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 03-Jun-2021 00:21:53 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q2M2I5/2_msa/Q2M2I5_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q2M2I5/3_mltree/Q2M2I5 --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/020621_run/phylogeny-snakemake/results/Q2M2I5/2_msa/Q2M2I5_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 307 sites WARNING: Sequences tr_A0A1D5PA18_A0A1D5PA18_CHICK_9031 and tr_A0A226N7Y4_A0A226N7Y4_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PZ89_A0A1D5PZ89_CHICK_9031 and sp_Q6PVZ1_K1C14_CHICK_9031 are exactly identical! WARNING: Sequences sp_Q8VCW2_K1C25_MOUSE_10090 and sp_Q6IFX0_K1C25_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YT82_M3YT82_MUSPF_9669 and tr_A0A2Y9JVH8_A0A2Y9JVH8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1QNX1_G1QNX1_NOMLE_61853 and tr_F7B5G7_F7B5G7_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1QNX1_G1QNX1_NOMLE_61853 and tr_G7PUP9_G7PUP9_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1QNX1_G1QNX1_NOMLE_61853 and tr_A0A2I3LE14_A0A2I3LE14_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1QNX1_G1QNX1_NOMLE_61853 and tr_A0A2K6CKL7_A0A2K6CKL7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1QNX1_G1QNX1_NOMLE_61853 and tr_A0A2K5XS94_A0A2K5XS94_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RIS7_G1RIS7_NOMLE_61853 and tr_H2NU31_H2NU31_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1RIS7_G1RIS7_NOMLE_61853 and sp_P08727_K1C19_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2Z0J1_A0A2I2Z0J1_GORGO_9595 and sp_P19012_K1C15_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QDX0_G3QDX0_GORGO_9595 and tr_H2QCX3_H2QCX3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QDX0_G3QDX0_GORGO_9595 and sp_P13645_K1C10_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3QDX0_G3QDX0_GORGO_9595 and tr_A0A2R9BVY1_A0A2R9BVY1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3RBU8_G3RBU8_GORGO_9595 and sp_A5A6N2_K1C25_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RBU8_G3RBU8_GORGO_9595 and tr_H2QCW9_H2QCW9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RBU8_G3RBU8_GORGO_9595 and sp_Q7Z3Z0_K1C25_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RBU8_G3RBU8_GORGO_9595 and tr_A0A2R9AJU2_A0A2R9AJU2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NU66_H2NU66_PONAB_9601 and tr_H2QCX1_H2QCX1_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NU66_H2NU66_PONAB_9601 and tr_A0A2R9BZA1_A0A2R9BZA1_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NU68_H2NU68_PONAB_9601 and tr_A0A0D9S2Y9_A0A0D9S2Y9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NU68_H2NU68_PONAB_9601 and tr_A0A2K6ADP2_A0A2K6ADP2_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_H2QCZ7_H2QCZ7_PANTR_9598 are exactly identical! WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and sp_P02533_K1C14_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_F7H312_F7H312_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A096P5N3_A0A096P5N3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A0D9S2F0_A0A0D9S2F0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A2K5NH02_A0A2K5NH02_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A2K6E2S6_A0A2K6E2S6_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A2K5ZWJ8_A0A2K5ZWJ8_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2NVQ7_H2NVQ7_PONAB_9601 