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 10:11:24 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/2_msa/Q3SXY7_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/3_mltree/Q3SXY7 --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/Q3SXY7/2_msa/Q3SXY7_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 301 sites WARNING: Sequences tr_F1P192_F1P192_CHICK_9031 and tr_G1MTF4_G1MTF4_MELGA_9103 are exactly identical! WARNING: Sequences sp_P0C192_LRC4B_MOUSE_10090 and sp_P0CC10_LRC4B_RAT_10116 are exactly identical! WARNING: Sequences sp_P0C192_LRC4B_MOUSE_10090 and tr_A0A1U7RAS4_A0A1U7RAS4_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3Z8E8_M3Z8E8_MUSPF_9669 and tr_A0A2Y9JQM1_A0A2Y9JQM1_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1R366_G1R366_NOMLE_61853 and tr_H2NCP7_H2NCP7_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1R366_G1R366_NOMLE_61853 and tr_K7D2Z3_K7D2Z3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1R366_G1R366_NOMLE_61853 and sp_Q6PJG9_LRFN4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R366_G1R366_NOMLE_61853 and tr_A0A096N284_A0A096N284_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1R366_G1R366_NOMLE_61853 and tr_A0A2K5L840_A0A2K5L840_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R366_G1R366_NOMLE_61853 and tr_A0A2K6D887_A0A2K6D887_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R366_G1R366_NOMLE_61853 and tr_A0A2R9A0Z5_A0A2R9A0Z5_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3I875_G3I875_CRIGR_10029 and tr_A0A1U7QDK3_A0A1U7QDK3_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3SJH4_G3SJH4_GORGO_9595 and sp_Q9BXN1_ASPN_HUMAN_9606 are exactly identical! WARNING: Sequences tr_C3ZS65_C3ZS65_BRAFL_7739 and tr_C3ZS67_C3ZS67_BRAFL_7739 are exactly identical! WARNING: Sequences tr_A0A2J8W5J4_A0A2J8W5J4_PONAB_9601 and sp_O43155_FLRT2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2J8W5J4_A0A2J8W5J4_PONAB_9601 and tr_A0A2R8MR44_A0A2R8MR44_CALJA_9483 are exactly identical! WARNING: Sequences tr_H2ND12_H2ND12_PONAB_9601 and tr_F6YJL6_F6YJL6_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2ND12_H2ND12_PONAB_9601 and tr_A0A096NDZ4_A0A096NDZ4_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2ND12_H2ND12_PONAB_9601 and tr_A0A0D9SCU5_A0A0D9SCU5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2ND12_H2ND12_PONAB_9601 and tr_A0A2K5KJA4_A0A2K5KJA4_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2ND12_H2ND12_PONAB_9601 and tr_A0A2K6AXI0_A0A2K6AXI0_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2ND12_H2ND12_PONAB_9601 and tr_A0A2K5XU37_A0A2K5XU37_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1NRU8_G1NRU8_MELGA_9103 and tr_A0A226MZ26_A0A226MZ26_CALSU_9009 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_D2GWR2_D2GWR2_AILME_9646 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_L5KR26_L5KR26_PTEAL_9402 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_A0A2U3UZJ5_A0A2U3UZJ5_TURTR_9739 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_A0A2U3VS62_A0A2U3VS62_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_A0A2U3YUV5_A0A2U3YUV5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_A0A2Y9K2T6_A0A2Y9K2T6_ENHLU_391180 