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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM RAxML-NG was called at 26-Jul-2021 00:10:21 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15265/2_msa/O15265_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15265/3_mltree/O15265 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15265/2_msa/O15265_trimmed_msa.fasta [00:00:00] Loaded alignment with 646 taxa and 218 sites WARNING: Sequences tr_M3YZR7_M3YZR7_MUSPF_9669 and tr_A0A2Y9IZV7_A0A2Y9IZV7_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z3I0_M3Z3I0_MUSPF_9669 and tr_A0A2Y9KBS0_A0A2Y9KBS0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Z3I0_M3Z3I0_MUSPF_9669 and tr_A0A384D3Y4_A0A384D3Y4_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1RCB0_G1RCB0_NOMLE_61853 and sp_Q3T136_AT7L1_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2I2Y2X6_A0A2I2Y2X6_GORGO_9595 and tr_H2PPB4_H2PPB4_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2Y2X6_A0A2I2Y2X6_GORGO_9595 and sp_Q9ULK2_AT7L1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Y2X6_A0A2I2Y2X6_GORGO_9595 and tr_A0A2R9CFZ5_A0A2R9CFZ5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S5V1_G3S5V1_GORGO_9595 and tr_A0A2I3T8Q1_A0A2I3T8Q1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S5V1_G3S5V1_GORGO_9595 and sp_O15265_ATX7_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S5V1_G3S5V1_GORGO_9595 and tr_A0A0D9RHS3_A0A0D9RHS3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2N6I3_H2N6I3_PONAB_9601 and sp_Q5T6C5_AT7L2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_J4KLQ9_J4KLQ9_BEAB2_655819 and tr_A0A0A2VP33_A0A0A2VP33_BEABA_1245745 are exactly identical! WARNING: Sequences tr_F6VLC1_F6VLC1_MACMU_9544 and tr_A0A0D9S6J1_A0A0D9S6J1_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WZJ3_F6WZJ3_MACMU_9544 and tr_G7P2E8_G7P2E8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WZJ3_F6WZJ3_MACMU_9544 and tr_A0A096NGU1_A0A096NGU1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6WZJ3_F6WZJ3_MACMU_9544 and tr_A0A0D9RG98_A0A0D9RG98_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WZJ3_F6WZJ3_MACMU_9544 and tr_A0A2K5KP56_A0A2K5KP56_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6WZJ3_F6WZJ3_MACMU_9544 and tr_A0A2K6DZS6_A0A2K6DZS6_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6WZJ3_F6WZJ3_MACMU_9544 and tr_A0A2K5Y2X0_A0A2K5Y2X0_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7GFQ4_F7GFQ4_MACMU_9544 and tr_A0A2K5P349_A0A2K5P349_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GFQ4_F7GFQ4_MACMU_9544 and tr_A0A2K6CVV3_A0A2K6CVV3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7NV57_G7NV57_MACFA_9541 and tr_A0A2K5ZU92_A0A2K5ZU92_MANLE_9568 are exactly identical! WARNING: Sequences tr_G7NZA5_G7NZA5_MACFA_9541 and tr_A0A2K5ZCZ2_A0A2K5ZCZ2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F2PLX5_F2PLX5_TRIEC_559882 and tr_A0A059J849_A0A059J849_9EURO_1215338 are exactly identical! WARNING: Sequences tr_A0A015JJP7_A0A015JJP7_9GLOM_1432141 and tr_A0A2I1G0H2_A0A2I1G0H2_9GLOM_588596 are exactly identical! WARNING: Sequences tr_A0A0F9ZBB3_A0A0F9ZBB3_TRIHA_5544 and tr_A0A2T3ZSX8_A0A2T3ZSX8_TRIHA_983964 are exactly identical! WARNING: Sequences tr_A0A0A1MN87_A0A0A1MN87_9FUNG_58291 and tr_A0A367K6D2_A0A367K6D2_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0Q3UQ40_A0A0Q3UQ40_AMAAE_12930 and tr_A0A093PC52_A0A093PC52_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A0Q3UQ40_A0A0Q3UQ40_AMAAE_12930 