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 13:52:14 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00139/2_msa/O00139_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00139/3_mltree/O00139 --seed 2 --threads 7 --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 (7 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00139/2_msa/O00139_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 464 sites WARNING: Sequences tr_A0A1D5PBU5_A0A1D5PBU5_CHICK_9031 and sp_Q5ZKV8_KIF2A_CHICK_9031 are exactly identical! WARNING: Sequences tr_G1PIW8_G1PIW8_MYOLU_59463 and tr_W5PAF9_W5PAF9_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1PIW8_G1PIW8_MYOLU_59463 and tr_A0A1D5QCA7_A0A1D5QCA7_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and sp_Q5R9Y9_KIF2A_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_J9P9X3_J9P9X3_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_H2RDI1_H2RDI1_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_F6Z551_F6Z551_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_G1LC09_G1LC09_AILME_9646 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_G3N277_G3N277_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_L5L2N5_L5L2N5_PTEAL_9402 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_M3W081_M3W081_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A0D9RU07_A0A0D9RU07_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A2K5KXZ0_A0A2K5KXZ0_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A2K6BPL4_A0A2K6BPL4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A2K5ZCF8_A0A2K5ZCF8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A2R9AXY9_A0A2R9AXY9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A2U4AX67_A0A2U4AX67_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A2U3X1W2_A0A2U3X1W2_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A2U3XIH9_A0A2U3XIH9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A2Y9KIL9_A0A2Y9KIL9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A2Y9Q091_A0A2Y9Q091_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2I2Z8R8_A0A2I2Z8R8_GORGO_9595 and tr_A0A2Y9TD17_A0A2Y9TD17_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1TTN7_G1TTN7_RABIT_9986 and tr_F7BVC4_F7BVC4_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1TTN7_G1TTN7_RABIT_9986 and tr_G3T4P9_G3T4P9_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G1TTN7_G1TTN7_RABIT_9986 and tr_A0A384C3Z5_A0A384C3Z5_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1TTN7_G1TTN7_RABIT_9986 and tr_A0A383ZLS9_A0A383ZLS9_BALAS_310752 are exactly identical! WARNING: Sequences tr_H2PYW2_H2PYW2_PANTR_9598 and tr_A0A2R9CTM1_A0A2R9CTM1_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0FPQ1_A0A0E0FPQ1_ORYNI_4536 and tr_B8ABY9_B8ABY9_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0FPQ1_A0A0E0FPQ1_ORYNI_4536 and tr_I1NPU1_I1NPU1_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0FPQ1_A0A0E0FPQ1_ORYNI_4536 and tr_A0A0E0MZG8_A0A0E0MZG8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0FPQ1_A0A0E0FPQ1_ORYNI_4536 and tr_A0A0D3ERF1_A0A0D3ERF1_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0FPQ1_A0A0E0FPQ1_ORYNI_4536 and tr_A0A0D9YBX7_A0A0D9YBX7_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A0A0E0FPQ1_A0A0E0FPQ1_ORYNI_4536 and sp_B9EY52_KN13B_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0H9T1_A0A0E0H9T1_ORYNI_4536 and tr_A0A0E0DM85_A0A0E0DM85_9ORYZ_40149 are exactly identical! WARNING: Sequences tr_A0A0E0H9T1_A0A0E0H9T1_ORYNI_4536 and tr_A0A0E0PHQ8_A0A0E0PHQ8_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0H9T1_A0A0E0H9T1_ORYNI_4536 and sp_B9FMJ3_KN13A_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_F7HEG1_F7HEG1_MACMU_9544 and tr_A0A2I3N0B5_A0A2I3N0B5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HEG1_F7HEG1_MACMU_9544 and tr_A0A2K5NJ81_A0A2K5NJ81_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MGN3_G7MGN3_MACMU_9544 and tr_A0A2K5LQC9_A0A2K5LQC9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7MGN3_G7MGN3_MACMU_9544 and tr_A0A2K6D0R7_A0A2K6D0R7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7MGN3_G7MGN3_MACMU_9544 and tr_A0A2K6A9I9_A0A2K6A9I9_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K1ZLF6_A0A2K1ZLF6_POPTR_3694 and tr_A0A2K1ZLK8_A0A2K1ZLK8_POPTR_3694 are exactly identical! WARNING: Sequences tr_I1PSK8_I1PSK8_ORYGL_4538 and tr_A0A0D3G3E4_A0A0D3G3E4_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A8XSE1_A8XSE1_CAEBR_6238 and tr_A0A2G5UTF1_A0A2G5UTF1_9PELO_1611254 are exactly identical! WARNING: Sequences tr_I1M5K9_I1M5K9_SOYBN_3847 and tr_I1MCP5_I1MCP5_SOYBN_3847 are exactly identical! WARNING: Sequences tr_W2Q332_W2Q332_PHYPN_761204 and tr_W2GKZ7_W2GKZ7_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A044VJB0_A0A044VJB0_ONCVO_6282 and tr_A0A182ECV9_A0A182ECV9_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A0E0JLD2_A0A0E0JLD2_ORYPU_4537 and tr_A0A0E0JLD3_A0A0E0JLD3_ORYPU_4537 are exactly identical! WARNING: Sequences tr_A0A078GT26_A0A078GT26_BRANA_3708 and tr_A0A078HB17_A0A078HB17_BRANA_3708 are exactly identical! WARNING: Sequences tr_V4S264_V4S264_9ROSI_85681 and tr_A0A2H5N6Q0_A0A2H5N6Q0_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0L9TB52_A0A0L9TB52_PHAAN_3914 and tr_A0A1S3V9W3_A0A1S3V9W3_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A087QP42_A0A087QP42_APTFO_9233 and tr_A0A093HX24_A0A093HX24_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A087QP42_A0A087QP42_APTFO_9233 and