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 11-Jul-2021 03:08:05 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O00567/2_msa/O00567_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O00567/3_mltree/O00567 --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_300621/phylogeny-snakemake/results/O00567/2_msa/O00567_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 479 sites WARNING: Sequences tr_B4R013_B4R013_DROSI_7240 and tr_B4HE83_B4HE83_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1RD85_G1RD85_NOMLE_61853 and tr_F6R553_F6R553_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1RD85_G1RD85_NOMLE_61853 and tr_A0A096NV77_A0A096NV77_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RD85_G1RD85_NOMLE_61853 and tr_A0A2K5LMR6_A0A2K5LMR6_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RD85_G1RD85_NOMLE_61853 and tr_A0A2K6C4I2_A0A2K6C4I2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RD85_G1RD85_NOMLE_61853 and tr_A0A2K5XMU6_A0A2K5XMU6_MANLE_9568 are exactly identical! WARNING: Sequences tr_J3KK68_J3KK68_COCIM_246410 and tr_A0A0J6Y2G7_A0A0J6Y2G7_COCIT_404692 are exactly identical! WARNING: Sequences tr_B2W8M0_B2W8M0_PYRTR_426418 and tr_A0A2W1GIL8_A0A2W1GIL8_9PLEO_45151 are exactly identical! WARNING: Sequences tr_H2P1E5_H2P1E5_PONAB_9601 and tr_G2HGR6_G2HGR6_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2P1E5_H2P1E5_PONAB_9601 and tr_A0A2R8ZU94_A0A2R8ZU94_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q7S0H3_Q7S0H3_NEUCR_367110 and tr_G4UX08_G4UX08_NEUT9_510952 are exactly identical! WARNING: Sequences tr_B8MZN8_B8MZN8_ASPFN_332952 and tr_Q2UQD8_Q2UQD8_ASPOR_510516 are exactly identical! WARNING: Sequences tr_B8MZN8_B8MZN8_ASPFN_332952 and tr_A0A1S9DTZ9_A0A1S9DTZ9_ASPOZ_5062 are exactly identical! WARNING: Sequences tr_E2QU53_E2QU53_CANLF_9615 and tr_A0A2U3ZDI8_A0A2U3ZDI8_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2QU53_E2QU53_CANLF_9615 and tr_A0A2Y9IUC5_A0A2Y9IUC5_ENHLU_391180 are exactly identical! WARNING: Sequences tr_W5P916_W5P916_SHEEP_9940 and tr_F1MW06_F1MW06_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F9FJG4_F9FJG4_FUSOF_660025 and tr_A0A0D2Y9B3_A0A0D2Y9B3_FUSO4_426428 are exactly identical! WARNING: Sequences tr_F9FJG4_F9FJG4_FUSOF_660025 and tr_N4U6Z4_N4U6Z4_FUSC1_1229664 are exactly identical! WARNING: Sequences tr_F9FJG4_F9FJG4_FUSOF_660025 and tr_X0CPS8_X0CPS8_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_F9FJG4_F9FJG4_FUSOF_660025 and tr_A0A2H3TJ50_A0A2H3TJ50_FUSOX_5507 are exactly identical! WARNING: Sequences tr_E9EXF2_E9EXF2_METRA_655844 and tr_A0A0D9PE65_A0A0D9PE65_METAN_1291518 are exactly identical! WARNING: Sequences tr_C6H772_C6H772_AJECH_544712 and tr_F0U6I6_F0U6I6_AJEC8_544711 are exactly identical! WARNING: Sequences tr_A0A0E0IPM3_A0A0E0IPM3_ORYNI_4536 and tr_A2XGQ0_A2XGQ0_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0IPM3_A0A0E0IPM3_ORYNI_4536 and tr_A0A0E0NV33_A0A0E0NV33_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0IPM3_A0A0E0IPM3_ORYNI_4536 and tr_Q10LF8_Q10LF8_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0K0JGI3_A0A0K0JGI3_BRUMA_6279 and tr_A0A0R3QS23_A0A0R3QS23_9BILA_42155 are exactly identical! WARNING: Sequences tr_A2R7C9_A2R7C9_ASPNC_425011 and tr_G3Y5R7_G3Y5R7_ASPNA_380704 are exactly identical! WARNING: Sequences tr_A2R7C9_A2R7C9_ASPNC_425011 and tr_A0A319B4F4_A0A319B4F4_9EURO_1450533 are exactly identical! WARNING: Sequences tr_G7XDS1_G7XDS1_ASPKW_1033177 and tr_A0A117E0X0_A0A117E0X0_ASPNG_5061 are exactly identical! WARNING: Sequences tr_G7XDS1_G7XDS1_ASPKW_1033177 and tr_A0A146FFW3_A0A146FFW3_9EURO_1069201 are exactly identical! WARNING: Sequences tr_G7XDS1_G7XDS1_ASPKW_1033177 and tr_A0A1L9N3E4_A0A1L9N3E4_ASPTU_767770 are exactly identical! WARNING: Sequences tr_G2XRL1_G2XRL1_BOTF4_999810 and tr_M7TZJ5_M7TZJ5_BOTF1_1290391 are exactly identical! WARNING: Sequences tr_E3MQP1_E3MQP1_CAERE_31234 and tr_A0A261BVY1_A0A261BVY1_9PELO_1503980 are exactly identical! WARNING: Sequences tr_A8X8Q7_A8X8Q7_CAEBR_6238 and tr_A0A2G5TJ85_A0A2G5TJ85_9PELO_1611254 are exactly identical! WARNING: Sequences tr_F2SE60_F2SE60_TRIRC_559305 and tr_A0A178EUK4_A0A178EUK4_TRIRU_5551 are exactly identical! WARNING: Sequences tr_M4EWB0_M4EWB0_BRARP_51351 and tr_A0A078I5H1_A0A078I5H1_BRANA_3708 are exactly identical! WARNING: Sequences tr_M4FI56_M4FI56_BRARP_51351 and tr_A0A078J8W4_A0A078J8W4_BRANA_3708 are exactly identical! WARNING: Sequences tr_M8A287_M8A287_TRIUA_4572 and tr_A0A3B5Y6T1_A0A3B5Y6T1_WHEAT_4565 are exactly identical! WARNING: Sequences tr_M8A287_M8A287_TRIUA_4572 and tr_A0A3B6A0B1_A0A3B6A0B1_WHEAT_4565 are exactly identical! WARNING: Sequences tr_S0EGZ6_S0EGZ6_GIBF5_1279085 and tr_A0A365NPQ7_A0A365NPQ7_GIBIN_948311 are exactly identical! WARNING: Sequences tr_W2RCJ0_W2RCJ0_PHYPN_761204 and tr_A0A0W8BY89_A0A0W8BY89_PHYNI_4790 are exactly identical! WARNING: Sequences tr_W2RCJ0_W2RCJ0_PHYPN_761204 and tr_W2H4H3_W2H4H3_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A015L8Y7_A0A015L8Y7_9GLOM_1432141 and tr_U9T875_U9T875_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044QVH6_A0A044QVH6_ONCVO_6282 and tr_A0A182E437_A0A182E437_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A094E842_A0A094E842_9PEZI_1420912 and tr_A0A1B8GFX7_A0A1B8GFX7_9PEZI_342668 are exactly identical! WARNING: Sequences tr_A0A0D2R135_A0A0D2R135_GOSRA_29730 and tr_A0A1U8HY21_A0A1U8HY21_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2R135_A0A0D2R135_GOSRA_29730 and tr_A0A1U8M483_A0A1U8M483_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2W7V6_A0A0D2W7V6_GOSRA_29730 