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 07:46:32 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0D4/2_msa/Q9C0D4_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0D4/3_mltree/Q9C0D4 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0D4/2_msa/Q9C0D4_trimmed_msa.fasta [00:00:00] Loaded alignment with 445 taxa and 229 sites WARNING: Sequences tr_M3Z1N5_M3Z1N5_MUSPF_9669 and tr_A0A2Y9IRR3_A0A2Y9IRR3_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3G238_A0A2I3G238_NOMLE_61853 and tr_G3RCJ8_G3RCJ8_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3G238_A0A2I3G238_NOMLE_61853 and tr_F6S565_F6S565_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3G238_A0A2I3G238_NOMLE_61853 and tr_F7I5H1_F7I5H1_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I3G238_A0A2I3G238_NOMLE_61853 and tr_G7PG42_G7PG42_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3G238_A0A2I3G238_NOMLE_61853 and tr_A0A096NX24_A0A096NX24_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3G238_A0A2I3G238_NOMLE_61853 and tr_A0A0D9RQ48_A0A0D9RQ48_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3G238_A0A2I3G238_NOMLE_61853 and tr_A0A2K5N3E7_A0A2K5N3E7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3G238_A0A2I3G238_NOMLE_61853 and tr_A0A2K6CSE2_A0A2K6CSE2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3G238_A0A2I3G238_NOMLE_61853 and tr_A0A2K5YZC4_A0A2K5YZC4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_H2QEQ6_H2QEQ6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and sp_Q9UL36_ZN236_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A1D5QSW3_A0A1D5QSW3_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_G7PW99_G7PW99_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A2I3MNE4_A0A2I3MNE4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A0D9S067_A0A0D9S067_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A2K5M0C3_A0A2K5M0C3_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A2K6D1J3_A0A2K6D1J3_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RDR1_G1RDR1_NOMLE_61853 and tr_A0A2R9BWH1_A0A2R9BWH1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3HWH0_G3HWH0_CRIGR_10029 and tr_A0A1U8BPG2_A0A1U8BPG2_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3I5C3_G3I5C3_CRIGR_10029 and tr_A0A3Q0DDN9_A0A3Q0DDN9_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A2I2Y3M2_A0A2I2Y3M2_GORGO_9595 and sp_Q6AHZ1_Z518A_HUMAN_9606 are exactly identical! WARNING: Sequences tr_K7CQ46_K7CQ46_PANTR_9598 and tr_A0A2R9CBC3_A0A2R9CBC3_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7EZ91_F7EZ91_MACMU_9544 and tr_G7P598_G7P598_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7EZ91_F7EZ91_MACMU_9544 and tr_A0A2K6B2N3_A0A2K6B2N3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GCU9_F7GCU9_MACMU_9544 and tr_G7PDM8_G7PDM8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GCU9_F7GCU9_MACMU_9544 and tr_A0A0D9SAU8_A0A0D9SAU8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7GCU9_F7GCU9_MACMU_9544 and tr_A0A2K5KQN3_A0A2K5KQN3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7GCU9_F7GCU9_MACMU_9544 and tr_A0A2K6B7P2_A0A2K6B7P2_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GCU9_F7GCU9_MACMU_9544 and tr_A0A2K5XMQ0_A0A2K5XMQ0_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0ZHW6_H0ZHW6_TAEGU_59729 and tr_A0A218VCU2_A0A218VCU2_9PASE_299123 are exactly identical! WARNING: Sequences tr_F7ISS8_F7ISS8_CALJA_9483 and tr_A0A2K5Z066_A0A2K5Z066_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1M279_G1M279_AILME_9646 and tr_A0A2U3WAD5_A0A2U3WAD5_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1M279_G1M279_AILME_9646 and tr_A0A384CPN1_A0A384CPN1_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A0D9SEA7_A0A0D9SEA7_CHLSB_60711 