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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 23-Jun-2021 14:14:23 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q99959/2_msa/Q99959_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q99959/3_mltree/Q99959 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q99959/2_msa/Q99959_trimmed_msa.fasta [00:00:00] Loaded alignment with 807 taxa and 562 sites WARNING: Sequences tr_E1C1N1_E1C1N1_CHICK_9031 and tr_A0A226NI90_A0A226NI90_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1C1N1_E1C1N1_CHICK_9031 and tr_A0A226NY55_A0A226NY55_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2I3HTS3_A0A2I3HTS3_NOMLE_61853 and tr_A0A2I2ZRH7_A0A2I2ZRH7_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3HTS3_A0A2I3HTS3_NOMLE_61853 and sp_Q99569_PKP4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3HTS3_A0A2I3HTS3_NOMLE_61853 and tr_F6PTU9_F6PTU9_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3HTS3_A0A2I3HTS3_NOMLE_61853 and tr_A0A0D9RTP4_A0A0D9RTP4_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3HTS3_A0A2I3HTS3_NOMLE_61853 and tr_A0A2K5NST1_A0A2K5NST1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3HTS3_A0A2I3HTS3_NOMLE_61853 and tr_A0A2K6C6D3_A0A2K6C6D3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3HTS3_A0A2I3HTS3_NOMLE_61853 and tr_A0A2K6A6L1_A0A2K6A6L1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3HTS3_A0A2I3HTS3_NOMLE_61853 and tr_A0A2R9BFT5_A0A2R9BFT5_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZX57_A0A2I2ZX57_GORGO_9595 and tr_A0A2I3TU76_A0A2I3TU76_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZX57_A0A2I2ZX57_GORGO_9595 and tr_A0A2R9B0M0_A0A2R9B0M0_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NDF0_H2NDF0_PONAB_9601 and tr_A0A0D9R121_A0A0D9R121_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NDF0_H2NDF0_PONAB_9601 and tr_A0A2K6A8L4_A0A2K6A8L4_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2PF71_H2PF71_PONAB_9601 and tr_A0A2I3RS45_A0A2I3RS45_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2PF71_H2PF71_PONAB_9601 and sp_Q9UQB3_CTND2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2PF71_H2PF71_PONAB_9601 and tr_A0A2K5LYT5_A0A2K5LYT5_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PF71_H2PF71_PONAB_9601 and tr_A0A2K6BRH1_A0A2K6BRH1_MACNE_9545 are exactly identical! WARNING: Sequences tr_E2R434_E2R434_CANLF_9615 and tr_A0A287D0L2_A0A287D0L2_ICTTR_43179 are exactly identical! WARNING: Sequences tr_E2R434_E2R434_CANLF_9615 and tr_A0A2U3XBA6_A0A2U3XBA6_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A2J8KHS3_A0A2J8KHS3_PANTR_9598 and sp_Q13835_PKP1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8KHS3_A0A2J8KHS3_PANTR_9598 and tr_A0A2R8ZKP2_A0A2R8ZKP2_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5R0S1_A0A1D5R0S1_MACMU_9544 and tr_A0A2K5N982_A0A2K5N982_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5R0S1_A0A1D5R0S1_MACMU_9544 and tr_A0A2K6BTC9_A0A2K6BTC9_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5R5N9_A0A1D5R5N9_MACMU_9544 and tr_A0A2I3NEV3_A0A2I3NEV3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5R5N9_A0A1D5R5N9_MACMU_9544 and tr_A0A2K5KJ19_A0A2K5KJ19_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5R5N9_A0A1D5R5N9_MACMU_9544 and tr_A0A2K6AR32_A0A2K6AR32_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6ZE57_F6ZE57_MACMU_9544 and tr_G7NWF8_G7NWF8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6ZE57_F6ZE57_MACMU_9544 and tr_A0A0D9RN26_A0A0D9RN26_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6ZE57_F6ZE57_MACMU_9544 and tr_A0A2K6CY12_A0A2K6CY12_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6ZE57_F6ZE57_MACMU_9544 and tr_A0A2K5ZNT1_A0A2K5ZNT1_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7F965_F7F965_MACMU_9544 and tr_A0A2K5XCG3_A0A2K5XCG3_MANLE_9568 are exactly identical! WARNING: Sequences tr_H0Z9R0_H0Z9R0_TAEGU_59729 and tr_A0A218UV72_A0A218UV72_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZB23_H0ZB23_TAEGU_59729 and tr_A0A091FKE9_A0A091FKE9_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZB23_H0ZB23_TAEGU_59729 and tr_A0A091J2G7_A0A091J2G7_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0ZB23_H0ZB23_TAEGU_59729 and tr_A0A087QXL3_A0A087QXL3_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0ZB23_H0ZB23_TAEGU_59729 and tr_A0A091FP28_A0A091FP28_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0ZB23_H0ZB23_TAEGU_59729 and tr_A0A0A0ADL3_A0A0A0ADL3_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0ZB23_H0ZB23_TAEGU_59729 and tr_A0A093G8L7_A0A093G8L7_DRYPU_118200 are exactly identical! WARNING: Sequences tr_G7PQ26_G7PQ26_MACFA_9541 and tr_A0A2K6CU05_A0A2K6CU05_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A337SDE9_A0A337SDE9_FELCA_9685 and tr_A0A384BSL7_A0A384BSL7_URSMA_29073 are exactly identical! WARNING: Sequences tr_R0LTB9_R0LTB9_ANAPL_8839 and tr_A0A091WU52_A0A091WU52_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A2I3LDG9_A0A2I3LDG9_PAPAN_9555 and tr_A0A2K6BXN0_A0A2K6BXN0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3LMC3_A0A2I3LMC3_PAPAN_9555 and tr_A0A2K5M1U1_A0A2K5M1U1_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3LMC3_A0A2I3LMC3_PAPAN_9555 and tr_A0A2K5XQZ3_A0A2K5XQZ3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MU41_A0A2I3MU41_PAPAN_9555 and tr_A0A2K5ZHY4_A0A2K5ZHY4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3N206_A0A2I3N206_PAPAN_9555 and tr_A0A2K5NBB6_A0A2K5NBB6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A195FV32_A0A195FV32_9HYME_34720 and tr_A0A195CX35_A0A195CX35_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A226MWU3_A0A226MWU3_CALSU_9009 and tr_A0A226P2W6_A0A226P2W6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MWY6_A0A226MWY6_CALSU_9009 