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 11:04:47 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52746/2_msa/P52746_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52746/3_mltree/P52746 --seed 2 --threads 5 --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 (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52746/2_msa/P52746_trimmed_msa.fasta [00:00:00] Loaded alignment with 646 taxa and 245 sites WARNING: Sequences tr_A0A0G2KUB4_A0A0G2KUB4_DANRE_7955 and tr_E9QEN1_E9QEN1_DANRE_7955 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_G1RJK9_G1RJK9_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_G3SCV4_G3SCV4_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_H2P0F4_H2P0F4_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_J9NX34_J9NX34_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_H2R5T2_H2R5T2_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_F6UYP8_F6UYP8_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and sp_Q8WXB4_ZN606_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_F6VJ47_F6VJ47_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_G3T2B3_G3T2B3_LOXAF_9785 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_F1SC26_F1SC26_PIG_9823 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_G1LLA8_G1LLA8_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_G7PZB1_G7PZB1_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_E1BLQ2_E1BLQ2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A2I2V352_A0A2I2V352_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A0A0MV87_A0A0A0MV87_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A0D9S6C3_A0A0D9S6C3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A2K5LBT8_A0A2K5LBT8_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A2K6CMN0_A0A2K6CMN0_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A2K5YJT1_A0A2K5YJT1_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A2R9B9N8_A0A2R9B9N8_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A2U4AUJ9_A0A2U4AUJ9_TURTR_9739 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A2U3ZL27_A0A2U3ZL27_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A2U3Z0Q3_A0A2U3Z0Q3_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3YAK2_M3YAK2_MUSPF_9669 and tr_A0A384DCH9_A0A384DCH9_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1QL70_G1QL70_NOMLE_61853 and tr_K7EVS2_K7EVS2_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QL70_G1QL70_NOMLE_61853 and tr_G7P725_G7P725_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QL70_G1QL70_NOMLE_61853 and tr_A0A2I3LTF8_A0A2I3LTF8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QL70_G1QL70_NOMLE_61853 and tr_A0A0D9R811_A0A0D9R811_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1QL70_G1QL70_NOMLE_61853 and tr_A0A2K5LBC9_A0A2K5LBC9_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1QL70_G1QL70_NOMLE_61853 and tr_A0A2K6ALD2_A0A2K6ALD2_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RBU6_G1RBU6_NOMLE_61853 and tr_H2P8L4_H2P8L4_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2Y594_A0A2I2Y594_GORGO_9595 and tr_A0A2I3SSM4_A0A2I3SSM4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2Y594_A0A2I2Y594_GORGO_9595 and sp_P51814_ZNF41_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Y594_A0A2I2Y594_GORGO_9595 and tr_A0A2R9B6G9_A0A2R9B6G9_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2YEB7_A0A2I2YEB7_GORGO_9595 and tr_A0A2I3S1M4_A0A2I3S1M4_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2YEB7_A0A2I2YEB7_GORGO_9595 and