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_A0A384DAI9_A0A384DAI9_URSMA_29073 are exactly identical! WARNING: Sequences tr_E2RH90_E2RH90_CANLF_9615 and tr_A0A383ZQ82_A0A383ZQ82_BALAS_310752 are exactly identical! WARNING: Sequences tr_F1PZW2_F1PZW2_CANLF_9615 and tr_H0XRH7_H0XRH7_OTOGA_30611 are exactly identical! WARNING: Sequences tr_F1PZW2_F1PZW2_CANLF_9615 and tr_A0A286ZY04_A0A286ZY04_PIG_9823 are exactly identical! WARNING: Sequences tr_F1PZW2_F1PZW2_CANLF_9615 and tr_E1BPK8_E1BPK8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_F1PZW2_F1PZW2_CANLF_9615 and tr_M3XBN4_M3XBN4_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1PZW2_F1PZW2_CANLF_9615 and tr_A0A2U3WLZ6_A0A2U3WLZ6_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PZW2_F1PZW2_CANLF_9615 and tr_A0A2U3YWN5_A0A2U3YWN5_LEPWE_9713 are exactly identical! WARNING: Sequences tr_F1PZW2_F1PZW2_CANLF_9615 and tr_A0A2Y9P997_A0A2Y9P997_DELLE_9749 are exactly identical! WARNING: Sequences tr_F1PZW2_F1PZW2_CANLF_9615 and tr_A0A2Y9EKM0_A0A2Y9EKM0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2I3STB8_A0A2I3STB8_PANTR_9598 and tr_A0A2R9B2G8_A0A2R9B2G8_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2Q8Q8_H2Q8Q8_PANTR_9598 and tr_A0A2R8Z827_A0A2R8Z827_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QGY2_H2QGY2_PANTR_9598 and sp_Q9NT99_LRC4B_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QGY2_H2QGY2_PANTR_9598 and tr_A0A2R8ZF23_A0A2R8ZF23_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QVB4_H2QVB4_PANTR_9598 and tr_A0A2R9A6Z7_A0A2R9A6Z7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R5B4_H2R5B4_PANTR_9598 and tr_A0A2R8ZJY6_A0A2R8ZJY6_PANPA_9597 are exactly identical! WARNING: Sequences tr_M4AYQ2_M4AYQ2_XIPMA_8083 and tr_A0A087YRR4_A0A087YRR4_POEFO_48698 are exactly identical! WARNING: Sequences sp_A6NDA9_LRIT2_HUMAN_9606 and tr_A0A2R9A5N3_A0A2R9A5N3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A1D5R520_A0A1D5R520_MACMU_9544 and tr_G7PEW6_G7PEW6_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6Q3P7_F6Q3P7_MACMU_9544 and tr_A0A0D9SCQ8_A0A0D9SCQ8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6WZ84_F6WZ84_MACMU_9544 and tr_G7PEW5_G7PEW5_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6WZ84_F6WZ84_MACMU_9544 and tr_A0A2K6BRT8_A0A2K6BRT8_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7BEN4_F7BEN4_MACMU_9544 and tr_G7PB44_G7PB44_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7BEN4_F7BEN4_MACMU_9544 and tr_A0A096MMQ8_A0A096MMQ8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7BEN4_F7BEN4_MACMU_9544 and tr_A0A0D9SDY6_A0A0D9SDY6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7BEN4_F7BEN4_MACMU_9544 and tr_A0A2K6AU17_A0A2K6AU17_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H0A3_F7H0A3_MACMU_9544 and tr_G3SWE9_G3SWE9_LOXAF_9785 are exactly identical! WARNING: Sequences tr_F7H0A3_F7H0A3_MACMU_9544 and tr_A0A0A0MVU1_A0A0A0MVU1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7H0A3_F7H0A3_MACMU_9544 and tr_A0A2K5KY06_A0A2K5KY06_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7H0A3_F7H0A3_MACMU_9544 and tr_A0A2K6BPY9_A0A2K6BPY9_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7H0A3_F7H0A3_MACMU_9544 and tr_A0A2K5XDC3_A0A2K5XDC3_MANLE_9568 are