and tr_A0A226P0Q1_A0A226P0Q1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226N962_A0A226N962_CALSU_9009 and tr_A0A226PZB1_A0A226PZB1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226NC43_A0A226NC43_CALSU_9009 and tr_A0A226P375_A0A226P375_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0RCX3_A0A2D0RCX3_ICTPU_7998 and tr_A0A2D0RCX4_A0A2D0RCX4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RCX3_A0A2D0RCX3_ICTPU_7998 and tr_A0A2D0RE31_A0A2D0RE31_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4AB49_A0A2U4AB49_TURTR_9739 and tr_A0A2Y9N8C2_A0A2Y9N8C2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CDB2_A0A2U4CDB2_TURTR_9739 and tr_A0A2Y9PPI8_A0A2Y9PPI8_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CDB2_A0A2U4CDB2_TURTR_9739 and tr_A0A2Y9FBM2_A0A2Y9FBM2_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 57 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q99959/3_mltree/Q99959.raxml.reduced.phy Alignment comprises 1 partitions and 562 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 562 / 562 Gaps: 15.62 % Invariant sites: 0.00 % NOTE: Binary MSA file already exists: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q99959/3_mltree/Q99959.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 807 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 81 / 6480 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -683590.655962] Initial branch length optimization [00:00:03 -552159.473663] Model parameter optimization (eps = 10.000000) [00:00:27 -550819.813915] AUTODETECT spr round 1 (radius: 5) [00:01:44 -306707.283868] AUTODETECT spr round 2 (radius: 10) [00:03:02 -210792.671173] AUTODETECT spr round 3 (radius: 15) [00:04:30 -172080.013192] AUTODETECT spr round 4 (radius: 20) [00:06:13 -144021.753525] AUTODETECT spr round 5 (radius: 25) [00:08:42 -135934.341541] SPR radius for FAST iterations: 25 (autodetect) [00:08:42 -135934.341541] Model parameter optimization (eps = 3.000000) [00:09:03 -135603.004440] FAST spr round 1 (radius: 25) [00:10:31 -118045.584657] FAST spr round 2 (radius: 25) [00:11:48 -116762.501910] FAST spr round 3 (radius: 25) [00:12:58 -116641.909256] FAST spr round 4 (radius: 25) [00:14:06 -116616.115643] FAST spr round 5 (radius: 25) [00:15:09 -116615.561910] FAST spr round 6 (radius: 25) [00:16:11 -116615.561678] Model parameter optimization (eps = 1.000000) [00:16:24 -116599.407940] SLOW spr round 1 (radius: 5) [00:17:44 -116577.922260] SLOW spr round 2 (radius: 5) [00:19:03 -116575.874273] SLOW spr round 3 (radius: 5) [00:20:21 -116575.873621] SLOW spr round 4 (radius: 10) [00:21:40 -116574.607394] SLOW spr round 5 (radius: 5) [00:23:14 -116574.607300] SLOW spr round 6 (radius: 10) [00:24:43 -116574.607248] SLOW spr round 7 (radius: 15) [00:26:50 -116574.607203] SLOW spr round 8 (radius: 20) [00:30:09 -116572.726329] SLOW spr round 9 (radius: 5) [00:31:49 -116572.726133] SLOW spr round 10 (radius: 10) [00:33:28 -116572.726087] SLOW spr round 11 (radius: 15) [00:35:32 -116572.726064] SLOW spr round 12 (radius: 20) [00:38:50 -116572.726062] SLOW spr round 13 (radius: 25) [00:43:02 -116572.726060] Model parameter optimization (eps = 0.100000) [00:43:10] ML tree search #1, logLikelihood: -116572.496330 [00:43:10 -689175.614677] Initial branch length optimization [00:43:13 -559458.048322] Model parameter optimization (eps = 10.000000) [00:43:45 -558179.788725] AUTODETECT spr round 1 (radius: 5) [00:45:01 -297495.504076] AUTODETECT spr round 2 (radius: 10) [00:46:19 -188375.262153] AUTODETECT spr round 3 (radius: 15) [00:47:44 -155969.900891] AUTODETECT spr round 4 (radius: 20) [00:49:29 -141557.445788] AUTODETECT spr round 5 (radius: 25) [00:51:33 -134772.108027] SPR radius for FAST iterations: 25 (autodetect) [00:51:33 -134772.108027] Model parameter optimization (eps = 3.000000) [00:51:59 -134401.004053] FAST spr round 1 (radius: 25) [00:53:37 -117510.844479] FAST spr round 2 (radius: 25) [00:55:01 -116700.007236] FAST spr round 3 (radius: 25) [00:56:15 -116619.445843] FAST spr round 4 (radius: 25) [00:57:19 -116610.807328] FAST spr round 5 (radius: 25) [00:58:20 -116610.806402] Model parameter optimization (eps = 1.000000) [00:58:30 -116607.272125] SLOW spr round 1 (radius: 5) [00:59:50 -116573.027325] SLOW spr round 2 (radius: 5) [01:01:07 -116571.923829] SLOW spr round 3 (radius: 5) [01:02:23 -116571.917397] SLOW spr round 4 (radius: 10) [01:03:39 -116571.068311] SLOW spr round 5 (radius: 5) [01:05:12 -116570.748045] SLOW spr round 6 (radius: 5) [01:06:35 -116570.747236] SLOW spr round 7 (radius: 10) [01:07:56 -116570.747179] SLOW spr round 8 (radius: 15) [01:10:07 -116570.035210] SLOW spr round 9 (radius: 5) [01:11:43 -116568.800647] SLOW spr round 10 (radius: 5) [01:13:08 -116568.800482] SLOW spr round 11 (radius: 10) [01:14:30 -116568.800419] SLOW spr round 12 (radius: 15) [01:16:39 -116568.800371] SLOW spr round 13 (radius: 20) [01:20:07 -116568.630763] SLOW spr round 14 (radius: 5) [01:21:44 -116568.629991] SLOW spr round 15 (radius: 10) [01:23:23 -116568.629588] SLOW spr round 16 (radius: 15) [01:25:28 -116568.629368] SLOW spr round 17 (radius: 20) [01:28:59 -116568.629239] SLOW spr round 18 (radius: 25) [01:33:26 -116568.629153] Model parameter optimization (eps = 0.100000) [01:33:31] ML tree search #2, logLikelihood: -116568.587503 [01:33:31 -686812.278984] Initial branch length optimization [01:33:34 -555211.324386] Model parameter optimization (eps = 10.000000) [01:33:55 -553949.818666] AUTODETECT spr round 1 (radius: 5) [01:35:16 -304801.176915] AUTODETECT spr round 2 (radius: 10) [01:36:38 -205273.177402] AUTODETECT spr round 3 (radius: 15) [01:38:10 -153980.176778] AUTODETECT spr round 