RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 01-Jul-2021 11:59:07 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A6/2_msa/Q9C0A6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A6/3_mltree/Q9C0A6 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A6/2_msa/Q9C0A6_trimmed_msa.fasta [00:00:00] Loaded alignment with 416 taxa and 155 sites WARNING: Sequences tr_E1BUU2_E1BUU2_CHICK_9031 and tr_G1N790_G1N790_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1BUU2_E1BUU2_CHICK_9031 and tr_U3KE44_U3KE44_FICAL_59894 are exactly identical! WARNING: Sequences tr_E1BUU2_E1BUU2_CHICK_9031 and tr_U3IHN8_U3IHN8_ANAPL_8839 are exactly identical! WARNING: Sequences tr_E1BUU2_E1BUU2_CHICK_9031 and tr_A0A1V4JIH1_A0A1V4JIH1_PATFA_372326 are exactly identical! WARNING: Sequences tr_E1BUU2_E1BUU2_CHICK_9031 and tr_A0A218VD61_A0A218VD61_9PASE_299123 are exactly identical! WARNING: Sequences tr_E1BUU2_E1BUU2_CHICK_9031 and tr_A0A226NFE9_A0A226NFE9_CALSU_9009 are exactly identical! WARNING: Sequences tr_E1BUU2_E1BUU2_CHICK_9031 and tr_A0A226PH06_A0A226PH06_COLVI_9014 are exactly identical! WARNING: Sequences tr_E1C7R9_E1C7R9_CHICK_9031 and tr_G1N4D5_G1N4D5_MELGA_9103 are exactly identical! WARNING: Sequences tr_E1C7R9_E1C7R9_CHICK_9031 and tr_U3I6A1_U3I6A1_ANAPL_8839 are exactly identical! WARNING: Sequences tr_E1C7R9_E1C7R9_CHICK_9031 and tr_A0A0A0ADU9_A0A0A0ADU9_CHAVO_50402 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_M3Z048_M3Z048_MUSPF_9669 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_G1QV07_G1QV07_NOMLE_61853 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_G1PBT6_G1PBT6_MYOLU_59463 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_G3GX85_G3GX85_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_G3QN50_G3QN50_GORGO_9595 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_H2PA58_H2PA58_PONAB_9601 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_G1T4Y5_G1T4Y5_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_E2RLT0_E2RLT0_CANLF_9615 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_K7D0P7_K7D0P7_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_F6XT59_F6XT59_HORSE_9796 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_D4A2W7_D4A2W7_RAT_10116 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A287DD08_A0A287DD08_ICTTR_43179 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_H0WV35_H0WV35_OTOGA_30611 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_H0V7Z2_H0V7Z2_CAVPO_10141 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and sp_Q9C0A6_SETD5_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_F7H017_F7H017_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_G5BX92_G5BX92_HETGA_10181 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_G3T2N2_G3T2N2_LOXAF_9785 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2R8N9R1_A0A2R8N9R1_CALJA_9483 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_G1LXT9_G1LXT9_AILME_9646 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_G7NYV2_G7NYV2_MACFA_9541 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_L5KAQ5_L5KAQ5_PTEAL_9402 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2I2V1C6_A0A2I2V1C6_FELCA_9685 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A091E1U5_A0A091E1U5_FUKDA_885580 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A0D9REB0_A0A0D9REB0_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A1S3WAA1_A0A1S3WAA1_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A1S3EQT0_A0A1S3EQT0_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A3Q0CJ35_A0A3Q0CJ35_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2K5N2Y1_A0A2K5N2Y1_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2K6EBA2_A0A2K6EBA2_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2K5ZC34_A0A2K5ZC34_MANLE_9568 