and tr_A0A091UWI0_A0A091UWI0_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A0Q3UQ40_A0A0Q3UQ40_AMAAE_12930 and tr_A0A0A0ADV3_A0A0A0ADV3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091IQQ5_A0A091IQQ5_EGRGA_188379 and tr_A0A091WBA3_A0A091WBA3_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091IQQ5_A0A091IQQ5_EGRGA_188379 and tr_A0A0A0AGG2_A0A0A0AGG2_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A195BTY0_A0A195BTY0_9HYME_520822 and tr_A0A195FU14_A0A195FU14_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A2I4C4B1_A0A2I4C4B1_9TELE_52670 and tr_A0A2I4D3C0_A0A2I4D3C0_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A2D0PJ72_A0A2D0PJ72_ICTPU_7998 and tr_A0A2D0PKU0_A0A2D0PKU0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5NVW4_A0A2K5NVW4_CERAT_9531 and tr_A0A2K6BZX0_A0A2K6BZX0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2U3W3E9_A0A2U3W3E9_ODORO_9708 and tr_A0A2U3XX66_A0A2U3XX66_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2U3ZNQ2_A0A2U3ZNQ2_ODORO_9708 and tr_A0A2U3Z1C7_A0A2U3Z1C7_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 38 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15265/3_mltree/O15265.raxml.reduced.phy Alignment comprises 1 partitions and 218 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 218 / 218 Gaps: 13.86 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15265/3_mltree/O15265.raxml.rba Parallelization scheme autoconfig: 4 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 646 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 218 / 17440 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -242615.950924] Initial branch length optimization [00:00:08 -198250.739880] Model parameter optimization (eps = 10.000000) [00:01:22 -197661.773529] AUTODETECT spr round 1 (radius: 5) [00:03:52 -134684.803806] AUTODETECT spr round 2 (radius: 10) [00:06:41 -104449.264160] AUTODETECT spr round 3 (radius: 15) [00:09:45 -92345.959492] AUTODETECT spr round 4 (radius: 20) [00:13:36 -84303.103792] AUTODETECT spr round 5 (radius: 25) [00:18:10 -83218.530232] SPR radius for FAST iterations: 25 (autodetect) [00:18:10 -83218.530232] Model parameter optimization (eps = 3.000000) [00:18:56 -83066.310491] FAST spr round 1 (radius: 25) [00:22:35 -73935.564884] FAST spr round 2 (radius: 25) [00:25:18 -73556.934982] FAST spr round 3 (radius: 25) [00:27:46 -73521.738360] FAST spr round 4 (radius: 25) [00:29:53 -73513.707018] FAST spr round 5 (radius: 25) [00:31:50 -73510.938520] FAST spr round 6 (radius: 25) [00:33:40 -73510.938512] Model parameter optimization (eps = 1.000000) [00:34:01 -73507.754067] SLOW spr round 1 (radius: 5) [00:36:52 -73493.474552] SLOW spr round 2 (radius: 5) [00:39:43 -73488.399967] SLOW spr round 3 (radius: 5) [00:42:27 -73488.135431] SLOW spr round 4 (radius: 5) [00:45:05 -73488.135012] SLOW spr round 5 (radius: 10) [00:47:52 -73487.435276] SLOW spr round 6 (radius: 5) [00:51:12 -73487.434920] SLOW spr round 7 (radius: 10) [00:54:25 -73487.434887] SLOW spr round 8 (radius: 15) [00:58:43 -73487.358979] SLOW spr round 9 (radius: 20) [01:04:51 -73487.358974] SLOW spr round 10 (radius: 25) [01:10:25] [worker #3] ML tree search #4, logLikelihood: -73464.234898 [01:11:15 -73487.358973] Model parameter optimization (eps = 0.100000) [01:11:27] [worker #0] ML tree search #1, logLikelihood: -73487.324267 [01:11:28 -244221.504368] Initial branch