4 (radius: 20) [01:39:53 -134633.845058] AUTODETECT spr round 5 (radius: 25) [01:42:04 -134271.709089] SPR radius for FAST iterations: 25 (autodetect) [01:42:04 -134271.709089] Model parameter optimization (eps = 3.000000) [01:42:28 -133915.733191] FAST spr round 1 (radius: 25) [01:43:58 -118049.920156] FAST spr round 2 (radius: 25) [01:45:19 -116759.345581] FAST spr round 3 (radius: 25) [01:46:34 -116653.161481] FAST spr round 4 (radius: 25) [01:47:41 -116649.807082] FAST spr round 5 (radius: 25) [01:48:47 -116649.794064] Model parameter optimization (eps = 1.000000) [01:49:01 -116636.723975] SLOW spr round 1 (radius: 5) [01:50:25 -116604.962134] SLOW spr round 2 (radius: 5) [01:51:49 -116597.446852] SLOW spr round 3 (radius: 5) [01:53:09 -116596.734612] SLOW spr round 4 (radius: 5) [01:54:28 -116596.732688] SLOW spr round 5 (radius: 10) [01:55:50 -116590.939334] SLOW spr round 6 (radius: 5) [01:57:29 -116574.078237] SLOW spr round 7 (radius: 5) [01:58:58 -116572.084890] SLOW spr round 8 (radius: 5) [02:00:20 -116572.084704] SLOW spr round 9 (radius: 10) [02:01:42 -116572.084635] SLOW spr round 10 (radius: 15) [02:03:57 -116572.084594] SLOW spr round 11 (radius: 20) [02:07:23 -116568.041832] SLOW spr round 12 (radius: 5) [02:09:06 -116567.374107] SLOW spr round 13 (radius: 5) [02:10:39 -116567.374010] SLOW spr round 14 (radius: 10) [02:12:07 -116567.373983] SLOW spr round 15 (radius: 15) [02:14:19 -116567.373967] SLOW spr round 16 (radius: 20) [02:17:43 -116567.373956] SLOW spr round 17 (radius: 25) [02:21:58 -116567.373947] Model parameter optimization (eps = 0.100000) [02:22:07] ML tree search #3, logLikelihood: -116566.942246 [02:22:07 -684735.486678] Initial branch length optimization [02:22:10 -551236.028649] Model parameter optimization (eps = 10.000000) [02:22:34 -550111.767442] AUTODETECT spr round 1 (radius: 5) [02:23:53 -318262.191154] AUTODETECT spr round 2 (radius: 10) [02:25:13 -204469.802491] AUTODETECT spr round 3 (radius: 15) [02:26:45 -148071.162023] AUTODETECT spr round 4 (radius: 20) [02:28:34 -131966.267434] AUTODETECT spr round 5 (radius: 25) [02:30:34 -130858.586516] SPR radius for FAST iterations: 25 (autodetect) [02:30:34 -130858.586516] Model parameter optimization (eps = 3.000000) [02:30:58 -130501.085982] FAST spr round 1 (radius: 25) [02:32:36 -117370.524392] FAST spr round 2 (radius: 25) [02:33:56 -116670.548359] FAST spr round 3 (radius: 25) [02:35:07 -116627.075859] FAST spr round 4 (radius: 25) [02:36:14 -116620.111844] FAST spr round 5 (radius: 25) [02:37:17 -116620.099724] Model parameter optimization (eps = 1.000000) [02:37:28 -116615.261187] SLOW spr round 1 (radius: 5) [02:38:52 -116585.631497] SLOW spr round 2 (radius: 5) [02:40:12 -116584.761049] SLOW spr round 3 (radius: 5) [02:41:32 -116581.724850] SLOW spr round 4 (radius: 5) [02:42:51 -116579.241989] SLOW spr round 5 (radius: 5) [02:44:08 -116579.240201] SLOW spr round 6 (radius: 10) [02:45:27 -116572.243890] SLOW spr round 7 (radius: 5) [02:47:03 -116572.182465] SLOW spr round 8 (radius: 10) [02:48:36 -116572.181587] SLOW spr round 9 (radius: 15) [02:50:42 -116572.094395] SLOW spr round 10 (radius: 20) [02:54:09 -116572.093299] SLOW spr round 11 (radius: 25) [02:58:26 -116572.092641] Model parameter optimization (eps = 0.100000) [02:58:32] ML tree search #4, logLikelihood: -116572.024438 [02:58:32 -687042.820242] Initial branch length optimization [02:58:35 -554625.891533] Model parameter optimization (eps = 10.000000) [02:59:09 -553374.987589] AUTODETECT spr round 1 (radius: 5) [03:00:26 -316913.496702] AUTODETECT spr round 2 (radius: 10) [03:01:45 -213972.284991] AUTODETECT spr round 3 (radius: 15) [03:03:15 -164286.549693] AUTODETECT spr round 4 (radius: 20) [03:05:13 -144103.595990] AUTODETECT spr round 5 (radius: 25) [03:07:33 -137435.735840] SPR radius for FAST iterations: 25 (autodetect) [03:07:33 -137435.735840] Model parameter optimization (eps = 3.000000) [03:08:02 -137082.450006] FAST spr round 1 (radius: 25) [03:09:41 -118158.862664] FAST spr round 2 (radius: 25) [03:10:57 -116741.653550] FAST spr round 3 (radius: 25) [03:12:06 -116660.605845] FAST spr round 4 (radius: 25) [03:13:10 -116659.396738] FAST spr round 5 (radius: 25) [03:14:12 -116659.350665] Model parameter optimization (eps = 1.000000) [03:14:23 -116649.747744] SLOW spr round 1 (radius: 5) [03:15:44 -116604.513581] SLOW spr round 2 (radius: 5) [03:17:02 -116598.660980] SLOW spr round 3 (radius: 5) [03:18:18 -116598.658466] SLOW spr round 4 (radius: 10) [03:19:34 -116597.542517] SLOW spr round 5 (radius: 5) [03:21:07 -116597.236047] SLOW spr round 6 (radius: 5) [03:22:32 -116597.236010] SLOW spr round 7 (radius: 10) [03:23:54 -116597.235998] SLOW spr round 8 (radius: 15) [03:26:06 -116597.143269] SLOW spr round 9 (radius: 20) [03:29:29 -116597.142949] SLOW spr round 10 (radius: 25) [03:33:47 -116597.142941] Model parameter optimization (eps = 0.100000) [03:33:54] ML tree search #5, logLikelihood: -116596.825152 [03:33:54 -683878.186196] Initial branch length optimization [03:33:58 -552534.314539] Model parameter optimization (eps = 10.000000) [03:34:19 -551271.614113] AUTODETECT spr round 1 (radius: 5) [03:35:37 -307219.380767] AUTODETECT spr round 2 (radius: 10) [03:36:55 -209944.545563] AUTODETECT spr round 3 (radius: 15) [03:38:21 -172989.994517] AUTODETECT spr round 4 (radius: 20) [03:40:10 -155738.322010] AUTODETECT spr round 5 (radius: 25) [03:41:56 -143873.752705] SPR radius for FAST iterations: 25 (autodetect) [03:41:56 -143873.752705] Model parameter optimization (eps = 3.000000) [03:42:17 -143512.111976] FAST spr round 1 (radius: 25) [03:43:53 -119049.389895] FAST spr round 2 (radius: 25) [03:45:17 -116879.035560] FAST spr round 3 (radius: 25) [03:46:27 -116695.674324] FAST spr round 4 (radius: 25) [03:47:32 -116685.810202] FAST spr round 5 (radius: 25) [03:48:33 -116680.165389] FAST spr round 6 (radius: 25) [03:49:33 -116680.165104] Model parameter optimization (eps = 1.000000) [03:49:52 -116637.506522] SLOW spr round 1 (radius: 5) [03:51:09 -116586.821753] SLOW spr round 2 (radius: 5) [03:52:28 -116584.575852] SLOW spr round 3 (radius: 5) [03:53:44 -116584.575382] SLOW spr round 4 (radius: 10) [03:55:01 -116583.245942] SLOW spr round 5 (radius: 5) [03:56:34 -116582.675951] SLOW spr round 6 (radius: 5) [03:57:56 -116582.675905] SLOW spr round 7 (radius: 10) [03:59:16 -116582.675863] SLOW spr round 8 (radius: 15) [04:01:23 -116582.503027] SLOW spr round 9 (radius: 5) [04:02:58 -116582.502166] SLOW spr round 10 (radius: 10) [04:04:32 -116582.502092] SLOW spr round 11 (radius: 15) [04:06:34 -116582.266564] SLOW spr round 12 (radius: 5) [04:08:10 -116581.973901] SLOW spr round 13 (radius: 5) [04:09:36 -116581.973872] SLOW spr round 14 (radius: 10) [04:11:05 -116580.936281] SLOW spr round 15 (radius: 5) [04:12:42 -116580.936245] SLOW spr round 16 (radius: 10) [04:14:16 -116580.936242] SLOW spr round 17 (radius: 15) [04:16:28 -116580.936240] SLOW spr round 18 (radius: 20) [04:19:53 -116580.936237] SLOW spr round 19 (radius: 25) [04:24:17 -116580.936235] Model parameter optimization (eps = 0.100000) [04:24:24] ML tree search #6, logLikelihood: -116580.681211 [04:24:24 -686391.441939] Initial branch length optimization [04:24:27 -556695.095190] Model parameter optimization (eps = 10.000000) [04:24:58 -555542.411522] AUTODETECT spr round 1 (radius: 5) [04:26:20 -301827.394386] AUTODETECT spr round 2 (radius: 10) [04:27:43 -206419.639887] AUTODETECT spr round 3 (radius: 15) [04:29:13 -162789.306256] AUTODETECT spr round 4 (radius: 20) [04:30:56 -138116.342183] AUTODETECT spr round 5 (radius: 25) [04:33:06 -135230.985844] SPR radius for FAST iterations: 25 (autodetect) [04:33:06 -135230.985844] Model parameter optimization (eps = 3.000000) [04:33:30 -134843.655924] FAST spr round 1 (radius: 25) [04:35:07 -117650.756165] FAST spr round 2 (radius: 25) [04:36:32 -116691.497857] FAST spr round 3 (radius: 25) [04:37:47 -116642.254670] FAST spr round 4 (radius: 25) [04:38:56 -116637.064254] FAST spr round 5 (radius: 25) [04:40:01 -116637.052836] Model parameter optimization (eps = 1.000000) [04:40:15 -116629.290314] SLOW spr round 1 (radius: 5) [04:41:38 -116584.118665] SLOW spr round 2 (radius: 5) [04:43:00 -116578.552006] SLOW spr round 3 (radius: 5) [04:44:21 -116578.325388] SLOW spr round 4 (radius: 5) [04:45:37 -116578.325332] SLOW spr round 5 (radius: 10) [04:46:58 -116574.253451] SLOW spr round 6 (radius: 5) [04:48:35 -116573.431786] SLOW spr round 7 (radius: 5) [04:50:02 -116573.431735] SLOW spr round 8 (radius: 10) [04:51:26 -116573.431698] SLOW spr round 9 (radius: 15) [04:53:41 -116573.431664] SLOW spr round 10 (radius: 20) [04:57:14 -116573.431631] SLOW spr round 11 (radius: 25) [05:01:33 -116573.431599] Model parameter optimization (eps = 0.100000) [05:01:41] ML tree search #7, logLikelihood: -116573.258849 [05:01:41 -686882.673329] Initial branch length optimization [05:01:44 -554818.462901] Model parameter optimization (eps = 10.000000) [05:02:12 -553722.629756] AUTODETECT spr round 1 (radius: 5) [05:03:30 -307360.033596] AUTODETECT spr round 2 (radius: 10) [05:04:53 -217703.845282] AUTODETECT spr round 3 (radius: 15) [05:06:23 -169511.869954] AUTODETECT spr round 4 (radius: 20) [05:08:04 -138604.585807] AUTODETECT spr round 5 (radius: 25) [05:10:23 -136297.356975] SPR radius for FAST iterations: 25 (autodetect) [05:10:23 -136297.356975] Model parameter optimization (eps = 3.000000) [05:10:44 -135871.639617] FAST spr round 1 (radius: 25) [05:12:18 -117591.976298] FAST spr round 2 (radius: 25) [05:13:39 -116723.911168] FAST spr round 3 (radius: 25) [05:14:52 -116648.181154] FAST spr round 4 (radius: 25) [05:15:59 -116636.356131] FAST spr round 5 (radius: 25) [05:17:03 -116632.996871] FAST spr round 6 (radius: 25) [05:18:05 -116631.678831] FAST spr round 7 (radius: 25) [05:19:07 -116631.678094] Model parameter optimization (eps = 1.000000) [05:19:20 -116619.533952] SLOW spr round 1 (radius: 5) [05:20:42 -116584.885540] SLOW spr round 2 (radius: 5) [05:22:04 -116581.005107] SLOW spr round 3 (radius: 5) [05:23:23 -116577.685826] SLOW spr round 4 (radius: 5) [05:24:41 -116577.680722] SLOW spr round 5 (radius: 10) [05:26:01 -116576.321639] SLOW spr round 6 (radius: 5) [05:27:37 -116575.750293] SLOW spr round 7 (radius: 5) [05:29:04 -116575.750253] SLOW spr round 8 (radius: 10) [05:30:28 -116575.581790] SLOW spr round 9 (radius: 5) [05:32:02 -116575.581286] SLOW spr round 10 (radius: 10) [05:33:34 -116575.581022] SLOW spr round 11 (radius: 15) [05:35:44 -116575.580875] SLOW spr round 12 (radius: 20) [05:39:12 -116575.580786] SLOW spr round 13 (radius: 25) [05:43:38 -116575.580716] Model parameter optimization (eps = 0.100000) [05:43:50] ML tree search #8, logLikelihood: -116575.079890 [05:43:50 -684812.950932] Initial branch length optimization [05:43:53 -552456.767011] Model parameter optimization (eps = 10.000000) [05:44:22 -551257.567040] AUTODETECT spr round 1 (radius: 5) [05:45:40 -300414.372467] AUTODETECT spr round 2 (radius: 10) [05:47:02 -201627.461426] AUTODETECT spr round 3 (radius: 15) [05:48:31 -157423.210712] AUTODETECT spr round 4 (radius: 20) [05:50:16 -138062.759493] AUTODETECT spr round 5 (radius: 25) [05:52:22 -133042.154691] SPR radius for FAST iterations: 25 (autodetect) [05:52:22 -133042.154691] Model parameter optimization (eps = 3.000000) [05:52:42 -132681.337555] FAST spr round 1 (radius: 25) [05:54:16 -117392.891775] FAST