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2R9C607_A0A2R9C607_PANPA_9597 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2U4C3Y2_A0A2U4C3Y2_TURTR_9739 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2U3VE75_A0A2U3VE75_ODORO_9708 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2Y9RE24_A0A2Y9RE24_TRIMA_127582 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2Y9J3Q1_A0A2Y9J3Q1_ENHLU_391180 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2Y9MDV4_A0A2Y9MDV4_DELLE_9749 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A2Y9FFV1_A0A2Y9FFV1_PHYCD_9755 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A384CMV8_A0A384CMV8_URSMA_29073 are exactly identical! WARNING: Sequences sp_Q5XJV7_SETD5_MOUSE_10090 and tr_A0A384AYV3_A0A384AYV3_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3Z3I5_M3Z3I5_MUSPF_9669 and tr_E2RQA5_E2RQA5_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Z3I5_M3Z3I5_MUSPF_9669 and tr_I3LJ07_I3LJ07_PIG_9823 are exactly identical! WARNING: Sequences tr_M3Z3I5_M3Z3I5_MUSPF_9669 and tr_G1M3B5_G1M3B5_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Z3I5_M3Z3I5_MUSPF_9669 and tr_A0A384D4Y4_A0A384D4Y4_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1RCT7_G1RCT7_NOMLE_61853 and tr_G3QE82_G3QE82_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RCT7_G1RCT7_NOMLE_61853 and tr_H2PN53_H2PN53_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RCT7_G1RCT7_NOMLE_61853 and tr_A0A2I3RZ98_A0A2I3RZ98_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RCT7_G1RCT7_NOMLE_61853 and sp_Q8IZD2_KMT2E_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RCT7_G1RCT7_NOMLE_61853 and tr_A0A2R9B4V4_A0A2R9B4V4_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6WJG5_F6WJG5_MONDO_13616 and tr_G3WP99_G3WP99_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5NW93_W5NW93_SHEEP_9940 and tr_F1MFD2_F1MFD2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A158NK48_A0A158NK48_ATTCE_12957 and tr_A0A195BA46_A0A195BA46_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158P0I0_A0A158P0I0_ATTCE_12957 and tr_F4WID5_F4WID5_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158P0I0_A0A158P0I0_ATTCE_12957 and tr_A0A151X0H3_A0A151X0H3_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158P0I0_A0A158P0I0_ATTCE_12957 and tr_A0A151J2E4_A0A151J2E4_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158P0I0_A0A158P0I0_ATTCE_12957 and tr_A0A195BMW5_A0A195BMW5_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158P0I0_A0A158P0I0_ATTCE_12957 and tr_A0A195F3H2_A0A195F3H2_9HYME_34720 are exactly identical! WARNING: Sequences tr_F7GG04_F7GG04_MACMU_9544 and tr_G7P2E3_G7P2E3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7GG04_F7GG04_MACMU_9544 and tr_A0A096NGS5_A0A096NGS5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GG04_F7GG04_MACMU_9544 and tr_A0A2K6DK87_A0A2K6DK87_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GG04_F7GG04_MACMU_9544 and tr_A0A2K5YKI3_A0A2K5YKI3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3SU58_G3SU58_LOXAF_9785 and tr_A0A2Y9RMU4_A0A2Y9RMU4_TRIMA_127582 are exactly identical! WARNING: Sequences tr_H0YXJ7_H0YXJ7_TAEGU_59729 and tr_A0A093PC46_A0A093PC46_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZDV4_H0ZDV4_TAEGU_59729 and tr_A0A091F882_A0A091F882_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZDV4_H0ZDV4_TAEGU_59729 and tr_A0A091ITE9_A0A091ITE9_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0ZDV4_H0ZDV4_TAEGU_59729 and tr_A0A093Q0G3_A0A093Q0G3_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZDV4_H0ZDV4_TAEGU_59729 and tr_A0A091VGL8_A0A091VGL8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZDV4_H0ZDV4_TAEGU_59729 