length optimization [01:11:35 -198504.089421] Model parameter optimization (eps = 10.000000) [01:13:04 -198008.961508] AUTODETECT spr round 1 (radius: 5) [01:15:40 -138555.128347] AUTODETECT spr round 2 (radius: 10) [01:18:28 -111474.570856] AUTODETECT spr round 3 (radius: 15) [01:20:38] [worker #2] ML tree search #3, logLikelihood: -73463.183906 [01:21:56 -93431.804269] AUTODETECT spr round 4 (radius: 20) [01:26:07 -83686.130406] AUTODETECT spr round 5 (radius: 25) [01:29:49 -82685.812837] SPR radius for FAST iterations: 25 (autodetect) [01:29:49 -82685.812837] Model parameter optimization (eps = 3.000000) [01:30:33 -82482.406076] FAST spr round 1 (radius: 25) [01:32:55] [worker #1] ML tree search #2, logLikelihood: -73457.235933 [01:33:49 -73990.039552] FAST spr round 2 (radius: 25) [01:36:23 -73538.773647] FAST spr round 3 (radius: 25) [01:38:42 -73495.473626] FAST spr round 4 (radius: 25) [01:40:47 -73487.367151] FAST spr round 5 (radius: 25) [01:42:44 -73486.986015] FAST spr round 6 (radius: 25) [01:44:38 -73486.985956] Model parameter optimization (eps = 1.000000) [01:45:03 -73483.359020] SLOW spr round 1 (radius: 5) [01:47:56 -73471.701464] SLOW spr round 2 (radius: 5) [01:50:44 -73467.886046] SLOW spr round 3 (radius: 5) [01:53:31 -73467.386429] SLOW spr round 4 (radius: 5) [01:56:10 -73467.385832] SLOW spr round 5 (radius: 10) [01:58:57 -73466.494824] SLOW spr round 6 (radius: 5) [02:02:22 -73465.492018] SLOW spr round 7 (radius: 5) [02:05:19 -73465.446673] SLOW spr round 8 (radius: 10) [02:08:17 -73465.446057] SLOW spr round 9 (radius: 15) [02:12:55 -73464.194263] SLOW spr round 10 (radius: 5) [02:16:30 -73464.194219] SLOW spr round 11 (radius: 10) [02:19:54 -73464.194200] SLOW spr round 12 (radius: 15) [02:21:26] [worker #3] ML tree search #8, logLikelihood: -73456.977911 [02:24:23 -73464.194182] SLOW spr round 13 (radius: 20) [02:31:01 -73460.074829] SLOW spr round 14 (radius: 5) [02:34:49 -73449.841530] SLOW spr round 15 (radius: 5) [02:37:56 -73449.514221] SLOW spr round 16 (radius: 5) [02:40:45 -73449.512538] SLOW spr round 17 (radius: 10) [02:43:41 -73446.450470] SLOW spr round 18 (radius: 5) [02:44:52] [worker #1] ML tree search #6, logLikelihood: -73448.464396 [02:46:56 -73446.447916] SLOW spr round 19 (radius: 10) [02:50:06 -73446.447818] SLOW spr round 20 (radius: 15) [02:52:36] [worker #2] ML tree search #7, logLikelihood: -73466.170115 [02:54:37 -73446.280441] SLOW spr round 21 (radius: 5) [02:58:11 -73446.280301] SLOW spr round 22 (radius: 10) [03:01:33 -73446.280282] SLOW spr round 23 (radius: 15) [03:05:59 -73446.280263] SLOW spr round 24 (radius: 20) [03:12:17 -73446.280244] SLOW spr round 25 (radius: 25) [03:18:55 -73446.280226] Model parameter optimization (eps = 0.100000) [03:19:10] [worker #0] ML tree search #5, logLikelihood: -73445.571675 [03:19:10 -244205.456862] Initial branch length optimization [03:19:18 -198986.980649] Model parameter optimization (eps = 10.000000) [03:20:21 -198303.289591] AUTODETECT spr round 1 (radius: 5) [03:22:52 -134106.443791] AUTODETECT spr round 2 (radius: 10) [03:25:37 -103708.384214] AUTODETECT spr round 3 (radius: 15) [03:28:56 -88858.564290] AUTODETECT spr round 4 (radius: 20) [03:32:53 -85504.014484] AUTODETECT spr round 5 (radius: 25) [03:37:02 -85149.913269] SPR radius for FAST iterations: 25 (autodetect) [03:37:02 -85149.913269] Model parameter optimization (eps = 3.000000) [03:37:46 -84984.953967] FAST