sp_Q9UJW8_ZN180_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YEB7_A0A2I2YEB7_GORGO_9595 and tr_A0A2R9A1Z5_A0A2R9A1Z5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2J8SK65_A0A2J8SK65_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2I3T1I2_A0A2I3T1I2_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and sp_Q99676_ZN184_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2R8PJ98_A0A2R8PJ98_CALJA_9483 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2K6EBM5_A0A2K6EBM5_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2K5XY05_A0A2K5XY05_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3S228_G3S228_GORGO_9595 and tr_A0A2R9C8X5_A0A2R9C8X5_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NZ55_H2NZ55_PONAB_9601 and tr_A0A0D9S1J8_A0A0D9S1J8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2QXP9_H2QXP9_PANTR_9598 and sp_Q9Y6Q3_ZFP37_HUMAN_9606 are exactly identical! WARNING: Sequences tr_W5QAN3_W5QAN3_SHEEP_9940 and sp_A6QLU5_ZN184_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A0G2K9M2_A0A0G2K9M2_RAT_10116 and tr_A0A0G2QC13_A0A0G2QC13_RAT_10116 are exactly identical! WARNING: Sequences tr_G3V8H6_G3V8H6_RAT_10116 and tr_A0A1U7R7P4_A0A1U7R7P4_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A286XQ14_A0A286XQ14_CAVPO_10141 and tr_A0A091DER8_A0A091DER8_FUKDA_885580 are exactly identical! WARNING: Sequences sp_B4DU55_ZN879_HUMAN_9606 and tr_A0A2R9ACJ3_A0A2R9ACJ3_PANPA_9597 are exactly identical! WARNING: Sequences sp_P52746_ZN142_HUMAN_9606 and tr_A0A2R9APM6_A0A2R9APM6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5R7W1_A0A1D5R7W1_MACMU_9544 and tr_G7PZZ5_G7PZZ5_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5R7W1_A0A1D5R7W1_MACMU_9544 and tr_A0A2K5M8D8_A0A2K5M8D8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7C6K6_F7C6K6_MACMU_9544 and tr_G7P2Q1_G7P2Q1_MACFA_9541 are exactly identical! WARNING: Sequences tr_G7P2D2_G7P2D2_MACFA_9541 and tr_A0A2K6DK49_A0A2K6DK49_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PRN1_G7PRN1_MACFA_9541 and tr_A0A2K5NBR7_A0A2K5NBR7_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PRN1_G7PRN1_MACFA_9541 and tr_A0A2K6DYU0_A0A2K6DYU0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PRN1_G7PRN1_MACFA_9541 and tr_A0A2K5XS25_A0A2K5XS25_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I2ULF6_A0A2I2ULF6_FELCA_9685 and tr_A0A2U3XMZ1_A0A2U3XMZ1_LEPWE_9713 are exactly identical! WARNING: Sequences tr_A0A0A0MUN0_A0A0A0MUN0_PAPAN_9555 and tr_A0A2K5L8E5_A0A2K5L8E5_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0A0MUN0_A0A0A0MUN0_PAPAN_9555 and tr_A0A2K5YCD8_A0A2K5YCD8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3LH46_A0A2I3LH46_PAPAN_9555 and tr_A0A0D9R6H9_A0A0D9R6H9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3LH46_A0A2I3LH46_PAPAN_9555 and tr_A0A1U7TCK5_A0A1U7TCK5_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A151N926_A0A151N926_ALLMI_8496 and tr_A0A1U8DV96_A0A1U8DV96_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A226NN44_A0A226NN44_CALSU_9009 and tr_A0A226PAR0_A0A226PAR0_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2K6DDK0_A0A2K6DDK0_MACNE_9545 and tr_A0A2K5ZF03_A0A2K5ZF03_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4AU84_A0A2U4AU84_TURTR_9739 and tr_A0A2Y9F3K7_A0A2Y9F3K7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4C4P0_A0A2U4C4P0_TURTR_9739 and tr_A0A2U4C4S2_A0A2U4C4S2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4C4P0_A0A2U4C4P0_TURTR_9739 and tr_A0A2Y9M7X8_A0A2Y9M7X8_DELLE_9749 are exactly identical! WARNING: Duplicate sequences found: 71 