tr_A0A0A0A4J8_A0A0A0A4J8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A0V1CKF8_A0A0V1CKF8_TRIBR_45882 and tr_A0A0V0VUD0_A0A0V0VUD0_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1NZ38_A0A0V1NZ38_9BILA_92180 and tr_A0A0V0UBV7_A0A0V0UBV7_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S2ZBV5_A0A1S2ZBV5_ERIEU_9365 and tr_A0A1U7TAA1_A0A1U7TAA1_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A1S3ZAG9_A0A1S3ZAG9_TOBAC_4097 and tr_A0A1U7W991_A0A1U7W991_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S3ZRB3_A0A1S3ZRB3_TOBAC_4097 and tr_A0A1U7YLV6_A0A1U7YLV6_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4DDQ3_A0A1S4DDQ3_TOBAC_4097 and tr_A0A1U7XZR8_A0A1U7XZR8_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A2A2J4I8_A0A2A2J4I8_9BILA_2018661 and tr_A0A2A2KS06_A0A2A2KS06_9BILA_2018661 are exactly identical! WARNING: Sequences tr_A0A1U8FV04_A0A1U8FV04_CAPAN_4072 and tr_A0A2G3D055_A0A2G3D055_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2U3VYP3_A0A2U3VYP3_ODORO_9708 and tr_A0A2U3XC65_A0A2U3XC65_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 62 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/O00139/3_mltree/O00139.raxml.reduced.phy Alignment comprises 1 partitions and 464 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 464 / 464 Gaps: 6.67 % Invariant sites: 0.43 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00139/3_mltree/O00139.raxml.rba Parallelization scheme autoconfig: 1 worker(s) x 7 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 / 67 / 5360 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -663251.341027] Initial branch length optimization [00:00:03 -553464.203678] Model parameter optimization (eps = 10.000000) [00:00:22 -553450.524984] AUTODETECT spr round 1 (radius: 5) [00:01:58 -373966.179952] AUTODETECT spr round 2 (radius: 10) [00:03:49 -288033.084404] AUTODETECT spr round 3 (radius: 15) [00:05:54 -226926.657293] AUTODETECT spr round 4 (radius: 20) [00:08:00 -201493.639696] AUTODETECT spr round 5 (radius: 25) [00:10:10 -199135.832368] SPR radius for FAST iterations: 25 (autodetect) [00:10:10 -199135.832368] Model parameter optimization (eps = 3.000000) [00:10:25 -198890.392885] FAST spr round 1 (radius: 25) [00:12:24 -170097.502527] FAST spr round 2 (radius: 25) [00:13:58 -169053.192642] FAST spr round 3 (radius: 25) [00:15:26 -169009.467858] FAST spr round 4 (radius: 25) [00:16:50 -168986.277615] FAST spr round 5 (radius: 25) [00:18:08 -168984.014158] FAST spr round 6 (radius: 25) [00:19:25 -168984.013614] Model parameter optimization (eps = 1.000000) [00:19:34 -168980.411005] SLOW spr round 1 (radius: 5) [00:21:11 -168950.366575] SLOW spr round 2 (radius: 5) [00:22:47 -168944.998795] SLOW spr round 3 (radius: 5) [00:24:19 -168944.442045] SLOW spr round 4 (radius: 5) [00:25:52 -168944.441499] SLOW spr round 5 (radius: 10) [00:27:31 -168941.493515] SLOW spr round 6 (radius: 5) [00:29:24 -168941.486391] SLOW spr round 7 (radius: 10) [00:31:11 -168940.334128] SLOW spr round 8 (radius: 5) [00:33:02 -168940.333590] SLOW spr round 9 (radius: 10) [00:34:48 -168940.333083] SLOW spr round 10 (radius: 15) [00:37:08 -168940.332571] SLOW spr round 11 (radius: 20) [00:40:32 -168940.332052] SLOW spr round 12 (radius: 25) [00:45:13 -168940.331528] Model parameter optimization (eps = 0.100000) [00:45:20] ML tree search #1, logLikelihood: -168940.212111 [00:45:20 -661409.181275] Initial branch length optimization [00:45:23 -554706.477975] Model parameter optimization (eps = 10.000000) [00:45:40 -554681.764739] AUTODETECT spr round 1 (radius: 5) [00:47:26 -377646.622295] AUTODETECT spr round 2 (radius: 10) [00:49:28 -291949.230088] AUTODETECT spr round 3 (radius: 15) [00:51:34 -243026.008680] AUTODETECT spr round 4 (radius: 20) [00:53:41 -212026.557152] AUTODETECT spr round 5 (radius: 25) [00:55:44 -202434.371649] SPR radius for FAST iterations: 25 (autodetect) [00:55:44 -202434.371649] Model parameter optimization (eps = 3.000000) [00:56:00 -202134.393834] FAST spr round 1 (radius: 25) [00:57:59 -171030.409826] FAST spr round 2 (radius: 25) [00:59:40 -169088.738579] FAST spr round 3 (radius: 25) [01:01:08 -168978.890650] FAST spr round 4 (radius: 25) [01:02:30 -168971.197922] FAST spr round 5 (radius: 25) [01:03:48 -168971.197500] Model parameter optimization (eps = 1.000000) [01:04:00 -168966.853956] SLOW spr round 1 (radius: 5) [01:05:36 -168932.397088] SLOW spr round 2 (radius: 5) [01:07:12 -168929.952710] SLOW spr round 3 (radius: 5) [01:08:45 -168929.951006] SLOW spr round 4 (radius: 10) [01:10:23 -168926.380686] SLOW spr round 5 (radius: 5) [01:12:18 -168921.888321] SLOW spr round 6 (radius: 5) [01:14:01 -168921.887754] SLOW spr round 7 (radius: 10) [01:15:40 -168921.887283] SLOW spr round 8 (radius: 15) [01:17:59 -168921.886399] SLOW spr round 9 (radius: 20) [01:20:57 -168921.874906] SLOW spr round 10 (radius: 25) [01:24:40 -168921.874431] Model parameter optimization (eps = 0.100000) [01:24:47] ML tree search #2, logLikelihood: -168921.708461 [01:24:47 -657688.277181] Initial branch length optimization [01:24:49 -551094.605594] Model parameter optimization (eps = 10.000000) [01:24:59 -551086.480566] AUTODETECT spr round 1 (radius: 5) [01:26:34 -376796.262568] AUTODETECT spr round 2 (radius: 10) [01:28:29 -278723.796740] AUTODETECT spr round 3 (radius: 15) [01:30:33 -226650.817013] AUTODETECT spr round 4 (radius: 20) [01:32:42 -205123.990940] AUTODETECT spr round 5 (radius: 25) [01:34:56 -200482.380370] SPR radius for FAST iterations: 25 (autodetect) [01:34:56 -200482.380370] Model parameter optimization (eps = 3.000000) [01:35:09 -200223.604240] FAST spr round 1 (radius: 25) [01:37:10 -170601.516501] FAST spr round 2 (radius: 25) [01:38:45 -169034.134184] FAST spr round 3 (radius: 25) [01:40:14 -168969.745665] FAST spr round 4 (radius: 25) [01:41:38 -168949.512780] FAST spr round 5 (radius: 25) [01:42:56 -168947.840370] FAST spr round 6 (radius: 25) [01:44:13 -168947.840093] Model parameter optimization (eps = 1.000000) [01:44:20 -168946.961671] SLOW spr round 1 (radius: 5) [01:45:55 -168919.763808] SLOW spr round 2 (radius: 5) [01:47:29 -168917.035086] SLOW spr round 3 (radius: 5) [01:49:02 -168917.034440] SLOW spr round 4 (radius: 10) [01:50:39 -168914.724860] SLOW spr round 5 (radius: 5) [01:52:31 -168914.554798] SLOW spr round 6 (radius: 5) [01:54:13 -168914.554485] SLOW spr round 7 (radius: 10) [01:55:52 -168914.554171] SLOW spr round 8 (radius: 15) [01:58:16 -168914.553435] SLOW spr round 9 (radius: 20) [02:01:27 -168914.553115] SLOW spr round 10 (radius: 25) [02:05:29 -168914.207814] SLOW spr round 11 (radius: 5) [02:07:31 -168914.207359] SLOW spr round 12 (radius: 10) [02:09:27 -168914.207035] SLOW spr round 13 (radius: 15) [02:11:42 -168914.206708] SLOW spr round 14 (radius: 20) [02:14:58 -168914.206377] SLOW spr round 15 (radius: 25) [02:18:59 -168914.206043] Model parameter optimization (eps = 0.100000) [02:19:05] ML tree search #3, logLikelihood: -168914.097361 [02:19:05 -660756.090076] Initial branch length optimization [02:19:07 -552545.384720] Model parameter optimization (eps = 10.000000) [02:19:19 -552535.790840] AUTODETECT spr round 1 (radius: 5) [02:20:57 -377780.206953] AUTODETECT spr round 2 (radius: 10) [02:22:49 -292892.053364] AUTODETECT spr round 3 (radius: 15) [02:24:52 -238281.811576] AUTODETECT spr round 4 (radius: 20) [02:27:05 -204524.562872] AUTODETECT spr round 5 (radius: 25) [02:29:20 -199050.274078] SPR radius for FAST iterations: 25 (autodetect) [02:29:20 -199050.274078] Model parameter optimization (eps = 3.000000) [02:29:35 -198814.603278] FAST spr round 1 (radius: 25) [02:31:34 -170021.441688] FAST spr round 2 (radius: 25) [02:33:12 -169058.145150] FAST spr round 3 (radius: 25) [02:34:44 -168995.211921] FAST spr round 4 (radius: 25) [02:36:04 -168977.743887] FAST spr round 5 (radius: 25) [02:37:21 -168973.334100] FAST spr round 6 (radius: 25) [02:38:38 -168973.333633] Model parameter optimization (eps = 1.000000) [02:38:50 -168972.273650] SLOW spr round 1 (radius: 5) [02:40:26 -168937.466862] SLOW spr round 2 (radius: 5) [02:42:02 -168929.959833] SLOW spr round 3 (radius: 5) [02:43:36 -168927.123158] SLOW spr round 4 (radius: 5) [02:45:10 -168927.122640] SLOW spr round 5 (radius: 10) [02:46:48 -168925.155915] SLOW spr round 6 (radius: 5) [02:48:44 -168921.040444] SLOW spr round 7 (radius: 5) [02:50:27 -168921.039836] SLOW spr round 8 (radius: 10) [02:52:08 -168921.039312] SLOW spr round 9 (radius: 15) [02:54:31 -168921.038793] SLOW spr round 10 (radius: 20) [02:57:47 -168921.038269] SLOW spr round 11 (radius: 25) [03:01:59 -168921.037739] Model parameter optimization (eps = 0.100000) [03:02:06] ML tree search #4, logLikelihood: -168920.930727 [03:02:06 -657934.322714] Initial branch length optimization [03:02:09 -550280.388294] Model parameter optimization (eps = 10.000000) [03:02:24 -550263.042516] AUTODETECT spr round 1 (radius: 5) [03:04:00 -379319.499060] AUTODETECT spr round 2 (radius: 10) [03:05:54 -288082.120260] AUTODETECT spr round 3 (radius: 15) [03:07:54 -249106.915423] AUTODETECT spr round 4 (radius: 20) [03:10:02 -230941.666707] AUTODETECT spr round 5 (radius: 25) [03:12:23 -218661.080364] SPR radius for FAST iterations: 25 (autodetect) [03:12:23 -218661.080364] Model parameter optimization (eps = 3.000000) [03:12:41 -218327.505945] FAST spr round 1 (radius: 25) [03:14:51 -171498.035746] FAST spr round 2 (radius: 25) [03:16:30 -169078.932781] FAST spr round 3 (radius: 25) [03:17:56 -168995.173033] FAST spr round 4 (radius: 25) [03:19:16 -168986.819396] FAST spr round 5 (radius: 25) [03:20:32 -168985.902216] FAST spr round 6 (radius: 25) [03:21:47 -168985.901316] Model parameter optimization (eps = 1.000000) [03:22:01 -168983.444993] SLOW spr round 1 (radius: 5) [03:23:34 -168939.974642] SLOW spr round 2 (radius: 5) [03:25:07 -168938.429945] SLOW spr round 3 (radius: 5) [03:26:39 -168938.429582] SLOW spr round 4 (radius: 10) [03:28:14 -168936.459378] SLOW spr round 5 (radius: 5) [03:30:07 -168936.459185] SLOW spr round 6 (radius: 10) [03:31:53 -168936.459081] SLOW spr round 7 (radius: 15) [03:34:11 -168936.459070] SLOW spr round 8 (radius: 20) [03:37:35 -168936.459061] SLOW spr round 9 (radius: 25) [03:41:52 -168935.821961] SLOW spr round 10 (radius: 5) [03:43:52 -168935.821795] SLOW spr round 11 (radius: 10) [03:45:48 -168935.821794] SLOW spr round 12 (radius: 15) [03:48:02 -168935.821794] SLOW spr round 13 (radius: 20) [03:51:26 -168935.821794] SLOW spr round 14 (radius: 25) [03:55:43 -168935.821794] Model parameter optimization (eps = 0.100000) [03:55:55] ML tree search #5, logLikelihood: -168934.780281 [03:55:56 -652681.790522] Initial branch length optimization [03:55:58 -545050.612423] Model parameter optimization (eps = 10.000000) [03:56:11 -545028.621020] AUTODETECT spr round 1 (radius: 5) [03:57:48 -373110.249466] AUTODETECT spr round 2 (radius: 10) [03:59:40 -285443.712509] AUTODETECT spr round 3 (radius: 15) [04:01:42 -237533.456284] AUTODETECT spr round 4 (radius: 