spr round 1 (radius: 25) [03:41:26 -74160.981720] FAST spr round 2 (radius: 25) [03:44:12 -73556.592308] FAST spr round 3 (radius: 25) [03:46:34 -73486.651100] FAST spr round 4 (radius: 25) [03:48:34 -73473.797034] FAST spr round 5 (radius: 25) [03:50:28 -73472.246425] FAST spr round 6 (radius: 25) [03:52:19 -73472.246200] Model parameter optimization (eps = 1.000000) [03:52:43 -73468.521752] SLOW spr round 1 (radius: 5) [03:55:36 -73457.790748] SLOW spr round 2 (radius: 5) [03:58:20 -73456.124427] SLOW spr round 3 (radius: 5) [04:00:56 -73456.123838] SLOW spr round 4 (radius: 10) [04:03:42 -73455.043365] SLOW spr round 5 (radius: 5) [04:07:02 -73453.156831] SLOW spr round 6 (radius: 5) [04:09:56 -73453.156745] SLOW spr round 7 (radius: 10) [04:10:45] [worker #1] ML tree search #10, logLikelihood: -73452.873382 [04:11:56] [worker #3] ML tree search #12, logLikelihood: -73443.516052 [04:12:52 -73451.694042] SLOW spr round 8 (radius: 5) [04:16:10 -73451.567426] SLOW spr round 9 (radius: 5) [04:19:02 -73451.567192] SLOW spr round 10 (radius: 10) [04:21:55 -73451.567184] SLOW spr round 11 (radius: 15) [04:26:25 -73451.267757] SLOW spr round 12 (radius: 5) [04:30:01 -73450.238949] SLOW spr round 13 (radius: 5) [04:33:03 -73450.236920] SLOW spr round 14 (radius: 10) [04:36:01 -73450.236838] SLOW spr round 15 (radius: 15) [04:40:20 -73450.236835] SLOW spr round 16 (radius: 20) [04:46:37 -73450.236834] SLOW spr round 17 (radius: 25) [04:53:16 -73450.236832] Model parameter optimization (eps = 0.100000) [04:53:30] [worker #0] ML tree search #9, logLikelihood: -73450.194514 [04:53:30 -245779.967607] Initial branch length optimization [04:53:37 -198416.162594] Model parameter optimization (eps = 10.000000) [04:54:58 -197931.898378] AUTODETECT spr round 1 (radius: 5) [04:57:34 -137229.917650] AUTODETECT spr round 2 (radius: 10) [05:00:24 -107748.825756] AUTODETECT spr round 3 (radius: 15) [05:03:42 -89075.267636] AUTODETECT spr round 4 (radius: 20) [05:07:19 -85083.102784] AUTODETECT spr round 5 (radius: 25) [05:07:22] [worker #2] ML tree search #11, logLikelihood: -73448.403881 [05:11:19 -83492.139430] SPR radius for FAST iterations: 25 (autodetect) [05:11:19 -83492.139430] Model parameter optimization (eps = 3.000000) [05:12:04 -83366.512211] FAST spr round 1 (radius: 25) [05:15:47 -74085.307128] FAST spr round 2 (radius: 25) [05:18:27 -73569.381773] FAST spr round 3 (radius: 25) [05:20:50 -73525.938836] FAST spr round 4 (radius: 25) [05:22:54 -73512.320846] FAST spr round 5 (radius: 25) [05:24:49 -73511.668613] FAST spr round 6 (radius: 25) [05:26:41 -73511.667174] Model parameter optimization (eps = 1.000000) [05:27:08 -73501.621724] SLOW spr round 1 (radius: 5) [05:29:55 -73480.840011] SLOW spr round 2 (radius: 5) [05:32:30] [worker #1] ML tree search #14, logLikelihood: -73459.949982 [05:32:41 -73479.757648] SLOW spr round 3 (radius: 5) [05:35:21 -73479.751179] SLOW spr round 4 (radius: 10) [05:37:30] [worker #3] ML tree search #16, logLikelihood: -73471.191638 [05:38:08 -73476.878481] SLOW spr round 5 (radius: 5) [05:41:30 -73476.878024] SLOW spr round 6 (radius: 10) [05:44:46 -73476.877821] SLOW spr round 7 (radius: 15) [05:49:10 -73475.692580] SLOW spr round 8 (radius: 5) [05:52:49 -73475.692443] SLOW spr round 9 (radius: 10) [05:56:17 -73475.692380] SLOW spr round 10 (radius: 15) [06:00:37 -73475.692337] SLOW spr round 11 (radius: 20) [06:07:06 -73470.499949] SLOW