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 06-Jul-2021 11:03:35 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW5/2_msa/Q9UPW5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW5/3_mltree/Q9UPW5 --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/Q9UPW5/2_msa/Q9UPW5_trimmed_msa.fasta [00:00:00] Loaded alignment with 923 taxa and 366 sites WARNING: Sequences sp_E1C3P4_CBPC1_CHICK_9031 and tr_R9PXP2_R9PXP2_CHICK_9031 are exactly identical! WARNING: Sequences sp_Q9VY99_NNAD_DROME_7227 and tr_B4IG55_B4IG55_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A2I3H6U0_A0A2I3H6U0_NOMLE_61853 and tr_A0A2I2YS08_A0A2I2YS08_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3H6U0_A0A2I3H6U0_NOMLE_61853 and tr_A0A2I3TGJ5_A0A2I3TGJ5_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3H6U0_A0A2I3H6U0_NOMLE_61853 and tr_A0A2R9AWW6_A0A2R9AWW6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1QUD4_G1QUD4_NOMLE_61853 and tr_G3QXW2_G3QXW2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QUD4_G1QUD4_NOMLE_61853 and tr_H2PSJ4_H2PSJ4_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1QUD4_G1QUD4_NOMLE_61853 and tr_I3LZI6_I3LZI6_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1QUD4_G1QUD4_NOMLE_61853 and tr_A0A2R9CLD9_A0A2R9CLD9_PANPA_9597 are exactly identical! WARNING: Sequences tr_J9NSE2_J9NSE2_CANLF_9615 and tr_A0A2I2V394_A0A2I2V394_FELCA_9685 are exactly identical! WARNING: Sequences tr_J9NSE2_J9NSE2_CANLF_9615 and tr_A0A2Y9K5N9_A0A2Y9K5N9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_A0A2J8QTK0_A0A2J8QTK0_PANTR_9598 and sp_Q8NEM8_CBPC3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8QTK0_A0A2J8QTK0_PANTR_9598 and tr_A0A2I3M2S1_A0A2I3M2S1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2J8QTK0_A0A2J8QTK0_PANTR_9598 and tr_A0A2K5NT02_A0A2K5NT02_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2J8QTK0_A0A2J8QTK0_PANTR_9598 and tr_A0A2K6E0F5_A0A2K6E0F5_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2J8QTK0_A0A2J8QTK0_PANTR_9598 and tr_A0A2R9CBM6_A0A2R9CBM6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R0I0_H2R0I0_PANTR_9598 and tr_A0A2R8Z9F3_A0A2R8Z9F3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A088ADR5_A0A088ADR5_APIME_7460 and tr_A0A2A3EPE4_A0A2A3EPE4_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A0K0JEX3_A0A0K0JEX3_BRUMA_6279 and tr_A0A0N4TKG1_A0A0N4TKG1_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A0A1D5QCQ5_A0A1D5QCQ5_MACMU_9544 and tr_G7PSM2_G7PSM2_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A1D5QCQ5_A0A1D5QCQ5_MACMU_9544 and tr_A0A096P1W5_A0A096P1W5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A1D5QCQ5_A0A1D5QCQ5_MACMU_9544 and tr_A0A0D9R547_A0A0D9R547_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A1D5QCQ5_A0A1D5QCQ5_MACMU_9544 and tr_A0A2K5P3E8_A0A2K5P3E8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A1D5QCQ5_A0A1D5QCQ5_MACMU_9544 and tr_A0A2K6B573_A0A2K6B573_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1D5QCQ5_A0A1D5QCQ5_MACMU_9544 and tr_A0A2K5YNI2_A0A2K5YNI2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6SFN7_F6SFN7_MACMU_9544 and tr_A0A2I3N1F1_A0A2I3N1F1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6SFN7_F6SFN7_MACMU_9544 and tr_A0A0D9R0H9_A0A0D9R0H9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6SFN7_F6SFN7_MACMU_9544 and tr_A0A2K6B9J7_A0A2K6B9J7_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6SFN7_F6SFN7_MACMU_9544 and tr_A0A2K5YLF5_A0A2K5YLF5_MANLE_9568 are exactly identical! WARNING: Sequences