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/P52746/3_mltree/P52746.raxml.reduced.phy Alignment comprises 1 partitions and 245 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 245 / 245 Gaps: 5.27 % Invariant sites: 2.04 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52746/3_mltree/P52746.raxml.rba Parallelization scheme autoconfig: 5 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 646 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 245 / 19600 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -237225.371361] Initial branch length optimization [00:00:03 -203603.735117] Model parameter optimization (eps = 10.000000) [00:00:39 -203381.733553] AUTODETECT spr round 1 (radius: 5) [00:02:19 -152613.739386] AUTODETECT spr round 2 (radius: 10) [00:04:37 -114844.448931] AUTODETECT spr round 3 (radius: 15) [00:06:54 -97404.793985] AUTODETECT spr round 4 (radius: 20) [00:09:31 -93756.083747] AUTODETECT spr round 5 (radius: 25) [00:12:37 -92055.191868] SPR radius for FAST iterations: 25 (autodetect) [00:12:37 -92055.191868] Model parameter optimization (eps = 3.000000) [00:12:57 -91837.257197] FAST spr round 1 (radius: 25) [00:15:21 -85318.696220] FAST spr round 2 (radius: 25) [00:17:15 -84745.450039] FAST spr round 3 (radius: 25) [00:18:54 -84684.383314] FAST spr round 4 (radius: 25) [00:20:22 -84677.162934] FAST spr round 5 (radius: 25) [00:21:36 -84675.722915] FAST spr round 6 (radius: 25) [00:22:48 -84675.722239] Model parameter optimization (eps = 1.000000) [00:23:02 -84673.918086] SLOW spr round 1 (radius: 5) [00:24:59 -84654.857508] SLOW spr round 2 (radius: 5) [00:26:52 -84643.844418] SLOW spr round 3 (radius: 5) [00:28:41 -84643.305665] SLOW spr round 4 (radius: 5) [00:30:25 -84643.305019] SLOW spr round 5 (radius: 10) [00:32:05 -84639.900358] SLOW spr round 6 (radius: 5) [00:34:15 -84636.872309] SLOW spr round 7 (radius: 5) [00:36:11 -84636.633743] SLOW spr round 8 (radius: 5) [00:38:00 -84636.154072] SLOW spr round 9 (radius: 5) [00:39:44 -84636.154057] SLOW spr round 10 (radius: 10) [00:41:25 -84636.154046] SLOW spr round 11 (radius: 15) [00:44:17 -84633.839461] SLOW spr round 12 (radius: 5) [00:46:28 -84628.885335] SLOW spr round 13 (radius: 5) [00:48:22 -84628.885247] SLOW spr round 14 (radius: 10) [00:50:09 -84628.885245] SLOW spr round 15 (radius: 15) [00:50:17] [worker #4] ML tree search #5, logLikelihood: -84687.571365 [00:52:56 -84628.885244] SLOW spr round 16 (radius: 20) [00:55:40] [worker #2] ML tree search #3, logLikelihood: -84671.264769 [00:57:17 -84628.522312] SLOW spr round 17 (radius: 5) [00:59:24] [worker #3] ML tree search #4, logLikelihood: -84633.447534 [00:59:30 -84628.521872] SLOW spr round 18 (radius: 10) [01:01:34 -84628.521857] SLOW spr round 19 (radius: 15) [01:04:13 -84628.521853] SLOW spr round 20 (radius: 20) [01:08:39 -84628.521850] SLOW spr round 21 (radius: 25) [01:13:45 -84628.521848] Model parameter optimization (eps = 0.100000) [01:13:58] [worker #0] ML tree search #1, logLikelihood: -84628.363863 [01:13:58 -235467.209802] Initial branch length optimization [01:14:01 -202567.806464] Model parameter optimization (eps = 10.000000) [01:14:33 -202326.727818] AUTODETECT spr round 1 (radius: 5) [01:16:12 -149350.322030] AUTODETECT spr round 2 (radius: 10) [01:18:17 -113999.400160] AUTODETECT spr round 3 (radius: 15) [01:20:34 -99654.389857] AUTODETECT spr round 4 (radius: 20) [01:23:18 -95780.040248] AUTODETECT spr round 5 (radius: 25) [01:26:33 -93764.423238] SPR radius for FAST iterations: 25 (autodetect) [01:26:33 -93764.423238] Model parameter