round 4 (radius: 10) [01:24:41 -201185.799960] SLOW spr round 5 (radius: 5) [01:29:58 -201179.704695] SLOW spr round 6 (radius: 5) [01:34:43 -201178.772101] SLOW spr round 7 (radius: 5) [01:39:12 -201178.770013] SLOW spr round 8 (radius: 10) [01:44:08 -201178.386605] SLOW spr round 9 (radius: 5) [01:49:25 -201174.920212] SLOW spr round 10 (radius: 5) [01:54:04 -201174.919627] SLOW spr round 11 (radius: 10) [01:59:15 -201168.832712] SLOW spr round 12 (radius: 5) [02:04:29 -201163.699009] SLOW spr round 13 (radius: 5) [02:09:08 -201163.640450] SLOW spr round 14 (radius: 10) [02:14:12 -201163.362889] SLOW spr round 15 (radius: 5) [02:19:16 -201163.222723] SLOW spr round 16 (radius: 5) [02:23:53 -201163.222331] SLOW spr round 17 (radius: 10) [02:28:55 -201162.402794] SLOW spr round 18 (radius: 5) [02:34:00 -201161.982674] SLOW spr round 19 (radius: 5) [02:38:37 -201161.982416] SLOW spr round 20 (radius: 10) [02:43:39 -201161.982365] SLOW spr round 21 (radius: 15) [02:52:12 -201157.134973] SLOW spr round 22 (radius: 5) [02:57:39 -201153.457616] SLOW spr round 23 (radius: 5) [03:02:28 -201152.580535] SLOW spr round 24 (radius: 5) [03:07:00 -201152.384632] SLOW spr round 25 (radius: 5) [03:11:22 -201152.384578] SLOW spr round 26 (radius: 10) [03:16:13 -201152.360596] SLOW spr round 27 (radius: 15) [03:24:47 -201151.525254] SLOW spr round 28 (radius: 5) [03:30:10 -201147.697066] SLOW spr round 29 (radius: 5) [03:34:55 -201147.694952] SLOW spr round 30 (radius: 10) [03:40:02 -201147.694300] SLOW spr round 31 (radius: 15) [03:48:17 -201147.694101] SLOW spr round 32 (radius: 20) [03:58:48 -201142.619846] SLOW spr round 33 (radius: 5) [04:04:10 -201142.590909] SLOW spr round 34 (radius: 10) [04:09:51] [worker #5] ML tree search #6, logLikelihood: -201111.738664 [04:10:09 -201142.590684] SLOW spr round 35 (radius: 15) [04:18:13 -201142.590678] SLOW spr round 36 (radius: 20) [04:28:45 -201142.590677] SLOW spr round 37 (radius: 25) [04:40:12 -201142.590676] Model parameter optimization (eps = 0.100000) [04:40:27] [worker #0] ML tree search #1, logLikelihood: -201142.436476 [04:40:27 -465017.431527] Initial branch length optimization [04:40:33 -401997.112383] Model parameter optimization (eps = 10.000000) [04:41:38 -401013.939094] AUTODETECT spr round 1 (radius: 5) [04:46:05 -323209.026009] AUTODETECT spr round 2 (radius: 10) [04:51:03 -250936.849492] AUTODETECT spr round 3 (radius: 15) [04:56:12 -226930.069779] AUTODETECT spr round 4 (radius: 20) [05:01:56 -218955.008141] AUTODETECT spr round 5 (radius: 25) [05:09:16 -215864.728393] SPR radius for FAST iterations: 25 (autodetect) [05:09:16 -215864.728393] Model parameter optimization (eps = 3.000000) [05:09:26 -215863.992031] FAST spr round 1 (radius: 25) [05:17:57 -202209.221409] FAST spr round 2 (radius: 25) [05:24:26 -201539.987254] FAST spr round 3 (radius: 25) [05:29:44 -201447.182516] FAST spr round 4 (radius: 25) [05:34:15 -201428.187228] FAST spr round 5 (radius: 25) [05:38:12 -201422.225556] FAST spr round 6 (radius: 25) [05:41:53 -201421.051349] FAST spr round 7 (radius: 25) [05:45:28 -201421.049895] Model parameter optimization (eps = 1.000000) [05:45:37 -201421.032706] SLOW spr round 1 (radius: 5) [05:50:33 -201367.921646] SLOW spr round 2 (radius: 5) [05:55:21 -201361.402294] SLOW spr round 3 (radius: 5) [05:59:53 -201360.010058] SLOW spr round 4 (radius: 5) [06:04:20 -201360.006801] SLOW spr round 5 (radius: 10) [06:09:17 -201347.661161] SLOW spr round 6 (radius: 5) [06:14:48 -201331.519136] SLOW spr round 7 (radius: 5) [06:16:45] [worker #4] ML tree search #5, logLikelihood: -201291.768883 [06:19:42 -201330.010405] SLOW spr round 8 (radius: 5) [06:24:18 -201329.872522] SLOW spr round 9 (radius: 5) [06:28:46 -201329.871948] SLOW spr round 10 (radius: 10) [06:33:43 -201329.288314] SLOW spr round 11 (radius: 5) [06:38:55 -201329.288010] SLOW spr round 12 (radius: 10) [06:42:43] [worker #2] ML tree search #3, logLikelihood: -201351.393789 [06:44:40 -201329.287848] SLOW spr round 13 (radius: 15) [06:53:31 -201322.255352] SLOW spr round 14 (radius: 5) [06:59:09 -201316.922708] SLOW spr round 15 (radius: 5) [07:04:15 -201314.565263] SLOW spr round 16 (radius: 5) [07:08:51 -201314.559407] SLOW spr round 17 (radius: 10) [07:13:55 -201313.648959] SLOW spr round 18 (radius: 5) [07:19:18 -201311.735047] SLOW spr round 19 (radius: 5) [07:24:11 -201308.065971] SLOW spr round 20 (radius: 5) [07:28:48 -201307.910259] SLOW spr round 21 (radius: 5) [07:32:28] [worker #3] ML tree search #4, logLikelihood: -201047.385961 [07:33:17 -201307.909555] SLOW spr round 22 (radius: 10) [07:38:17 -201307.549634] SLOW spr round 23 (radius: 5) [07:43:37 -201302.890046] SLOW spr round 24 (radius: 5) [07:48:23 -201302.890007] SLOW spr round 25 (radius: 10) [07:50:57] [worker #5] ML tree search #12, logLikelihood: -201212.378708 [07:52:59] [worker #1] ML tree search #2, logLikelihood: -201336.885851 [07:53:35 -201302.249330] SLOW spr round 26 (radius: 5) [07:58:49 -201301.176578] SLOW spr round 27 (radius: 5) [08:03:33 -201301.176524] SLOW spr round 28 (radius: 10) [08:08:43 -201301.176522] SLOW spr round 29 (radius: 15) [08:17:42 -201301.176522] SLOW spr round 30 (radius: 20) [08:29:11 -201301.176521] SLOW spr round 31 (radius: 25) [08:42:04 -201301.176521] Model parameter optimization (eps = 0.100000) [08:42:20] [worker #0] ML tree search #7, logLikelihood: -201301.058862 [08:42:20 -464858.381662] Initial branch length optimization [08:42:27 -401568.479705] Model parameter optimization (eps = 10.000000) [08:43:37 -400563.536880] AUTODETECT spr round 1 (radius: 5) [08:48:02 -322274.611880] AUTODETECT spr round 2 (radius: 10) [08:52:51 -256481.950858] AUTODETECT spr round 3 (radius: 15) [08:58:02 -229609.195643] AUTODETECT spr round 4 (radius: 20) [09:03:47 -220482.153647] AUTODETECT spr round 5 (radius: 25) [09:10:22 -218087.815654] SPR radius for FAST iterations: 25 (autodetect) [09:10:22 -218087.815654] Model parameter optimization (eps = 3.000000) [09:10:32 -218087.111653] FAST spr round 1 (radius: 25) [09:18:38 -202532.786225] FAST spr round 2 (radius: 25) [09:24:50 -201625.323964] FAST spr round 3 (radius: 25) [09:29:52 -201516.499393] FAST spr round 4 (radius: 25) [09:34:20 -201483.730219] FAST spr round 5 (radius: 25) [09:38:14 -201478.603384] FAST spr round 6 (radius: 25) [09:41:53 -201478.602751] Model parameter optimization (eps = 1.000000) [09:42:03 -201478.418382] SLOW spr round 1 (radius: 5) [09:47:00 -201404.596908] SLOW spr round 2 (radius: 5) [09:51:04] [worker #2] ML tree search #9, logLikelihood: -201235.104086 [09:51:46 -201375.755683] SLOW spr round 3 (radius: 5) [09:56:29 -201366.145678] SLOW spr round 4 (radius: 5) [10:00:56 -201366.144410] SLOW spr round 5 (radius: 10) [10:05:59 -201340.783603] SLOW spr round 6 (radius: 5) [10:11:16 -201339.978490] SLOW spr round 7 (radius: 5) [10:16:07 -201339.732280] SLOW spr round 8 (radius: 5) [10:20:41 -201339.732190] SLOW spr round 9 (radius: 10) [10:25:40 -201338.312489] SLOW spr round 10 (radius: 5) [10:30:53 -201338.312293] SLOW spr round 11 (radius: 10) [10:36:30 -201338.196294] SLOW spr round 12 (radius: 5) [10:41:42 -201338.196263] SLOW spr