tr_F6TGX6_F6TGX6_MACMU_9544 and tr_A0A096NN36_A0A096NN36_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6TGX6_F6TGX6_MACMU_9544 and tr_A0A2K5MMJ3_A0A2K5MMJ3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6TGX6_F6TGX6_MACMU_9544 and tr_A0A2K6E6L9_A0A2K6E6L9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7GRB8_F7GRB8_MACMU_9544 and tr_A0A2I3M6C6_A0A2I3M6C6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7GRB8_F7GRB8_MACMU_9544 and tr_A0A2K6BBV5_A0A2K6BBV5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H4K8_F7H4K8_MACMU_9544 and tr_G7P0V7_G7P0V7_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1LBM6_G1LBM6_AILME_9646 and tr_A0A384CGQ6_A0A384CGQ6_URSMA_29073 are exactly identical! WARNING: Sequences sp_E1B9D8_CBPC3_BOVIN_9913 and tr_G5E5V2_G5E5V2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_W2REU5_W2REU5_PHYPN_761204 and tr_W2LEN1_W2LEN1_PHYPR_4792 are exactly identical! WARNING: Sequences tr_A0A0V1CX59_A0A0V1CX59_TRIBR_45882 and tr_A0A0V0V3Z6_A0A0V0V3Z6_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1CX59_A0A0V1CX59_TRIBR_45882 and tr_A0A0V1LFN4_A0A0V1LFN4_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1CX59_A0A0V1CX59_TRIBR_45882 and tr_A0A0V1PCA0_A0A0V1PCA0_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CX59_A0A0V1CX59_TRIBR_45882 and tr_A0A0V0U678_A0A0V0U678_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S3JFE1_A0A1S3JFE1_LINUN_7574 and tr_A0A1S3JGN5_A0A1S3JGN5_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1D1W0E8_A0A1D1W0E8_RAMVA_947166 and tr_A0A1D1W0F4_A0A1D1W0F4_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A1D1W0E8_A0A1D1W0E8_RAMVA_947166 and tr_A0A1D1W1C9_A0A1D1W1C9_RAMVA_947166 are exactly identical! WARNING: Sequences tr_A0A226MUA7_A0A226MUA7_CALSU_9009 and tr_A0A226PIM5_A0A226PIM5_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0QX90_A0A2D0QX90_ICTPU_7998 and tr_A0A2D0QX93_A0A2D0QX93_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QX90_A0A2D0QX90_ICTPU_7998 and tr_A0A2D0QXJ8_A0A2D0QXJ8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SBN0_A0A2D0SBN0_ICTPU_7998 and tr_A0A2D0SBN3_A0A2D0SBN3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SBN0_A0A2D0SBN0_ICTPU_7998 and tr_A0A2D0SD13_A0A2D0SD13_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4BRW3_A0A2U4BRW3_TURTR_9739 and tr_A0A2Y9LXU2_A0A2Y9LXU2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4BRW3_A0A2U4BRW3_TURTR_9739 and tr_A0A2Y9TCN4_A0A2Y9TCN4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4BRW3_A0A2U4BRW3_TURTR_9739 and tr_A0A383ZPI2_A0A383ZPI2_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 53 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/Q9UPW5/3_mltree/Q9UPW5.raxml.reduced.phy Alignment comprises 1 partitions and 366 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 366 / 366 Gaps: 13.73 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW5/3_mltree/Q9UPW5.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 923 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 366 / 29280 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -522273.686929] Initial branch length optimization [00:00:10 -437308.109459] Model parameter optimization (eps = 10.000000) [00:01:15 -434853.694518] AUTODETECT spr round 1 (radius: 5) [00:05:34 -321961.122438] AUTODETECT spr round 2 (radius: 10) [00:10:28 -250761.379284] AUTODETECT spr round 3 (radius: 15) [00:15:26 -226834.640594] AUTODETECT spr round 4 (radius: 20) [00:21:54 -198497.668013] AUTODETECT spr round 5 (radius: 25) [00:29:15 -196363.158386] SPR radius for FAST iterations: 25 (autodetect) [00:29:15 -196363.158386] Model parameter optimization (eps = 3.000000) [00:29:53 -196073.672885] FAST spr round 1 (radius: 25) [00:36:50 -170334.777785] FAST spr round 2 (radius: 25) [00:41:35 -169224.741370] FAST spr round 3 (radius: 25) [00:45:20 -169090.675757] FAST spr round 4 (radius: 25) [00:48:35 -169076.663307] FAST spr round 5 (radius: 25) [00:51:38 -169069.377731] FAST spr round 6 (radius: 25) [00:54:29 -169069.377067] Model parameter optimization (eps = 1.000000) [00:55:05 -169044.456964] SLOW spr round 1 (radius: 5) [00:59:11 -168985.177389] SLOW spr round 2 (radius: 5) [01:03:16 -168981.359283] SLOW spr round 3 (radius: 5) [01:07:16 -168981.358728] SLOW spr round 4 (radius: 10) [01:11:31 -168972.276990] SLOW spr round 5 (radius: 5) [01:16:32 -168970.711384] SLOW spr round 6 (radius: 5) [01:20:54 -168970.710787] SLOW spr round 7 (radius: 10) [01:25:09 -168970.710712] SLOW spr round 8 (radius: 15) [01:31:44 -168970.710686] SLOW spr round 9 (radius: 20) [01:40:36 -168970.710676] SLOW spr round 10 (radius: 25) [01:51:08 -168970.710671] Model parameter optimization (eps = 0.100000) [01:51:30] [worker #0] ML tree search #1, logLikelihood: -168969.520305 [01:51:30 -520281.060742] Initial branch length optimization [01:51:41 -438316.720137] Model parameter optimization (eps = 10.000000) [01:52:52 -435952.965424] AUTODETECT spr round 1 (radius: 5) [01:52:57] [worker #1] ML tree search #2, logLikelihood: -168956.622985 [01:57:10 -322999.843651] AUTODETECT spr round 2 (radius: 10) [02:02:02 -244443.587130] AUTODETECT spr round 3 (radius: 15) [02:07:21 -212397.710576] AUTODETECT spr round 4 (radius: 20) [02:13:09 -194149.431219] AUTODETECT spr round 5 (radius: 25) [02:19:42 -190625.267765] SPR radius for FAST iterations: 25 (autodetect) [02:19:42 -190625.267765] Model parameter optimization (eps = 3.000000) [02:20:45 -190408.349830] FAST spr round 1 (radius: 25) [02:27:17 -169962.474489] FAST spr round 2 (radius: 25) [02:29:15] [worker #4] ML tree search #5, logLikelihood: -168951.837399 [02:31:54 -169217.487660] FAST spr round 3 (radius: 25) [02:35:45 -169075.185831] FAST spr round 4 (radius: 25) [02:39:14 -169049.590861] FAST spr round 5 (radius: 25) [02:39:59] [worker #2] ML tree search #3, logLikelihood: -168972.965378 [02:42:14 -169048.670714] FAST spr round 6 (radius: 25) [02:45:07 -169048.670592] Model parameter optimization (eps = 1.000000) [02:45:42 -169041.366134] SLOW spr round 1 (radius: 5) [02:49:45 -168997.861020] SLOW spr round 2 (radius: 5) [02:53:49 -168982.804266] SLOW spr round 3 (radius: 5) [02:57:53 -168981.895669] SLOW spr round 4 (radius: 5) [03:01:50 -168981.876001] SLOW spr round 5 (radius: 10) [03:06:12 -168972.731802] SLOW spr round 6 (radius: 5) [03:11:13 -168971.113208] SLOW spr round 7 (radius: 5) [03:15:36 -168971.108076] SLOW spr round 8 (radius: 10) [03:15:44] [worker #3] ML tree search #4, logLikelihood: -168955.020209 [03:19:53 -168971.107815] SLOW spr round 9 (radius: 15) [03:26:46 -168969.966353] SLOW spr round 10 (radius: 5) [03:31:57 -168969.963306] SLOW spr round 11 (radius: 10) [03:36:51 -168969.963276] SLOW spr round 12 (radius: 15) [03:43:26 -168969.059492] SLOW spr round 13 (radius: 5) [03:48:36 -168969.010437] SLOW spr round 14 (radius: 10) [03:53:33 -168969.009471] SLOW spr round 15 (radius: 15) [04:00:04 -168968.252435] SLOW spr round 16 (radius: 5) [04:05:12 -168968.252206] SLOW spr round 17 (radius: 10) [04:10:09 -168968.252056] SLOW spr round 