and tr_A0A2R9CHA8_A0A2R9CHA8_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1MVS0_G1MVS0_MELGA_9103 and tr_A0A091UUY7_A0A091UUY7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1MVS0_G1MVS0_MELGA_9103 and tr_A0A091GDA1_A0A091GDA1_9AVES_55661 are exactly identical! WARNING: Sequences tr_G1MVS0_G1MVS0_MELGA_9103 and tr_A0A0A0ART4_A0A0A0ART4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_G1MVS0_G1MVS0_MELGA_9103 and tr_A0A2I0LLZ1_A0A2I0LLZ1_COLLI_8932 are exactly identical! WARNING: Sequences tr_G1MVS0_G1MVS0_MELGA_9103 and tr_A0A1V4JQQ9_A0A1V4JQQ9_PATFA_372326 are exactly identical! WARNING: Sequences tr_F1PYU9_F1PYU9_CANLF_9615 and sp_Q6EIZ0_K1C10_CANLF_9615 are exactly identical! WARNING: Sequences tr_H2QCC4_H2QCC4_PANTR_9598 and tr_A0A2R9BI07_A0A2R9BI07_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCX2_H2QCX2_PANTR_9598 and tr_A0A2R8ZZ64_A0A2R8ZZ64_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCX4_H2QCX4_PANTR_9598 and sp_Q99456_K1C12_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QCX4_H2QCX4_PANTR_9598 and tr_A0A2R9B0H7_A0A2R9B0H7_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCX5_H2QCX5_PANTR_9598 and tr_A0A2R9AN97_A0A2R9AN97_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCZ0_H2QCZ0_PANTR_9598 and tr_A0A2R9BRN9_A0A2R9BRN9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCZ2_H2QCZ2_PANTR_9598 and tr_A0A2R9ATZ6_A0A2R9ATZ6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCZ4_H2QCZ4_PANTR_9598 and tr_A0A2R8ZHV6_A0A2R8ZHV6_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QCZ8_H2QCZ8_PANTR_9598 and sp_Q04695_K1C17_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QCZ8_H2QCZ8_PANTR_9598 and tr_A0A2R9BML2_A0A2R9BML2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R114_H2R114_PANTR_9598 and tr_A0A2R9ALU5_A0A2R9ALU5_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6SS14_F6SS14_HORSE_9796 and tr_F6WDW3_F6WDW3_HORSE_9796 are exactly identical! WARNING: Sequences sp_B0LKP1_KRT35_SHEEP_9940 and tr_W5Q5N5_W5Q5N5_SHEEP_9940 are exactly identical! WARNING: Sequences tr_W5Q0H4_W5Q0H4_SHEEP_9940 and sp_Q0P5J4_K1C25_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A1D5Q3N1_A0A1D5Q3N1_MACMU_9544 and tr_G7PUS3_G7PUS3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6YKA7_F6YKA7_MACMU_9544 and tr_A0A2K6C8U3_A0A2K6C8U3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7A635_F7A635_MACMU_9544 and tr_A0A2I3MA29_A0A2I3MA29_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7A635_F7A635_MACMU_9544 and tr_A0A0D9S2G2_A0A0D9S2G2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7A670_F7A670_MACMU_9544 and tr_G7PUS4_G7PUS4_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7ACB4_F7ACB4_MACMU_9544 and tr_G7PUS1_G7PUS1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7B5A6_F7B5A6_MACMU_9544 and tr_G7PUQ1_G7PUQ1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_G7PUQ0_G7PUQ0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_A0A096P5J0_A0A096P5J0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_A0A0D9S2W8_A0A0D9S2W8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7B5C2_F7B5C2_MACMU_9544 and tr_A0A2K6AP56_A0A2K6AP56_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B5I4_F7B5I4_MACMU_9544 and