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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM RAxML-NG was called at 26-Jul-2021 00:10:20 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8K979/2_msa/A8K979_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8K979/3_mltree/A8K979 --seed 2 --threads 4 --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 (4 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8K979/2_msa/A8K979_trimmed_msa.fasta [00:00:00] Loaded alignment with 734 taxa and 178 sites WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_H0ZB84_H0ZB84_TAEGU_59729 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_U3JRU2_U3JRU2_FICAL_59894 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A0Q3MQT1_A0A0Q3MQT1_AMAAE_12930 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A091FTK5_A0A091FTK5_CORBR_85066 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A093SF29_A0A093SF29_9PASS_328815 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A091VBY3_A0A091VBY3_NIPNI_128390 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A087RHI9_A0A087RHI9_APTFO_9233 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A099Z8C9_A0A099Z8C9_TINGU_94827 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A091FZQ7_A0A091FZQ7_9AVES_55661 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A0A0AGJ1_A0A0A0AGJ1_CHAVO_50402 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A2I0LP84_A0A2I0LP84_COLLI_8932 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A093IP55_A0A093IP55_DRYPU_118200 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A091HTW0_A0A091HTW0_CALAN_9244 are exactly identical! WARNING: Sequences tr_F1NBT2_F1NBT2_CHICK_9031 and tr_A0A1V4JXA2_A0A1V4JXA2_PATFA_372326 are exactly identical! WARNING: Sequences sp_Q8C460_ERI3_MOUSE_10090 and tr_M0R8C5_M0R8C5_RAT_10116 are exactly identical! WARNING: Sequences tr_M3YJ14_M3YJ14_MUSPF_9669 and tr_A0A2U3WUP2_A0A2U3WUP2_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3YJ14_M3YJ14_MUSPF_9669 and tr_A0A2Y9J119_A0A2Y9J119_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YQ28_M3YQ28_MUSPF_9669 and tr_W5NRQ9_W5NRQ9_SHEEP_9940 are exactly identical! WARNING: Sequences tr_C5XHC7_C5XHC7_SORBI_4558 and tr_K3XI71_K3XI71_SETIT_4555 are exactly identical! WARNING: Sequences tr_C5XHC7_C5XHC7_SORBI_4558 and tr_A0A2T7DNU1_A0A2T7DNU1_9POAL_1504633 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A2I2ZSW9_A0A2I2ZSW9_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_G1SVG5_G1SVG5_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_H2PYW0_H2PYW0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_F7C592_F7C592_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_H0VPY5_H0VPY5_CAVPO_10141 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and sp_O43414_ERI3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_G5ARV9_G5ARV9_HETGA_10181 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_G3SRP7_G3SRP7_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_F6RWU0_F6RWU0_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_G7NUY4_G7NUY4_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and sp_A6QLH5_ERI3_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_L5KQV1_L5KQV1_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A096N7D8_A0A096N7D8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A091CSK0_A0A091CSK0_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A0D9S7H7_A0A0D9S7H7_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A1S3A8N1_A0A1S3A8N1_ERIEU_9365 