18 (radius: 15) [04:16:44 -168968.251932] SLOW spr round 19 (radius: 20) [04:26:29 -168966.769584] SLOW spr round 20 (radius: 5) [04:31:44 -168966.769268] SLOW spr round 21 (radius: 10) [04:36:48 -168966.769174] SLOW spr round 22 (radius: 15) [04:43:23 -168966.769062] SLOW spr round 23 (radius: 20) [04:45:33] [worker #1] ML tree search #7, logLikelihood: -168952.176812 [04:53:11 -168966.768975] SLOW spr round 24 (radius: 25) [05:05:11 -168966.768894] Model parameter optimization (eps = 0.100000) [05:05:32] [worker #0] ML tree search #6, logLikelihood: -168966.344185 [05:05:32 -522914.048686] Initial branch length optimization [05:05:40 -440797.687994] Model parameter optimization (eps = 10.000000) [05:06:49 -438352.674280] AUTODETECT spr round 1 (radius: 5) [05:11:14 -325188.277999] AUTODETECT spr round 2 (radius: 10) [05:16:03 -252426.223425] AUTODETECT spr round 3 (radius: 15) [05:21:17 -213466.598178] AUTODETECT spr round 4 (radius: 20) [05:27:32 -199659.919242] AUTODETECT spr round 5 (radius: 25) [05:34:14 -197263.990424] SPR radius for FAST iterations: 25 (autodetect) [05:34:14 -197263.990424] Model parameter optimization (eps = 3.000000) [05:35:01 -197042.055332] FAST spr round 1 (radius: 25) [05:41:56 -171243.958781] FAST spr round 2 (radius: 25) [05:46:53 -169926.183169] FAST spr round 3 (radius: 25) [05:49:29] [worker #2] ML tree search #8, logLikelihood: -168948.303722 [05:50:53 -169796.436285] FAST spr round 4 (radius: 25) [05:54:13 -169771.727251] FAST spr round 5 (radius: 25) [05:55:57] [worker #3] ML tree search #9, logLikelihood: -168971.844675 [05:57:31 -169752.755640] FAST spr round 6 (radius: 25) [06:00:39 -169073.844791] FAST spr round 7 (radius: 25) [06:03:27 -169072.990887] FAST spr round 8 (radius: 25) [06:04:16] [worker #4] ML tree search #10, logLikelihood: -168942.921144 [06:06:13 -169072.989361] Model parameter optimization (eps = 1.000000) [06:06:40 -169044.556869] SLOW spr round 1 (radius: 5) [06:10:51 -169011.106957] SLOW spr round 2 (radius: 5) [06:15:01 -169006.469892] SLOW spr round 3 (radius: 5) [06:19:15 -169000.143867] SLOW spr round 4 (radius: 5) [06:23:08 -169000.143539] SLOW spr round 5 (radius: 10) [06:27:17 -168995.456161] SLOW spr round 6 (radius: 5) [06:32:20 -168989.431565] SLOW spr round 7 (radius: 5) [06:36:42 -168989.431030] SLOW spr round 8 (radius: 10) [06:41:00 -168989.430809] SLOW spr round 9 (radius: 15) [06:47:43 -168989.430691] SLOW spr round 10 (radius: 20) [06:57:01 -168988.979984] SLOW spr round 11 (radius: 5) [07:02:15 -168988.979941] SLOW spr round 12 (radius: 10) [07:07:19 -168988.979920] SLOW spr round 13 (radius: 15) [07:13:45 -168988.979907] SLOW spr round 14 (radius: 20) [07:23:08 -168988.979899] SLOW spr round 15 (radius: 25) [07:26:10] [worker #1] ML tree search #12, logLikelihood: -168961.212414 [07:34:25 -168988.979893] Model parameter optimization (eps = 0.100000) [07:34:34] [worker #0] ML tree search #11, logLikelihood: -168988.903104 [07:34:34 -521688.978212] Initial branch length optimization [07:34:44 -439548.140265] Model parameter optimization (eps = 10.000000) [07:36:13 -436981.353111] AUTODETECT spr round 1 (radius: 5) [07:40:43 -325144.354910] AUTODETECT spr round 2 (radius: 10) [07:45:38 -254477.292867] AUTODETECT spr round 3 (radius: 15) [07:50:32 -216886.827427] AUTODETECT spr round 4 (radius: 20) [07:56:36 -197082.163620] AUTODETECT spr round 5 (radius: 25) [08:03:00 -191201.742779] SPR radius for FAST iterations: 25 (autodetect) [08:03:00 -191201.742779] Model parameter