optimization (eps = 3.000000) [01:26:58 -93541.402230] FAST spr round 1 (radius: 25) [01:29:23 -85878.477546] FAST spr round 2 (radius: 25) [01:31:12 -85178.284957] FAST spr round 3 (radius: 25) [01:32:46 -84952.993507] FAST spr round 4 (radius: 25) [01:34:16 -84846.927514] FAST spr round 5 (radius: 25) [01:35:34 -84836.277761] FAST spr round 6 (radius: 25) [01:36:49 -84833.642699] FAST spr round 7 (radius: 25) [01:37:59 -84833.642633] Model parameter optimization (eps = 1.000000) [01:38:12 -84833.070973] SLOW spr round 1 (radius: 5) [01:40:06 -84786.493055] SLOW spr round 2 (radius: 5) [01:41:58 -84783.172976] SLOW spr round 3 (radius: 5) [01:43:46 -84782.223433] SLOW spr round 4 (radius: 5) [01:44:58] [worker #2] ML tree search #8, logLikelihood: -84659.627158 [01:45:15] [worker #3] ML tree search #9, logLikelihood: -84661.884177 [01:45:31 -84782.223152] SLOW spr round 5 (radius: 10) [01:47:14 -84780.537431] SLOW spr round 6 (radius: 5) [01:49:23 -84777.087912] SLOW spr round 7 (radius: 5) [01:51:16 -84777.087896] SLOW spr round 8 (radius: 10) [01:52:20] [worker #1] ML tree search #2, logLikelihood: -84674.114323 [01:53:03 -84777.087894] SLOW spr round 9 (radius: 15) [01:53:22] [worker #4] ML tree search #10, logLikelihood: -84617.744156 [01:56:14 -84777.087893] SLOW spr round 10 (radius: 20) [02:01:02 -84754.580203] SLOW spr round 11 (radius: 5) [02:03:22 -84692.869487] SLOW spr round 12 (radius: 5) [02:05:24 -84691.105209] SLOW spr round 13 (radius: 5) [02:07:13 -84691.103906] SLOW spr round 14 (radius: 10) [02:08:58 -84691.103857] SLOW spr round 15 (radius: 15) [02:12:08 -84691.103854] SLOW spr round 16 (radius: 20) [02:16:56 -84691.103853] SLOW spr round 17 (radius: 25) [02:22:12 -84691.103852] Model parameter optimization (eps = 0.100000) [02:22:22] [worker #0] ML tree search #6, logLikelihood: -84690.422936 [02:22:22 -233704.771795] Initial branch length optimization [02:22:25 -200499.334572] Model parameter optimization (eps = 10.000000) [02:22:55 -200260.974638] AUTODETECT spr round 1 (radius: 5) [02:24:33 -147440.325129] AUTODETECT spr round 2 (radius: 10) [02:26:38 -111856.646164] AUTODETECT spr round 3 (radius: 15) [02:29:01 -99176.284627] AUTODETECT spr round 4 (radius: 20) [02:31:44 -94582.084992] AUTODETECT spr round 5 (radius: 25) [02:34:35 -93849.960521] SPR radius for FAST iterations: 25 (autodetect) [02:34:35 -93849.960521] Model parameter optimization (eps = 3.000000) [02:34:56 -93685.849229] FAST spr round 1 (radius: 25) [02:37:20 -87817.147149] FAST spr round 2 (radius: 25) [02:39:09 -85310.902192] FAST spr round 3 (radius: 25) [02:40:46 -84797.255803] FAST spr round 4 (radius: 25) [02:42:12 -84775.845387] FAST spr round 5 (radius: 25) [02:43:32 -84760.001702] FAST spr round 6 (radius: 25) [02:44:45 -84759.043823] FAST spr round 7 (radius: 25) [02:45:55 -84759.043792] Model parameter optimization (eps = 1.000000) [02:46:09] [worker #4] ML tree search #15, logLikelihood: -84652.094099 [02:46:10 -84754.645821] SLOW spr round 1 (radius: 5) [02:47:01] [worker #2] ML tree search #13, logLikelihood: -84628.759329 [02:48:07 -84730.944890] SLOW spr round 2 (radius: 5) [02:49:58 -84727.452830] SLOW spr round 3 (radius: 5) [02:51:42 -84727.452752] SLOW spr round 4 (radius: 10) [02:52:47] [worker #3] ML tree search #14, logLikelihood: -84671.144366 [02:53:21 -84724.037976] SLOW spr round 5 (radius: 5) [02:55:27 -84723.442793] SLOW spr round 6 (radius: 5) [02:57:21 -84723.442190] SLOW spr round 7 (radius: 10) [02:59:04 -84723.442185] SLOW spr round 8 (radius: 15) [03:01:51 -84723.442185] SLOW spr round 9 (radius: 20) [03:05:52 -84723.442185] SLOW spr round 10 (radius: 25) [03:10:19 -84723.442185] Model parameter optimization (eps = 0.100000) [03:10:28] [worker #0] ML tree search #11, logLikelihood: -84723.326060 [03:10:29 -235466.161690] Initial branch length optimization [03:10:31 -201379.276188] Model parameter optimization (eps = 10.000000) [03:11:06 -201120.560762] AUTODETECT spr round 1 (radius: 5) [03:12:45 -151723.377951] AUTODETECT spr round 2 (radius: 10) [03:14:50 -113577.956931] AUTODETECT spr round 3 (radius: 15) [03:17:15 -98488.186560] AUTODETECT spr round 4 (radius: 20) [03:20:13 -93396.142388] AUTODETECT spr round 5 (radius: 25) [03:23:29 -91676.073602] SPR radius for FAST iterations: 25 (autodetect) [03:23:29 -91676.073602] Model parameter optimization (eps = 3.000000) [03:23:46 -91533.101102] FAST spr round 1 (radius: 25) [03:26:08 -85533.555681] FAST spr round 2 (radius: 25) [03:28:01 -84805.297612] FAST spr round 3 (radius: 25) [03:29:38 -84708.253230] FAST spr round 4 (radius: 25) [03:31:00 -84697.546492] FAST spr round 5 (radius: 25) [03:32:15 -84695.485917] FAST spr round 6 (radius: 25) [03:33:31 -84692.665608] FAST spr round 7 (radius: 25) [03:34:44 -84688.879815] FAST spr round 8 (radius: 25) [03:35:55 -84688.879644] Model parameter optimization (eps = 1.000000) [03:36:10 -84683.122591] SLOW spr round 1 (radius: 5) [03:36:54] [worker #4] ML tree search #20, logLikelihood: -84664.474534 [03:38:01 -84638.910755] SLOW spr round 2 (radius: 5) [03:39:47 -84635.239131] SLOW spr round 3 (radius: 5) [03:41:31 -84635.238633] SLOW spr round 4 (radius: 10) [03:43:09 -84635.238631] SLOW spr round 5 (radius: 15) [03:45:50 -84635.238630] SLOW spr round 6 (radius: 20) [03:50:07 -84635.238629] SLOW spr round 7 (radius: 25) [03:55:15 -84634.931578] SLOW spr round 8 (radius: 5) [03:57:31 -84631.782081] SLOW spr round 9 (radius: 5) [03:59:28 -84631.781910] SLOW spr round 10 (radius: 10) [04:01:14 -84631.781909] SLOW spr round 11 (radius: 15) [04:03:49 -84631.781908] SLOW spr round 12 (radius: 20) [04:07:48] [worker #2] ML tree search #18, logLikelihood: -84676.065347 [04:08:06 -84631.781907] SLOW spr round 13 (radius: 25) [04:11:58] [worker #3] ML tree search #19, logLikelihood: -84977.521776 [04:13:09 -84631.781906] Model parameter optimization (eps = 0.100000) [04:13:16] [worker #0] ML tree search #16, logLikelihood: -84631.718459 [05:13:37] [worker #1] ML tree search #7, logLikelihood: -84875.217379 [06:17:51] [worker #1] ML tree search #12, logLikelihood: -84649.268998 [07:49:26] [worker #1] ML tree search #17, logLikelihood: -84653.349475 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.245580,0.237121) (0.117516,0.400439) (0.369552,0.867392) (0.267352,2.147592) 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: -84617.744156 AIC score: 171825.488313 / AICc score: 3528465.488313 / BIC score: 176359.617695 Free parameters (model + branch lengths): 1295 WARNING: Number of free parameters (K=1295) is larger than alignment size (n=245). 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/P52746/3_mltree/P52746.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52746/3_mltree/P52746.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52746/3_mltree/P52746.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52746/3_mltree/P52746.raxml.log Analysis started: 01-Jul-2021 11:04:47 / finished: 01-Jul-2021 18:54:13 Elapsed time: 28166.344 seconds Consumed energy: 1432.301 Wh (= 7 km in an electric car, or 36 km with an e-scooter!)