tr_A0A2K6EC66_A0A2K6EC66_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B5M7_F7B5M7_MACMU_9544 and tr_A0A2K5KWM8_A0A2K5KWM8_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7B5M7_F7B5M7_MACMU_9544 and tr_A0A2K6BB16_A0A2K6BB16_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7B5M7_F7B5M7_MACMU_9544 and tr_A0A2K6AF67_A0A2K6AF67_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7BBR0_F7BBR0_MACMU_9544 and tr_A0A2K6CHN1_A0A2K6CHN1_MACNE_9545 are exactly identical! WARNING: Sequences tr_H0YVX6_H0YVX6_TAEGU_59729 and tr_A0A218UN40_A0A218UN40_9PASE_299123 are exactly identical! WARNING: Sequences tr_H1A2Y8_H1A2Y8_TAEGU_59729 and tr_U3JC30_U3JC30_FICAL_59894 are exactly identical! WARNING: Sequences tr_H1A2Y8_H1A2Y8_TAEGU_59729 and tr_A0A091ESI5_A0A091ESI5_CORBR_85066 are exactly identical! WARNING: Sequences tr_H1A2Y8_H1A2Y8_TAEGU_59729 and tr_A0A093PX43_A0A093PX43_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A1B8Y9F2_A0A1B8Y9F2_XENTR_8364 and tr_F6RG86_F6RG86_XENTR_8364 are exactly identical! WARNING: Sequences tr_B0BMG5_B0BMG5_XENTR_8364 and tr_F6S8K4_F6S8K4_XENTR_8364 are exactly identical! WARNING: Sequences tr_B0BMI8_B0BMI8_XENTR_8364 and tr_F6RGW5_F6RGW5_XENTR_8364 are exactly identical! WARNING: Sequences tr_G7PUP4_G7PUP4_MACFA_9541 and tr_A0A2K6DXA7_A0A2K6DXA7_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A140T867_A0A140T867_BOVIN_9913 and sp_A1L595_K1C17_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A096P5M5_A0A096P5M5_PAPAN_9555 and tr_A0A0D9S2H7_A0A0D9S2H7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3LFF0_A0A2I3LFF0_PAPAN_9555 and tr_A0A2K5YQY4_A0A2K5YQY4_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2I3MX15_A0A2I3MX15_PAPAN_9555 and tr_A0A2K5KRV7_A0A2K5KRV7_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A2I3MX15_A0A2I3MX15_PAPAN_9555 and tr_A0A2K6A821_A0A2K6A821_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0D9S2G3_A0A0D9S2G3_CHLSB_60711 and tr_A0A2K6A0P8_A0A2K6A0P8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151PC64_A0A151PC64_ALLMI_8496 and tr_A0A1U7RR64_A0A1U7RR64_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151PC95_A0A151PC95_ALLMI_8496 and tr_A0A1U7RME3_A0A1U7RME3_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091UVR9_A0A091UVR9_NIPNI_128390 and tr_A0A0A0ASS1_A0A0A0ASS1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091VY56_A0A091VY56_NIPNI_128390 and tr_A0A0A0APW4_A0A0A0APW4_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A226N7Z7_A0A226N7Z7_CALSU_9009 and tr_A0A226NRM3_A0A226NRM3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226N891_A0A226N891_CALSU_9009 and tr_A0A226NT37_A0A226NT37_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226N8V0_A0A226N8V0_CALSU_9009 and tr_A0A226NP08_A0A226NP08_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0PWP1_A0A2D0PWP1_ICTPU_7998 and tr_A0A2D0PXJ4_A0A2D0PXJ4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KJ84_A0A2K5KJ84_CERAT_9531 and tr_A0A2K6A2M2_A0A2K6A2M2_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K5LTL8_A0A2K5LTL8_CERAT_9531 and tr_A0A2K6E9C0_A0A2K6E9C0_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K5P1B1_A0A2K5P1B1_CERAT_9531 and tr_A0A2K5ZJV4_A0A2K5ZJV4_MANLE_9568 are exactly identical! WARNING: Duplicate sequences found: 93 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q2M2I5/3_mltree/Q2M2I5.raxml.reduced.phy Alignment comprises 1 partitions and 307 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 307 / 307 Gaps: 0.41 % Invariant sites: 0.65 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q2M2I5/3_mltree/Q2M2I5.