and tr_A0A087RC45_A0A087RC45_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0ZDV4_H0ZDV4_TAEGU_59729 and tr_A0A0A0AVM6_A0A0A0AVM6_CHAVO_50402 are exactly identical! WARNING: Sequences tr_H0ZDV4_H0ZDV4_TAEGU_59729 and tr_A0A091HHP3_A0A091HHP3_CALAN_9244 are exactly identical! WARNING: Sequences tr_F4W8D6_F4W8D6_ACREC_103372 and tr_A0A195FB03_A0A195FB03_9HYME_34720 are exactly identical! WARNING: Sequences tr_L0PF09_L0PF09_PNEJ8_1209962 and tr_A0A0W4ZNR3_A0A0W4ZNR3_PNEJ7_1408657 are exactly identical! WARNING: Sequences tr_A0A3B1J565_A0A3B1J565_ASTMX_7994 and tr_A0A099ZER4_A0A099ZER4_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A3B1J565_A0A3B1J565_ASTMX_7994 and tr_A0A060YYD6_A0A060YYD6_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A151MP75_A0A151MP75_ALLMI_8496 and tr_A0A1U7SU39_A0A1U7SU39_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A2I0MH86_A0A2I0MH86_COLLI_8932 and tr_A0A1V4JZZ2_A0A1V4JZZ2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S4B2S7_A0A1S4B2S7_TOBAC_4097 and tr_A0A1U7YLA4_A0A1U7YLA4_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1V8UJM8_A0A1V8UJM8_9PEZI_1974281 and tr_A0A1V8UWI5_A0A1V8UWI5_9PEZI_1974281 are exactly identical! WARNING: Sequences tr_A0A1V8UJM8_A0A1V8UJM8_9PEZI_1974281 and tr_A0A1V8T2D3_A0A1V8T2D3_9PEZI_1507870 are exactly identical! WARNING: Sequences tr_A0A2D0RY84_A0A2D0RY84_ICTPU_7998 and tr_A0A2D0RY85_A0A2D0RY85_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RY84_A0A2D0RY84_ICTPU_7998 and tr_A0A2D0RY88_A0A2D0RY88_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RY84_A0A2D0RY84_ICTPU_7998 and tr_A0A2D0RZS3_A0A2D0RZS3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4BSD5_A0A2U4BSD5_TURTR_9739 and tr_A0A2Y9LMW6_A0A2Y9LMW6_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BSD5_A0A2U4BSD5_TURTR_9739 and tr_A0A2Y9S771_A0A2Y9S771_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3XX73_A0A2U3XX73_LEPWE_9713 and tr_A0A2Y9KC15_A0A2Y9KC15_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 95 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A6/3_mltree/Q9C0A6.raxml.reduced.phy Alignment comprises 1 partitions and 155 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 155 / 155 Gaps: 8.08 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A6/3_mltree/Q9C0A6.raxml.rba Parallelization scheme autoconfig: 3 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 416 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 155 / 12400 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -106967.974225] Initial branch length optimization [00:00:01 -81863.585643] Model parameter optimization (eps = 10.000000) [00:00:24 -81278.478820] AUTODETECT spr round 1 (radius: 5) [00:00:49 -59506.513774] AUTODETECT spr round 2 (radius: 10) [00:01:18 -50634.883240] AUTODETECT spr round 3 (radius: 15) [00:01:53 -44338.491060] AUTODETECT spr round 4 (radius: 20) [00:02:37 -37100.365935] AUTODETECT spr round 5 (radius: 25) [00:03:27 -35663.855363] SPR radius for FAST iterations: 25 (autodetect) [00:03:27 -35663.855363] Model parameter optimization (eps = 3.000000) [00:03:42 -35270.656260] FAST spr round 1 (radius: 25) [00:04:18 -29625.045835] FAST spr round 2 (radius: 25) [00:04:45 -29306.317858] FAST spr round 3 (radius: 25) [00:05:09 -29285.692380] FAST spr round 4 (radius: 25) [00:05:31 -29268.536834] FAST spr round 5 (radius: 25) [00:05:49 -29268.536773] Model parameter optimization (eps = 1.000000) [00:05:56 -29257.261170] SLOW spr round 1 (radius: 5) [00:06:20 -29252.101285] SLOW spr round 2 (radius: 5) [00:06:46 -29251.319777] SLOW spr round 3 (radius: 5) [00:07:14 -29249.329442] SLOW spr round 4 (radius: 5) [00:07:41 -29249.084389] SLOW spr round 5 (radius: 5) [00:08:07 -29249.083310] SLOW spr round 6 (radius: 10) [00:08:36 -29249.083042] SLOW spr round 7 (radius: 15) [00:09:24 -29249.082855] SLOW spr round 8 (radius: 20) [00:10:39 -29249.082811] SLOW spr round 9 (radius: 25) [00:10:45] [worker #1] ML tree search #2, logLikelihood: -29239.130429 [00:11:56 -29249.082776] Model parameter optimization (eps = 0.100000) [00:11:58] [worker #0] ML tree search #1, logLikelihood: -29249.069309 [00:11:58 -107276.788589] Initial branch length optimization [00:11:59 -81378.898711] Model parameter optimization (eps = 10.000000) [00:12:04] [worker #2] ML tree search #3, logLikelihood: -29245.363555 [00:12:32 -80841.958343] AUTODETECT spr round 1 (radius: 5) [00:12:59 -60301.301491] AUTODETECT spr round 2 (radius: 10) [00:13:29 -49732.757182] AUTODETECT spr round 3 (radius: 15) [00:14:08 -40419.122237] AUTODETECT spr round 4 (radius: 20) [00:14:49 -38355.273627] AUTODETECT spr round 5 (radius: 25) [00:15:50 -36072.075629] SPR radius for FAST iterations: 25 (autodetect) [00:15:50 -36072.075629] Model parameter optimization (eps = 3.000000) [00:16:09 -35684.523523] FAST spr round 1 (radius: 25) [00:16:43 -30253.014804] FAST spr round 2 (radius: 25) [00:17:08 -29329.624489] FAST spr round 3 (radius: 25) [00:17:29 -29257.006949] FAST spr round 4 (radius: 25) [00:17:51 -29254.119073] FAST spr round 5 (radius: 25) [00:18:11 -29254.118607] Model parameter optimization (eps = 1.000000) [00:18:17 -29250.331095] SLOW spr round 1 (radius: 5) [00:18:44 -29243.591932] SLOW spr round 2 (radius: 5) [00:19:10 -29242.432922] SLOW spr round 3 (radius: 5) [00:19:36 -29242.432513] SLOW spr round 4 (radius: 10) [00:20:04 -29242.349367] SLOW spr round 5 (radius: 15) [00:20:49 -29242.349206] SLOW spr round 6 (radius: 20) [00:21:28] [worker #1] ML tree search #5, logLikelihood: -29243.383355 [00:21:59 -29242.349008] SLOW spr round 7 (radius: 25) [00:22:23] [worker #2] ML tree search #6, logLikelihood: -29237.552865 [00:23:13 -29242.349008] Model parameter optimization (eps = 0.100000) [00:23:16] [worker #0] ML tree search #4, logLikelihood: -29242.265019 [00:23:16 -106066.937965] Initial branch length optimization [00:23:17 -81077.826484] Model parameter optimization (eps = 10.000000) [00:23:51 -80690.882241] AUTODETECT spr round 1 (radius: 5) [00:24:18 -59535.638451] AUTODETECT spr round 2 (radius: 10) [00:24:52 -48123.092126] AUTODETECT spr round 3 (radius: 15) [00:25:29 -39787.674756] AUTODETECT spr round 4 (radius: 20) [00:26:15 -38150.425857] AUTODETECT spr round 5 (radius: 25) [00:27:13 -37151.751174] SPR radius for FAST iterations: 25 (autodetect) [00:27:13 -37151.751174] Model parameter optimization (eps = 3.000000) [00:27:34 -36694.617421] FAST spr round 1 (radius: 25) [00:28:15 -29736.171583] FAST spr round 2 (radius: 25) [00:28:44 -29344.701699] FAST spr round 3 (radius: 25) [00:29:05 -29268.473267] FAST spr round 4 (radius: 25) [00:29:27 -29251.106635] FAST spr round 5 (radius: 25) [00:29:45 -29248.057458] FAST spr round 6 (radius: 25) [00:30:04 -29248.057104] Model parameter optimization (eps = 1.000000) [00:30:11 -29242.261242] SLOW spr round 1 (radius: 5) [00:30:35 -29236.200519] SLOW spr round 2 (radius: 5) [00:31:01 -29236.199797] SLOW spr round 3 (radius: 10) [00:31:28 -29236.089262] SLOW spr round 4 (radius: 5) [00:32:06 -29236.089023] SLOW spr round 5 (radius: 10) [00:32:35] [worker #1] ML tree search #8, logLikelihood: -29240.632947 [00:32:37 -29236.088840] SLOW spr round 6 (radius: 15) [00:33:17 -29236.088821] SLOW spr round 7 (radius: 20) [00:34:25 -29236.088820] SLOW spr round 8 (radius: 25) [00:34:31] [worker #2] ML tree search #9, logLikelihood: -29236.917658 [00:35:36 -29236.088820] Model parameter optimization (eps = 0.100000) [00:35:38] [worker #0] ML tree search #7, logLikelihood: -29236.086291 [00:35:38 -106473.014473] Initial branch length optimization [00:35:39 -80246.809431] Model parameter optimization (eps = 10.000000) [00:36:06 -79741.718063] AUTODETECT spr round 1 (radius: 5) [00:36:32 -59771.995256] AUTODETECT spr round 2 (radius: 10) [00:37:03 -48432.598754] AUTODETECT spr round 3 (radius: 15) [00:37:39 -43641.042964] AUTODETECT spr round 4 (radius: 20) [00:38:32 -35764.729228] AUTODETECT spr round 5 (radius: 25) [00:39:15 -35525.590934] SPR radius for FAST iterations: 25 (autodetect) [00:39:15 -35525.590934] Model parameter optimization (eps = 3.000000) [00:39:30 -35071.541946] FAST spr round 1 (radius: 25) [00:40:06 -29627.611270] FAST spr round 2 (radius: 25) [00:40:35 -29299.081922] FAST spr round 3 (radius: 25) [00:40:59 -29267.381864] FAST spr round 4 (radius: 25) [00:41:18 -29261.943506] FAST spr round 5 (radius: 25) [00:41:38 -29261.943238] Model parameter optimization (eps = 1.000000) [00:41:46 -29257.609870] SLOW spr round 1 (radius: 5) [00:42:14 -29246.463698] SLOW spr round 2 (radius: 5) [00:42:43 -29243.305065] SLOW spr round 3 (radius: 5) [00:43:12 -29242.142747] SLOW spr round 4 (radius: 5) [00:43:39 -29242.142506] SLOW spr round 5 (radius: 10) [00:43:55] [worker #1] ML tree search #11, logLikelihood: -29247.070161 [00:44:07 -29242.142452] SLOW spr round 6 (radius: 15) [00:44:57 -29242.142409] SLOW spr round 7 (radius: 20) [00:46:07 -29242.142357] SLOW spr round 8 (radius: 25) [00:47:01] [worker #2] ML tree search #12, logLikelihood: -29242.295880 [00:47:25 -29242.142357] Model parameter optimization (eps = 0.100000) [00:47:29] [worker #0] ML tree search #10, logLikelihood: -29241.927960 [00:47:29 -104699.527968] Initial branch length optimization [00:47:30 -79745.529736] Model parameter optimization (eps = 10.000000) [00:47:57 -79377.549536] AUTODETECT spr round 1 (radius: 5) [00:48:23 -58236.591754] AUTODETECT spr round 2 (radius: 10) [00:48:53 -47230.094966] AUTODETECT spr round 3 (radius: 15) [00:49:31 -42383.921139] AUTODETECT spr round 4 (radius: 20) [00:50:14 -40849.789067] AUTODETECT spr round 5 (radius: 25) [00:51:02 -37048.314876] SPR radius for FAST iterations: 25 (autodetect) [00:51:02 -37048.314876] Model parameter optimization (eps = 3.000000) [00:51:17 -36611.812168] FAST spr round 1 (radius: 25) [00:51:52 -29620.428083] FAST spr round 2 (radius: 25) [00:52:15 -29283.110535] FAST spr round 3 (radius: 25) [00:52:37 -29270.708248] FAST spr round 4 (radius: 25) [00:52:58 -29261.082722] FAST spr round 5 (radius: 25) [00:53:18 -29259.133338] FAST spr round 6 (radius: 25) [00:53:36 -29259.132718] Model parameter optimization (eps = 1.000000) [00:53:43 -29250.994151] SLOW spr round 1 (radius: 5) [00:54:08 -29242.742369] SLOW spr round 2 (radius: 5) [00:54:34 -29240.714201] SLOW spr round 3 (radius: 5) [00:54:57] [worker #1] ML tree search #14, logLikelihood: -29238.187772 [00:55:00 -29240.713759] SLOW spr round 4 (radius: 10) [00:55:29 -29240.613887] SLOW spr round 5 (radius: 15) [00:56:13 -29240.613850] SLOW spr round 6 (radius: 20) [00:57:19 -29240.613824] SLOW spr round 7 (radius: 25) [00:58:33 -29240.613823] Model parameter optimization (eps = 0.100000) [00:58:36] [worker #0] ML tree search #13, logLikelihood: -29240.497190 [00:58:36 -106744.642573] Initial branch length optimization [00:58:37 -80463.295788] Model parameter optimization (eps = 10.000000) [00:58:59 -79977.224731] AUTODETECT spr round 1 (radius: 5) [00:59:27 -61173.923524] AUTODETECT spr round 2 (radius: 10) [00:59:45] [worker #2] ML tree search #15, logLikelihood: -29242.529983 [01:00:00 -50852.038356] AUTODETECT spr round 3 (radius: 15) [01:00:36 -41328.947023] AUTODETECT spr