and tr_A0A1U8HWV7_A0A1U8HWV7_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0F0I4V5_A0A0F0I4V5_ASPPU_1403190 and tr_A0A2G7G609_A0A2G7G609_9EURO_656916 are exactly identical! WARNING: Sequences tr_A0A0V0XCG3_A0A0V0XCG3_9BILA_92179 and tr_A0A0V1LG76_A0A0V1LG76_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V0XCG3_A0A0V0XCG3_9BILA_92179 and tr_A0A0V0ZY88_A0A0V0ZY88_9BILA_990121 are exactly identical! WARNING: Sequences tr_A0A0V0XCG3_A0A0V0XCG3_9BILA_92179 and tr_A0A0V1NXT0_A0A0V1NXT0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A1S4AF91_A0A1S4AF91_TOBAC_4097 and tr_A0A1U7X774_A0A1U7X774_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1S4D4Q6_A0A1S4D4Q6_TOBAC_4097 and tr_A0A1J6HZ39_A0A1J6HZ39_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1U8JZA9_A0A1U8JZA9_GOSHI_3635 and tr_A0A1U8L6Y1_A0A1U8L6Y1_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A1V8UA77_A0A1V8UA77_9PEZI_1974281 and tr_A0A1V8SIC8_A0A1V8SIC8_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A1U8DUW6_A0A1U8DUW6_CAPAN_4072 and tr_A0A2G3AWV8_A0A2G3AWV8_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2U4CLW3_A0A2U4CLW3_TURTR_9739 and tr_A0A2Y9PTJ2_A0A2Y9PTJ2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CLW3_A0A2U4CLW3_TURTR_9739 and tr_A0A2Y9FQK1_A0A2Y9FQK1_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2V5I0Z2_A0A2V5I0Z2_9EURO_1450541 and tr_A0A2V5H6C1_A0A2V5H6C1_9EURO_1450538 are exactly identical! WARNING: Duplicate sequences found: 60 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O00567/3_mltree/O00567.raxml.reduced.phy Alignment comprises 1 partitions and 479 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 479 / 479 Gaps: 3.44 % Invariant sites: 0.63 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O00567/3_mltree/O00567.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 / 69 / 5520 [00:00:00] Data distribution: max. searches per worker: 20 Starting ML tree search with 20 distinct starting trees [00:00:00 -609262.646407] Initial branch length optimization [00:00:03 -535187.496723] Model parameter optimization (eps = 10.000000) [00:00:26 -533555.340806] AUTODETECT spr round 1 (radius: 5) [00:02:10 -377019.373368] AUTODETECT spr round 2 (radius: 10) [00:04:04 -265111.806742] AUTODETECT spr round 3 (radius: 15) [00:05:58 -219494.804706] AUTODETECT spr round 4 (radius: 20) [00:08:06 -210297.960207] AUTODETECT spr round 5 (radius: 25) [00:10:28 -208788.328069] SPR radius for FAST iterations: 25 (autodetect) [00:10:28 -208788.328069] Model parameter optimization (eps = 3.000000) [00:10:44 -208724.619025] FAST spr round 1 (radius: 25) [00:12:43 -179569.414402] FAST spr round 2 (radius: 25) [00:14:21 -178686.545555] FAST spr round 3 (radius: 25) [00:15:49 -178614.713459] FAST spr round 4 (radius: 25) [00:17:10 -178611.165204] FAST spr round 5 (radius: 25) [00:18:29 -178610.571136] FAST spr round 6 (radius: 25) [00:19:47 -178610.571126] Model parameter optimization (eps = 1.000000) [00:19:55 -178609.670338] SLOW spr round 1 (radius: 5) [00:21:41 -178563.764493] SLOW spr round 2 (radius: 5) [00:23:24 -178537.179296] SLOW spr round 3 (radius: 5) [00:25:01 -178535.631144] SLOW spr round 4 (radius: 5) [00:26:37 -178535.631109] SLOW spr round 5 (radius: 10) [00:28:18 -178533.571804] SLOW spr round 6 (radius: 5) [00:30:18 -178531.839349] SLOW spr round 7 (radius: 5) [00:32:06 -178531.839340] SLOW spr round 8 (radius: 10) [00:33:50 -178531.738478] SLOW spr round 9 (radius: 5) [00:35:50 -178528.704283] SLOW spr round 10 (radius: 5) [00:37:38 -178527.977392] SLOW spr round 11 (radius: 5) [00:39:19 -178527.977334] SLOW spr round 12 (radius: 10) [00:41:00 -178527.977334] SLOW spr round 13 (radius: 15) [00:43:34 -178527.977334] SLOW spr round 14 (radius: 20) [00:47:14 -178527.977334] SLOW spr round 15 (radius: 25) [00:51:33 -178527.977334] Model parameter optimization (eps = 0.100000) [00:51:40] ML tree search #1, logLikelihood: -178527.409385 [00:51:40 -607181.988592] Initial branch length optimization [00:51:43 -532917.666566] Model parameter optimization (eps = 10.000000) [00:52:05 -531151.606892] AUTODETECT spr round 1 (radius: 5) [00:53:49 -385854.482645] AUTODETECT spr round 2 (radius: 10) [00:55:53 -281935.574998] AUTODETECT spr round 3 (radius: 15) [00:58:05 -225701.085272] AUTODETECT spr round 4 (radius: 20) [01:00:15 -210213.584813] AUTODETECT spr round 5 (radius: 25) [01:02:35 -207608.488474] SPR radius for FAST iterations: 25 (autodetect) [01:02:35 -207608.488474] Model parameter optimization (eps = 3.000000) [01:02:51 -207549.003561] FAST spr round 1 (radius: 25) [01:04:50 -179475.514688] FAST spr round 2 (radius: 25) [01:06:30 -178669.966272] FAST spr round 3 (radius: 25) [01:08:04 -178612.859078] FAST spr round 4 (radius: 25) [01:09:26 -178605.454167] FAST spr round 5 (radius: 25) [01:10:46 -178602.885857] FAST spr round 6 (radius: 25) [01:12:05 -178602.885806] Model parameter optimization (eps = 1.000000) [01:12:18 -178598.675370] SLOW spr round 1 (radius: 5) [01:14:04 -178555.677406] SLOW spr round 2 (radius: 5) [01:15:45 -178552.589901] SLOW spr round 3 (radius: 5) [01:17:23 -178552.546336] SLOW spr round 4 (radius: 10) [01:19:04 -178552.546202] SLOW spr round 5 (radius: 15) [01:21:41 -178552.546201] SLOW spr round 6 (radius: 20) [01:25:23 -178552.546201] SLOW spr round 7 (radius: 25) [01:29:57 -178552.546201] Model parameter optimization (eps = 0.100000) [01:30:03] ML tree search #2, logLikelihood: -178552.501046 [01:30:03 -606032.122211] Initial