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 / 307 / 24560 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -353306.571445] Initial branch length optimization [00:00:08 -309872.012359] Model parameter optimization (eps = 10.000000) [00:01:03 -308131.673329] AUTODETECT spr round 1 (radius: 5) [00:04:44 -198026.845374] AUTODETECT spr round 2 (radius: 10) [00:08:26 -137240.370369] AUTODETECT spr round 3 (radius: 15) [00:12:41 -116343.294047] AUTODETECT spr round 4 (radius: 20) [00:17:29 -109759.597606] AUTODETECT spr round 5 (radius: 25) [00:24:03 -102815.055286] SPR radius for FAST iterations: 25 (autodetect) [00:24:03 -102815.055286] Model parameter optimization (eps = 3.000000) [00:24:31 -102662.378641] FAST spr round 1 (radius: 25) [00:28:31 -87116.763327] FAST spr round 2 (radius: 25) [00:31:26 -86236.554179] FAST spr round 3 (radius: 25) [00:33:57 -86183.121648] FAST spr round 4 (radius: 25) [00:36:11 -86177.954927] FAST spr round 5 (radius: 25) [00:38:19 -86177.954927] Model parameter optimization (eps = 1.000000) [00:38:43 -86159.077248] SLOW spr round 1 (radius: 5) [00:41:52 -86120.661054] SLOW spr round 2 (radius: 5) [00:45:00 -86118.169587] SLOW spr round 3 (radius: 5) [00:47:52 -86115.771402] SLOW spr round 4 (radius: 5) [00:50:39 -86115.763528] SLOW spr round 5 (radius: 10) [00:53:19 -86114.680892] SLOW spr round 6 (radius: 5) [00:57:01 -86106.679059] SLOW spr round 7 (radius: 5) [01:00:10 -86106.678888] SLOW spr round 8 (radius: 10) [01:02:54 -86106.678888] SLOW spr round 9 (radius: 15) [01:07:00 -86106.678888] SLOW spr round 10 (radius: 20) [01:13:20 -86106.678888] SLOW spr round 11 (radius: 25) [01:17:15] [worker #3] ML tree search #4, logLikelihood: -86137.555974 [01:20:38] [worker #2] ML tree search #3, logLikelihood: -86134.270019 [01:22:03] [worker #4] ML tree search #5, logLikelihood: -86124.649728 [01:22:11 -86106.678888] Model parameter optimization (eps = 0.100000) [01:22:19] [worker #0] ML tree search #1, logLikelihood: -86106.606191 [01:22:19 -354146.237551] Initial branch length optimization [01:22:26 -311253.922099] Model parameter optimization (eps = 10.000000) [01:23:18 -309454.084431] AUTODETECT spr round 1 (radius: 5) [01:26:36 -207004.504617] AUTODETECT spr round 2 (radius: 10) [01:29:59 -142853.940439] AUTODETECT spr round 3 (radius: 15) [01:33:47 -118315.338858] AUTODETECT spr round 4 (radius: 20) [01:38:52 -106544.444706] AUTODETECT spr round 5 (radius: 25) [01:44:47 -104075.092656] SPR radius for FAST iterations: 25 (autodetect) [01:44:47 -104075.092656] Model parameter optimization (eps = 3.000000) [01:45:12 -103926.722916] FAST spr round 1 (radius: 25) [01:48:44 -90248.978278] FAST spr round 2 (radius: 25) [01:51:26 -87530.484779] FAST spr round 3 (radius: 25) [01:53:54 -86792.581202] FAST spr round 4 (radius: 25) [01:56:12 -86699.547674] FAST spr round 5 (radius: 25) [01:58:14 -86699.397979] FAST spr round 6 (radius: 25) [02:00:13 -86699.396563] Model parameter optimization (eps = 1.000000) [02:00:33 -86667.023200] SLOW spr round 1 (radius: 5) [02:03:35 -86638.158433] SLOW spr round 2 (radius: 5) [02:06:32 -86632.299122] SLOW