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A1S3F711_A0A1S3F711_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A2K5MDU5_A0A2K5MDU5_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A2K6CJW2_A0A2K6CJW2_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A2K5XIB5_A0A2K5XIB5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A2R9CPC6_A0A2R9CPC6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A2Y9DCL5_A0A2Y9DCL5_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A2Y9NPI8_A0A2Y9NPI8_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A2Y9F9Z8_A0A2Y9F9Z8_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1RUX5_G1RUX5_NOMLE_61853 and tr_A0A383YPI5_A0A383YPI5_BALAS_310752 are exactly identical! WARNING: Sequences tr_G3GYS4_G3GYS4_CRIGR_10029 and tr_A0A1U7R1V3_A0A1U7R1V3_MESAU_10036 are exactly identical! WARNING: Sequences tr_G3QPF3_G3QPF3_GORGO_9595 and tr_A0A2J8Q5V4_A0A2J8Q5V4_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QPF3_G3QPF3_GORGO_9595 and tr_F7APV0_F7APV0_MACMU_9544 are exactly identical! WARNING: Sequences tr_G3QPF3_G3QPF3_GORGO_9595 and tr_A0A2K6E578_A0A2K6E578_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3RBA0_G3RBA0_GORGO_9595 and tr_A0A2I3TXS5_A0A2I3TXS5_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3RBA0_G3RBA0_GORGO_9595 and sp_Q8IV48_ERI1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3RBA0_G3RBA0_GORGO_9595 and tr_A0A2R9AV92_A0A2R9AV92_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2PPL0_H2PPL0_PONAB_9601 and tr_H9EX66_H9EX66_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PPL0_H2PPL0_PONAB_9601 and tr_G7PCK8_G7PCK8_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2PPL0_H2PPL0_PONAB_9601 and tr_A0A096MZD1_A0A096MZD1_PAPAN_9555 are exactly identical! WARNING: Sequences tr_H2PPL0_H2PPL0_PONAB_9601 and tr_A0A0D9RWC8_A0A0D9RWC8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_H2PPL0_H2PPL0_PONAB_9601 and tr_A0A2K5MVY5_A0A2K5MVY5_CERAT_9531 are exactly identical! WARNING: Sequences tr_H2PPL0_H2PPL0_PONAB_9601 and tr_A0A2K6AMY8_A0A2K6AMY8_MACNE_9545 are exactly identical! WARNING: Sequences tr_H2PPL0_H2PPL0_PONAB_9601 and tr_A0A2K5ZUD3_A0A2K5ZUD3_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0R3NPH6_A0A0R3NPH6_DROPS_46245 and tr_B4GHB7_B4GHB7_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2RAN5_E2RAN5_CANLF_9615 and tr_G1M619_G1M619_AILME_9646 are exactly identical! WARNING: Sequences tr_E2RAN5_E2RAN5_CANLF_9615 and tr_M3W3T3_M3W3T3_FELCA_9685 are exactly identical! WARNING: Sequences tr_E2RAN5_E2RAN5_CANLF_9615 and tr_A0A2U3XC31_A0A2U3XC31_LEPWE_9713 are exactly identical! WARNING: Sequences tr_E2RAN5_E2RAN5_CANLF_9615 and tr_A0A2Y9IUW9_A0A2Y9IUW9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_E2RAN5_E2RAN5_CANLF_9615 and tr_A0A384CRS3_A0A384CRS3_URSMA_29073 are exactly identical! WARNING: Sequences tr_Q4D8C8_Q4D8C8_TRYCC_353153 and tr_Q4DHR3_Q4DHR3_TRYCC_353153 are exactly identical! WARNING: Sequences tr_B0WX94_B0WX94_CULQU_7176 and tr_B0WZT0_B0WZT0_CULQU_7176 are exactly identical! WARNING: Sequences tr_W5PJX8_W5PJX8_SHEEP_9940 and tr_Q32LA2_Q32LA2_BOVIN_9913 are exactly identical! WARNING: Sequences tr_K4B045_K4B045_SOLLC_4081 and tr_M0ZUM5_M0ZUM5_SOLTU_4113 are exactly identical! WARNING: Sequences tr_A0A368PYP8_A0A368PYP8_SETIT_4555 and tr_K3ZUY1_K3ZUY1_SETIT_4555 are exactly identical! WARNING: Sequences tr_A0A368PZM4_A0A368PZM4_SETIT_4555 and tr_K4A284_K4A284_SETIT_4555 are exactly identical! WARNING: Sequences sp_A8K979_ERI2_HUMAN_9606 and tr_A0A2R8ZZ97_A0A2R8ZZ97_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A0E0FK60_A0A0E0FK60_ORYNI_4536 and tr_B8ACK2_B8ACK2_ORYSI_39946 are exactly identical! WARNING: Sequences tr_A0A0E0FK60_A0A0E0FK60_ORYNI_4536 and tr_A0A0D3EMG3_A0A0D3EMG3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A0E0FK60_A0A0E0FK60_ORYNI_4536 and tr_A0A0E0JH50_A0A0E0JH50_ORYPU_4537 are exactly identical! WARNING: Sequences tr_A0A0E0FK60_A0A0E0FK60_ORYNI_4536 and tr_A0A0P0V145_A0A0P0V145_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_A0A0E0J2I7_A0A0E0J2I7_ORYNI_4536 and tr_I1R0L1_I1R0L1_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0J2I7_A0A0E0J2I7_ORYNI_4536 and tr_A0A0E0R952_A0A0E0R952_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0J2I7_A0A0E0J2I7_ORYNI_4536 and tr_A0A0D3HMG5_A0A0D3HMG5_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A0A1P6C659_A0A1P6C659_BRUMA_6279 and tr_A0A0N4TIC3_A0A0N4TIC3_BRUPA_6280 are exactly identical! WARNING: Sequences tr_A2WSN4_A2WSN4_ORYSI_39946 and tr_I1NPP7_I1NPP7_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A2WSN4_A2WSN4_ORYSI_39946 and tr_A0A0E0MZB4_A0A0E0MZB4_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A2WSN4_A2WSN4_ORYSI_39946 and tr_A0A0D3ERA3_A0A0D3ERA3_9ORYZ_65489 are exactly identical! WARNING: Sequences tr_A2WSN4_A2WSN4_ORYSI_39946 and tr_A0A0D9YBR1_A0A0D9YBR1_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A2WSN4_A2WSN4_ORYSI_39946 and tr_Q5ZDI4_Q5ZDI4_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_H0Z3A4_H0Z3A4_TAEGU_59729 and tr_A0A218UMX3_A0A218UMX3_9PASE_299123 are exactly identical! WARNING: Sequences tr_B3RN57_B3RN57_TRIAD_10228 and tr_A0A369SBF8_A0A369SBF8_9METZ_287889 are exactly identical! WARNING: Sequences tr_G7Q0N1_G7Q0N1_MACFA_9541 and tr_A0A096NH86_A0A096NH86_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7Q0N1_G7Q0N1_MACFA_9541 and tr_A0A0D9R5G5_A0A0D9R5G5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G7Q0N1_G7Q0N1_MACFA_9541 and tr_A0A2K5ME61_A0A2K5ME61_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7Q0N1_G7Q0N1_MACFA_9541 and tr_A0A2K5YA19_A0A2K5YA19_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A3B6GPG3_A0A3B6GPG3_WHEAT_4565 and tr_A0A3B6GU06_A0A3B6GU06_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A067DP17_A0A067DP17_CITSI_2711 and tr_V4T2S7_V4T2S7_9ROSI_85681 are exactly identical! WARNING: Sequences tr_A0A067DP17_A0A067DP17_CITSI_2711 and tr_A0A2H5Q1V4_A0A2H5Q1V4_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0A0KDW9_A0A0A0KDW9_CUCSA_3659 and tr_A0A1S3BCJ6_A0A1S3BCJ6_CUCME_3656 are exactly identical! WARNING: Sequences tr_W9RJ81_W9RJ81_9ROSA_981085 and tr_W9RSX2_W9RSX2_9ROSA_981085 are exactly identical! WARNING: Sequences tr_V4RXQ1_V4RXQ1_9ROSI_85681 and tr_V4SRF9_V4SRF9_9ROSI_85681 are exactly identical! WARNING: Sequences tr_V4SLH0_V4SLH0_9ROSI_85681 and tr_A0A2H5NF00_A0A2H5NF00_CITUN_55188 are exactly identical! WARNING: Sequences tr_A0A0D2UWN1_A0A0D2UWN1_GOSRA_29730 and tr_A0A1U8KGJ0_A0A1U8KGJ0_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A091J5Y3_A0A091J5Y3_EGRGA_188379 and tr_A0A093K1H8_A0A093K1H8_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A0V1CIS5_A0A0V1CIS5_TRIBR_45882 and tr_A0A0V1NJ03_A0A0V1NJ03_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1CIS5_A0A0V1CIS5_TRIBR_45882 and tr_A0A0V0T8Q3_A0A0V0T8Q3_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1DJ05_A0A0V1DJ05_TRIBR_45882 and