spr round 2 (radius: 25) [05:55:35 -116678.871951] FAST spr round 3 (radius: 25) [05:56:45 -116655.763234] FAST spr round 4 (radius: 25) [05:57:52 -116647.727408] FAST spr round 5 (radius: 25) [05:58:55 -116647.726775] Model parameter optimization (eps = 1.000000) [05:59:07 -116639.197808] SLOW spr round 1 (radius: 5) [06:00:30 -116585.942211] SLOW spr round 2 (radius: 5) [06:01:51 -116574.635758] SLOW spr round 3 (radius: 5) [06:03:11 -116569.570034] SLOW spr round 4 (radius: 5) [06:04:28 -116569.567431] SLOW spr round 5 (radius: 10) [06:05:47 -116569.183729] SLOW spr round 6 (radius: 5) [06:07:21 -116569.181618] SLOW spr round 7 (radius: 10) [06:08:52 -116569.181351] SLOW spr round 8 (radius: 15) [06:10:55 -116569.181234] SLOW spr round 9 (radius: 20) [06:14:16 -116569.181144] SLOW spr round 10 (radius: 25) [06:18:31 -116569.181068] Model parameter optimization (eps = 0.100000) [06:18:39] ML tree search #9, logLikelihood: -116568.955231 [06:18:39 -686358.796337] Initial branch length optimization [06:18:42 -556673.911661] Model parameter optimization (eps = 10.000000) [06:19:08 -555408.923238] AUTODETECT spr round 1 (radius: 5) [06:20:25 -318653.635651] AUTODETECT spr round 2 (radius: 10) [06:21:44 -210233.545366] AUTODETECT spr round 3 (radius: 15) [06:23:12 -169026.190541] AUTODETECT spr round 4 (radius: 20) [06:24:48 -142901.378535] AUTODETECT spr round 5 (radius: 25) [06:26:39 -136456.890166] SPR radius for FAST iterations: 25 (autodetect) [06:26:39 -136456.890166] Model parameter optimization (eps = 3.000000) [06:27:04 -136092.166888] FAST spr round 1 (radius: 25) [06:28:32 -117278.718496] FAST spr round 2 (radius: 25) [06:29:48 -116727.376527] FAST spr round 3 (radius: 25) [06:30:59 -116637.387323] FAST spr round 4 (radius: 25) [06:32:06 -116622.526496] FAST spr round 5 (radius: 25) [06:33:08 -116620.518291] FAST spr round 6 (radius: 25) [06:34:09 -116620.517684] Model parameter optimization (eps = 1.000000) [06:34:22 -116612.404828] SLOW spr round 1 (radius: 5) [06:35:43 -116590.678503] SLOW spr round 2 (radius: 5) [06:37:01 -116584.449921] SLOW spr round 3 (radius: 5) [06:38:18 -116583.292345] SLOW spr round 4 (radius: 5) [06:39:31 -116583.291029] SLOW spr round 5 (radius: 10) [06:40:48 -116580.848262] SLOW spr round 6 (radius: 5) [06:42:19 -116580.782651] SLOW spr round 7 (radius: 10) [06:43:49 -116580.781880] SLOW spr round 8 (radius: 15) [06:45:54 -116580.781404] SLOW spr round 9 (radius: 20) [06:49:10 -116580.781045] SLOW spr round 10 (radius: 25) [06:53:18 -116580.780771] Model parameter optimization (eps = 0.100000) [06:53:23] ML tree search #10, logLikelihood: -116580.685150 [06:53:23 -689669.432979] Initial branch length optimization [06:53:25 -555465.913015] Model parameter optimization (eps = 10.000000) [06:53:44 -554292.943555] AUTODETECT spr round 1 (radius: 5) [06:55:01 -314241.710085] AUTODETECT spr round 2 (radius: 10) [06:56:18 -196449.219327] AUTODETECT spr round 3 (radius: 15) [06:57:43 -149557.351613] AUTODETECT spr round 4 (radius: 20) [06:59:16 -134766.594418] AUTODETECT spr round 5 (radius: 25) [07:01:07 -132714.855428] SPR radius for FAST iterations: 25 (autodetect) [07:01:07 -132714.855428] Model parameter optimization (eps = 3.000000) [07:01:28 -132352.576711] FAST spr round 1 (radius: 25) [07:03:02 -117446.798213] FAST spr round 2 (radius: 25) [07:04:21 -116705.395968] FAST spr round 3 (radius: 25) [07:05:33 -116647.433968] FAST spr round 4 (radius: 25) [07:06:40 -116641.164643] FAST spr round 5 (radius: 25) [07:07:43 -116639.977250] FAST spr round 6 (radius: 25) [07:08:45 -116638.459329] FAST spr round 7 (radius: 25) [07:09:47 -116638.458686] Model parameter optimization (eps = 1.000000) [07:10:00 -116625.716485] SLOW spr round 1 (radius: 5) [07:11:21 -116581.068338] SLOW spr round 2 (radius: 5) [07:12:41 -116578.292183] SLOW spr round 3 (radius: 5) [07:13:59 -116578.290726] SLOW spr round 4 (radius: 10) [07:15:18 -116577.014924] SLOW spr round 5 (radius: 5) [07:16:52 -116576.509917] SLOW spr round 6 (radius: 5) [07:18:17 -116576.509068] SLOW spr round 7 (radius: 10) [07:19:40 -116576.508724] SLOW spr round 8 (radius: 15) [07:21:48 -116576.508715] SLOW spr round 9 (radius: 20) [07:25:02 -116576.508706] SLOW spr round 10 (radius: 25) [07:29:10 -116576.508698] Model parameter optimization (eps = 0.100000) [07:29:22] ML tree search #11, logLikelihood: -116576.328247 [07:29:22 -679269.660755] Initial branch length optimization [07:29:26 -546969.294519] Model parameter optimization (eps = 10.000000) [07:29:53 -545737.937724] AUTODETECT spr round 1 (radius: 5) [07:31:09 -313392.367199] AUTODETECT spr round 2 (radius: 10) [07:32:27 -208761.353701] AUTODETECT spr round 3 (radius: 15) [07:33:50 -164845.977802] AUTODETECT spr round 4 (radius: 20) [07:35:21 -148747.303739] AUTODETECT spr round 5 (radius: 25) [07:37:01 -138476.662381] SPR radius for FAST iterations: 25 (autodetect) [07:37:01 -138476.662381] Model parameter optimization (eps = 3.000000) [07:37:22 -138127.177713] FAST spr round 1 (radius: 25) [07:38:56 -118265.196900] FAST spr round 2 (radius: 25) [07:40:14 -116715.673029] FAST spr round 3 (radius: 25) [07:41:22 -116638.380963] FAST spr round 4 (radius: 25) [07:42:26 -116627.751602] FAST spr round 5 (radius: 25) [07:43:28 -116627.263660] FAST spr round 6 (radius: 25) [07:44:28 -116627.167609] Model parameter optimization (eps = 1.000000) [07:44:41 -116609.744134] SLOW spr round 1 (radius: 5) [07:45:59 -116584.668664] SLOW spr round 2 (radius: 5) [07:47:16 -116582.034111] SLOW spr round 3 (radius: 5) [07:48:32 -116582.005296] SLOW spr round 4 (radius: 10) [07:49:49 -116580.410054] SLOW spr round 5 (radius: 5) [07:51:24 -116575.371949] SLOW spr round 6 (radius: 