exactly identical! WARNING: Sequences tr_G3TMK9_G3TMK9_LOXAF_9785 and tr_A0A1U7TDX1_A0A1U7TDX1_TARSY_1868482 are exactly identical! WARNING: Sequences tr_H0YW34_H0YW34_TAEGU_59729 and tr_A0A218US11_A0A218US11_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0YW98_H0YW98_TAEGU_59729 and tr_A0A091ENY6_A0A091ENY6_CORBR_85066 are exactly identical! WARNING: Sequences tr_G7PI19_G7PI19_MACFA_9541 and tr_A0A096MVL6_A0A096MVL6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PI19_G7PI19_MACFA_9541 and tr_A0A2K6E268_A0A2K6E268_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PI19_G7PI19_MACFA_9541 and tr_A0A2K5Y3N5_A0A2K5Y3N5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0A0MP87_A0A0A0MP87_BOVIN_9913 and sp_F1MLX5_LGR4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096NB36_A0A096NB36_PAPAN_9555 and tr_A0A2K6CU43_A0A2K6CU43_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A096P4E2_A0A096P4E2_PAPAN_9555 and tr_A0A2K5LJS6_A0A2K5LJS6_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A151N6V5_A0A151N6V5_ALLMI_8496 and tr_A0A1U7R1D4_A0A1U7R1D4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NLG0_A0A151NLG0_ALLMI_8496 and tr_A0A1U7SFS0_A0A1U7SFS0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151P9H4_A0A151P9H4_ALLMI_8496 and tr_A0A1U7SM99_A0A1U7SM99_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A226MA54_A0A226MA54_CALSU_9009 and tr_A0A226MBI0_A0A226MBI0_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A2D0PXC6_A0A2D0PXC6_ICTPU_7998 and tr_A0A2D0PXD1_A0A2D0PXD1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PXC6_A0A2D0PXC6_ICTPU_7998 and tr_A0A2D0PYP6_A0A2D0PYP6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PXC6_A0A2D0PXC6_ICTPU_7998 and tr_A0A2D0Q0D9_A0A2D0Q0D9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PXC6_A0A2D0PXC6_ICTPU_7998 and tr_A0A2D0Q1B1_A0A2D0Q1B1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U3VH26_A0A2U3VH26_ODORO_9708 and tr_A0A384DJH6_A0A384DJH6_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2U3WIV2_A0A2U3WIV2_ODORO_9708 and tr_A0A2U3X7C0_A0A2U3X7C0_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 79 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/Q3SXY7/3_mltree/Q3SXY7.raxml.reduced.phy Alignment comprises 1 partitions and 301 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 301 / 301 Gaps: 14.07 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/3_mltree/Q3SXY7.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 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 301 / 24080 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -596361.598109] Initial branch length optimization [00:00:08 -497723.655851] Model parameter optimization (eps = 10.000000) [00:01:22 -497002.361990] AUTODETECT spr round 1 (radius: 5) [00:05:39 -340025.139403] AUTODETECT spr round 2 (radius: 10) [00:10:07 -249422.999771] AUTODETECT spr round 3 (radius: 15) [00:15:04 -192444.247511] AUTODETECT spr round 4 (radius: 20) [00:20:31 -171112.203573] AUTODETECT spr round 5 (radius: 25) [00:27:51 -163527.856958] SPR radius for FAST iterations: 25 (autodetect) [00:27:52 -163527.856958] Model parameter optimization (eps = 3.000000) [00:28:30 -163329.070811] FAST spr round 1 (radius: 25) [00:33:40 -142932.851152] FAST spr round 2 (radius: 25) [00:37:42 -141113.456976] FAST spr round 3 (radius: 25) [00:41:05 -140477.215669] FAST spr round 4 (radius: 25) [00:44:10 -140412.751109] FAST spr round 5 (radius: 25) [00:46:52 -140412.749094] Model parameter optimization (eps = 1.000000) [00:47:24 -140398.701700] SLOW spr round 1 (radius: 5) [00:51:07 -140360.657131] SLOW spr round 2 (radius: 5) [00:54:38 -140354.813577] SLOW spr round 3 (radius: 5) [00:57:57 -140354.812890] SLOW spr round 4 (radius: 10) [01:01:34 -140350.880961] SLOW spr round 5 (radius: 5) [01:05:48 -140349.402811] SLOW spr round 6 (radius: 5) [01:09:31 -140349.401954] SLOW spr round 7 (radius: 10) [01:13:25 -140349.401726] SLOW spr round 8 (radius: 15) [01:21:06 -140346.444650] SLOW spr round 9 (radius: 5) [01:25:30 -140343.813013] SLOW spr round 10 (radius: 5) [01:29:18 -140343.812232] SLOW spr round 11 (radius: 10) [01:33:19 -140343.812211] SLOW spr round 12 (radius: 15) [01:40:49 -140343.812210] SLOW spr round 13 (radius: 20) [01:53:06 -140343.305155] SLOW spr round 14 (radius: 5) [01:57:32 -140343.304941] SLOW spr round 15 (radius: 10) [02:02:29 -140343.304939] SLOW spr round 16 (radius: 15) [02:09:37 -140343.304939] SLOW spr round 17 (radius: 20) [02:21:51 -140343.304939] SLOW spr round 18 (radius: 25) [02:36:18 -140343.304938] Model parameter optimization (eps = 0.100000) [02:36:32] [worker #0] ML tree search #1, logLikelihood: -140343.054259 [02:36:33 -597751.682045] Initial branch length optimization [02:36:42 -500380.008684] Model parameter optimization (eps = 10.000000) [02:37:46 -499552.654644] AUTODETECT spr round 1 (radius: 5) [02:39:09] [worker #2] ML tree search #3, logLikelihood: -140332.099128 [02:42:02] [worker #4] ML tree search #5, logLikelihood: -140333.869498 [02:42:03 -335224.050061] AUTODETECT spr round 2 (radius: 10) [02:46:23 -241703.837739] AUTODETECT spr round 3 (radius: 15) [02:50:55 -192301.146227] AUTODETECT spr round 4 (radius: 20) [02:51:54] [worker #3] ML tree search #4, logLikelihood: -140347.570842 [02:56:03 -177117.913682] AUTODETECT spr round 5 (radius: 25) [03:02:43 -163522.923064] SPR radius for FAST iterations: 25 (autodetect) [03:02:43 -163522.923064] Model parameter optimization (eps = 3.000000) [03:03:24 -163313.494811] FAST spr round 1 (radius: 25) [03:08:38 -141822.775719] FAST spr round 2 (radius: 25) [03:12:49 -140557.577681] FAST spr round 3 (radius: 25) [03:16:11 -140433.813097] FAST spr round 4 (radius: 25) [03:19:07 -140425.281579] FAST spr round 5 (radius: 25) [03:21:48 -140425.280573] Model parameter optimization (eps = 1.000000) [03:22:10 -140403.265943] SLOW spr round 1 (radius: 5) [03:25:53 -140368.133447] SLOW spr round 2 (radius: 5) [03:29:26 -140356.309066] SLOW spr round 3 (radius: 5) [03:32:52 -140355.691112] SLOW spr round 4 (radius: 5) [03:36:12 -140355.690602] SLOW spr round 5 (radius: 10) [03:39:43 -140355.690552] SLOW spr round 6 (radius: 15) [03:47:40 -140355.690547] SLOW spr round 7 (radius: 20) [03:50:16] [worker #1] ML tree search #2, logLikelihood: -140351.261636 [04:00:02 -140355.690546] SLOW spr round 8 (radius: 25) [04:15:06 -140355.690546] Model parameter optimization (eps = 0.100000) [04:15:21] [worker #0] ML tree search #6, logLikelihood: -140354.976219 [04:15:22 -597556.735447] Initial branch length optimization [04:15:30 -498991.255208] Model parameter optimization (eps = 10.000000) [04:17:26 -497646.938305] AUTODETECT spr round 1 (radius: 5) [04:21:43 -330247.203242] AUTODETECT spr round 2 (radius: 10) [04:26:06 -236845.031059] AUTODETECT spr round 3 (radius: 15) [04:30:49 -182417.810115] AUTODETECT spr round 4 (radius: 20) [04:36:13 -162857.786855] AUTODETECT spr round 5 (radius: 25) [04:42:18 -158350.434642] SPR radius for FAST iterations: 25 (autodetect) [04:42:18 -158350.434642] Model parameter optimization (eps = 3.000000) [04:42:48 -158140.116441] FAST spr round 1 (radius: 25) [04:47:56 -141628.214901] FAST spr round 2 (radius: 25) [04:51:49 -140533.514945] FAST spr round 3 (radius: 25) [04:55:19 -140427.430557] FAST spr round 4 (radius: 25) [04:58:10 -140416.828324] FAST spr round 5 (radius: 25) [05:00:48 -140414.523125] FAST spr round 6 (radius: 25) [05:03:21 -140412.643997] FAST spr round 7 (radius: 25) [05:05:50 -140412.643992] Model parameter optimization (eps = 1.000000) [05:06:04 -140410.447138] SLOW spr round 1 (radius: 5) [05:09:48 -140366.459328] SLOW spr round 2 (radius: 5) [05:13:17 -140361.781728] SLOW spr round 3 (radius: 5) [05:16:33] [worker #3] ML tree search #9, logLikelihood: -140341.801340 [05:16:35 -140361.778211] SLOW spr round 4 (radius: 10) [05:20:14 -140351.934720] SLOW spr round 5 (radius: 5) [05:23:08] [worker #2] ML tree search #8, logLikelihood: -140330.353187 [05:24:34 -140344.920579] SLOW spr round 6 (radius: 5) [05:25:15] [worker #4] ML tree search #10, logLikelihood: -140349.864112 [05:28:23 -140344.112830] SLOW spr round 7 (radius: 5) [05:31:55 -140343.911694] SLOW spr round 8 (radius: 5) [05:35:19 -140343.911121] SLOW spr round 9 (radius: 10) [05:38:59 -140341.235580] SLOW spr round 10 (radius: 5) [05:43:11 -140341.233072] SLOW spr round 11 (radius: 10) [05:47:35 -140341.233021] SLOW spr round 12 (radius: 15) [05:55:02 -140336.047514] SLOW spr round 13 (radius: 5) [05:59:22 -140336.047459] SLOW spr round 14 (radius: 10) [06:04:05 -140336.047457] SLOW spr round 15 (radius: 15) [06:11:33 -140336.047457] SLOW spr round 16 (radius: 20) [06:24:10 -140335.141144] SLOW spr round 17 (radius: 5) [06:28:41 -140335.140967] SLOW spr round 18 (radius: 10) [06:33:41 -140335.140965] SLOW spr round 19 (radius: 15) [06:41:01 -140335.140965] SLOW spr round 20 (radius: 20) [06:53:28 -140335.079953] SLOW spr round 21 (radius: 25) [07:07:54 -140335.079953] Model parameter optimization (eps = 0.100000) [07:08:05] [worker #0] ML tree search #11, logLikelihood: -140334.960662 [07:08:05 -597387.926610] Initial branch length optimization [07:08:15 -498333.815767] Model parameter optimization (eps = 10.000000) [07:09:43 -497565.648853] AUTODETECT spr round 1 (radius: 5) [07:11:13] [worker #1] ML tree search #7, logLikelihood: -140331.751373 [07:13:54 -332826.912728] AUTODETECT spr round 2 (radius: 10) [07:18:16 -247444.471972] AUTODETECT spr round 3 (radius: 15) [07:23:17 -195979.566555] AUTODETECT spr round 4 (radius: 20) [07:28:58 -168094.222578] AUTODETECT spr round 5 (radius: 25) [07:34:46 -162875.393177] SPR radius for FAST iterations: 25 (autodetect) [07:34:46 -162875.393177] Model parameter optimization (eps = 3.000000) [07:35:19 -162665.251253] FAST spr round 1 (radius: 25) [07:40:44 -141532.933229] FAST spr round 2 (radius: 25) [07:44:49 -140574.414405] FAST spr round 3 (radius: 25) [07:47:17] [worker #3] ML tree search #14, logLikelihood: -140332.925513 [07:48:11 -140416.761322] FAST spr round 4 (radius: 25) [07:51:07 -140407.303956] FAST spr round 5 (radius: 25) [07:53:50 -140403.752270] FAST spr round 6 (radius: 25) [07:56:27 -140403.282546] FAST spr round 7 (radius: 25) [07:58:58 -140403.282261] Model parameter optimization (eps = 1.000000) [07:59:17 -140397.570581] SLOW spr round 1 (radius: 5) [08:02:50 -140371.267814] SLOW spr round 2 (radius: 5) [08:06:14 -140371.091729] SLOW spr round 3 (radius: 5) [08:09:30 -140371.091207] SLOW spr round 4 (radius: 10) [08:13:02 -140368.649643] SLOW spr round 5 (radius: 5) [08:13:54] [worker #4] ML tree search #15, logLikelihood: -140337.365100 [08:17:20 -140365.574422] SLOW spr round 6 (radius: 5) [08:21:20 -140354.878694] SLOW spr round 7 (radius: 5) [08:24:53 -140353.748824] SLOW spr round 8 (radius: 5) [08:28:17 -140353.747433] SLOW spr round 9 (radius: 10) [08:31:53 -140350.692924] SLOW spr round 10 (radius: 5) [08:36:06 -140349.997881] SLOW spr round 11 (radius: 5) [08:37:29] [worker #2] ML tree search #13, logLikelihood: -140363.938451 [08:39:50 -140349.997822] SLOW spr round 12 (radius: 10) [08:43:42 -140349.997821] SLOW spr round 13 (radius: 15) [08:51:14 -140344.733151] SLOW spr round 14 (radius: 5) [08:55:33 -140344.733007] SLOW spr round 15 (radius: 10) [09:00:07 -140344.733005] SLOW spr round 16 (radius: 15) [09:07:03 -140344.733005] SLOW spr round 17 (radius: 20) [09:18:50 -140344.733005] SLOW spr round 18 (radius: 25) [09:32:57 -140344.733005] Model parameter optimization (eps = 0.100000) [09:33:10] [worker #0] ML tree search #16, logLikelihood: -140344.283189 [09:59:56] [worker #1] ML tree search #12, logLikelihood: -140358.254977 [10:12:55] [worker #2] ML tree search #18, logLikelihood: -140360.195663 [10:15:23] [worker #3] ML tree search #19, logLikelihood: -140343.945662 [10:50:41] [worker #4] ML tree search #20, logLikelihood: -140319.477126 [11:55:48] [worker #1] ML tree search #17, logLikelihood: -140350.215903 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.156067,0.429535) (0.122556,0.467343) (0.441621,1.080979) (0.279755,1.423760) 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: -140319.477126 AIC score: 284648.954252 / AICc score: 8328708.954252 / BIC score: 292081.710333 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=301). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 132 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/3_mltree/Q3SXY7.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/3_mltree/Q3SXY7.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/3_mltree/Q3SXY7.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/3_mltree/Q3SXY7.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q3SXY7/3_mltree/Q3SXY7.raxml.log Analysis started: 01-Jul-2021 10:11:24 / finished: 01-Jul-2021 22:07:13 Elapsed time: 42948.615 seconds Consumed energy: 3412.330 Wh (= 17 km in an electric car, or 85 km with an e-scooter!)