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 01-Jul-2021 22:50:17 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14766/2_msa/Q14766_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14766/3_mltree/Q14766 --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/Q14766/2_msa/Q14766_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 538 sites WARNING: Sequences tr_G3QLA9_G3QLA9_GORGO_9595 and sp_P35555_FBN1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S458_G3S458_GORGO_9595 and tr_H2QGC8_H2QGC8_PANTR_9598 are exactly identical! WARNING: Sequences tr_E2RS46_E2RS46_CANLF_9615 and tr_A0A2Y9IKT0_A0A2Y9IKT0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I3RC60_A0A2I3RC60_PANTR_9598 and tr_A0A2R9AKA2_A0A2R9AKA2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q433_H2Q433_PANTR_9598 and sp_Q9NS15_LTBP3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2R429_H2R429_PANTR_9598 and tr_A0A2R9BKP0_A0A2R9BKP0_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_G7PBA1_G7PBA1_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A096NM08_A0A096NM08_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A2K5L3Z1_A0A2K5L3Z1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5Q4D3_A0A1D5Q4D3_MACMU_9544 and tr_A0A2K6BW09_A0A2K6BW09_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6UHI1_F6UHI1_MACMU_9544 and tr_A0A2K5ZZV8_A0A2K5ZZV8_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7EB76_F7EB76_MACMU_9544 and tr_G7PM02_G7PM02_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7EB76_F7EB76_MACMU_9544 and tr_A0A096MQ74_A0A096MQ74_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7EB76_F7EB76_MACMU_9544 and tr_A0A0D9RGS8_A0A0D9RGS8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7EB76_F7EB76_MACMU_9544 and tr_A0A2K5LUR3_A0A2K5LUR3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7EB76_F7EB76_MACMU_9544 and tr_A0A2K6CH16_A0A2K6CH16_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7EB76_F7EB76_MACMU_9544 and tr_A0A2K6AJP7_A0A2K6AJP7_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1L4Y3_G1L4Y3_AILME_9646 and tr_A0A384DBL5_A0A384DBL5_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1LMU7_G1LMU7_AILME_9646 and tr_A0A384CUD7_A0A384CUD7_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A0D9R657_A0A0D9R657_CHLSB_60711 and tr_A0A2K5LP53_A0A2K5LP53_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151NCY9_A0A151NCY9_ALLMI_8496 and tr_A0A1U8DGN0_A0A1U8DGN0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091VNN5_A0A091VNN5_NIPNI_128390 and tr_A0A087R5P4_A0A087R5P4_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091VNN5_A0A091VNN5_NIPNI_128390 and tr_A0A091FSW9_A0A091FSW9_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091VNN5_A0A091VNN5_NIPNI_128390 and tr_A0A1V4K1A6_A0A1V4K1A6_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0UQZ3_A0A0V0UQZ3_9BILA_181606 and tr_A0A0V1L600_A0A0V1L600_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0UQZ3_A0A0V0UQZ3_9BILA_181606 and tr_A0A0V0TJX0_A0A0V0TJX0_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V0ZS65_A0A0V0ZS65_9BILA_990121 and tr_A0A0V1P4F3_A0A0V1P4F3_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A2D0QCE5_A0A2D0QCE5_ICTPU_7998 and tr_W5UJK4_W5UJK4_ICTPU_7998 are exactly identical! WARNING: Duplicate sequences found: 28 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/Q14766/3_mltree/Q14766.raxml.reduced.phy Alignment comprises 1 partitions and 538 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 538 / 538 Gaps: 18.62 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14766/3_mltree/Q14766.