20) [04:03:45 -210473.225115] AUTODETECT spr round 5 (radius: 25) [04:06:06 -201745.238335] SPR radius for FAST iterations: 25 (autodetect) [04:06:06 -201745.238335] Model parameter optimization (eps = 3.000000) [04:06:20 -201520.051726] FAST spr round 1 (radius: 25) [04:08:18 -170178.604106] FAST spr round 2 (radius: 25) [04:09:56 -169019.780999] FAST spr round 3 (radius: 25) [04:11:23 -168967.066199] FAST spr round 4 (radius: 25) [04:12:43 -168962.974439] FAST spr round 5 (radius: 25) [04:14:00 -168961.147974] FAST spr round 6 (radius: 25) [04:15:16 -168961.147744] Model parameter optimization (eps = 1.000000) [04:15:23 -168960.646637] SLOW spr round 1 (radius: 5) [04:16:57 -168934.802407] SLOW spr round 2 (radius: 5) [04:18:30 -168930.035943] SLOW spr round 3 (radius: 5) [04:20:02 -168930.033993] SLOW spr round 4 (radius: 10) [04:21:37 -168925.427205] SLOW spr round 5 (radius: 5) [04:23:29 -168922.213593] SLOW spr round 6 (radius: 5) [04:25:12 -168922.213500] SLOW spr round 7 (radius: 10) [04:26:51 -168922.213483] SLOW spr round 8 (radius: 15) [04:29:12 -168922.213479] SLOW spr round 9 (radius: 20) [04:32:35 -168922.213474] SLOW spr round 10 (radius: 25) [04:36:48 -168921.814413] SLOW spr round 11 (radius: 5) [04:38:47 -168921.814348] SLOW spr round 12 (radius: 10) [04:40:43 -168921.814334] SLOW spr round 13 (radius: 15) [04:43:00 -168921.814331] SLOW spr round 14 (radius: 20) [04:46:28 -168921.814330] SLOW spr round 15 (radius: 25) [04:50:39 -168921.814330] Model parameter optimization (eps = 0.100000) [04:50:49] ML tree search #6, logLikelihood: -168920.331202 [04:50:49 -661701.246261] Initial branch length optimization [04:50:52 -552420.669654] Model parameter optimization (eps = 10.000000) [04:51:12 -552396.633241] AUTODETECT spr round 1 (radius: 5) [04:52:50 -378198.530122] AUTODETECT spr round 2 (radius: 10) [04:54:46 -277399.681615] AUTODETECT spr round 3 (radius: 15) [04:56:44 -237213.113764] AUTODETECT spr round 4 (radius: 20) [04:59:03 -208441.675738] AUTODETECT spr round 5 (radius: 25) [05:01:21 -199029.656781] SPR radius for FAST iterations: 25 (autodetect) [05:01:21 -199029.656781] Model parameter optimization (eps = 3.000000) [05:01:36 -198777.507561] FAST spr round 1 (radius: 25) [05:03:37 -170716.673258] FAST spr round 2 (radius: 25) [05:05:13 -169046.080008] FAST spr round 3 (radius: 25) [05:06:38 -168991.495002] FAST spr round 4 (radius: 25) [05:07:56 -168991.480312] Model parameter optimization (eps = 1.000000) [05:08:05 -168986.482146] SLOW spr round 1 (radius: 5) [05:09:43 -168934.883035] SLOW spr round 2 (radius: 5) [05:11:18 -168922.491498] SLOW spr round 3 (radius: 5) [05:12:53 -168918.422072] SLOW spr round 4 (radius: 5) [05:14:25 -168918.266629] SLOW spr round 5 (radius: 5) [05:15:56 -168918.265818] SLOW spr round 6 (radius: 10) [05:17:31 -168918.265020] SLOW spr round 7 (radius: 15) [05:19:56 -168918.264222] SLOW spr round 8 (radius: 20) [05:23:13 -168918.263984] SLOW spr round 9 (radius: 25) [05:27:26 -168917.717345] SLOW spr round 10 (radius: 5) [05:29:26 -168917.717292] SLOW spr round 11 (radius: 10) [05:31:21 -168917.717290] SLOW spr round 12 (radius: 15) [05:33:35 -168917.717289] SLOW spr round 13 (radius: 20) [05:36:57 -168917.717289] SLOW spr round 14 (radius: 25) [05:41:08 -168917.717289] Model parameter optimization (eps = 0.100000) [05:41:15] ML tree search #7, logLikelihood: -168917.132146 [05:41:15 -660443.846416] Initial branch length optimization [05:41:18 -555909.620836] Model parameter optimization (eps = 10.000000) [05:41:39 -555875.836383] AUTODETECT spr round 1 (radius: 5) [05:43:16 -376289.936656] AUTODETECT spr round 2 (radius: 10) [05:45:09 -287018.096349] AUTODETECT spr round 3 (radius: 15) [05:47:09 -244543.781518] AUTODETECT spr round 4 (radius: 20) [05:49:20 -207331.472209] AUTODETECT spr round 5 (radius: 25) [05:51:37 -202083.886785] SPR radius for FAST iterations: 25 (autodetect) [05:51:37 -202083.886785] Model parameter optimization (eps = 3.000000) [05:51:54 -201841.978129] FAST spr round 1 (radius: 25) [05:54:00 -170444.090473] FAST spr round 2 (radius: 25) [05:55:38 -169053.226956] FAST spr round 3 (radius: 25) [05:57:07 -168984.523243] FAST spr round 4 (radius: 25) [05:58:29 -168979.040528] FAST spr round 5 (radius: 25) [05:59:46 -168978.160154] FAST spr round 6 (radius: 25) [06:01:02 -168978.159571] Model parameter optimization (eps = 1.000000) [06:01:13 -168975.826142] SLOW spr round 1 (radius: 5) [06:02:47 -168936.569708] SLOW spr round 2 (radius: 5) [06:04:21 -168930.165584] SLOW spr round 3 (radius: 5) [06:05:54 -168930.164996] SLOW spr round 4 (radius: 10) [06:07:32 -168928.168703] SLOW spr round 5 (radius: 5) [06:09:24 -168928.168138] SLOW spr round 6 (radius: 10) [06:11:11 -168928.167583] SLOW spr round 7 (radius: 15) [06:13:26 -168928.167032] SLOW spr round 8 (radius: 20) [06:16:35 -168928.166538] SLOW spr round 9 (radius: 25) [06:20:31 -168927.968552] SLOW spr round 10 (radius: 5) [06:22:31 -168927.968452] SLOW spr round 11 (radius: 10) [06:24:27 -168927.968451] SLOW spr round 12 (radius: 15) [06:26:40 -168927.968451] SLOW spr round 13 (radius: 20) [06:29:49 -168927.968451] SLOW spr round 14 (radius: 25) [06:33:46 -168927.968451] Model parameter optimization (eps = 0.100000) [06:33:54] ML tree search #8, logLikelihood: -168927.818839 [06:33:54 -656664.314816] Initial branch length optimization [06:33:56 -549162.849837] Model parameter optimization (eps = 10.000000) [06:34:09 -549148.629531] AUTODETECT spr round 1 (radius: 5) [06:35:45 -375624.100079] AUTODETECT spr round 2 (radius: 10) [06:37:40 -288369.897480] AUTODETECT spr round 3 (radius: 15) [06:39:41 -242317.662427] AUTODETECT spr round 4 (radius: 20) [06:41:48 -217584.408969] AUTODETECT spr round 5 (radius: 25) [06:44:07 -209627.458558] SPR radius for FAST iterations: 25 (autodetect) [06:44:07 -209627.458558] Model parameter optimization (eps = 3.000000) [06:44:21 -209355.980495] FAST spr round 1 (radius: 25) [06:46:34 -170363.489964] FAST spr round 2 (radius: 25) [06:48:15 -169107.247913] FAST spr round 3 (radius: 25) [06:49:47 -168980.930581] FAST spr round 4 (radius: 25) [06:51:08 -168975.360979] FAST spr round 5 (radius: 25) [06:52:26 -168972.717385] FAST spr round 6 (radius: 25) [06:53:42 -168972.716553] Model parameter optimization (eps = 1.000000) [06:53:52 -168971.217354] SLOW spr round 1 (radius: 5) [06:55:26 -168931.713801] SLOW spr round 2 (radius: 5) [06:56:59 -168928.310293] SLOW spr round 3 (radius: 5) [06:58:33 -168926.308159] SLOW spr round 4 (radius: 5) [07:00:06 -168925.080281] SLOW spr round 5 (radius: 5) [07:01:38 -168925.079457] SLOW spr round 6 (radius: 10) [07:03:14 -168925.078687] SLOW spr round 7 (radius: 15) [07:05:37 -168925.077971] SLOW spr round 8 (radius: 20) [07:08:44 -168925.077266] SLOW spr round 9 (radius: 25) [07:12:46 -168925.076573] Model parameter optimization (eps = 0.100000) [07:12:55] ML tree search #9, logLikelihood: -168924.772879 [07:12:55 -660141.160856] Initial branch length optimization [07:12:57 -552723.888408] Model parameter optimization (eps = 10.000000) [07:13:16 -552711.886020] AUTODETECT spr round 1 (radius: 5) [07:14:53 -373630.456317] AUTODETECT spr round 2 (radius: 10) [07:16:43 -287286.145830] AUTODETECT spr round 3 (radius: 15) [07:18:39 -230391.608203] AUTODETECT spr round 4 (radius: 20) [07:20:47 -203862.636364] AUTODETECT spr round 5 (radius: 25) [07:22:55 -201437.085241] SPR radius for FAST iterations: 25 (autodetect) [07:22:55 -201437.085241] Model parameter optimization (eps = 3.000000) [07:23:12 -201180.591885] FAST spr round 1 (radius: 25) [07:25:16 -170153.861434] FAST spr round 2 (radius: 25) [07:26:55 -169048.587605] FAST spr round 3 (radius: 25) [07:28:23 -168972.593127] FAST spr round 4 (radius: 25) [07:29:42 -168955.197376] FAST spr round 5 (radius: 25) [07:31:01 -168954.221493] FAST spr round 6 (radius: 25) [07:32:17 -168954.220971] Model parameter optimization (eps = 1.000000) [07:32:26 -168951.415850] SLOW spr round 1 (radius: 5) [07:34:00 -168923.880697] SLOW spr round 2 (radius: 5) [07:35:32 -168919.700486] SLOW spr round 3 (radius: 5) [07:37:02 -168919.700472] SLOW spr round 4 (radius: 10) [07:38:38 -168919.627347] SLOW spr round 5 (radius: 15) [07:41:06 -168919.612179] SLOW spr round 6 (radius: 20) [07:44:23 -168919.611953] SLOW spr round 7 (radius: 25) [07:48:41 -168919.611950] Model parameter optimization (eps = 0.100000) [07:48:45] ML tree search #10, logLikelihood: -168919.595723 [07:48:46 -655068.805390] Initial branch length optimization [07:48:49 -545759.230091] Model parameter optimization (eps = 10.000000) [07:48:56 -545756.396051] AUTODETECT spr round 1 (radius: 5) [07:50:34 -371073.955287] AUTODETECT spr round 2 (radius: 10) [07:52:25 -292044.066339] AUTODETECT spr round 3 (radius: 15) [07:54:34 -257433.161960] AUTODETECT spr round 4 (radius: 20) [07:56:48 -229619.543269] AUTODETECT spr round 5 (radius: 25) [07:59:23 -207730.591209] SPR radius for FAST iterations: 25 (autodetect) [07:59:23 -207730.591209] Model parameter optimization (eps = 3.000000) [07:59:40 -207455.921809] FAST spr round 1 (radius: 25) [08:01:49 -171049.617049] FAST spr round 2 (radius: 25) [08:03:27 -169158.581295] FAST spr round 3 (radius: 25) [08:04:58 -168998.221032] FAST spr round 4 (radius: 25) [08:06:19 -168978.776984] FAST spr round 5 (radius: 25) [08:07:36 -168978.776682] Model parameter optimization (eps = 1.000000) [08:07:53 -168974.717286] SLOW spr round 1 (radius: 5) [08:09:30 -168928.763256] SLOW spr round 2 (radius: 5) [08:11:06 -168922.198813] SLOW spr round 3 (radius: 5) [08:12:39 -168919.532283] SLOW spr round 4 (radius: 5) [08:14:11 -168918.972035] SLOW spr round 5 (radius: 5) [08:15:42 -168918.971699] SLOW spr round 6 (radius: 10) [08:17:18 -168914.619777] SLOW spr round 7 (radius: 5) [08:19:11 -168914.454798] SLOW spr round 8 (radius: 5) [08:20:54 -168914.013500] SLOW spr round 9 (radius: 5) [08:22:29 -168914.013087] SLOW spr round 10 (radius: 10) [08:24:05 -168914.012764] SLOW spr round 11 (radius: 15) [08:26:26 -168914.012446] SLOW spr round 12 (radius: 20) [08:29:23 -168914.012126] SLOW spr round 13 (radius: 25) [08:33:09 -168914.011803] Model parameter optimization (eps = 0.100000) [08:33:16] ML tree search #11, logLikelihood: -168913.295648 [08:33:16 -656680.359149] Initial branch length optimization [08:33:19 -548546.057203] Model parameter optimization (eps = 10.000000) [08:33:32 -548527.454977] AUTODETECT spr round 1 (radius: 5) [08:35:08 -374907.596267] AUTODETECT spr round 2 (radius: 10) [08:37:00 -296397.269610] AUTODETECT spr round 3 (radius: 15) [08:39:05 -234860.071427] AUTODETECT spr round 4 (radius: 20) [08:41:09 -203889.617331] AUTODETECT spr round 5 (radius: 25) [08:43:23 -198901.886627] SPR radius for FAST iterations: 25 (autodetect) [08:43:23 -198901.886627] Model parameter optimization (eps = 3.000000) [08:43:39 -198660.234976] FAST spr round 1 (radius: 25) [08:45:43 -170101.674431] FAST spr round 2 (radius: 25) [08:47:21 -169025.261272] FAST