branch length optimization [01:30:05 -532953.953313] Model parameter optimization (eps = 10.000000) [01:30:28 -531284.317740] AUTODETECT spr round 1 (radius: 5) [01:32:10 -381060.728345] AUTODETECT spr round 2 (radius: 10) [01:34:11 -280912.506597] AUTODETECT spr round 3 (radius: 15) [01:36:12 -237433.308625] AUTODETECT spr round 4 (radius: 20) [01:38:24 -218054.679462] AUTODETECT spr round 5 (radius: 25) [01:40:48 -212895.856600] SPR radius for FAST iterations: 25 (autodetect) [01:40:48 -212895.856600] Model parameter optimization (eps = 3.000000) [01:41:05 -212840.415463] FAST spr round 1 (radius: 25) [01:43:05 -181866.031388] FAST spr round 2 (radius: 25) [01:44:46 -179083.362269] FAST spr round 3 (radius: 25) [01:46:18 -178600.171519] FAST spr round 4 (radius: 25) [01:47:41 -178588.356113] FAST spr round 5 (radius: 25) [01:49:02 -178585.901414] FAST spr round 6 (radius: 25) [01:50:21 -178585.901410] Model parameter optimization (eps = 1.000000) [01:50:29 -178584.574713] SLOW spr round 1 (radius: 5) [01:52:16 -178557.096843] SLOW spr round 2 (radius: 5) [01:53:58 -178551.525444] SLOW spr round 3 (radius: 5) [01:55:38 -178545.801606] SLOW spr round 4 (radius: 5) [01:57:15 -178545.801343] SLOW spr round 5 (radius: 10) [01:58:57 -178544.620258] SLOW spr round 6 (radius: 5) [02:00:59 -178541.338680] SLOW spr round 7 (radius: 5) [02:02:49 -178539.793086] SLOW spr round 8 (radius: 5) [02:04:31 -178539.702525] SLOW spr round 9 (radius: 10) [02:06:14 -178539.702142] SLOW spr round 10 (radius: 15) [02:08:52 -178539.702138] SLOW spr round 11 (radius: 20) [02:12:43 -178539.702136] SLOW spr round 12 (radius: 25) [02:17:24 -178539.702133] Model parameter optimization (eps = 0.100000) [02:17:32] ML tree search #3, logLikelihood: -178539.403424 [02:17:32 -606518.477701] Initial branch length optimization [02:17:35 -532194.195895] Model parameter optimization (eps = 10.000000) [02:18:04 -530497.886438] AUTODETECT spr round 1 (radius: 5) [02:19:46 -380332.727718] AUTODETECT spr round 2 (radius: 10) [02:21:40 -275707.002815] AUTODETECT spr round 3 (radius: 15) [02:23:46 -230199.942675] AUTODETECT spr round 4 (radius: 20) [02:26:01 -212231.552437] AUTODETECT spr round 5 (radius: 25) [02:28:36 -206005.459338] SPR radius for FAST iterations: 25 (autodetect) [02:28:36 -206005.459338] Model parameter optimization (eps = 3.000000) [02:28:52 -205946.901441] FAST spr round 1 (radius: 25) [02:30:46 -179488.541773] FAST spr round 2 (radius: 25) [02:32:17 -178711.791322] FAST spr round 3 (radius: 25) [02:33:45 -178655.070302] FAST spr round 4 (radius: 25) [02:35:07 -178643.325994] FAST spr round 5 (radius: 25) [02:36:27 -178643.165461] FAST spr round 6 (radius: 25) [02:37:46 -178643.164452] Model parameter optimization (eps = 1.000000) [02:37:58 -178636.398289] SLOW spr round 1 (radius: 5) [02:39:46 -178601.873730] SLOW spr round 2 (radius: 5) [02:41:27 -178591.430682] SLOW spr round 3 (radius: 5) [02:43:05 -178591.430647] SLOW spr round 4 (radius: 10) [02:44:46 -178589.906663] SLOW spr round 5 (radius: 5) [02:46:47 -178589.906660] SLOW spr round 6 (radius: 10) [02:48:38 -178589.462251] SLOW spr round 7 (radius: 5) [02:50:38 -178587.639322] SLOW spr round 8 (radius: 5) [02:52:26 -178585.250878] SLOW spr round 9 (radius: 5) [02:54:08 -178585.250725] SLOW spr round 10 (radius: 10) [02:55:52 -178585.250716] SLOW spr round 11 (radius: 15) [02:58:25 -178585.250713] SLOW spr round 12 (radius: 20) [03:02:01 -178585.250710] SLOW spr round 13 (radius: 25) [03:06:12 -178585.250708] Model parameter optimization (eps = 0.100000) [03:06:20] ML tree search #4, logLikelihood: -178585.117200 [03:06:20 -608088.296532] Initial branch length optimization [03:06:22 -533420.516845] Model parameter optimization (eps = 10.000000) [03:06:50 -531649.222346] AUTODETECT spr round 1 (radius: 5) [03:08:32 -378844.591958] AUTODETECT spr round 2 (radius: 10) [03:10:31 -268748.977498] AUTODETECT spr round 3 (radius: 15) [03:12:33 -220915.665197] AUTODETECT spr round 4 (radius: 20) [03:14:58 -205506.559461] AUTODETECT spr round 5 (radius: 25) [03:17:34 -203694.741381] SPR radius for FAST iterations: 25 (autodetect) [03:17:34 -203694.741381] Model parameter optimization (eps = 3.000000) [03:17:54 -203630.732929] FAST spr round 1 (radius: 25) [03:19:53 -179703.862256] FAST spr round 2 (radius: 25) [03:21:30 -178685.279796] FAST spr round 3 (radius: 25) [03:23:01 -178632.668729] FAST spr round 4 (radius: 25) [03:24:23 -178625.408014] FAST spr round 5 (radius: 25) [03:25:43 -178625.406902] Model parameter optimization (eps = 1.000000) [03:25:55 -178624.105523] SLOW spr round 1 (radius: 5) [03:27:44 -178551.419691] SLOW spr round 2 (radius: 5) [03:29:26 -178540.331157] SLOW spr round 3 (radius: 5) [03:31:05 -178540.331076] SLOW spr round 4 (radius: 10) [03:32:46 -178537.019858] SLOW spr round 5 (radius: 5) [03:34:48 -178534.425765] SLOW spr round 6 (radius: 5) [03:36:37 -178534.425621] SLOW spr round 7 (radius: 10) [03:38:20 -178534.425618] SLOW spr round 8 (radius: 15) [03:40:52 -178534.425616] SLOW spr round 9 (radius: 20) [03:44:32 -178534.425613] SLOW spr round 10 (radius: 25) [03:48:52 -178534.425610] Model parameter optimization (eps = 0.100000) [03:49:01] ML tree search #5, logLikelihood: -178534.229026 [03:49:01 -609285.227724] Initial branch length optimization [03:49:04 -536120.051150] Model parameter optimization (eps = 10.000000) [03:49:27 -534327.159533] AUTODETECT spr round 1 (radius: 5) [03:51:09 -383727.281552] AUTODETECT spr round 2 (radius: 10) [03:53:07 -272518.471430] AUTODETECT