spr round 3 (radius: 5) [02:09:21 -86632.299039] SLOW spr round 4 (radius: 10) [02:11:30] [worker #1] ML tree search #2, logLikelihood: -86148.095486 [02:12:02 -86627.030500] SLOW spr round 5 (radius: 5) [02:15:38 -86627.030450] SLOW spr round 6 (radius: 10) [02:18:38 -86627.030445] SLOW spr round 7 (radius: 15) [02:22:48 -86627.030442] SLOW spr round 8 (radius: 20) [02:30:06 -86561.228253] SLOW spr round 9 (radius: 5) [02:34:04 -86260.970060] SLOW spr round 10 (radius: 5) [02:36:13] [worker #3] ML tree search #9, logLikelihood: -86138.390095 [02:37:28 -86130.743290] SLOW spr round 11 (radius: 5) [02:40:28 -86130.743229] SLOW spr round 12 (radius: 10) [02:43:09 -86130.743226] SLOW spr round 13 (radius: 15) [02:47:33 -86130.743224] SLOW spr round 14 (radius: 20) [02:52:04] [worker #2] ML tree search #8, logLikelihood: -86141.063153 [02:54:30 -86130.743224] SLOW spr round 15 (radius: 25) [03:03:56 -86130.743223] Model parameter optimization (eps = 0.100000) [03:04:09] [worker #0] ML tree search #6, logLikelihood: -86130.420987 [03:04:09 -353507.194269] Initial branch length optimization [03:04:15 -310110.247204] Model parameter optimization (eps = 10.000000) [03:05:07 -308359.579142] AUTODETECT spr round 1 (radius: 5) [03:08:22 -198298.931130] AUTODETECT spr round 2 (radius: 10) [03:10:21] [worker #4] ML tree search #10, logLikelihood: -86113.697154 [03:11:45 -136572.085964] AUTODETECT spr round 3 (radius: 15) [03:15:27 -113447.268659] AUTODETECT spr round 4 (radius: 20) [03:19:56 -106215.819259] AUTODETECT spr round 5 (radius: 25) [03:25:53 -101699.148707] SPR radius for FAST iterations: 25 (autodetect) [03:25:53 -101699.148707] Model parameter optimization (eps = 3.000000) [03:26:15 -101617.588259] FAST spr round 1 (radius: 25) [03:29:44 -86956.886572] FAST spr round 2 (radius: 25) [03:32:32 -86293.839413] FAST spr round 3 (radius: 25) [03:34:49 -86222.396585] FAST spr round 4 (radius: 25) [03:36:56 -86211.909755] FAST spr round 5 (radius: 25) [03:38:56 -86211.909715] Model parameter optimization (eps = 1.000000) [03:39:16 -86186.835147] SLOW spr round 1 (radius: 5) [03:41:32] [worker #1] ML tree search #7, logLikelihood: -86118.587632 [03:42:19 -86149.934484] SLOW spr round 2 (radius: 5) [03:45:11 -86145.123318] SLOW spr round 3 (radius: 5) [03:47:53 -86145.123202] SLOW spr round 4 (radius: 10) [03:50:37 -86141.959440] SLOW spr round 5 (radius: 5) [03:54:16 -86141.920141] SLOW spr round 6 (radius: 10) [03:57:23 -86138.125453] SLOW spr round 7 (radius: 5) [04:00:52 -86138.125274] SLOW spr round 8 (radius: 10) [04:03:51 -86138.125274] SLOW spr round 9 (radius: 15) [04:04:12] [worker #3] ML tree search #14, logLikelihood: -86106.581744 [04:08:07 -86133.261605] SLOW spr round 10 (radius: 5) [04:11:55 -86127.737826] SLOW spr round 11 (radius: 5) [04:15:14 -86127.737824] SLOW spr round 12 (radius: 10) [04:15:56] [worker #2] ML tree search #13, logLikelihood: -86159.107973 [04:18:04 -86127.737824] SLOW spr round 13 (radius: 15) [04:22:26 -86127.737824] SLOW spr round 14 (radius: 20) [04:29:53 -86127.737824] SLOW spr round 15 (radius: 25) [04:39:41 -86127.737824] Model parameter optimization (eps = 0.100000) [04:39:51] [worker #0] ML tree search #11, logLikelihood: -86127.630893 [04:39:51 -355846.077195] Initial branch length optimization [04:39:57 -311687.083868] Model