spr round 3 (radius: 25) [08:48:49 -168987.088674] FAST spr round 4 (radius: 25) [08:50:09 -168983.272871] FAST spr round 5 (radius: 25) [08:51:26 -168982.785295] FAST spr round 6 (radius: 25) [08:52:42 -168982.784848] Model parameter optimization (eps = 1.000000) [08:52:50 -168980.093543] SLOW spr round 1 (radius: 5) [08:54:28 -168930.215176] SLOW spr round 2 (radius: 5) [08:56:00 -168925.516342] SLOW spr round 3 (radius: 5) [08:57:32 -168925.515782] SLOW spr round 4 (radius: 10) [08:59:09 -168920.314320] SLOW spr round 5 (radius: 5) [09:01:03 -168917.636055] SLOW spr round 6 (radius: 5) [09:02:46 -168910.775184] SLOW spr round 7 (radius: 5) [09:04:22 -168910.774560] SLOW spr round 8 (radius: 10) [09:05:57 -168910.774091] SLOW spr round 9 (radius: 15) [09:08:18 -168910.773616] SLOW spr round 10 (radius: 20) [09:11:27 -168910.773137] SLOW spr round 11 (radius: 25) [09:15:29 -168910.772651] Model parameter optimization (eps = 0.100000) [09:15:35] ML tree search #12, logLikelihood: -168910.640341 [09:15:35 -660117.301851] Initial branch length optimization [09:15:38 -552081.734004] Model parameter optimization (eps = 10.000000) [09:15:57 -552068.467319] AUTODETECT spr round 1 (radius: 5) [09:17:34 -374697.009036] AUTODETECT spr round 2 (radius: 10) [09:19:25 -291385.934479] AUTODETECT spr round 3 (radius: 15) [09:21:24 -252242.231590] AUTODETECT spr round 4 (radius: 20) [09:23:33 -210090.701527] AUTODETECT spr round 5 (radius: 25) [09:25:38 -202653.763228] SPR radius for FAST iterations: 25 (autodetect) [09:25:38 -202653.763228] Model parameter optimization (eps = 3.000000) [09:25:55 -202447.796802] FAST spr round 1 (radius: 25) [09:27:56 -170155.024753] FAST spr round 2 (radius: 25) [09:29:33 -169043.580436] FAST spr round 3 (radius: 25) [09:30:59 -168966.921399] FAST spr round 4 (radius: 25) [09:32:18 -168957.082783] FAST spr round 5 (radius: 25) [09:33:34 -168957.082121] Model parameter optimization (eps = 1.000000) [09:33:44 -168951.455372] SLOW spr round 1 (radius: 5) [09:35:18 -168926.629768] SLOW spr round 2 (radius: 5) [09:36:52 -168925.550893] SLOW spr round 3 (radius: 5) [09:38:25 -168925.550378] SLOW spr round 4 (radius: 10) [09:40:02 -168922.488064] SLOW spr round 5 (radius: 5) [09:41:55 -168921.845441] SLOW spr round 6 (radius: 5) [09:43:36 -168920.664545] SLOW spr round 7 (radius: 5) [09:45:13 -168920.663996] SLOW spr round 8 (radius: 10) [09:46:50 -168920.663050] SLOW spr round 9 (radius: 15) [09:49:11 -168920.662519] SLOW spr round 10 (radius: 20) [09:52:08 -168920.661627] SLOW spr round 11 (radius: 25) [09:55:51 -168920.545403] SLOW spr round 12 (radius: 5) [09:57:52 -168920.544522] SLOW spr round 13 (radius: 10) [09:59:47 -168920.543969] SLOW spr round 14 (radius: 15) [10:01:58 -168920.543428] SLOW spr round 15 (radius: 20) [10:04:59 -168920.543016] SLOW spr round 16 (radius: 25) [10:08:42 -168920.543014] Model parameter optimization (eps = 0.100000) [10:08:52] ML tree search #13, logLikelihood: -168919.696933 [10:08:52 -658792.950051] Initial branch length optimization [10:08:55 -550613.819903] Model parameter optimization (eps = 10.000000) [10:09:13 -550586.644522] AUTODETECT spr round 1 (radius: 5) [10:10:53 -378836.255383] AUTODETECT spr round 2 (radius: 10) [10:12:46 -290405.581102] AUTODETECT spr round 3 (radius: 15) [10:14:56 -224738.956971] AUTODETECT spr round 4 (radius: 20) [10:16:56 -197453.745089] AUTODETECT spr round 5 (radius: 25) [10:19:05 -194159.890121] SPR radius for FAST iterations: 25 (autodetect) [10:19:05 -194159.890121] Model parameter optimization (eps = 3.000000) [10:19:20 -193960.311269] FAST spr round 1 (radius: 25) [10:21:22 -169844.667048] FAST spr round 2 (radius: 25) [10:23:00 -169051.241550] FAST spr round 3 (radius: 25) [10:24:30 -168984.372738] FAST spr round 4 (radius: 25) [10:25:47 -168980.257061] FAST spr round 5 (radius: 25) [10:27:05 -168976.077741] FAST spr round 6 (radius: 25) [10:28:21 -168976.071804] Model parameter optimization (eps = 1.000000) [10:28:32 -168972.747326] SLOW spr round 1 (radius: 5) [10:30:07 -168925.834674] SLOW spr round 2 (radius: 5) [10:31:41 -168921.320079] SLOW spr round 3 (radius: 5) [10:33:15 -168919.525745] SLOW spr round 4 (radius: 5) [10:34:45 -168919.525179] SLOW spr round 5 (radius: 10) [10:36:22 -168917.568378] SLOW spr round 6 (radius: 5) [10:38:15 -168917.567698] SLOW spr round 7 (radius: 10) [10:40:01 -168917.567108] SLOW spr round 8 (radius: 15) [10:42:20 -168917.566541] SLOW spr round 9 (radius: 20) [10:45:48 -168917.565971] SLOW spr round 10 (radius: 25) [10:50:09 -168917.171903] SLOW spr round 11 (radius: 5) [10:52:08 -168917.171178] SLOW spr round 12 (radius: 10) [10:54:03 -168917.170665] SLOW spr round 13 (radius: 15) [10:56:19 -168917.170148] SLOW spr round 14 (radius: 20) [10:59:49 -168917.169626] SLOW spr round 15 (radius: 25) [11:04:09 -168917.169097] Model parameter optimization (eps = 0.100000) [11:04:17] ML tree search #14, logLikelihood: -168916.863827 [11:04:17 -662910.007683] Initial branch length optimization [11:04:20 -554760.304965] Model parameter optimization (eps = 10.000000) [11:04:39 -554696.976581] AUTODETECT spr round 1 (radius: 5) [11:06:17 -376767.452823] AUTODETECT spr round 2 (radius: 10) [11:08:11 -290842.288336] AUTODETECT spr round 3 (radius: 15) [11:10:21 -219642.719875] AUTODETECT spr round 4 (radius: 20) [11:12:18 -196220.324342] AUTODETECT spr round 5 (radius: 25) [11:14:34 -193953.128450] SPR radius for FAST iterations: 25 (autodetect) [11:14:34 -193953.128450] Model parameter optimization (eps = 3.000000) [11:14:47 -193729.073307] FAST spr round 1 (radius: 25) [11:16:38 -169925.249292] FAST spr round 2 (radius: 25) [11:18:06 -169039.199525] FAST spr round 3 (radius: 25) [11:19:31 -168992.115465] FAST spr round 4 (radius: 25) [11:20:51 -168984.186950] FAST spr round 5 (radius: 25) [11:22:06 -168984.186233] Model parameter optimization (eps = 1.000000) [11:22:18 -168981.062872] SLOW spr round 1 (radius: 5) [11:23:53 -168931.154742] SLOW spr round 2 (radius: 5) [11:25:27 -168930.110703] SLOW spr round 3 (radius: 5) [11:26:58 -168930.110130] SLOW spr round 4 (radius: 10) [11:28:34 -168928.040835] SLOW spr round 5 (radius: 5) [11:30:24 -168928.040328] SLOW spr round 6 (radius: 10) [11:32:09 -168928.039807] SLOW spr round 7 (radius: 15) [11:34:25 -168928.039290] SLOW spr round 8 (radius: 20) [11:37:47 -168928.038772] SLOW spr round 9 (radius: 25) [11:41:50 -168928.038248] Model parameter optimization (eps = 0.100000) [11:41:55] ML tree search #15, logLikelihood: -168927.958114 [11:41:55 -659557.841587] Initial branch length optimization [11:41:58 -553850.151715] Model parameter optimization (eps = 10.000000) [11:42:17 -553835.075843] AUTODETECT spr round 1 (radius: 5) [11:43:55 -381165.291477] AUTODETECT spr round 2 (radius: 10) [11:45:44 -284989.206379] AUTODETECT spr round 3 (radius: 15) [11:47:52 -231501.890595] AUTODETECT spr round 4 (radius: 20) [11:49:57 -215061.884046] AUTODETECT spr round 5 (radius: 25) [11:52:12 -202493.025425] SPR radius for FAST iterations: 25 (autodetect) [11:52:12 -202493.025425] Model parameter optimization (eps = 3.000000) [11:52:30 -202249.880272] FAST spr round 1 (radius: 25) [11:54:35 -170275.745773] FAST spr round 2 (radius: 25) [11:56:14 -169062.441576] FAST spr round 3 (radius: 25) [11:57:42 -168981.057489] FAST spr round 4 (radius: 25) [11:59:00 -168973.014022] FAST spr round 5 (radius: 25) [12:00:16 -168973.002651] Model parameter optimization (eps = 1.000000) [12:00:31 -168969.468077] SLOW spr round 1 (radius: 5) [12:02:08 -168927.000974] SLOW spr round 2 (radius: 5) [12:03:43 -168920.973109] SLOW spr round 3 (radius: 5) [12:05:14 -168920.961208] SLOW spr round 4 (radius: 10) [12:06:48 -168920.959987] SLOW spr round 5 (radius: 15) [12:09:10 -168920.958824] SLOW spr round 6 (radius: 20) [12:12:08 -168920.957709] SLOW spr round 7 (radius: 25) [12:15:53 -168920.956641] Model parameter optimization (eps = 0.100000) [12:16:00] ML tree search #16, logLikelihood: -168920.781006 [12:16:00 -659382.998210] Initial branch length optimization [12:16:03 -551750.011197] Model parameter optimization (eps = 10.000000) [12:16:16 -551746.309711] AUTODETECT spr round 1 (radius: 5) [12:17:53 -373435.207093] AUTODETECT spr round 2 (radius: 10) [12:19:48 -282219.336766] AUTODETECT spr round 3 (radius: 15) [12:21:47 -227724.558161] AUTODETECT spr round 4 (radius: 20) [12:23:58 -201290.612224] AUTODETECT spr round 5 (radius: 25) [12:26:11 -198613.142126] SPR radius for FAST iterations: 25 (autodetect) [12:26:11 -198613.142126] Model parameter optimization (eps = 3.000000) [12:26:24 -198359.869334] FAST spr round 1 (radius: 25) [12:28:24 -170118.499207] FAST spr round 2 (radius: 25) [12:30:01 -169026.228124] FAST spr round 3 (radius: 25) [12:31:29 -168985.493951] FAST spr round 4 (radius: 25) [12:32:49 -168984.494596] FAST spr round 5 (radius: 25) [12:34:05 -168984.494574] Model parameter optimization (eps = 1.000000) [12:34:17 -168981.921093] SLOW spr round 1 (radius: 5) [12:35:55 -168954.927132] SLOW spr round 2 (radius: 5) [12:37:32 -168946.053821] SLOW spr round 3 (radius: 5) [12:39:04 -168944.850832] SLOW spr round 4 (radius: 5) [12:40:35 -168944.838995] SLOW spr round 5 (radius: 10) [12:42:10 -168942.869275] SLOW spr round 6 (radius: 5) [12:44:02 -168942.868093] SLOW spr round 7 (radius: 10) [12:45:48 -168942.866953] SLOW spr round 8 (radius: 15) [12:48:08 -168942.865854] SLOW spr round 9 (radius: 20) [12:51:31 -168942.864793] SLOW spr round 10 (radius: 25) [12:55:51 -168942.863770] Model parameter optimization (eps = 0.100000) [12:55:59] ML tree search #17, logLikelihood: -168942.777783 [12:55:59 -655769.004669] Initial branch length optimization [12:56:01 -546526.134172] Model parameter optimization (eps = 10.000000) [12:56:12 -546517.297990] AUTODETECT spr round 1 (radius: 5) [12:57:49 -379448.719032] AUTODETECT spr round 2 (radius: 10) [12:59:40 -295520.877528] AUTODETECT spr round 3 (radius: 15) [13:01:48 -247110.016796] AUTODETECT spr round 4 (radius: 20) [13:03:50 -219571.711791] AUTODETECT spr round 5 (radius: 25) [13:06:03 -214414.858563] SPR radius for FAST iterations: 25 (autodetect) [13:06:03 -214414.858563] Model parameter optimization (eps = 3.000000) [13:06:18 -214147.247459] FAST spr round 1 (radius: 25) [13:08:23 -171306.478183] FAST spr round 2 (radius: 25) [13:10:00 -169097.027177] FAST spr round 3 (radius: 25) [13:11:29 -169020.945365] FAST spr round 4 (radius: 25) [13:12:51 -168977.294302] FAST spr round 5 (radius: 25) [13:14:09 -168973.602152] FAST spr round 6 (radius: 25) [13:15:25 -168973.601983] Model parameter optimization (eps = 1.000000) [13:15:37 -168970.667054] SLOW spr round 1 (radius: 5) [13:17:12 -168940.273726] SLOW spr round 2 (radius: 5) [13:18:46 -168939.013175] SLOW spr round 3 (radius: 5) [13:20:20 -168939.007835] SLOW spr round 4 (radius: 10) [13:21:57 -168933.890242] SLOW spr round 5 (radius: 5) [13:23:51 -168932.303216] SLOW spr round 6 (radius: 5) [13:25:33 -168930.763684] SLOW spr round 7 (radius: 5) [13:27:11 -168929.959295] SLOW spr round 8 (radius: 5) [13:28:46 -168929.958203] SLOW spr round 9 (radius: 10) [13:30:21 -168929.957952] SLOW spr round 10 (radius: 15) [13:32:43 -168929.957733] SLOW spr round 11 (radius: 20) [13:35:39 -168929.957515] SLOW spr round 12 (radius: 25) [13:39:20 -168929.957297] Model parameter optimization (eps = 0.100000) [13:39:27] ML tree search #18, logLikelihood: -168929.850996 [13:39:27 -655441.352510] Initial branch length optimization [13:39:30 -549968.495315] Model parameter optimization (eps = 10.000000) [13:39:45 -549956.298324] AUTODETECT spr round 1 (radius: 5) [13:41:22 -380913.629539] AUTODETECT spr round 2 (radius: 10) [13:43:16 -287116.620003] AUTODETECT spr round 3 (radius: 15) [13:45:23 -227154.508323] AUTODETECT spr round 4 (radius: 20) [13:47:27 -202747.199269] AUTODETECT spr round 5 (radius: 25) [13:49:38 -197301.527243] SPR radius for FAST iterations: 25 (autodetect) [13:49:38 -197301.527243] Model parameter optimization (eps = 3.000000) [13:49:52 -197061.751360] FAST spr round 1 (radius: 25) [13:51:53 -169861.372939] FAST spr round 2 (radius: 25) [13:53:30 -169024.385028] FAST spr round 3 (radius: 25) [13:54:57 -168981.270556] FAST spr round 4 (radius: 25) [13:56:17 -168975.980769] FAST spr round 5 (radius: 25) [13:57:34 -168975.979781] Model parameter optimization (eps = 1.000000) [13:57:45 -168974.024010] SLOW spr round 1 (radius: 5) [13:59:20 -168932.300864] SLOW spr round 2 (radius: 5) [14:00:54 -168926.486521] SLOW spr round 3 (radius: 5) [14:02:29 -168925.239518] SLOW spr round 4 (radius: 5) [14:04:01 -168925.238642] SLOW spr round 5 (radius: 10) [14:05:37 -168923.285765] SLOW spr round 6 (radius: 5) [14:07:28 -168923.285330] SLOW spr round 7 (radius: 10) [14:09:14 -168923.284901] SLOW spr round 8 (radius: 15) [14:11:29 -168923.284475] SLOW spr round 9 (radius: 20) [14:14:39 -168923.284050] SLOW spr round 10 (radius: 25) [14:18:41 -168922.892156] SLOW spr round 11 (radius: 5) [14:20:42 -168922.891676] SLOW spr round 12 (radius: 10) [14:22:38 -168922.891343] SLOW spr round 13 (radius: 15) [14:24:50 -168922.891007] SLOW spr round 14 (radius: 20) [14:28:01 -168922.890669] SLOW spr round 15 (radius: 25) [14:32:03 -168922.890326] Model parameter optimization (eps = 0.100000) [14:32:09] ML tree search #19, logLikelihood: -168922.813934 [14:32:09 -656303.762375] Initial branch length optimization [14:32:13 -549062.184146] Model parameter optimization (eps = 10.000000) [14:32:34 -549040.582481] AUTODETECT spr round 1 (radius: 5) [14:34:10 -373448.991378] AUTODETECT spr round 2 (radius: 10) [14:36:01 -299917.290072] AUTODETECT spr round 3 (radius: 15) [14:38:05 -250895.986113] AUTODETECT spr round 4 (radius: 20) [14:40:10 -223887.177970] AUTODETECT spr round 5 (radius: 25) [14:42:16 -204341.866437] SPR radius for FAST iterations: 25 (autodetect) [14:42:16 -204341.866437] Model parameter optimization (eps = 3.000000) [14:42:31 -204065.269169] FAST spr round 1 (radius: 25) [14:44:35 -171138.505689] FAST spr round 2 (radius: 25) [14:46:15 -169068.306658] FAST spr round 3 (radius: 25) [14:47:41 -169002.913181] FAST spr round 4 (radius: 25) [14:49:04 -168980.196896] FAST spr round 5 (radius: 25) [14:50:19 -168979.643990] FAST spr round 6 (radius: 25) [14:51:34 -168979.643352] Model parameter optimization (eps = 1.000000) [14:51:47 -168976.330077] SLOW spr round 1 (radius: 5) [14:53:23 -168925.933058] SLOW spr round 2 (radius: 5) [14:54:57 -168918.191960] SLOW spr round 3 (radius: 5) [14:56:28 -168918.191561] SLOW spr round 4 (radius: 10) [14:58:04 -168916.025727] SLOW spr round 5 (radius: 5) [14:59:55 -168913.386690] SLOW spr round 6 (radius: 5) [15:01:37 -168911.253254] SLOW spr round 7 (radius: 5) [15:03:13 -168911.036388] SLOW spr round 8 (radius: 5) [15:04:46 -168911.036122] SLOW spr round 9 (radius: 10) [15:06:21 -168911.035912] SLOW spr round 10 (radius: 15) [15:08:42 -168911.035711] SLOW spr round 11 (radius: 20) [15:11:44 -168911.035518] SLOW spr round 12 (radius: 25) [15:15:34 -168910.820538] SLOW spr round 13 (radius: 5) [15:17:38 -168908.872618] SLOW spr round 14 (radius: 5) [15:19:25 -168908.872077] SLOW spr round 15 (radius: 10) [15:21:07 -168908.872071] SLOW spr round 16 (radius: 15) [15:23:21 -168908.872070] SLOW spr round 17 (radius: 20) [15:26:20 -168908.872070] SLOW spr round 18 (radius: 25) [15:30:04 -168908.872070] Model parameter optimization (eps = 0.100000) [15:30:12] ML tree search #20, logLikelihood: -168908.372424 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.208981,0.161730) (0.213397,0.285450) (0.282017,0.943506) (0.295605,2.162355) 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: -168908.372424 AIC score: 341826.744847 / AICc score: 8385886.744847 / BIC score: 350127.213374 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=464). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 130 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00139/3_mltree/O00139.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00139/3_mltree/O00139.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00139/3_mltree/O00139.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00139/3_mltree/O00139.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/O00139/3_mltree/O00139.raxml.log Analysis started: 02-Jul-2021 13:52:14 / finished: 03-Jul-2021 05:22:26 Elapsed time: 55812.575 seconds Consumed energy: 5022.503 Wh (= 25 km in an electric car, or 126 km with an e-scooter!)