and tr_A0A2K5KVA6_A0A2K5KVA6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0D9SEA7_A0A0D9SEA7_CHLSB_60711 and tr_A0A2K5XKF5_A0A2K5XKF5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151MPP5_A0A151MPP5_ALLMI_8496 and tr_A0A1U7SBY9_A0A1U7SBY9_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091IYU7_A0A091IYU7_EGRGA_188379 and tr_A0A091VZJ8_A0A091VZJ8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IYU7_A0A091IYU7_EGRGA_188379 and tr_A0A087R9R0_A0A087R9R0_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IYU7_A0A091IYU7_EGRGA_188379 and tr_A0A093HW31_A0A093HW31_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091IYU7_A0A091IYU7_EGRGA_188379 and tr_A0A0A0B2Y1_A0A0A0B2Y1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091IYU7_A0A091IYU7_EGRGA_188379 and tr_A0A093G3V8_A0A093G3V8_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A2I0LXN2_A0A2I0LXN2_COLLI_8932 and tr_A0A1V4JT41_A0A1V4JT41_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2Y9K7X4_A0A2Y9K7X4_ENHLU_391180 and tr_A0A2Y9K8U2_A0A2Y9K8U2_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2Y9MVG3_A0A2Y9MVG3_DELLE_9749 and tr_A0A2Y9FC95_A0A2Y9FC95_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 45 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/Q9C0D4/3_mltree/Q9C0D4.raxml.reduced.phy Alignment comprises 1 partitions and 229 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 229 / 229 Gaps: 11.40 % Invariant sites: 0.44 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0D4/3_mltree/Q9C0D4.raxml.rba Parallelization scheme autoconfig: 5 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 445 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 229 / 18320 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -208394.972762] Initial branch length optimization [00:00:02 -170845.083262] Model parameter optimization (eps = 10.000000) [00:00:23 -170439.373613] AUTODETECT spr round 1 (radius: 5) [00:01:01 -107360.757351] AUTODETECT spr round 2 (radius: 10) [00:01:47 -75348.295406] AUTODETECT spr round 3 (radius: 15) [00:02:38 -64867.592831] AUTODETECT spr round 4 (radius: 20) [00:03:36 -59337.679365] AUTODETECT spr round 5 (radius: 25) [00:04:42 -58639.108927] SPR radius for FAST iterations: 25 (autodetect) [00:04:42 -58639.108927] Model parameter optimization (eps = 3.000000) [00:04:52 -58628.486740] FAST spr round 1 (radius: 25) [00:05:49 -51505.251725] FAST spr round 2 (radius: 25) [00:06:29 -51153.650874] FAST spr round 3 (radius: 25) [00:07:03 -51133.104989] FAST spr round 4 (radius: 25) [00:07:33 -51129.865534] FAST spr round 5 (radius: 25) [00:08:01 -51128.180756] FAST spr round 6 (radius: 25) [00:08:29 -51128.178873] Model parameter optimization (eps = 1.000000) [00:08:37 -51117.978144] SLOW spr round 1 (radius: 5) [00:09:27 -51109.106388] SLOW spr round 2 (radius: 5) [00:10:12 -51108.273002] SLOW spr round 3 (radius: 5) [00:10:58 -51105.877937] SLOW spr round 4 (radius: 5) [00:11:41 -51105.877692] SLOW spr round 5 (radius: 10) [00:12:25 -51104.105360] SLOW spr round 6 (radius: 5) [00:13:24 -51102.953149] SLOW spr round 7 (radius: 5) [00:14:17 -51097.735568] SLOW spr round 8 (radius: 5) [00:15:05 -51095.853530] SLOW spr round 9 (radius: 5) [00:15:50 -51095.853337] SLOW spr round 10 (radius: 10) [00:16:33 -51095.853334] SLOW spr round 11 (radius: 15) [00:17:51 -51095.157502] SLOW spr round 12 (radius: 5) [00:18:54 -51093.868457] SLOW spr round 13 (radius: 5) [00:19:35] [worker #3] ML tree search #4, logLikelihood: -51108.928084 [00:19:47 -51093.867888] SLOW spr round 14 (radius: 10) [00:20:36 -51093.867873] SLOW spr round 15 (radius: 15) [00:21:12] [worker #4] ML tree search #5, logLikelihood: -51121.716308 [00:21:48 -51093.867873] SLOW spr round 16 (radius: 20) [00:23:23 -51093.867872] SLOW spr round 17 (radius: 25) [00:25:22 -51093.867872] Model parameter optimization (eps = 0.100000) [00:25:25] [worker #0] ML tree search #1, logLikelihood: -51093.845694 [00:25:25 -205052.938858] Initial branch length optimization [00:25:28 -168524.623404] Model parameter optimization (eps = 10.000000) [00:25:49 -168097.962603] AUTODETECT spr round 1 (radius: 5) [00:26:29 -96390.914131] AUTODETECT spr round 2 (radius: 10) [00:27:12 -70574.509440] AUTODETECT spr round 3 (radius: 15) [00:28:06 -60245.085774] AUTODETECT spr round 4 (radius: 20) [00:28:09] [worker #1] ML tree search #2, logLikelihood: -51095.326523 [00:29:18 -56817.948666] AUTODETECT spr round 5 (radius: 25) [00:30:40 -56726.238818] SPR radius for FAST iterations: 25 (autodetect) [00:30:40 -56726.238818] Model parameter optimization (eps = 3.000000) [00:30:49 -56696.901763] FAST spr round 1 (radius: 25) [00:31:24] [worker #2] ML tree search #3, logLikelihood: -51086.974606 [00:31:41 -51335.750686] FAST spr round 2 (radius: 25) [00:32:21 -51186.448571] FAST spr round 3 (radius: 25) [00:32:57 -51155.001372] FAST spr round 4 (radius: 25) [00:33:33 -51148.216874] FAST spr round 5 (radius: 25) [00:34:02 -51148.215976] Model parameter optimization (eps = 1.000000) [00:34:11 -51132.623801] SLOW spr round 1 (radius: 5) [00:35:04 -51120.101674] SLOW spr round 2 (radius: 5) [00:35:53 -51119.173258] SLOW spr round 3 (radius: 5) [00:36:38 -51119.173141] SLOW spr round 4 (radius: 10) [00:37:24 -51114.304652] SLOW spr round 5 (radius: 5) [00:38:25 -51111.699335] SLOW spr round 6 (radius: 5) [00:39:18 -51110.691982] SLOW spr round 7 (radius: 5) [00:40:06 -51110.691883] SLOW spr round 8 (radius: 10) [00:40:49 -51110.691790] SLOW spr round 9 (radius: 15) [00:41:01] [worker #4] ML tree search #10, logLikelihood: -51096.598888 [00:42:12 -51110.691697] SLOW spr round 10 (radius: 20) [00:43:55] [worker #3] ML tree search #9, logLikelihood: -51127.239985 [00:44:08 -51110.691604] SLOW spr round 11 (radius: 25) [00:46:26 -51110.691512] Model parameter optimization (eps = 0.100000) [00:46:29] [worker #0] ML tree search #6, logLikelihood: -51110.689860 [00:46:29 -207141.377361] Initial branch length optimization [00:46:31 -172300.419676] Model parameter optimization (eps = 10.000000) [00:46:55 -171868.026648] AUTODETECT spr round 1 (radius: 5) [00:47:34 -97955.727093] AUTODETECT spr round 2 (radius: 10) [00:48:19 -71459.312111] AUTODETECT spr round 3 (radius: 15) [00:49:08 -60131.747215] AUTODETECT spr round 4 (radius: 20) [00:50:15 -55790.109973] AUTODETECT spr round 5 (radius: 25) [00:51:37 -55681.239794] SPR radius for FAST iterations: 25 (autodetect) [00:51:37 -55681.239794] Model parameter optimization (eps = 3.000000) [00:51:47 -55639.295022] FAST spr round 1 (radius: 25) [00:52:40 -51436.072803] FAST spr round 2 (radius: 25) [00:53:17 -51147.259694] FAST spr round 3 (radius: 25) [00:53:52 -51127.923096] FAST spr round 4 (radius: 25) [00:54:21 -51127.922399] Model parameter optimization (eps = 1.000000) [00:54:29 -51125.641930] SLOW spr round 1 (radius: 5) [00:55:19 -51106.916908] SLOW spr round 2 (radius: 5) [00:56:07 -51102.819712] SLOW spr round 3 (radius: 5) [00:56:51 -51102.819502] SLOW spr round 4 (radius: 10) [00:57:37 -51091.769805] SLOW spr round 5 (radius: 5) [00:58:01] [worker #1] ML tree search #7, logLikelihood: -51115.480879 [00:58:39 -51087.308702] SLOW spr round 6 (radius: 5) [00:59:32 -51087.302725] SLOW spr round 7 (radius: 10) [01:00:18 -51087.167069] SLOW spr round 8 (radius: 5) [01:00:19] [worker #2] ML tree search #8, logLikelihood: -51094.476680 [01:01:14 -51087.166903] SLOW spr round 9 (radius: 