round 13 (radius: 10) [10:47:15 -201338.142584] SLOW spr round 14 (radius: 15) [10:55:57 -201327.990399] SLOW spr round 15 (radius: 5) [11:01:30 -201325.604665] SLOW spr round 16 (radius: 5) [11:06:27 -201325.009519] SLOW spr round 17 (radius: 5) [11:11:04 -201325.009007] SLOW spr round 18 (radius: 10) [11:16:00 -201324.284652] SLOW spr round 19 (radius: 5) [11:21:15 -201322.862155] SLOW spr round 20 (radius: 5) [11:26:00 -201322.861454] SLOW spr round 21 (radius: 10) [11:31:03 -201322.861431] SLOW spr round 22 (radius: 15) [11:39:42 -201322.861427] SLOW spr round 23 (radius: 20) [11:51:10 -201322.861425] SLOW spr round 24 (radius: 25) [12:04:37 -201307.120956] SLOW spr round 25 (radius: 5) [12:10:26 -201271.546274] SLOW spr round 26 (radius: 5) [12:15:35 -201258.509851] SLOW spr round 27 (radius: 5) [12:20:15 -201258.446533] SLOW spr round 28 (radius: 10) [12:25:16 -201258.446219] SLOW spr round 29 (radius: 15) [12:30:49] [worker #4] ML tree search #11, logLikelihood: -201717.772871 [12:34:09 -201246.046253] SLOW spr round 30 (radius: 5) [12:39:42 -201237.369321] SLOW spr round 31 (radius: 5) [12:44:36 -201237.369306] SLOW spr round 32 (radius: 10) [12:49:48 -201237.369302] SLOW spr round 33 (radius: 15) [12:54:35] [worker #3] ML tree search #10, logLikelihood: -201127.063044 [12:58:28 -201237.369300] SLOW spr round 34 (radius: 20) [13:02:44] [worker #1] ML tree search #8, logLikelihood: -201319.232495 [13:10:06 -201237.369298] SLOW spr round 35 (radius: 25) [13:23:45 -201237.369296] Model parameter optimization (eps = 0.100000) [13:23:53] [worker #0] ML tree search #13, logLikelihood: -201237.326295 [13:23:53 -467582.071826] Initial branch length optimization [13:24:00 -403306.536630] Model parameter optimization (eps = 10.000000) [13:25:10 -402411.802528] AUTODETECT spr round 1 (radius: 5) [13:29:34 -324195.388675] AUTODETECT spr round 2 (radius: 10) [13:34:32 -258374.135667] AUTODETECT spr round 3 (radius: 15) [13:40:07 -226864.489765] AUTODETECT spr round 4 (radius: 20) [13:44:22] [worker #2] ML tree search #15, logLikelihood: -201386.691847 [13:46:36 -220090.831298] AUTODETECT spr round 5 (radius: 25) [13:54:09 -216837.924906] SPR radius for FAST iterations: 25 (autodetect) [13:54:09 -216837.924906] Model parameter optimization (eps = 3.000000) [13:54:44 -216587.249763] FAST spr round 1 (radius: 25) [14:03:32 -202260.500351] FAST spr round 2 (radius: 25) [14:09:57 -201433.859513] FAST spr round 3 (radius: 25) [14:14:55 -201278.552761] FAST spr round 4 (radius: 25) [14:19:16 -201255.796106] FAST spr round 5 (radius: 25) [14:23:08 -201252.755716] FAST spr round 6 (radius: 25) [14:26:55 -201239.403310] FAST spr round 7 (radius: 25) [14:30:36 -201207.668727] FAST spr round 8 (radius: 25) [14:34:03 -201207.667104] Model parameter optimization (eps = 1.000000) [14:34:38 -201205.480275] SLOW spr round 1 (radius: 5) [14:39:20 -201150.933153] SLOW spr round 2 (radius: 5) [14:43:57 -201147.037232] SLOW spr round 3 (radius: 5) [14:48:28 -201147.012535] SLOW spr round 4 (radius: 10) [14:53:25 -201142.496351] SLOW spr round 5 (radius: 5) [14:58:47 -201131.516476] SLOW spr round 6 (radius: 5) [15:03:35 -201124.751604] SLOW spr round 7 (radius: 5) [15:08:08 -201122.648661] SLOW spr round 8 (radius: 5) [15:12:33 -201122.648282] SLOW spr round 9 (radius: 10) [15:17:29 -201122.163193] SLOW spr round 10 (radius: 5) [15:19:20] [worker #5] ML tree search #18, logLikelihood: -201082.796876 [15:22:36 -201122.163062] SLOW spr round 11 (radius: 10) [15:28:18 -201111.952064] SLOW spr round 12 (radius: 5) [15:33:24 -201106.096955] SLOW