spr round 3 (radius: 15) [03:55:07 -223425.607931] AUTODETECT spr round 4 (radius: 20) [03:57:26 -208317.121609] AUTODETECT spr round 5 (radius: 25) [04:00:14 -207338.695545] SPR radius for FAST iterations: 25 (autodetect) [04:00:14 -207338.695545] Model parameter optimization (eps = 3.000000) [04:00:29 -207282.804292] FAST spr round 1 (radius: 25) [04:02:23 -179741.814795] FAST spr round 2 (radius: 25) [04:03:57 -178720.931254] FAST spr round 3 (radius: 25) [04:05:27 -178624.664680] FAST spr round 4 (radius: 25) [04:06:48 -178621.075206] FAST spr round 5 (radius: 25) [04:08:07 -178621.074405] Model parameter optimization (eps = 1.000000) [04:08:17 -178618.187751] SLOW spr round 1 (radius: 5) [04:10:03 -178576.911810] SLOW spr round 2 (radius: 5) [04:11:46 -178568.551371] SLOW spr round 3 (radius: 5) [04:13:26 -178568.303659] SLOW spr round 4 (radius: 5) [04:15:04 -178568.303620] SLOW spr round 5 (radius: 10) [04:16:46 -178560.061664] SLOW spr round 6 (radius: 5) [04:18:48 -178556.694290] SLOW spr round 7 (radius: 5) [04:20:38 -178552.000620] SLOW spr round 8 (radius: 5) [04:22:20 -178552.000592] SLOW spr round 9 (radius: 10) [04:24:02 -178550.566615] SLOW spr round 10 (radius: 5) [04:26:02 -178550.566615] SLOW spr round 11 (radius: 10) [04:27:52 -178549.848978] SLOW spr round 12 (radius: 5) [04:29:50 -178549.848955] SLOW spr round 13 (radius: 10) [04:31:39 -178549.612710] SLOW spr round 14 (radius: 5) [04:33:37 -178549.612704] SLOW spr round 15 (radius: 10) [04:35:25 -178549.477262] SLOW spr round 16 (radius: 5) [04:37:25 -178546.471241] SLOW spr round 17 (radius: 5) [04:39:13 -178545.752442] SLOW spr round 18 (radius: 5) [04:40:54 -178545.752388] SLOW spr round 19 (radius: 10) [04:42:37 -178545.752388] SLOW spr round 20 (radius: 15) [04:45:11 -178545.752388] SLOW spr round 21 (radius: 20) [04:48:50 -178545.752388] SLOW spr round 22 (radius: 25) [04:53:15 -178545.752388] Model parameter optimization (eps = 0.100000) [04:53:20] ML tree search #6, logLikelihood: -178545.665734 [04:53:20 -606754.875108] Initial branch length optimization [04:53:22 -532639.149720] Model parameter optimization (eps = 10.000000) [04:53:46 -530882.231762] AUTODETECT spr round 1 (radius: 5) [04:55:27 -378576.510213] AUTODETECT spr round 2 (radius: 10) [04:57:21 -269349.987988] AUTODETECT spr round 3 (radius: 15) [04:59:21 -222409.458317] AUTODETECT spr round 4 (radius: 20) [05:01:39 -207056.383522] AUTODETECT spr round 5 (radius: 25) [05:03:58 -204622.684924] SPR radius for FAST iterations: 25 (autodetect) [05:03:58 -204622.684924] Model parameter optimization (eps = 3.000000) [05:04:14 -204575.172905] FAST spr round 1 (radius: 25) [05:06:13 -179563.446236] FAST spr round 2 (radius: 25) [05:07:50 -178688.059109] FAST spr round 3 (radius: 25) [05:09:22 -178630.791675] FAST spr round 4 (radius: 25) [05:10:45 -178607.364457] FAST spr round 5 (radius: 25) [05:12:05 -178607.361101] Model parameter optimization (eps = 1.000000) [05:12:17 -178599.844010] SLOW spr round 1 (radius: 5) [05:14:03 -178572.039849] SLOW spr round 2 (radius: 5) [05:15:46 -178563.566465] SLOW spr round 3 (radius: 5) [05:17:25 -178563.480724] SLOW spr round 4 (radius: 10) [05:19:06 -178555.185562] SLOW spr round 5 (radius: 5) [05:21:07 -178555.185364] SLOW spr round 6 (radius: 10) [05:22:57 -178554.894805] SLOW spr round 7 (radius: 5) [05:24:56 -178554.894780] SLOW spr round 8 (radius: 10) [05:26:43 -178554.894779] SLOW spr round 9 (radius: 15) [05:29:09 -178554.894779] SLOW spr round 10 (radius: 20) [05:32:51 -178554.894779] SLOW spr round 11 (radius: 25) [05:37:07 -178554.894779] Model parameter optimization (eps = 0.100000) [05:37:18] ML tree search #7, logLikelihood: -178554.439240 [05:37:18 -608674.488527] Initial branch length optimization [05:37:20 -534113.027615] Model parameter optimization (eps = 10.000000) [05:37:42 -532318.079490] AUTODETECT spr round 1 (radius: 5) [05:39:23 -386252.589564] AUTODETECT spr round 2 (radius: 10) [05:41:24 -265588.833409] AUTODETECT spr round 3 (radius: 15) [05:43:23 -222451.377961] AUTODETECT spr round 4 (radius: 20) [05:45:52 -206877.177592] AUTODETECT spr round 5 (radius: 25) [05:48:50 -206561.658119] SPR radius for FAST iterations: 25 (autodetect) [05:48:50 -206561.658119] Model parameter optimization (eps = 3.000000) [05:49:07 -206499.144603] FAST spr round 1 (radius: 25) [05:51:04 -179891.003130] FAST spr round 2 (radius: 25) [05:52:42 -178677.002617] FAST spr round 3 (radius: 25) [05:54:12 -178618.863885] FAST spr round 4 (radius: 25) [05:55:33 -178617.021273] FAST spr round 5 (radius: 25) [05:56:53 -178617.021262] Model parameter optimization (eps = 1.000000) [05:57:04 -178610.247285] SLOW spr round 1 (radius: 5) [05:58:51 -178547.176433] SLOW spr round 2 (radius: 5) [06:00:32 -178545.660512] SLOW spr round 3 (radius: 5) [06:02:10 -178545.660410] SLOW spr round 4 (radius: 10) [06:03:52 -178544.941634] SLOW spr round 5 (radius: 5) [06:05:56 -178541.727736] SLOW spr round 6 (radius: 5) [06:07:44 -178541.727708] SLOW spr round 7 (radius: 10) [06:09:28 -178541.727705] SLOW spr round 8 (radius: 15) [06:11:58 -178541.727703] SLOW spr round 9 (radius: 20) [06:15:35 -178541.727700] SLOW spr round 10 (radius: 25) [06:19:53 -178541.727697] Model parameter optimization (eps = 0.100000) [06:20:02] ML tree search #8, logLikelihood: -178541.143066 [06:20:02 -606803.091468] Initial branch length optimization [06:20:04 -532762.301471] Model parameter optimization (eps = 10.000000) [06:20:27 -531047.558367] AUTODETECT spr round 1 (radius: 5) [06:22:09 -381134.349943] AUTODETECT spr round 2 (radius: 10) [06:24:05 -264472.388487] AUTODETECT spr round 3 (radius: 15) [06:26:03 -222772.072880] AUTODETECT spr round 4 (radius: 20) [06:28:20 -210540.206053] AUTODETECT spr round 5 (radius: 25) [06:31:02 -208639.591837] SPR radius for FAST iterations: 25 (autodetect) [06:31:02 -208639.591837] Model parameter optimization (eps = 3.000000) [06:31:23 -208572.191043] FAST spr round 1 (radius: 25) [06:33:23 -180229.430278] FAST spr round 2 (radius: 25) [06:35:03 -178691.662076] FAST spr round 3 (radius: 25) [06:36:33 -178624.064751] FAST spr round 4 (radius: 25) [06:37:56 -178616.181178] FAST spr round 5 (radius: 25) [06:39:18 -178613.831252] FAST spr round 6 (radius: 25) [06:40:38 -178613.831241] Model parameter optimization (eps = 1.000000) [06:40:44 -178613.279252] SLOW spr round 1 (radius: 5) [06:42:31 -178567.203055] SLOW spr round 2 (radius: 5) [06:44:13 -178557.584961] SLOW spr round 3 (radius: 5) [06:45:52 -178557.391116] SLOW spr round 4 (radius: 5) [06:47:30 -178557.391114] SLOW spr round 5 (radius: 10) [06:49:12 -178546.314468] SLOW spr round 6 (radius: 5) [06:51:13 -178545.073989] SLOW spr round 7 (radius: 5) [06:53:03 -178545.073984] SLOW spr round 8 (radius: 10) [06:54:48 -178545.073984] SLOW spr round 9 (radius: 15) [06:57:21 -178545.073984] SLOW spr round 10 (radius: 20) [07:01:06 -178545.073984] SLOW spr round 11 (radius: 25) [07:05:28 -178545.073984] Model parameter optimization (eps = 0.100000) [07:05:36] ML tree search #9, logLikelihood: -178544.752249 [07:05:36 -608708.871359] Initial branch length optimization [07:05:39 -534980.074348] Model parameter optimization (eps = 10.000000) [07:06:03 -533229.721198] AUTODETECT spr round 1 (radius: 5) [07:07:45 -378764.372639] AUTODETECT spr round 2 (radius: 10) [07:09:46 -271958.449886] AUTODETECT spr round 3 (radius: 15) [07:11:47 -220925.572554] AUTODETECT spr round 4 (radius: 20) [07:14:02 -211171.999451] AUTODETECT spr round 5 (radius: 25) [07:16:46 -208220.025099] SPR radius for FAST iterations: 25 (autodetect) [07:16:46 -208220.025099] Model parameter optimization (eps = 3.000000) [07:17:04 -208151.540550] FAST spr round 1 (radius: 25) [07:19:03 -179566.925155] FAST spr round 2 (radius: 25) [07:20:40 -178674.576480] FAST spr round 3 (radius: 25) [07:22:08 -178614.986744] FAST spr round 4 (radius: 25) [07:23:29 -178614.420198] FAST spr round 5 (radius: 25) [07:24:49 -178614.420189] Model parameter optimization (eps = 1.000000) [07:25:00 -178607.418672] SLOW spr round 1 (radius: 5) [07:26:48 -178550.847640] SLOW spr round 2 (radius: 5) [07:28:30 -178542.307138] SLOW spr round 3 (radius: 5) [07:30:09 -178542.307101] SLOW spr round 4 (radius: 10) [07:31:50 -178541.521121] SLOW spr round 5 (radius: 5) [07:33:51 -178538.109314] SLOW spr round 6 (radius: 5) [07:35:39 -178537.197800] SLOW spr round 7 (radius: 5) [07:37:22 -178537.056016] SLOW spr round 8 (radius: 5) [07:39:01 -178537.055900] SLOW spr round 9 (radius: 10) [07:40:43 -178536.568526] SLOW spr round 10 (radius: 5) [07:42:43 -178536.568239] SLOW spr round 11 (radius: 10) [07:44:32 -178536.568236] SLOW spr round 12 (radius: 15) [07:47:00 -178536.568234] SLOW spr round 13 (radius: 20) [07:50:48 -178536.568232] SLOW spr round 14 (radius: 25) [07:55:13 -178536.568230] Model parameter optimization (eps = 0.100000) [07:55:25] ML tree search #10, logLikelihood: -178535.664907 [07:55:25 -604565.549978] Initial branch length optimization [07:55:28 -531679.130729] Model parameter optimization (eps = 10.000000) [07:55:50 -529917.908455] AUTODETECT spr round 1 (radius: 5) [07:57:32 -387440.275051] AUTODETECT spr round 2 (radius: 10) [07:59:34 -269994.617297] AUTODETECT spr round 3 (radius: 15) [08:01:36 -221471.313858] AUTODETECT spr round 4 (radius: 20) [08:03:54 -207261.591422] AUTODETECT spr round 5 (radius: 25) [08:07:01 -206602.990162] SPR radius for FAST iterations: 25 (autodetect) [08:07:01 -206602.990162] Model parameter optimization (eps = 3.000000) [08:07:16 -206538.138742] FAST spr round 1 (radius: 25) [08:09:12 -179509.156206] FAST spr round 2 (radius: 25) [08:10:49 -178715.910116] FAST spr round 3 (radius: 25) [08:12:20 -178611.816925] FAST spr round 4 (radius: 25) [08:13:42 -178602.213528] FAST spr round 5 (radius: 25) [08:15:03 -178601.512280] FAST spr round 6 (radius: 25) [08:16:22 -178601.512250] Model parameter optimization (eps = 1.000000) [08:16:31 -178599.511069] SLOW spr round 1 (radius: 5) [08:18:16 -178559.197441] SLOW spr round 2 (radius: 5) [08:19:59 -178557.551351] SLOW spr round 3 (radius: 5) [08:21:38 -178557.551298] SLOW spr round 4 (radius: 10) [08:23:18 -178557.480613] SLOW spr round 5 (radius: 15) [08:25:55 -178557.480411] SLOW spr round 6 (radius: 20) [08:29:36 -178557.480411] SLOW spr round 7 (radius: 25) [08:34:03 -178557.480411] Model parameter optimization (eps = 0.100000) [08:34:07] ML tree search #11, logLikelihood: -178557.458253 [08:34:07 -611802.448700] Initial branch length optimization [08:34:10 -536350.839223] Model parameter optimization (eps = 10.000000) [08:34:33 -534659.735984] AUTODETECT spr round 1 (radius: 5) [08:36:16 -380500.625668] AUTODETECT spr round 2 (radius: 10) [08:38:15 -276488.461860] AUTODETECT spr round 3 (radius: 15) [08:40:17 -231976.317402] AUTODETECT spr round 4 (radius: 20) [08:42:26 -207484.290848] AUTODETECT spr round 5 (radius: 25) [08:44:53 -206395.384435] SPR radius for FAST iterations: 25 (autodetect) [08:44:53 -206395.384435] Model parameter optimization (eps = 3.000000) [08:45:11 -206351.532460] FAST spr