spr round 12 (radius: 5) [06:10:53 -73461.401242] SLOW spr round 13 (radius: 5) [06:14:00 -73461.400913] SLOW spr round 14 (radius: 10) [06:17:01 -73461.400886] SLOW spr round 15 (radius: 15) [06:21:25 -73461.400874] SLOW spr round 16 (radius: 20) [06:27:36 -73461.400865] SLOW spr round 17 (radius: 25) [06:34:00 -73461.400858] Model parameter optimization (eps = 0.100000) [06:34:11] [worker #0] ML tree search #13, logLikelihood: -73461.156928 [06:34:12 -242327.405305] Initial branch length optimization [06:34:19 -198665.123048] Model parameter optimization (eps = 10.000000) [06:35:31 -198120.104470] AUTODETECT spr round 1 (radius: 5) [06:37:06] [worker #2] ML tree search #15, logLikelihood: -73456.770616 [06:38:04 -136357.153322] AUTODETECT spr round 2 (radius: 10) [06:40:49 -105847.634729] AUTODETECT spr round 3 (radius: 15) [06:44:00 -93884.619737] AUTODETECT spr round 4 (radius: 20) [06:47:37 -83684.799610] AUTODETECT spr round 5 (radius: 25) [06:51:23 -82037.613866] SPR radius for FAST iterations: 25 (autodetect) [06:51:23 -82037.613866] Model parameter optimization (eps = 3.000000) [06:52:07 -81887.942014] FAST spr round 1 (radius: 25) [06:55:39 -74244.462479] FAST spr round 2 (radius: 25) [06:57:09] [worker #1] ML tree search #18, logLikelihood: -73453.552833 [06:58:19 -73584.327282] FAST spr round 3 (radius: 25) [06:58:53] [worker #3] ML tree search #20, logLikelihood: -73452.955176 [07:00:38 -73512.957246] FAST spr round 4 (radius: 25) [07:02:41 -73502.687655] FAST spr round 5 (radius: 25) [07:04:34 -73502.686708] Model parameter optimization (eps = 1.000000) [07:05:03 -73496.168972] SLOW spr round 1 (radius: 5) [07:07:49 -73468.825817] SLOW spr round 2 (radius: 5) [07:10:35 -73463.318432] SLOW spr round 3 (radius: 5) [07:13:19 -73461.913171] SLOW spr round 4 (radius: 5) [07:15:56 -73461.912483] SLOW spr round 5 (radius: 10) [07:18:40 -73460.271503] SLOW spr round 6 (radius: 5) [07:22:01 -73460.177025] SLOW spr round 7 (radius: 10) [07:25:07 -73460.176599] SLOW spr round 8 (radius: 15) [07:29:31 -73458.616619] SLOW spr round 9 (radius: 5) [07:33:07 -73458.573965] SLOW spr round 10 (radius: 10) [07:36:27 -73458.571041] SLOW spr round 11 (radius: 15) [07:40:45 -73458.570367] SLOW spr round 12 (radius: 20) [07:47:12 -73458.570113] SLOW spr round 13 (radius: 25) [07:53:40 -73458.569947] Model parameter optimization (eps = 0.100000) [07:53:54] [worker #0] ML tree search #17, logLikelihood: -73458.389653 [08:14:46] [worker #2] ML tree search #19, logLikelihood: -73453.305118 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.118691,0.243554) (0.111930,1.239282) (0.300416,0.675588) (0.468964,1.342156) 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: -73443.516052 AIC score: 149477.032103 / AICc score: 3506117.032103 / BIC score: 153859.953210 Free parameters (model + branch lengths): 1295 WARNING: Number of free parameters (K=1295) is larger than alignment size (n=218). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15265/3_mltree/O15265.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15265/3_mltree/O15265.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15265/3_mltree/O15265.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/O15265/3_mltree/O15265.raxml.log Analysis started: 26-Jul-2021 00:10:21 / finished: 26-Jul-2021 08:25:07 Elapsed time: 29686.490 seconds Consumed energy: 1181.213 Wh (= 6 km in an electric car, or 30 km with an e-scooter!)