5) [07:52:48 -116574.104359] SLOW spr round 7 (radius: 5) [07:54:09 -116574.103290] SLOW spr round 8 (radius: 10) [07:55:33 -116574.103282] SLOW spr round 9 (radius: 15) [07:57:52 -116573.917469] SLOW spr round 10 (radius: 5) [07:59:35 -116573.917107] SLOW spr round 11 (radius: 10) [08:01:15 -116573.917099] SLOW spr round 12 (radius: 15) [08:03:27 -116573.917083] SLOW spr round 13 (radius: 20) [08:07:01 -116571.718225] SLOW spr round 14 (radius: 5) [08:08:45 -116571.718198] SLOW spr round 15 (radius: 10) [08:10:30 -116569.478245] SLOW spr round 16 (radius: 5) [08:12:03 -116569.478243] SLOW spr round 17 (radius: 10) [08:13:34 -116569.478241] SLOW spr round 18 (radius: 15) [08:15:46 -116569.478241] SLOW spr round 19 (radius: 20) [08:19:20 -116569.478240] SLOW spr round 20 (radius: 25) [08:23:38 -116569.478240] Model parameter optimization (eps = 0.100000) [08:23:46] ML tree search #12, logLikelihood: -116569.115758 [08:23:46 -683702.027785] Initial branch length optimization [08:23:49 -554890.768775] Model parameter optimization (eps = 10.000000) [08:24:09 -553777.999676] AUTODETECT spr round 1 (radius: 5) [08:25:30 -321673.709152] AUTODETECT spr round 2 (radius: 10) [08:26:51 -211010.914681] AUTODETECT spr round 3 (radius: 15) [08:28:21 -163109.123229] AUTODETECT spr round 4 (radius: 20) [08:30:07 -141871.597510] AUTODETECT spr round 5 (radius: 25) [08:32:00 -134813.300852] SPR radius for FAST iterations: 25 (autodetect) [08:32:00 -134813.300852] Model parameter optimization (eps = 3.000000) [08:32:34 -134505.614073] FAST spr round 1 (radius: 25) [08:34:09 -117814.626022] FAST spr round 2 (radius: 25) [08:35:31 -116701.112925] FAST spr round 3 (radius: 25) [08:36:46 -116650.037925] FAST spr round 4 (radius: 25) [08:37:55 -116646.220387] FAST spr round 5 (radius: 25) [08:39:00 -116644.789179] FAST spr round 6 (radius: 25) [08:40:06 -116644.788093] Model parameter optimization (eps = 1.000000) [08:40:19 -116633.430320] SLOW spr round 1 (radius: 5) [08:41:42 -116592.669234] SLOW spr round 2 (radius: 5) [08:43:04 -116583.421506] SLOW spr round 3 (radius: 5) [08:44:26 -116583.421267] SLOW spr round 4 (radius: 10) [08:45:47 -116581.906396] SLOW spr round 5 (radius: 5) [08:47:27 -116581.339798] SLOW spr round 6 (radius: 5) [08:48:57 -116581.339145] SLOW spr round 7 (radius: 10) [08:50:25 -116581.338869] SLOW spr round 8 (radius: 15) [08:52:34 -116581.167597] SLOW spr round 9 (radius: 5) [08:54:15 -116581.167491] SLOW spr round 10 (radius: 10) [08:55:54 -116581.167432] SLOW spr round 11 (radius: 15) [08:57:57 -116581.167385] SLOW spr round 12 (radius: 20) [09:01:16 -116578.956466] SLOW spr round 13 (radius: 5) [09:02:58 -116578.956417] SLOW spr round 14 (radius: 10) [09:04:40 -116576.709833] SLOW spr round 15 (radius: 5) [09:06:13 -116576.709796] SLOW spr round 16 (radius: 10) [09:07:42 -116576.709760] SLOW spr round 17 (radius: 15) [09:09:48 -116576.709724] SLOW spr round 18 (radius: 20) [09:13:05 -116576.709688] SLOW spr round 19 (radius: 25) [09:17:13 -116576.709652] Model parameter optimization (eps = 0.100000) [09:17:21] ML tree search #13, logLikelihood: -116576.321406 [09:17:22 -688679.423377] Initial branch length optimization [09:17:25 -557123.508564] Model parameter optimization (eps = 10.000000) [09:17:50 -555809.075298] AUTODETECT spr round 1 (radius: 5) [09:19:07 -329882.024743] AUTODETECT spr round 2 (radius: 10) [09:20:28 -222502.368885] AUTODETECT spr round 3 (radius: 15) [09:21:56 -174700.621031] AUTODETECT spr round 4 (radius: 20) [09:23:36 -146070.616428] AUTODETECT spr round 5 (radius: 25) [09:25:29 -137049.281640] SPR radius for FAST iterations: 25 (autodetect) [09:25:29 -137049.281640] Model parameter optimization (eps = 3.000000) [09:26:07 -136669.988857] FAST spr round 1 (radius: 25) [09:27:39 -118378.593649] FAST spr round 2 (radius: 25) [09:28:57 -116758.342738] FAST spr round 3 (radius: 25) [09:30:09 -116632.069009] FAST spr round 4 (radius: 25) [09:31:15 -116631.675266] FAST spr round 5 (radius: 25) [09:32:18 -116631.674343] Model parameter optimization (eps = 1.000000) [09:32:30 -116622.901441] SLOW spr round 1 (radius: 5) [09:33:52 -116586.755202] SLOW spr round 2 (radius: 5) [09:35:14 -116578.719683] SLOW spr round 3 (radius: 5) [09:36:33 -116574.438964] SLOW spr round 4 (radius: 5) [09:37:49 -116570.653653] SLOW spr round 5 (radius: 5) [09:39:05 -116569.448848] SLOW spr round 6 (radius: 5) [09:40:20 -116569.441987] SLOW spr round 7 (radius: 10) [09:41:38 -116564.723697] SLOW spr round 8 (radius: 5) [09:43:10 -116564.393557] SLOW spr round 9 (radius: 5) [09:44:34 -116564.393456] SLOW spr round 10 (radius: 10) [09:45:55 -116564.393382] SLOW spr round 11 (radius: 15) [09:48:03 -116564.393319] SLOW spr round 12 (radius: 20) [09:51:22 -116564.393264] SLOW spr round 13 (radius: 25) [09:55:41 -116564.393246] Model parameter optimization (eps = 0.100000) [09:55:48] ML tree search #14, logLikelihood: -116564.101557 [09:55:48 -691020.999567] Initial branch length optimization [09:55:51 -556943.573770] Model parameter optimization (eps = 10.000000) [09:56:13 -555494.806543] AUTODETECT spr round 1 (radius: 5) [09:57:29 -319474.677942] AUTODETECT spr round 2 (radius: 10) [09:58:45 -216739.458274] AUTODETECT spr round 3 (radius: 15) [10:00:10 -174270.461944] AUTODETECT spr round 4 (radius: 20) [10:01:58 -152082.780846] AUTODETECT spr round 5 (radius: 25) [10:03:54 -139943.285003] SPR radius for FAST iterations: 25 (autodetect) [10:03:54 -139943.285003] Model parameter optimization (eps = 3.000000) [10:04:19 -139537.391991] FAST spr round 1 (radius: 25) [10:05:47 -119358.040644] FAST spr round 2 (radius: 25) [10:07:04 -116958.619573] FAST spr round 3 (radius: 25) [10:08:16 -116809.326061] FAST spr round 