round 1 (radius: 25) [08:47:09 -180032.329068] FAST spr round 2 (radius: 25) [08:48:48 -178747.018179] FAST spr round 3 (radius: 25) [08:50:18 -178648.787819] FAST spr round 4 (radius: 25) [08:51:41 -178639.265613] FAST spr round 5 (radius: 25) [08:53:01 -178638.280303] FAST spr round 6 (radius: 25) [08:54:20 -178638.280298] Model parameter optimization (eps = 1.000000) [08:54:28 -178637.223451] SLOW spr round 1 (radius: 5) [08:56:15 -178581.184186] SLOW spr round 2 (radius: 5) [08:57:56 -178576.262515] SLOW spr round 3 (radius: 5) [08:59:34 -178576.262286] SLOW spr round 4 (radius: 10) [09:01:16 -178575.258475] SLOW spr round 5 (radius: 5) [09:03:17 -178574.766538] SLOW spr round 6 (radius: 5) [09:05:07 -178569.392282] SLOW spr round 7 (radius: 5) [09:06:50 -178568.622535] SLOW spr round 8 (radius: 5) [09:08:30 -178568.622517] SLOW spr round 9 (radius: 10) [09:10:11 -178568.622517] SLOW spr round 10 (radius: 15) [09:12:46 -178568.622517] SLOW spr round 11 (radius: 20) [09:16:23 -178568.622517] SLOW spr round 12 (radius: 25) [09:20:48 -178568.622517] Model parameter optimization (eps = 0.100000) [09:20:57] ML tree search #12, logLikelihood: -178568.167463 [09:20:57 -607894.891948] Initial branch length optimization [09:21:00 -533209.324898] Model parameter optimization (eps = 10.000000) [09:21:22 -531476.400281] AUTODETECT spr round 1 (radius: 5) [09:23:05 -382387.721537] AUTODETECT spr round 2 (radius: 10) [09:25:10 -256442.597607] AUTODETECT spr round 3 (radius: 15) [09:27:07 -219228.821792] AUTODETECT spr round 4 (radius: 20) [09:29:21 -208184.386893] AUTODETECT spr round 5 (radius: 25) [09:31:44 -207469.627415] SPR radius for FAST iterations: 25 (autodetect) [09:31:44 -207469.627415] Model parameter optimization (eps = 3.000000) [09:32:00 -207398.609746] FAST spr round 1 (radius: 25) [09:33:59 -179467.439196] FAST spr round 2 (radius: 25) [09:35:39 -178682.373358] FAST spr round 3 (radius: 25) [09:37:11 -178622.991362] FAST spr round 4 (radius: 25) [09:38:33 -178618.703987] FAST spr round 5 (radius: 25) [09:39:54 -178617.076671] FAST spr round 6 (radius: 25) [09:41:13 -178617.073787] Model parameter optimization (eps = 1.000000) [09:41:26 -178599.422402] SLOW spr round 1 (radius: 5) [09:43:14 -178559.392112] SLOW spr round 2 (radius: 5) [09:44:56 -178557.164629] SLOW spr round 3 (radius: 5) [09:46:37 -178551.328026] SLOW spr round 4 (radius: 5) [09:48:15 -178551.327884] SLOW spr round 5 (radius: 10) [09:49:55 -178547.570532] SLOW spr round 6 (radius: 5) [09:51:57 -178545.080425] SLOW spr round 7 (radius: 5) [09:53:46 -178540.839008] SLOW spr round 8 (radius: 5) [09:55:28 -178540.838954] SLOW spr round 9 (radius: 10) [09:57:10 -178540.838951] SLOW spr round 10 (radius: 15) [09:59:43 -178540.838949] SLOW spr round 11 (radius: 20) [10:03:22 -178540.838946] SLOW spr round 12 (radius: 25) [10:07:49 -178540.838944] Model parameter optimization (eps = 0.100000) [10:07:55] ML tree search #13, logLikelihood: -178540.756805 [10:07:55 -607867.120443] Initial branch length optimization [10:07:58 -532165.159469] Model parameter optimization (eps = 10.000000) [10:08:23 -530476.620851] AUTODETECT spr round 1 (radius: 5) [10:10:06 -385506.200009] AUTODETECT spr round 2 (radius: 10) [10:12:01 -281843.131917] AUTODETECT spr round 3 (radius: 15) [10:14:06 -229268.354679] AUTODETECT spr round 4 (radius: 20) [10:16:15 -208052.030214] AUTODETECT spr round 5 (radius: 25) [10:18:47 -206662.049014] SPR radius for FAST iterations: 25 (autodetect) [10:18:48 -206662.049014] Model parameter optimization (eps = 3.000000) [10:19:04 -206589.739671] FAST spr round 1 (radius: 25) [10:20:55 -179654.535947] FAST spr round 2 (radius: 25) [10:22:32 -178655.676598] FAST spr round 3 (radius: 25) [10:24:04 -178616.074978] FAST spr round 4 (radius: 25) [10:25:26 -178612.068551] FAST spr round 5 (radius: 25) [10:26:46 -178611.216145] FAST spr round 6 (radius: 25) [10:28:06 -178611.216117] Model parameter optimization (eps = 1.000000) [10:28:16 -178605.988041] SLOW spr round 1 (radius: 5) [10:30:01 -178566.553055] SLOW spr round 2 (radius: 5) [10:31:45 -178555.654509] SLOW spr round 3 (radius: 5) [10:33:25 -178554.010359] SLOW spr round 4 (radius: 5) [10:35:04 -178554.010343] SLOW spr round 5 (radius: 10) [10:36:47 -178553.091233] SLOW spr round 6 (radius: 5) [10:38:48 -178553.091085] SLOW spr round 7 (radius: 10) [10:40:38 -178552.951341] SLOW spr round 8 (radius: 5) [10:42:40 -178546.465495] SLOW spr round 9 (radius: 5) [10:44:29 -178545.314087] SLOW spr round 10 (radius: 5) [10:46:13 -178540.877638] SLOW spr round 11 (radius: 5) [10:47:53 -178540.877634] SLOW spr round 12 (radius: 10) [10:49:35 -178540.877634] SLOW spr round 13 (radius: 15) [10:52:09 -178540.877634] SLOW spr round 14 (radius: 20) [10:55:43 -178540.877634] SLOW spr round 15 (radius: 25) [10:59:54 -178540.877634] Model parameter optimization (eps = 0.100000) [11:00:04] ML tree search #14, logLikelihood: -178540.547149 [11:00:04 -607415.844859] Initial branch length optimization [11:00:07 -532910.381615] Model parameter optimization (eps = 10.000000) [11:00:28 -531245.909721] AUTODETECT spr round 1 (radius: 5) [11:02:12 -389011.258963] AUTODETECT spr round 2 (radius: 10) [11:04:19 -271891.387773] AUTODETECT spr round 3 (radius: 15) [11:06:24 -218661.979865] AUTODETECT spr round 4 (radius: 20) [11:08:39 -212200.089024] AUTODETECT spr round 5 (radius: 25) [11:11:00 -210599.050270] SPR radius for FAST iterations: 25 (autodetect) [11:11:00 -210599.050270] Model parameter optimization (eps = 3.000000) [11:11:16 -210554.775181] FAST spr round 1 (radius: 25) [11:13:17 -179912.248953] FAST spr round 2 (radius: 25) [11:14:52 -178662.526103] FAST spr round 3 (radius: 25) [11:16:21 -178594.917715] FAST spr round 4 (radius: 25) [11:17:42 -178594.644570] FAST spr round 5 (radius: 25) [11:19:01 -178594.644566] Model parameter optimization (eps = 1.000000) [11:19:14 -178587.234940] SLOW spr round 1 (radius: 5) [11:21:02 -178548.232507] SLOW spr round 2 (radius: 5) [11:22:44 -178543.794081] SLOW spr round 3 (radius: 5) [11:24:22 -178543.793954] SLOW spr round 4 (radius: 10) [11:26:04 -178539.910285] SLOW spr round 5 (radius: 5) [11:28:08 -178528.443109] SLOW spr round 6 (radius: 5) [11:29:57 -178528.299228] SLOW spr round 7 (radius: 5) [11:31:39 -178528.299155] SLOW spr round 8 (radius: 10) [11:33:22 -178528.299152] SLOW spr round 9 (radius: 15) [11:35:57 -178528.299149] SLOW spr round 10 (radius: 20) [11:39:40 -178528.299147] SLOW spr round 11 (radius: 25) [11:44:13 -178528.299144] Model parameter optimization (eps = 0.100000) [11:44:23] ML tree search #15, logLikelihood: -178528.192624 [11:44:23 -609042.856885] Initial branch length optimization [11:44:26 -534312.429436] Model parameter optimization (eps = 10.000000) [11:44:50 -532620.076412] AUTODETECT spr round 1 (radius: 5) [11:46:32 -381865.315387] AUTODETECT spr round 2 (radius: 10) [11:48:35 -248849.249632] AUTODETECT spr round 3 (radius: 15) [11:50:31 -210281.666028] AUTODETECT spr round 4 (radius: 20) [11:52:40 -203191.894200] AUTODETECT spr round 5 (radius: 25) [11:55:02 -203133.812214] SPR radius for FAST iterations: 25 (autodetect) [11:55:02 -203133.812214] Model parameter optimization (eps = 3.000000) [11:55:18 -203069.310002] FAST spr round 1 (radius: 25) [11:57:15 -179451.968701] FAST spr round 2 (radius: 25) [11:58:48 -178719.186875] FAST spr round 3 (radius: 25) [12:00:17 -178640.015923] FAST spr round 4 (radius: 25) [12:01:39 -178632.425064] FAST spr round 5 (radius: 25) [12:02:59 -178630.742049] FAST spr round 6 (radius: 25) [12:04:17 -178629.732552] FAST spr round 7 (radius: 25) [12:05:36 -178629.732310] Model parameter optimization (eps = 1.000000) [12:05:46 -178624.407911] SLOW spr round 1 (radius: 5) [12:07:30 -178578.258730] SLOW spr round 2 (radius: 5) [12:09:11 -178567.228135] SLOW spr round 3 (radius: 5) [12:10:48 -178567.228125] SLOW spr round 4 (radius: 10) [12:12:30 -178563.492356] SLOW spr round 5 (radius: 5) [12:14:33 -178554.293312] SLOW spr round 6 (radius: 5) [12:16:20 -178554.293227] SLOW spr round 7 (radius: 10) [12:18:04 -178554.293227] SLOW spr round 8 (radius: 15) [12:20:34 -178554.293227] SLOW spr round 9 (radius: 20) [12:24:13 -178554.293227] SLOW spr round 10 (radius: 25) [12:28:30 -178554.293227] Model parameter optimization (eps = 0.100000) [12:28:38] ML tree search #16, logLikelihood: -178553.898101 [12:28:38 -607532.360161] Initial branch length optimization [12:28:42 -532958.813376] Model parameter optimization (eps = 10.000000) [12:29:05 -531227.406726] AUTODETECT spr round 1 (radius: 5) [12:30:49 -380605.880320] AUTODETECT spr round 2 (radius: 10) [12:32:43 -268101.131610] AUTODETECT spr round 3 (radius: 15) [12:34:42 -217187.867472] AUTODETECT spr round 4 (radius: 20) [12:36:53 -203778.451384] AUTODETECT spr round 5 (radius: 25) [12:39:39 -203685.255755] SPR radius for FAST iterations: 25 (autodetect) [12:39:39 -203685.255755] Model parameter optimization (eps = 3.000000) [12:39:53 -203650.886290] FAST spr round 1 (radius: 25) [12:41:48 -180058.857825] FAST spr round 2 (radius: 25) [12:43:22 -178730.916388] FAST spr round 3 (radius: 25) [12:44:51 -178641.086684] FAST spr round 4 (radius: 25) [12:46:12 -178632.288144] FAST spr round 5 (radius: 25) [12:47:32 -178632.288105] Model parameter optimization (eps = 1.000000) [12:47:45 -178624.593294] SLOW spr round 1 (radius: 5) [12:49:30 -178574.678775] SLOW spr round 2 (radius: 5) [12:51:13 -178561.335106] SLOW spr round 3 (radius: 5) [12:52:52 -178561.335072] SLOW spr round 4 (radius: 10) [12:54:35 -178560.085316] SLOW spr round 5 (radius: 5) [12:56:38 -178546.032007] SLOW spr round 6 (radius: 5) [12:58:28 -178545.000756] SLOW spr round 7 (radius: 5) [13:00:10 -178545.000727] SLOW spr round 8 (radius: 10) [13:01:52 -178544.601425] SLOW spr round 9 (radius: 5) [13:03:53 -178540.866116] SLOW spr round 10 (radius: 5) [13:05:43 -178536.481564] SLOW spr round 11 (radius: 5) [13:07:25 -178536.481523] SLOW spr round 12 (radius: 10) [13:09:06 -178536.481520] SLOW spr round 13 (radius: 15) [13:11:44 -178536.481518] SLOW spr round 14 (radius: 20) [13:15:33 -178536.481515] SLOW spr round 15 (radius: 25) [13:20:07 -178536.481512] Model parameter optimization (eps = 0.100000) [13:20:12] ML tree search #17, logLikelihood: -178536.462250 [13:20:12 -607623.048827] Initial branch length optimization [13:20:15 -533122.618684] Model parameter optimization (eps = 10.000000) [13:20:40 -531488.569977] AUTODETECT spr round 1 (radius: 5) [13:22:21 -380515.898768] AUTODETECT spr round 2 (radius: 10) [13:24:28 -267998.166883] AUTODETECT spr round 3 (radius: 15) [13:26:24 -229737.242189] AUTODETECT spr round 4 (radius: 20) [13:28:48 -211382.474805] AUTODETECT spr round 5 (radius: 25) [13:31:28 -208797.072731] SPR radius for FAST iterations: 25 (autodetect) [13:31:28 -208797.072731] Model parameter optimization (eps = 3.000000) [13:31:49 -208733.100003] FAST spr round 1 (radius: 25) [13:33:49 -179764.714197] FAST spr round 2 (radius: 25) [13:35:30 -178657.487307] FAST spr round 3 (radius: 25) [13:36:57 -178602.797471] FAST spr