10) [01:02:05 -51087.166874] SLOW spr round 10 (radius: 15) [01:03:01] [worker #4] ML tree search #15, logLikelihood: -51097.967037 [01:03:21 -51086.840811] SLOW spr round 11 (radius: 5) [01:04:22 -51086.840517] SLOW spr round 12 (radius: 10) [01:05:20 -51086.840515] SLOW spr round 13 (radius: 15) [01:06:35 -51086.840514] SLOW spr round 14 (radius: 20) [01:08:19 -51086.840514] SLOW spr round 15 (radius: 25) [01:09:26] [worker #3] ML tree search #14, logLikelihood: -51071.470900 [01:10:39 -51086.840514] Model parameter optimization (eps = 0.100000) [01:10:45] [worker #0] ML tree search #11, logLikelihood: -51085.956054 [01:10:46 -208733.246448] Initial branch length optimization [01:10:48 -170711.767142] Model parameter optimization (eps = 10.000000) [01:11:09 -170299.982220] AUTODETECT spr round 1 (radius: 5) [01:11:51 -103505.608102] AUTODETECT spr round 2 (radius: 10) [01:12:37 -75977.248672] AUTODETECT spr round 3 (radius: 15) [01:13:32 -61688.383866] AUTODETECT spr round 4 (radius: 20) [01:14:36 -56600.329683] AUTODETECT spr round 5 (radius: 25) [01:15:41 -56256.404874] SPR radius for FAST iterations: 25 (autodetect) [01:15:41 -56256.404874] Model parameter optimization (eps = 3.000000) [01:15:57 -56211.953696] FAST spr round 1 (radius: 25) [01:16:53 -51381.311455] FAST spr round 2 (radius: 25) [01:17:37 -51157.132157] FAST spr round 3 (radius: 25) [01:18:11 -51146.171799] FAST spr round 4 (radius: 25) [01:18:17] [worker #1] ML tree search #12, logLikelihood: -51106.851590 [01:18:41 -51146.170993] Model parameter optimization (eps = 1.000000) [01:18:48 -51144.672429] SLOW spr round 1 (radius: 5) [01:19:41 -51113.066692] SLOW spr round 2 (radius: 5) [01:20:29 -51110.490286] SLOW spr round 3 (radius: 5) [01:21:16 -51109.811508] SLOW spr round 4 (radius: 5) [01:22:02 -51109.800736] SLOW spr round 5 (radius: 10) [01:22:48 -51107.923646] SLOW spr round 6 (radius: 5) [01:23:50 -51105.752288] SLOW spr round 7 (radius: 5) [01:24:43 -51105.751965] SLOW spr round 8 (radius: 10) [01:24:55] [worker #4] ML tree search #20, logLikelihood: -51077.364326 [01:25:01] [worker #2] ML tree search #13, logLikelihood: -51105.302343 [01:25:32 -51105.751957] SLOW spr round 9 (radius: 15) [01:26:52 -51105.751957] SLOW spr round 10 (radius: 20) [01:28:42 -51105.751956] SLOW spr round 11 (radius: 25) [01:30:55 -51105.751956] Model parameter optimization (eps = 0.100000) [01:31:01] [worker #0] ML tree search #16, logLikelihood: -51105.629134 [01:34:14] [worker #3] ML tree search #19, logLikelihood: -51110.901557 [01:49:21] [worker #1] ML tree search #17, logLikelihood: -51093.293793 [01:55:57] [worker #2] ML tree search #18, logLikelihood: -51106.370491 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.128263,0.217491) (0.136099,0.523324) (0.513127,1.111228) (0.222511,1.486126) 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: -51071.470900 AIC score: 103928.941799 / AICc score: 1700612.941799 / BIC score: 106995.255548 Free parameters (model + branch lengths): 893 WARNING: Number of free parameters (K=893) is larger than alignment size (n=229). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 74 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0D4/3_mltree/Q9C0D4.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0D4/3_mltree/Q9C0D4.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0D4/3_mltree/Q9C0D4.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0D4/3_mltree/Q9C0D4.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0D4/3_mltree/Q9C0D4.raxml.log Analysis started: 02-Jul-2021 07:46:32 / finished: 02-Jul-2021 09:42:29 Elapsed time: 6957.373 seconds Consumed energy: 577.002 Wh (= 3 km in an electric car, or 14 km with an e-scooter!)