parameter optimization (eps = 10.000000) [04:40:44 -309907.117073] AUTODETECT spr round 1 (radius: 5) [04:42:13] [worker #4] ML tree search #15, logLikelihood: -86112.412637 [04:44:05 -198844.390244] AUTODETECT spr round 2 (radius: 10) [04:47:28 -132358.594149] AUTODETECT spr round 3 (radius: 15) [04:51:25 -112479.006060] AUTODETECT spr round 4 (radius: 20) [04:56:10 -104671.936253] AUTODETECT spr round 5 (radius: 25) [05:01:42 -103148.365078] SPR radius for FAST iterations: 25 (autodetect) [05:01:42 -103148.365078] Model parameter optimization (eps = 3.000000) [05:02:08 -103062.307763] FAST spr round 1 (radius: 25) [05:05:42 -86847.705733] FAST spr round 2 (radius: 25) [05:08:22 -86358.676973] FAST spr round 3 (radius: 25) [05:10:42 -86294.056207] FAST spr round 4 (radius: 25) [05:12:54 -86277.578734] FAST spr round 5 (radius: 25) [05:14:56 -86276.095325] FAST spr round 6 (radius: 25) [05:16:55 -86276.095325] Model parameter optimization (eps = 1.000000) [05:17:14 -86256.783612] SLOW spr round 1 (radius: 5) [05:20:17 -86208.308942] SLOW spr round 2 (radius: 5) [05:23:16 -86183.072076] SLOW spr round 3 (radius: 5) [05:25:34] [worker #3] ML tree search #19, logLikelihood: -86100.497476 [05:26:09 -86182.588098] SLOW spr round 4 (radius: 5) [05:28:54 -86182.588070] SLOW spr round 5 (radius: 10) [05:31:34 -86178.282164] SLOW spr round 6 (radius: 5) [05:35:10 -86177.355099] SLOW spr round 7 (radius: 5) [05:38:20 -86177.355081] SLOW spr round 8 (radius: 10) [05:41:04 -86177.355078] SLOW spr round 9 (radius: 15) [05:45:09 -86177.355075] SLOW spr round 10 (radius: 20) [05:51:41 -86173.528795] SLOW spr round 11 (radius: 5) [05:53:03] [worker #1] ML tree search #12, logLikelihood: -86123.581803 [05:53:19] [worker #2] ML tree search #18, logLikelihood: -86119.814588 [05:55:17 -86170.749458] SLOW spr round 12 (radius: 5) [05:58:24 -86170.749427] SLOW spr round 13 (radius: 10) [06:01:03 -86170.749425] SLOW spr round 14 (radius: 15) [06:05:02 -86170.749423] SLOW spr round 15 (radius: 20) [06:11:35 -86170.749421] SLOW spr round 16 (radius: 25) [06:20:10 -86170.749419] Model parameter optimization (eps = 0.100000) [06:20:16] [worker #0] ML tree search #16, logLikelihood: -86170.692479 [06:33:05] [worker #4] ML tree search #20, logLikelihood: -86131.125153 [07:14:08] [worker #1] ML tree search #17, logLikelihood: -86140.101198 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.302370,0.434245) (0.187819,1.198777) (0.376679,0.986285) (0.133132,2.043316) 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: -86100.497476 AIC score: 176210.994951 / AICc score: 8220270.994951 / BIC score: 183683.324685 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=307). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 152 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q2M2I5/3_mltree/Q2M2I5.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q2M2I5/3_mltree/Q2M2I5.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q2M2I5/3_mltree/Q2M2I5.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q2M2I5/3_mltree/Q2M2I5.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/Q2M2I5/3_mltree/Q2M2I5.raxml.log Analysis started: 03-Jun-2021 00:21:53 / finished: 03-Jun-2021 07:36:02 Elapsed time: 26048.830 seconds Consumed energy: 1920.194 Wh (= 10 km in an electric car, or 48 km with an e-scooter!)