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 2 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 / 269 / 21520 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -779901.964138] Initial branch length optimization [00:00:15 -662580.213059] Model parameter optimization (eps = 10.000000) [00:01:29 -661796.643843] AUTODETECT spr round 1 (radius: 5) [00:05:23 -476127.416227] AUTODETECT spr round 2 (radius: 10) [00:09:46 -366862.187104] AUTODETECT spr round 3 (radius: 15) [00:15:13 -318893.306738] AUTODETECT spr round 4 (radius: 20) [00:20:28 -309207.495772] AUTODETECT spr round 5 (radius: 25) [00:26:43 -292208.071003] SPR radius for FAST iterations: 25 (autodetect) [00:26:43 -292208.071003] Model parameter optimization (eps = 3.000000) [00:27:52 -290866.101254] FAST spr round 1 (radius: 25) [00:35:49 -257593.983449] FAST spr round 2 (radius: 25) [00:40:01 -255484.318981] FAST spr round 3 (radius: 25) [00:43:31 -254901.745379] FAST spr round 4 (radius: 25) [00:46:44 -254819.431795] FAST spr round 5 (radius: 25) [00:49:34 -254816.792451] FAST spr round 6 (radius: 25) [00:52:19 -254811.144730] FAST spr round 7 (radius: 25) [00:54:59 -254809.968832] FAST spr round 8 (radius: 25) [00:57:36 -254809.967016] Model parameter optimization (eps = 1.000000) [00:58:04 -254784.568264] SLOW spr round 1 (radius: 5) [01:01:48 -254705.836545] SLOW spr round 2 (radius: 5) [01:05:27 -254703.325601] SLOW spr round 3 (radius: 5) [01:08:54 -254703.324845] SLOW spr round 4 (radius: 10) [01:12:33 -254701.063858] SLOW spr round 5 (radius: 5) [01:16:46 -254699.350321] SLOW spr round 6 (radius: 5) [01:20:31 -254699.350304] SLOW spr round 7 (radius: 10) [01:24:20 -254699.350302] SLOW spr round 8 (radius: 15) [01:31:02 -254699.350302] SLOW spr round 9 (radius: 20) [01:41:24 -254699.350302] SLOW spr round 10 (radius: 25) [01:55:18 -254699.350302] Model parameter optimization (eps = 0.100000) [01:55:35] [worker #0] ML tree search #1, logLikelihood: -254699.109572 [01:55:35 -779739.428138] Initial branch length optimization [01:55:46 -661471.404751] Model parameter optimization (eps = 10.000000) [01:56:55 -660676.766579] AUTODETECT spr round 1 (radius: 5) [02:00:47 -477411.036225] AUTODETECT spr round 2 (radius: 10) [02:05:17 -375622.635563] AUTODETECT spr round 3 (radius: 15) [02:11:14 -319126.925276] AUTODETECT spr round 4 (radius: 20) [02:17:05 -290156.309473] AUTODETECT spr round 5 (radius: 25) [02:22:42 -283664.925947] SPR radius for FAST iterations: 25 (autodetect) [02:22:42 -283664.925947] Model parameter optimization (eps = 3.000000) [02:22:55 -283646.670974] FAST spr round 1 (radius: 25) [02:30:35 -257387.430879] FAST spr round 2 (radius: 25) [02:30:52] [worker #2] ML tree search #3, logLikelihood: -254679.291824 [02:36:57 -256313.184846] FAST spr round 3 (radius: 25) [02:41:37 -256215.344823] FAST spr round 4 (radius: 25) [02:42:40] [worker #1] ML tree search #2, logLikelihood: -254684.706407 [02:45:34 -256200.987988] FAST spr round 5 (radius: 25) [02:49:02 -256195.267529] FAST spr round 6 (radius: 25) [02:52:14 -256195.265441] Model parameter optimization (eps = 1.000000) [02:52:23 -256194.640277] SLOW spr round 1 (radius: 5) [02:58:00 -256112.289837] SLOW spr round 2 (radius: 5) [03:03:16 -256071.907248] SLOW spr round 3 (radius: 5) [03:08:17 -256066.333802] SLOW spr round 4 (radius: 5) [03:13:02 -256062.339207] SLOW spr round 5 (radius: 5) [03:17:40 -256060.279803] SLOW spr round 6 (radius: 5) [03:22:12 -256060.279206] SLOW spr round 7 (radius: 10) [03:27:11 -256058.536070] SLOW spr round 8 (radius: 5) [03:33:02 -256058.234197] SLOW spr round 9 (radius: 5) [03:38:07 -256058.234052] SLOW spr round 10 (radius: 10) [03:43:28 -256053.798173] SLOW spr round 11 (radius: 5) [03:49:21 -256047.636659] SLOW spr round 12 (radius: 5) [03:54:25 -256046.849184] SLOW spr round 13 (radius: 5) [03:59:04 -256046.848856] SLOW spr round 14 (radius: 10) [04:04:05 -256046.696073] SLOW spr round 15 (radius: 5) [04:09:48 -256046.696058] SLOW spr round 16 (radius: 10) [04:15:34 -256046.696057] SLOW spr round 17 (radius: 15) [04:24:50 -256043.808020] SLOW spr round 18 (radius: 5) [04:31:03 -256041.040435] SLOW spr round 19 (radius: 5) [04:31:58] [worker #2] ML tree search #6, logLikelihood: -254699.280676 [04:36:18 -256041.040127] SLOW spr round 20 (radius: 10) [04:41:35 -256041.040117] SLOW spr round 21 (radius: 15) [04:50:55 -256041.040115] SLOW spr round 22 (radius: 20) [04:54:04] [worker #1] ML tree search #5, logLikelihood: -254677.131998 [05:07:23 -256037.666126] SLOW spr round 23 (radius: 5) [05:13:48 -256034.137091] SLOW spr round 24 (radius: 5) [05:19:09 -256033.926911] SLOW spr round 25 (radius: 5) [05:23:59 -256033.926861] SLOW spr round 26 (radius: 10) [05:28:59 -256033.926858] SLOW spr round 27 (radius: 15) [05:38:26 -256033.876242] SLOW spr round 28 (radius: 20) [05:54:35 -256033.875820] SLOW spr round 29 (radius: 25) [06:15:50 -256033.875810] Model parameter optimization (eps = 0.100000) [06:16:28] [worker #0] ML tree search #4, logLikelihood: -254722.912023 [06:16:28 -775883.106779] Initial branch length optimization [06:16:39 -658822.774752] Model parameter optimization (eps = 10.000000) [06:17:43 -658089.718084] AUTODETECT spr round 1 (radius: 5) [06:21:29 -478771.353230] AUTODETECT spr round 2 (radius: 10) [06:25:52 -377428.196838] AUTODETECT spr round 3 (radius: 15) [06:31:56 -323609.688025] AUTODETECT spr round 4 (radius: 20) [06:37:22 -295864.828043] AUTODETECT spr round 5 (radius: 25) [06:43:48 -284230.866663] SPR radius for FAST iterations: 25 (autodetect) [06:43:48 -284230.866663] Model parameter optimization (eps = 3.000000) [06:44:04 -284211.420254] FAST spr round 1 (radius: 25) [06:51:32 -257417.454700] FAST spr round 2 (radius: 25) [06:57:38 -256302.912310] FAST spr round 3 (radius: 25) [07:01:58 -256198.771361] FAST spr round 4 (radius: 25) [07:05:33 -256182.052271] FAST spr round 5 (radius: 25) [07:08:40 -256182.051399] Model parameter optimization (eps = 1.000000) [07:09:25 -254893.506878] SLOW spr round 1 (radius: 5) [07:13:01] [worker #2] ML tree search #9, logLikelihood: -254701.565175 [07:13:21 -254770.277749] SLOW spr round 2 (radius: 5) [07:17:02 -254756.993494] SLOW spr round 3 (radius: 5) [07:20:40 -254750.169305] SLOW spr round 4 (radius: 5) [07:24:12 -254749.751150] SLOW spr round 5 (radius: 5) [07:27:44 -254746.997017] SLOW spr round 6 (radius: 5) [07:31:11 -254746.996422] SLOW spr round 7 (radius: 10) [07:34:59 -254735.738166] SLOW spr round 8 (radius: 5) [07:39:17 -254731.961091] SLOW spr round 9 (radius: 5) [07:43:03 -254731.960613] SLOW spr round 10 (radius: 10) [07:47:01 -254728.895979] SLOW spr round 11 (radius: 5) [07:47:06] [worker #1] ML tree search #8, logLikelihood: -254669.518851 [07:51:18 -254724.846484] SLOW spr round 12 (radius: 5) [07:55:06 -254724.845245] SLOW spr round 13 (radius: 10) [07:59:03 -254722.818173] SLOW spr round 14 (radius: 5) [08:03:15 -254721.123608] SLOW spr round 15 (radius: 5) [08:07:02 -254720.828394] SLOW spr round 16 (radius: 5) [08:10:36 -254720.827731] SLOW spr round 17 (radius: 10) [08:14:26 -254718.914690] SLOW spr round 18 (radius: 5) [08:18:44 -254713.493537] SLOW spr round 19 (radius: 5) [08:22:29 -254713.493196] SLOW spr round 20 (radius: 10) [08:26:27 -254713.302651] SLOW spr round 21 (radius: 5) [08:30:43 -254712.276624] SLOW spr round 22 (radius: 5) [08:34:33 -254710.026878] SLOW spr round 23 (radius: 5) [08:38:08 -254708.662201] SLOW spr round 24 (radius: 5) [08:41:37 -254708.661415] SLOW spr round 25 (radius: 10) [08:45:23 -254708.661064] SLOW spr round 26 (radius: 15) [08:52:19 -254708.441096] SLOW spr round 27 (radius: 5) [08:56:51 -254697.806171] SLOW spr round 28 (radius: 5) [09:00:47 -254696.958590] SLOW spr round 29 (radius: 5) [09:04:24 -254696.958225] SLOW spr round 30 (radius: 10) [09:08:10 -254696.958218] SLOW spr round 31 (radius: 15) [09:14:53 -254696.958218] SLOW spr round 32 (radius: 20) [09:25:24 -254693.958150] SLOW spr round 33 (radius: 5) [09:30:03 -254688.349737] SLOW spr round 34 (radius: 5) [09:34:01 -254688.349388] SLOW spr round 35 (radius: 10) [09:38:08 -254688.349357] SLOW spr round 36 (radius: 15) [09:44:37 -254688.349339] SLOW spr round 37 (radius: 20) [09:55:06 -254688.349324] SLOW spr round 38 (radius: 25) [10:08:35 -254687.823319] SLOW spr round 39 (radius: 5) [10:13:09 -254687.823313] SLOW spr round 40 (radius: 10) [10:18:01 -254687.823308] SLOW spr round 41 (radius: 15) [10:19:41] [worker #1] ML tree search #11, logLikelihood: -254666.724176 [10:21:14] [worker #2] ML tree search #12, logLikelihood: -254696.648131 [10:24:20 -254687.823303] SLOW spr round 42 (radius: 20) [10:35:05 -254687.823300] SLOW spr round 43 (radius: 25) [10:48:36 -254687.789765] Model parameter optimization (eps = 0.100000) [10:48:52] [worker #0] ML tree search #7, logLikelihood: -254687.171831 [10:48:52 -773784.854445] Initial branch length optimization [10:49:02 -655429.665677] Model parameter optimization (eps = 10.000000) [10:49:58 -654781.445852] AUTODETECT spr round 1 (radius: 5) [10:53:47 -475687.893981] AUTODETECT spr round 2 (radius: 10) [10:58:10 -377396.612820] AUTODETECT spr round 3 (radius: 15) [11:03:52 -324756.754255] AUTODETECT spr round 4 (radius: 20) [11:09:15 -299376.807374] AUTODETECT spr round 5 (radius: 25) [11:15:42 -291844.103840] SPR radius for FAST iterations: 25 (autodetect) [11:15:42 -291844.103840] Model parameter optimization (eps = 3.000000) [11:16:36 -290481.007276] FAST spr round 1 (radius: 25) [11:23:49 -257064.842788] FAST spr round 2 (radius: 25) [11:28:03 -255069.893534] FAST spr round 3 (radius: 25) [11:31:35 -254905.343196] FAST spr round 4 (radius: 25) [11:34:53 -254895.698848] FAST spr round 5 (radius: 25) [11:37:47 -254891.208511] FAST spr round 6 (radius: 25) [11:40:32 -254890.216406] FAST spr round 7 (radius: 25) [11:43:13 -254890.216042] Model parameter optimization (eps = 1.000000) [11:43:42 -254859.744783] SLOW spr round 1 (radius: 5) [11:47:32 -254777.660126] SLOW spr round 2 (radius: 5) [11:51:09 -254771.547413] SLOW spr round 3 (radius: 5) [11:54:48 -254762.667953] SLOW spr round 4 (radius: 5) [11:58:24 -254728.972033] SLOW spr round 5 (radius: 5) [12:01:59 -254711.616645] SLOW spr round 6 (radius: 5) [12:05:36 -254694.265418] SLOW spr round 7 (radius: 5) [12:09:10 -254683.913032] SLOW spr round 8 (radius: 5) [12:12:38 -254680.604453] SLOW spr round 9 (radius: 5) [12:16:02 -254680.603352] SLOW spr round 10 (radius: 10) [12:19:42 -254676.098509] SLOW spr round 11 (radius: 5) [12:23:55 -254674.392065] SLOW spr round 12 (radius: 5) [12:27:43 -254674.096108] SLOW spr round 13 (radius: 5) [12:31:16 -254674.095797] SLOW spr round 14 (radius: 10) [12:35:02 -254674.095792] SLOW spr round 15 (radius: 15) [12:41:53 -254662.920020] SLOW spr round 16 (radius: 5) [12:45:01] [worker #1] ML tree search #14, logLikelihood: -254678.549583 [12:46:26 -254659.985361] SLOW spr round 17 (radius: 5) [12:50:28 -254654.353824] SLOW spr round 18 (radius: 5) [12:54:06 -254654.195304] SLOW spr round 19 (radius: 5) [12:57:36 -254654.195150] SLOW spr round 20 (radius: 10) [13:01:16 -254654.195128] SLOW spr round 21 (radius: 15) [13:08:21 -254654.195119] SLOW spr round 22 (radius: 20) [13:18:23 -254654.195115] SLOW spr round 23 (radius: 25) [13:22:06] [worker #2] ML tree search #15, logLikelihood: -254695.670065 [13:32:08 -254654.161962] Model parameter optimization (eps = 0.100000) [13:32:28] [worker #0] ML tree search #10, logLikelihood: -254652.558389 [13:32:28 -779082.127431] Initial branch length optimization [13:32:37 -660888.622201] Model parameter optimization (eps = 10.000000) [13:33:47 -659996.530765] AUTODETECT spr round 1 (radius: 5) [13:37:38 -484801.028558] AUTODETECT spr round 2 (radius: 10) [13:42:05 -376267.274368] AUTODETECT spr round 3 (radius: 15) [13:47:49 -316391.767002] AUTODETECT spr round 4 (radius: 20) [13:53:33 -293951.340896] AUTODETECT spr round 5 (radius: 25) [13:59:38 -289516.491018] SPR radius for FAST iterations: 25 (autodetect) [13:59:38 -289516.491018] Model parameter optimization (eps = 3.000000) [14:00:27 -288176.967168] FAST spr round 1 (radius: 25) [14:08:15 -257743.093806] FAST spr round 2 (radius: 25) [14:12:48 -255074.198246] FAST spr round 3 (radius: 25) [14:16:34 -254835.382061] FAST spr round 4 (radius: 25) [14:20:04 -254789.570286] FAST spr round 5 (radius: 25) [14:22:56 -254786.775703] FAST spr round 6 (radius: 25) [14:25:39 -254786.339487] FAST spr round 7 (radius: 25) [14:28:19 -254786.338580] Model parameter optimization (eps = 1.000000) [14:28:48 -254757.644854] SLOW spr round 1 (radius: 