4 (radius: 25) [10:09:21 -116803.031344] FAST spr round 5 (radius: 25) [10:10:24 -116800.943753] FAST spr round 6 (radius: 25) [10:11:25 -116799.973774] FAST spr round 7 (radius: 25) [10:12:25 -116799.972956] Model parameter optimization (eps = 1.000000) [10:12:39 -116787.277822] SLOW spr round 1 (radius: 5) [10:13:57 -116746.439695] SLOW spr round 2 (radius: 5) [10:15:15 -116742.899691] SLOW spr round 3 (radius: 5) [10:16:37 -116741.370986] SLOW spr round 4 (radius: 5) [10:18:00 -116741.370926] SLOW spr round 5 (radius: 10) [10:19:24 -116739.021040] SLOW spr round 6 (radius: 5) [10:21:03 -116738.686827] SLOW spr round 7 (radius: 5) [10:22:32 -116738.686769] SLOW spr round 8 (radius: 10) [10:23:59 -116738.686726] SLOW spr round 9 (radius: 15) [10:26:11 -116738.686687] SLOW spr round 10 (radius: 20) [10:29:32 -116738.686648] SLOW spr round 11 (radius: 25) [10:33:40 -116738.686609] Model parameter optimization (eps = 0.100000) [10:33:48] ML tree search #15, logLikelihood: -116738.501571 [10:33:48 -683020.152445] Initial branch length optimization [10:33:51 -552668.097284] Model parameter optimization (eps = 10.000000) [10:34:15 -551481.849567] AUTODETECT spr round 1 (radius: 5) [10:35:36 -311191.828578] AUTODETECT spr round 2 (radius: 10) [10:36:58 -205276.010485] AUTODETECT spr round 3 (radius: 15) [10:38:28 -151970.673018] AUTODETECT spr round 4 (radius: 20) [10:40:11 -136164.268422] AUTODETECT spr round 5 (radius: 25) [10:42:20 -135290.006347] SPR radius for FAST iterations: 25 (autodetect) [10:42:20 -135290.006347] Model parameter optimization (eps = 3.000000) [10:42:42 -135002.469637] FAST spr round 1 (radius: 25) [10:44:17 -117841.173897] FAST spr round 2 (radius: 25) [10:45:40 -116821.891754] FAST spr round 3 (radius: 25) [10:46:54 -116793.219386] FAST spr round 4 (radius: 25) [10:48:03 -116781.868180] FAST spr round 5 (radius: 25) [10:49:08 -116781.867043] Model parameter optimization (eps = 1.000000) [10:49:24 -116765.576548] SLOW spr round 1 (radius: 5) [10:50:46 -116736.612964] SLOW spr round 2 (radius: 5) [10:52:07 -116734.953207] SLOW spr round 3 (radius: 5) [10:53:28 -116734.853614] SLOW spr round 4 (radius: 10) [10:54:51 -116730.778241] SLOW spr round 5 (radius: 5) [10:56:27 -116730.435665] SLOW spr round 6 (radius: 5) [10:57:54 -116730.435639] SLOW spr round 7 (radius: 10) [10:59:20 -116730.435638] SLOW spr round 8 (radius: 15) [11:01:26 -116729.139586] SLOW spr round 9 (radius: 5) [11:03:09 -116728.498692] SLOW spr round 10 (radius: 5) [11:04:39 -116728.498690] SLOW spr round 11 (radius: 10) [11:06:07 -116728.498690] SLOW spr round 12 (radius: 15) [11:08:12 -116728.498690] SLOW spr round 13 (radius: 20) [11:11:17 -116728.498690] SLOW spr round 14 (radius: 25) [11:15:21 -116725.811685] SLOW spr round 15 (radius: 5) [11:17:04 -116723.984344] SLOW spr round 16 (radius: 5) [11:18:36 -116723.982147] SLOW spr round 17 (radius: 10) [11:20:05 -116717.973381] SLOW spr round 18 (radius: 5) [11:21:41 -116582.072535] SLOW spr round 19 (radius: 5) [11:23:06 -116582.068230] SLOW spr round 20 (radius: 10) [11:24:29 -116579.042321] SLOW spr round 21 (radius: 5) [11:26:03 -116577.536044] SLOW spr round 22 (radius: 5) [11:27:27 -116577.532064] SLOW spr round 23 (radius: 10) [11:28:48 -116577.530303] SLOW spr round 24 (radius: 15) [11:30:53 -116577.530249] SLOW spr round 25 (radius: 20) [11:33:54 -116577.530249] SLOW spr round 26 (radius: 25) [11:38:00 -116577.530249] Model parameter optimization (eps = 0.100000) [11:38:09] ML tree search #16, logLikelihood: -116576.887935 [11:38:09 -684265.410203] Initial branch length optimization [11:38:13 -556278.579547] Model parameter optimization (eps = 10.000000) [11:38:50 -555072.445369] AUTODETECT spr round 1 (radius: 5) [11:40:08 -312647.202545] AUTODETECT spr round 2 (radius: 10) [11:41:29 -206871.021666] AUTODETECT spr round 3 (radius: 15) [11:42:59 -166718.158915] AUTODETECT spr round 4 (radius: 20) [11:44:36 -144100.880073] AUTODETECT spr round 5 (radius: 25) [11:46:31 -135212.835491] SPR radius for FAST iterations: 25 (autodetect) [11:46:31 -135212.835491] Model parameter optimization (eps = 3.000000) [11:46:52 -134889.456988] FAST spr round 1 (radius: 25) [11:48:24 -117395.201198] FAST spr round 2 (radius: 25) [11:49:39 -116681.044109] FAST spr round 3 (radius: 25) [11:50:50 -116624.703976] FAST spr round 4 (radius: 25) [11:51:54 -116623.366607] FAST spr round 5 (radius: 25) [11:52:55 -116623.366028] Model parameter optimization (eps = 1.000000) [11:53:07 -116607.199737] SLOW spr round 1 (radius: 5) [11:54:26 -116579.302407] SLOW spr round 2 (radius: 5) [11:55:43 -116574.189136] SLOW spr round 3 (radius: 5) [11:56:59 -116574.188268] SLOW spr round 4 (radius: 10) [11:58:17 -116568.811649] SLOW spr round 5 (radius: 5) [11:59:50 -116568.346092] SLOW spr round 6 (radius: 5) [12:01:13 -116568.343149] SLOW spr round 7 (radius: 10) [12:02:34 -116568.342622] SLOW spr round 8 (radius: 15) [12:04:42 -116568.279726] SLOW spr round 9 (radius: 20) [12:07:57 -116568.279175] SLOW spr round 10 (radius: 25) [12:12:09 -116568.279130] Model parameter optimization (eps = 0.100000) [12:12:17] ML tree search #17, logLikelihood: -116568.085823 [12:12:17 -684205.846857] Initial branch length optimization [12:12:20 -557556.537236] Model parameter optimization (eps = 10.000000) [12:12:40 -556284.482410] AUTODETECT spr round 1 (radius: 5) [12:13:57 -300681.175881] AUTODETECT spr round 2 (radius: 10) [12:15:15 -200420.512058] AUTODETECT spr round 3 (radius: 15) [12:16:40 -161895.415047] AUTODETECT spr round 4 (radius: 20) [12:18:22 -144892.444335] AUTODETECT spr round 5 (radius: 25) [12:20:17 -133810.487138] SPR radius for FAST iterations: 25 (autodetect) [12:20:17 -133810.487138] Model