optimization (eps = 3.000000) [08:03:43 -190965.868666] FAST spr round 1 (radius: 25) [08:09:51 -170277.255735] FAST spr round 2 (radius: 25) [08:14:22 -169170.095919] FAST spr round 3 (radius: 25) [08:18:12 -169107.339226] FAST spr round 4 (radius: 25) [08:21:22 -169098.014472] FAST spr round 5 (radius: 25) [08:24:19 -169084.453447] FAST spr round 6 (radius: 25) [08:27:10 -169082.332778] FAST spr round 7 (radius: 25) [08:29:58 -169082.332508] Model parameter optimization (eps = 1.000000) [08:30:30 -169063.410582] SLOW spr round 1 (radius: 5) [08:34:34 -168999.103794] SLOW spr round 2 (radius: 5) [08:38:40 -168994.800909] SLOW spr round 3 (radius: 5) [08:39:53] [worker #2] ML tree search #13, logLikelihood: -168945.313979 [08:42:43 -168994.800070] SLOW spr round 4 (radius: 10) [08:46:56 -168987.402826] SLOW spr round 5 (radius: 5) [08:52:00 -168985.005825] SLOW spr round 6 (radius: 5) [08:56:22 -168985.005360] SLOW spr round 7 (radius: 10) [09:00:42 -168983.502659] SLOW spr round 8 (radius: 5) [09:03:16] [worker #4] ML tree search #15, logLikelihood: -168959.927182 [09:05:38 -168982.589659] SLOW spr round 9 (radius: 5) [09:05:46] [worker #3] ML tree search #14, logLikelihood: -168944.328156 [09:10:02 -168981.652486] SLOW spr round 10 (radius: 5) [09:14:09 -168981.652394] SLOW spr round 11 (radius: 10) [09:18:18 -168981.652382] SLOW spr round 12 (radius: 15) [09:25:04 -168978.421948] SLOW spr round 13 (radius: 5) [09:30:15 -168976.303511] SLOW spr round 14 (radius: 5) [09:34:44 -168976.303349] SLOW spr round 15 (radius: 10) [09:39:05 -168976.303342] SLOW spr round 16 (radius: 15) [09:44:14] [worker #1] ML tree search #17, logLikelihood: -168962.699323 [09:45:35 -168976.108632] SLOW spr round 17 (radius: 5) [09:50:45 -168973.007757] SLOW spr round 18 (radius: 5) [09:55:14 -168973.006693] SLOW spr round 19 (radius: 10) [09:59:36 -168973.006670] SLOW spr round 20 (radius: 15) [10:06:02 -168973.006669] SLOW spr round 21 (radius: 20) [10:15:10 -168971.577176] SLOW spr round 22 (radius: 5) [10:20:21 -168971.577176] SLOW spr round 23 (radius: 10) [10:25:25 -168971.577175] SLOW spr round 24 (radius: 15) [10:31:39 -168971.577175] SLOW spr round 25 (radius: 20) [10:40:53 -168971.577175] SLOW spr round 26 (radius: 25) [10:52:04 -168971.577175] Model parameter optimization (eps = 0.100000) [10:52:24] [worker #0] ML tree search #16, logLikelihood: -168971.147536 [11:55:10] [worker #2] ML tree search #18, logLikelihood: -168943.707262 [12:05:00] [worker #4] ML tree search #20, logLikelihood: -168977.833711 [12:22:00] [worker #3] ML tree search #19, logLikelihood: -168960.890225 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.180878,0.588178) (0.216254,0.556357) (0.377514,0.817765) (0.225354,2.061555) 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: -168942.921144 AIC score: 341583.842287 / AICc score: 7182883.842287 / BIC score: 348799.811321 Free parameters (model + branch lengths): 1849 WARNING: Number of free parameters (K=1849) is larger than alignment size (n=366). 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/Q9UPW5/3_mltree/Q9UPW5.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW5/3_mltree/Q9UPW5.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW5/3_mltree/Q9UPW5.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UPW5/3_mltree/Q9UPW5.raxml.log Analysis started: 06-Jul-2021 11:03:35 / finished: 06-Jul-2021 23:25:36 Elapsed time: 44520.895 seconds Consumed energy: 3660.978 Wh (= 18 km in an electric car, or 92 km with an e-scooter!)