round 4 (radius: 20) [01:01:19 -35787.443854] AUTODETECT spr round 5 (radius: 25) [01:02:06 -35237.061966] SPR radius for FAST iterations: 25 (autodetect) [01:02:06 -35237.061966] Model parameter optimization (eps = 3.000000) [01:02:25 -34870.864146] FAST spr round 1 (radius: 25) [01:02:58 -29741.841642] FAST spr round 2 (radius: 25) [01:03:23 -29296.110199] FAST spr round 3 (radius: 25) [01:03:45 -29256.085637] FAST spr round 4 (radius: 25) [01:04:07 -29256.085382] Model parameter optimization (eps = 1.000000) [01:04:12 -29253.296865] SLOW spr round 1 (radius: 5) [01:04:37 -29244.503481] SLOW spr round 2 (radius: 5) [01:05:02 -29243.696711] SLOW spr round 3 (radius: 5) [01:05:28 -29242.899706] SLOW spr round 4 (radius: 5) [01:05:53 -29242.899429] SLOW spr round 5 (radius: 10) [01:05:56] [worker #1] ML tree search #17, logLikelihood: -29238.277578 [01:06:21 -29242.816389] SLOW spr round 6 (radius: 15) [01:07:08 -29242.816306] SLOW spr round 7 (radius: 20) [01:08:20 -29242.816261] SLOW spr round 8 (radius: 25) [01:09:38 -29242.816261] Model parameter optimization (eps = 0.100000) [01:09:40] [worker #0] ML tree search #16, logLikelihood: -29242.774897 [01:09:40 -107780.268906] Initial branch length optimization [01:09:41 -81845.046140] Model parameter optimization (eps = 10.000000) [01:10:12 -81335.930168] AUTODETECT spr round 1 (radius: 5) [01:10:38 -58910.448636] AUTODETECT spr round 2 (radius: 10) [01:11:09 -46644.651977] AUTODETECT spr round 3 (radius: 15) [01:11:43 -40238.792330] AUTODETECT spr round 4 (radius: 20) [01:12:26 -36393.222405] AUTODETECT spr round 5 (radius: 25) [01:12:36] [worker #2] ML tree search #18, logLikelihood: -29245.934914 [01:13:15 -34180.145722] SPR radius for FAST iterations: 25 (autodetect) [01:13:15 -34180.145722] Model parameter optimization (eps = 3.000000) [01:13:42 -33767.577663] FAST spr round 1 (radius: 25) [01:14:20 -29501.550546] FAST spr round 2 (radius: 25) [01:14:47 -29298.194906] FAST spr round 3 (radius: 25) [01:15:10 -29283.455621] FAST spr round 4 (radius: 25) [01:15:32 -29278.496281] FAST spr round 5 (radius: 25) [01:15:53 -29278.495969] Model parameter optimization (eps = 1.000000) [01:15:59 -29272.609961] SLOW spr round 1 (radius: 5) [01:16:26 -29261.995602] SLOW spr round 2 (radius: 5) [01:16:53 -29260.660990] SLOW spr round 3 (radius: 5) [01:17:19 -29260.660503] SLOW spr round 4 (radius: 10) [01:17:46 -29260.563744] SLOW spr round 5 (radius: 15) [01:18:13] [worker #1] ML tree search #20, logLikelihood: -29237.711156 [01:18:36 -29260.563626] SLOW spr round 6 (radius: 20) [01:19:45 -29260.563605] SLOW spr round 7 (radius: 25) [01:21:05 -29260.563601] Model parameter optimization (eps = 0.100000) [01:21:07] [worker #0] ML tree search #19, logLikelihood: -29260.536282 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.064509,0.126194) (0.193272,0.314779) (0.334661,0.728148) (0.407558,1.686479) 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: -29236.086291 AIC score: 60142.172582 / AICc score: 1456262.172582 / BIC score: 62683.432555 Free parameters (model + branch lengths): 835 WARNING: Number of free parameters (K=835) is larger than alignment size (n=155). This might lead to overfitting and compromise tree inference results! Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A6/3_mltree/Q9C0A6.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A6/3_mltree/Q9C0A6.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A6/3_mltree/Q9C0A6.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9C0A6/3_mltree/Q9C0A6.raxml.log Analysis started: 01-Jul-2021 11:59:07 / finished: 01-Jul-2021 13:20:15 Elapsed time: 4867.839 seconds Consumed energy: 326.434 Wh (= 2 km in an electric car, or 8 km with an e-scooter!)