round 4 (radius: 25) [13:38:18 -178598.802535] FAST spr round 5 (radius: 25) [13:39:38 -178598.802001] Model parameter optimization (eps = 1.000000) [13:39:48 -178595.413692] SLOW spr round 1 (radius: 5) [13:41:35 -178546.550215] SLOW spr round 2 (radius: 5) [13:43:16 -178540.860998] SLOW spr round 3 (radius: 5) [13:44:55 -178540.774606] SLOW spr round 4 (radius: 10) [13:46:37 -178540.774584] SLOW spr round 5 (radius: 15) [13:49:13 -178540.774578] SLOW spr round 6 (radius: 20) [13:52:53 -178540.774575] SLOW spr round 7 (radius: 25) [13:57:23 -178540.774572] Model parameter optimization (eps = 0.100000) [13:57:35] ML tree search #18, logLikelihood: -178540.504723 [13:57:35 -611436.012393] Initial branch length optimization [13:57:38 -535454.326449] Model parameter optimization (eps = 10.000000) [13:58:00 -533801.955914] AUTODETECT spr round 1 (radius: 5) [13:59:43 -386934.275328] AUTODETECT spr round 2 (radius: 10) [14:01:47 -277212.298974] AUTODETECT spr round 3 (radius: 15) [14:03:51 -228668.068116] AUTODETECT spr round 4 (radius: 20) [14:06:04 -217886.328466] AUTODETECT spr round 5 (radius: 25) [14:08:47 -211454.565708] SPR radius for FAST iterations: 25 (autodetect) [14:08:47 -211454.565708] Model parameter optimization (eps = 3.000000) [14:09:03 -211391.568559] FAST spr round 1 (radius: 25) [14:11:04 -179547.566856] FAST spr round 2 (radius: 25) [14:12:44 -178697.534371] FAST spr round 3 (radius: 25) [14:14:16 -178616.049931] FAST spr round 4 (radius: 25) [14:15:39 -178608.706805] FAST spr round 5 (radius: 25) [14:16:59 -178606.450152] FAST spr round 6 (radius: 25) [14:18:19 -178606.449788] Model parameter optimization (eps = 1.000000) [14:18:31 -178601.248446] SLOW spr round 1 (radius: 5) [14:20:19 -178562.725928] SLOW spr round 2 (radius: 5) [14:22:01 -178557.430415] SLOW spr round 3 (radius: 5) [14:23:41 -178556.664549] SLOW spr round 4 (radius: 5) [14:25:20 -178556.664500] SLOW spr round 5 (radius: 10) [14:27:02 -178553.688508] SLOW spr round 6 (radius: 5) [14:29:05 -178552.806737] SLOW spr round 7 (radius: 5) [14:30:55 -178552.636712] SLOW spr round 8 (radius: 5) [14:32:38 -178551.213574] SLOW spr round 9 (radius: 5) [14:34:18 -178551.213574] SLOW spr round 10 (radius: 10) [14:36:01 -178548.094213] SLOW spr round 11 (radius: 5) [14:38:03 -178546.321292] SLOW spr round 12 (radius: 5) [14:39:53 -178542.558776] SLOW spr round 13 (radius: 5) [14:41:36 -178542.558728] SLOW spr round 14 (radius: 10) [14:43:19 -178541.806858] SLOW spr round 15 (radius: 5) [14:45:21 -178538.210283] SLOW spr round 16 (radius: 5) [14:47:09 -178538.210229] SLOW spr round 17 (radius: 10) [14:48:54 -178538.210228] SLOW spr round 18 (radius: 15) [14:51:26 -178538.210228] SLOW spr round 19 (radius: 20) [14:55:14 -178538.210228] SLOW spr round 20 (radius: 25) [14:59:48 -178538.210228] Model parameter optimization (eps = 0.100000) [14:59:53] ML tree search #19, logLikelihood: -178538.147549 [14:59:53 -609306.808569] Initial branch length optimization [14:59:55 -533934.901986] Model parameter optimization (eps = 10.000000) [15:00:20 -532266.347746] AUTODETECT spr round 1 (radius: 5) [15:02:03 -386807.041330] AUTODETECT spr round 2 (radius: 10) [15:04:13 -274506.000257] AUTODETECT spr round 3 (radius: 15) [15:06:18 -217326.438951] AUTODETECT spr round 4 (radius: 20) [15:08:33 -207773.503431] AUTODETECT spr round 5 (radius: 25) [15:11:10 -207400.675206] SPR radius for FAST iterations: 25 (autodetect) [15:11:10 -207400.675206] Model parameter optimization (eps = 3.000000) [15:11:26 -207327.230033] FAST spr round 1 (radius: 25) [15:13:22 -179800.924667] FAST spr round 2 (radius: 25) [15:15:00 -178647.282243] FAST spr round 3 (radius: 25) [15:16:27 -178620.602683] FAST spr round 4 (radius: 25) [15:17:47 -178620.602670] Model parameter optimization (eps = 1.000000) [15:17:57 -178619.356389] SLOW spr round 1 (radius: 5) [15:19:44 -178576.982561] SLOW spr round 2 (radius: 5) [15:21:25 -178572.953490] SLOW spr round 3 (radius: 5) [15:23:03 -178572.953450] SLOW spr round 4 (radius: 10) [15:24:45 -178569.882320] SLOW spr round 5 (radius: 5) [15:26:45 -178569.882319] SLOW spr round 6 (radius: 10) [15:28:35 -178568.906080] SLOW spr round 7 (radius: 5) [15:30:33 -178564.868549] SLOW spr round 8 (radius: 5) [15:32:20 -178562.661793] SLOW spr round 9 (radius: 5) [15:34:00 -178562.661792] SLOW spr round 10 (radius: 10) [15:35:43 -178562.448376] SLOW spr round 11 (radius: 5) [15:37:43 -178562.447595] SLOW spr round 12 (radius: 10) [15:39:33 -178562.447594] SLOW spr round 13 (radius: 15) [15:41:58 -178562.447594] SLOW spr round 14 (radius: 20) [15:45:43 -178562.447594] SLOW spr round 15 (radius: 25) [15:50:02 -178562.447594] Model parameter optimization (eps = 0.100000) [15:50:11] ML tree search #20, logLikelihood: -178561.737667 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.296351,0.319160) (0.270864,0.563761) (0.258463,1.234003) (0.174322,2.488329) 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: -178527.409385 AIC score: 361064.818770 / AICc score: 8405124.818770 / BIC score: 369429.078467 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=479). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O00567/3_mltree/O00567.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O00567/3_mltree/O00567.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O00567/3_mltree/O00567.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/O00567/3_mltree/O00567.raxml.log Analysis started: 11-Jul-2021 03:08:05 / finished: 11-Jul-2021 18:58:16 Elapsed time: 57011.525 seconds