spr round 13 (radius: 5) [15:38:06 -201105.718508] SLOW spr round 14 (radius: 5) [15:42:35 -201105.718267] SLOW spr round 15 (radius: 10) [15:47:32 -201104.803066] SLOW spr round 16 (radius: 5) [15:52:48 -201102.412120] SLOW spr round 17 (radius: 5) [15:57:31 -201101.954465] SLOW spr round 18 (radius: 5) [16:02:05 -201101.047987] SLOW spr round 19 (radius: 5) [16:06:31 -201100.590121] SLOW spr round 20 (radius: 5) [16:10:53 -201100.589729] SLOW spr round 21 (radius: 10) [16:14:08] [worker #3] ML tree search #16, logLikelihood: -201392.189746 [16:15:42 -201098.777860] SLOW spr round 22 (radius: 5) [16:20:48 -201098.776641] SLOW spr round 23 (radius: 10) [16:26:25 -201098.776562] SLOW spr round 24 (radius: 15) [16:34:52 -201094.365071] SLOW spr round 25 (radius: 5) [16:40:16 -201093.265908] SLOW spr round 26 (radius: 5) [16:45:05 -201093.265348] SLOW spr round 27 (radius: 10) [16:50:21 -201087.320120] SLOW spr round 28 (radius: 5) [16:55:29 -201085.678692] SLOW spr round 29 (radius: 5) [17:00:10 -201085.140507] SLOW spr round 30 (radius: 5) [17:04:38 -201085.139609] SLOW spr round 31 (radius: 10) [17:09:30 -201085.139512] SLOW spr round 32 (radius: 15) [17:18:13] [worker #4] ML tree search #17, logLikelihood: -201282.025493 [17:18:17 -201085.104943] SLOW spr round 33 (radius: 20) [17:29:34 -201081.215227] SLOW spr round 34 (radius: 5) [17:35:01 -201079.546403] SLOW spr round 35 (radius: 5) [17:39:51 -201079.514642] SLOW spr round 36 (radius: 10) [17:45:05 -201079.099366] SLOW spr round 37 (radius: 5) [17:50:11 -201076.695286] SLOW spr round 38 (radius: 5) [17:54:49 -201076.694975] SLOW spr round 39 (radius: 10) [17:59:50 -201076.694923] SLOW spr round 40 (radius: 15) [18:08:29 -201075.971090] SLOW spr round 41 (radius: 5) [18:13:45 -201072.171661] SLOW spr round 42 (radius: 5) [18:18:32 -201072.171223] SLOW spr round 43 (radius: 10) [18:20:37] [worker #1] ML tree search #14, logLikelihood: -201790.113858 [18:23:42 -201072.171213] SLOW spr round 44 (radius: 15) [18:32:14 -201072.171210] SLOW spr round 45 (radius: 20) [18:43:25 -201071.941355] SLOW spr round 46 (radius: 5) [18:48:49 -201067.713488] SLOW spr round 47 (radius: 5) [18:53:45 -201063.177645] SLOW spr round 48 (radius: 5) [18:58:17 -201063.177622] SLOW spr round 49 (radius: 10) [19:03:14 -201063.177619] SLOW spr round 50 (radius: 15) [19:12:01 -201063.177619] SLOW spr round 51 (radius: 20) [19:23:08 -201063.177618] SLOW spr round 52 (radius: 25) [19:36:07 -201063.177618] Model parameter optimization (eps = 0.100000) [19:36:33] [worker #0] ML tree search #19, logLikelihood: -201062.278136 [26:39:14] [worker #1] ML tree search #20, logLikelihood: -201446.469478 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.156372,0.462099) (0.145672,0.510554) (0.410895,0.940608) (0.287062,1.626399) 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: -201047.385961 AIC score: 406040.771922 / AICc score: 8195444.771922 / BIC score: 413219.245685 Free parameters (model + branch lengths): 1973 WARNING: Number of free parameters (K=1973) is larger than alignment size (n=281). 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/Q8IVF6/3_mltree/Q8IVF6.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IVF6/3_mltree/Q8IVF6.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IVF6/3_mltree/Q8IVF6.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q8IVF6/3_mltree/Q8IVF6.raxml.log Analysis started: 01-Jul-2021 12:32:43 / finished: 02-Jul-2021 15:11:57 Elapsed time: 95954.297 seconds Consumed energy: 5013.410 Wh (= 25 km in an electric car, or 125 km with an e-scooter!)