parameter optimization (eps = 3.000000) [12:20:39 -133471.613901] FAST spr round 1 (radius: 25) [12:22:11 -117797.283657] FAST spr round 2 (radius: 25) [12:23:30 -116805.377575] FAST spr round 3 (radius: 25) [12:24:45 -116674.858506] FAST spr round 4 (radius: 25) [12:25:55 -116665.518342] FAST spr round 5 (radius: 25) [12:27:02 -116665.517557] Model parameter optimization (eps = 1.000000) [12:27:20 -116630.516449] SLOW spr round 1 (radius: 5) [12:28:45 -116592.704695] SLOW spr round 2 (radius: 5) [12:30:08 -116581.003767] SLOW spr round 3 (radius: 5) [12:31:30 -116581.002473] SLOW spr round 4 (radius: 10) [12:32:51 -116580.080171] SLOW spr round 5 (radius: 5) [12:34:29 -116576.934960] SLOW spr round 6 (radius: 5) [12:35:57 -116576.043121] SLOW spr round 7 (radius: 5) [12:37:19 -116576.043072] SLOW spr round 8 (radius: 10) [12:38:40 -116576.043037] SLOW spr round 9 (radius: 15) [12:40:57 -116576.043003] SLOW spr round 10 (radius: 20) [12:44:19 -116576.042968] SLOW spr round 11 (radius: 25) [12:48:43 -116576.042934] Model parameter optimization (eps = 0.100000) [12:48:52] ML tree search #18, logLikelihood: -116575.872388 [12:48:52 -686385.463751] Initial branch length optimization [12:48:55 -554395.822311] Model parameter optimization (eps = 10.000000) [12:49:19 -553203.116964] AUTODETECT spr round 1 (radius: 5) [12:50:41 -309817.569682] AUTODETECT spr round 2 (radius: 10) [12:52:04 -197222.941424] AUTODETECT spr round 3 (radius: 15) [12:53:32 -159673.426807] AUTODETECT spr round 4 (radius: 20) [12:55:12 -146906.997060] AUTODETECT spr round 5 (radius: 25) [12:57:27 -139273.911886] SPR radius for FAST iterations: 25 (autodetect) [12:57:27 -139273.911886] Model parameter optimization (eps = 3.000000) [12:57:48 -138897.808209] FAST spr round 1 (radius: 25) [12:59:25 -119136.637528] FAST spr round 2 (radius: 25) [13:00:54 -116828.518193] FAST spr round 3 (radius: 25) [13:02:07 -116639.570992] FAST spr round 4 (radius: 25) [13:03:13 -116614.590867] FAST spr round 5 (radius: 25) [13:04:21 -116607.515860] FAST spr round 6 (radius: 25) [13:05:27 -116607.515612] Model parameter optimization (eps = 1.000000) [13:05:44 -116592.225462] SLOW spr round 1 (radius: 5) [13:07:06 -116567.204189] SLOW spr round 2 (radius: 5) [13:08:30 -116562.036155] SLOW spr round 3 (radius: 5) [13:09:51 -116562.035220] SLOW spr round 4 (radius: 10) [13:11:14 -116558.845899] SLOW spr round 5 (radius: 5) [13:12:53 -116555.953609] SLOW spr round 6 (radius: 5) [13:14:20 -116555.953406] SLOW spr round 7 (radius: 10) [13:15:45 -116555.953358] SLOW spr round 8 (radius: 15) [13:17:55 -116555.953319] SLOW spr round 9 (radius: 20) [13:21:22 -116555.953282] SLOW spr round 10 (radius: 25) [13:25:40 -116555.953245] Model parameter optimization (eps = 0.100000) [13:25:48] ML tree search #19, logLikelihood: -116555.773743 [13:25:49 -682940.159164] Initial branch length optimization [13:25:52 -555652.850374] Model parameter optimization (eps = 10.000000) [13:26:18 -554376.041530] AUTODETECT spr round 1 (radius: 5) [13:27:38 -307589.221164] AUTODETECT spr round 2 (radius: 10) [13:28:58 -200761.559967] AUTODETECT spr round 3 (radius: 15) [13:30:21 -170929.216697] AUTODETECT spr round 4 (radius: 20) [13:32:02 -158800.829402] AUTODETECT spr round 5 (radius: 25) [13:33:57 -148192.153675] SPR radius for FAST iterations: 25 (autodetect) [13:33:58 -148192.153675] Model parameter optimization (eps = 3.000000) [13:34:25 -147817.749008] FAST spr round 1 (radius: 25) [13:35:59 -122668.821191] FAST spr round 2 (radius: 25) [13:37:19 -117496.681060] FAST spr round 3 (radius: 25) [13:38:32 -116684.653786] FAST spr round 4 (radius: 25) [13:39:40 -116630.613920] FAST spr round 5 (radius: 25) [13:40:45 -116623.650438] FAST spr round 6 (radius: 25) [13:41:47 -116623.649884] Model parameter optimization (eps = 1.000000) [13:42:04 -116599.640262] SLOW spr round 1 (radius: 5) [13:43:25 -116579.303052] SLOW spr round 2 (radius: 5) [13:44:44 -116573.578345] SLOW spr round 3 (radius: 5) [13:46:02 -116573.574822] SLOW spr round 4 (radius: 10) [13:47:21 -116570.211140] SLOW spr round 5 (radius: 5) [13:48:57 -116567.480946] SLOW spr round 6 (radius: 5) [13:50:22 -116567.480663] SLOW spr round 7 (radius: 10) [13:51:45 -116567.480621] SLOW spr round 8 (radius: 15) [13:53:51 -116567.480583] SLOW spr round 9 (radius: 20) [13:57:06 -116567.312322] SLOW spr round 10 (radius: 5) [13:58:44 -116567.311584] SLOW spr round 11 (radius: 10) [14:00:23 -116567.311205] SLOW spr round 12 (radius: 15) [14:02:23 -116567.311002] SLOW spr round 13 (radius: 20) [14:05:38 -116567.310885] SLOW spr round 14 (radius: 25) [14:09:54 -116567.310810] Model parameter optimization (eps = 0.100000) [14:10:02] ML tree search #20, logLikelihood: -116566.931743 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.239988,0.581085) (0.113967,0.441996) (0.338180,0.852191) (0.307864,1.695484) 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: -116555.773743 AIC score: 236345.547486 / AICc score: 5468957.547486 / BIC score: 243349.585977 Free parameters (model + branch lengths): 1617 WARNING: Number of free parameters (K=1617) is larger than alignment size (n=562). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 1 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q99959/3_mltree/Q99959.raxml.bestTreeCollapsed Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q99959/3_mltree/Q99959.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q99959/3_mltree/Q99959.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q99959/3_mltree/Q99959.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q99959/3_mltree/Q99959.raxml.log Analysis started: 23-Jun-2021 14:14:23 / finished: 24-Jun-2021 04:24:26 Elapsed time: 51002.631 seconds