5) [14:32:48 -254702.138916] SLOW spr round 2 (radius: 5) [14:36:31 -254699.325761] SLOW spr round 3 (radius: 5) [14:39:56 -254699.325027] SLOW spr round 4 (radius: 10) [14:43:34 -254698.435265] SLOW spr round 5 (radius: 5) [14:47:47 -254696.035676] SLOW spr round 6 (radius: 5) [14:51:32 -254696.035215] SLOW spr round 7 (radius: 10) [14:55:23 -254695.922504] SLOW spr round 8 (radius: 5) [14:59:48 -254694.734189] SLOW spr round 9 (radius: 5) [15:03:54 -254694.731245] SLOW spr round 10 (radius: 10) [15:08:08 -254694.730320] SLOW spr round 11 (radius: 15) [15:15:52 -254694.729658] SLOW spr round 12 (radius: 20) [15:27:31 -254694.729107] SLOW spr round 13 (radius: 25) [15:43:08 -254694.728603] Model parameter optimization (eps = 0.100000) [15:43:20] [worker #0] ML tree search #13, logLikelihood: -254694.654506 [15:43:20 -776759.754193] Initial branch length optimization [15:43:36 -663263.173254] Model parameter optimization (eps = 10.000000) [15:44:30 -662453.514456] AUTODETECT spr round 1 (radius: 5) [15:48:34 -473937.520543] AUTODETECT spr round 2 (radius: 10) [15:50:46] [worker #1] ML tree search #17, logLikelihood: -254692.857684 [15:53:22 -351696.410589] AUTODETECT spr round 3 (radius: 15) [15:58:31 -306865.613263] AUTODETECT spr round 4 (radius: 20) [16:04:09 -284337.589939] AUTODETECT spr round 5 (radius: 25) [16:11:36 -278483.146239] SPR radius for FAST iterations: 25 (autodetect) [16:11:36 -278483.146239] Model parameter optimization (eps = 3.000000) [16:12:30 -277140.533248] FAST spr round 1 (radius: 25) [16:19:47 -256174.028357] FAST spr round 2 (radius: 25) [16:24:20 -255007.911283] FAST spr round 3 (radius: 25) [16:28:12 -254909.235399] FAST spr round 4 (radius: 25) [16:31:44 -254880.534043] FAST spr round 5 (radius: 25) [16:34:57 -254865.697204] FAST spr round 6 (radius: 25) [16:37:58 -254865.695678] Model parameter optimization (eps = 1.000000) [16:38:29 -254844.161231] SLOW spr round 1 (radius: 5) [16:42:38 -254796.416394] SLOW spr round 2 (radius: 5) [16:46:41 -254784.628683] SLOW spr round 3 (radius: 5) [16:50:35 -254784.628006] SLOW spr round 4 (radius: 10) [16:54:47 -254781.695007] SLOW spr round 5 (radius: 5) [16:59:24 -254780.104522] SLOW spr round 6 (radius: 5) [17:03:32 -254780.104472] SLOW spr round 7 (radius: 10) [17:07:58 -254778.713686] SLOW spr round 8 (radius: 5) [17:12:34 -254777.724094] SLOW spr round 9 (radius: 5) [17:16:43 -254776.444491] SLOW spr round 10 (radius: 5) [17:20:40 -254776.442872] SLOW spr round 11 (radius: 10) [17:24:57 -254775.674387] SLOW spr round 12 (radius: 5) [17:29:35 -254772.977798] SLOW spr round 13 (radius: 5) [17:33:46 -254772.977541] SLOW spr round 14 (radius: 10) [17:38:08 -254772.438547] SLOW spr round 15 (radius: 5) [17:42:41 -254772.437828] SLOW spr round 16 (radius: 10) [17:45:44] [worker #2] ML tree search #18, logLikelihood: -254698.477741 [17:47:27 -254772.437809] SLOW spr round 17 (radius: 15) [17:54:38 -254772.437806] SLOW spr round 18 (radius: 20) [18:05:35 -254717.625848] SLOW spr round 19 (radius: 5) [18:10:33 -254716.093801] SLOW spr round 20 (radius: 5) [18:14:52 -254716.093331] SLOW spr round 21 (radius: 10) [18:19:18 -254716.092879] SLOW spr round 22 (radius: 15) [18:26:33 -254716.092428] SLOW spr round 23 (radius: 20) [18:37:36 -254716.091978] SLOW spr round 24 (radius: 25) [18:53:03 -254716.091527] Model parameter optimization (eps = 0.100000) [18:53:20] [worker #0] ML tree search #16, logLikelihood: -254715.960460 [18:53:20 -780515.176079] Initial branch length optimization [18:53:34 -666106.871525] Model parameter optimization (eps = 10.000000) [18:54:54 -665291.163678] AUTODETECT spr round 1 (radius: 5) [18:59:08 -473714.161154] AUTODETECT spr round 2 (radius: 10) [19:03:58 -355385.570591] AUTODETECT spr round 3 (radius: 15) [19:09:07 -315379.566117] AUTODETECT spr round 4 (radius: 20) [19:09:17] [worker #1] ML tree search #20, logLikelihood: -254647.067077 [19:15:09 -293285.494852] AUTODETECT spr round 5 (radius: 25) [19:21:49 -285269.455903] SPR radius for FAST iterations: 25 (autodetect) [19:21:49 -285269.455903] Model parameter optimization (eps = 3.000000) [19:22:39 -283998.796093] FAST spr round 1 (radius: 25) [19:30:44 -256573.144076] FAST spr round 2 (radius: 25) [19:35:34 -255051.107017] FAST spr round 3 (radius: 25) [19:39:38 -254861.406868] FAST spr round 4 (radius: 25) [19:43:15 -254822.885861] FAST spr round 5 (radius: 25) [19:46:23 -254818.330400] FAST spr round 6 (radius: 25) [19:49:20 -254817.259792] FAST spr round 7 (radius: 25) [19:52:13 -254817.258440] Model parameter optimization (eps = 1.000000) [19:52:21 -254816.304231] SLOW spr round 1 (radius: 5) [19:56:29 -254765.810446] SLOW spr round 2 (radius: 5) [20:00:31 -254757.678330] SLOW spr round 3 (radius: 5) [20:04:15 -254757.627753] SLOW spr round 4 (radius: 10) [20:08:19 -254756.070041] SLOW spr round 5 (radius: 5) [20:13:14 -254746.838864] SLOW spr round 6 (radius: 5) [20:17:31 -254744.381161] SLOW spr round 7 (radius: 5) [20:21:28 -254742.107729] SLOW spr round 8 (radius: 5) [20:25:14 -254742.094067] SLOW spr round 9 (radius: 10) [20:29:17 -254741.813196] SLOW spr round 10 (radius: 5) [20:33:57 -254739.084516] SLOW spr round 11 (radius: 5) [20:38:06 -254738.158628] SLOW spr round 12 (radius: 5) [20:41:58 -254738.157835] SLOW spr round 13 (radius: 10) [20:46:04 -254738.157803] SLOW spr round 14 (radius: 15) [20:53:49 -254738.157800] SLOW spr round 15 (radius: 20) [21:05:02 -254738.157798] SLOW spr round 16 (radius: 25) [21:20:31 -254738.157797] Model parameter optimization (eps = 0.100000) [21:21:00] [worker #0] ML tree search #19, logLikelihood: -254697.802734 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.276991,0.231717) (0.092278,1.136284) (0.404558,1.053758) (0.226174,1.789139) 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: -254647.067077 AIC score: 513304.134153 / AICc score: 8557364.134153 / BIC score: 521901.290566 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=538). 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/Q14766/3_mltree/Q14766.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14766/3_mltree/Q14766.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14766/3_mltree/Q14766.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q14766/3_mltree/Q14766.raxml.log Analysis started: 01-Jul-2021 22:50:17 / finished: 02-Jul-2021 20:11:18 Elapsed time: 76860.803 seconds Consumed energy: 7184.431 Wh (= 36 km in an electric car, or 180 km with an e-scooter!)