tr_A0A0V0X538_A0A0V0X538_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1DJ05_A0A0V1DJ05_TRIBR_45882 and tr_A0A0V1L2L8_A0A0V1L2L8_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1DJ05_A0A0V1DJ05_TRIBR_45882 and tr_A0A0V0TW20_A0A0V0TW20_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A1S4DSE5_A0A1S4DSE5_TOBAC_4097 and tr_A0A1J6IRV3_A0A1J6IRV3_NICAT_49451 are exactly identical! WARNING: Sequences tr_A0A1S4DSE5_A0A1S4DSE5_TOBAC_4097 and tr_A0A1U7W2T7_A0A1U7W2T7_NICSY_4096 are exactly identical! WARNING: Sequences tr_A0A1I7T2A8_A0A1I7T2A8_9PELO_1561998 and tr_A0A1I7T2A9_A0A1I7T2A9_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1L8GFY6_A0A1L8GFY6_XENLA_8355 and tr_A0A1L8GM67_A0A1L8GM67_XENLA_8355 are exactly identical! WARNING: Sequences tr_A0A2G2YYH9_A0A2G2YYH9_CAPAN_4072 and tr_A0A2G3BTM2_A0A2G3BTM2_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2I1H577_A0A2I1H577_9GLOM_588596 and tr_U9TZG1_U9TZG1_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A2U4A829_A0A2U4A829_TURTR_9739 and tr_A0A2Y9NC69_A0A2Y9NC69_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A829_A0A2U4A829_TURTR_9739 and tr_A0A2Y9EG80_A0A2Y9EG80_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4A829_A0A2U4A829_TURTR_9739 and tr_A0A383ZGW2_A0A383ZGW2_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 114 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8K979/3_mltree/A8K979.raxml.reduced.phy Alignment comprises 1 partitions and 178 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 178 / 178 Gaps: 5.52 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8K979/3_mltree/A8K979.raxml.rba Parallelization scheme autoconfig: 4 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 734 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 178 / 14240 [00:00:00] Data distribution: max. searches per worker: 5 Starting ML tree search with 20 distinct starting trees [00:00:00 -231467.782390] Initial branch length optimization [00:00:07 -192688.083265] Model parameter optimization (eps = 10.000000) [00:01:12 -192244.878436] AUTODETECT spr round 1 (radius: 5) [00:04:07 -133102.860294] AUTODETECT spr round 2 (radius: 10) [00:07:17 -107360.265856] AUTODETECT spr round 3 (radius: 15) [00:10:53 -88248.506919] AUTODETECT spr round 4 (radius: 20) [00:14:27 -80747.444144] AUTODETECT spr round 5 (radius: 25) [00:18:42 -78693.900804] SPR radius for FAST iterations: 25 (autodetect) [00:18:42 -78693.900804] Model parameter optimization (eps = 3.000000) [00:19:16 -78604.181855] FAST spr round 1 (radius: 25) [00:23:04 -69679.449489] FAST spr round 2 (radius: 25) [00:25:48 -69193.806844] FAST spr round 3 (radius: 25) [00:28:12 -69172.579681] FAST spr round 4 (radius: 25) [00:30:25 -69163.014013] FAST spr round 5 (radius: 25) [00:32:28 -69163.012045] Model parameter optimization (eps = 1.000000) [00:32:52 -69158.988838] SLOW spr round 1 (radius: 5) [00:35:45 -69132.462740] SLOW spr round 2 (radius: 5) [00:38:32 -69132.460025] SLOW spr round 3 (radius: 10) [00:41:25 -69128.080594] SLOW spr round 4 (radius: 5) [00:45:00 -69114.508220] SLOW spr round 5 (radius: 5) [00:48:04 -69114.237306] SLOW spr round 6 (radius: 5) [00:50:53 -69114.237179] SLOW spr round 7 (radius: 10) [00:53:38 -69114.081915] SLOW spr round 8 (radius: 5) [00:57:04 -69111.836600] SLOW spr round 9 (radius: 5) [01:00:04 -69111.836596] SLOW spr round 10 (radius: 10) [01:00:58] [worker #1] ML tree search #2, logLikelihood: -69172.079677 [01:02:51 -69111.836571] SLOW spr round 11 (radius: 15) [01:06:45] [worker #3] ML tree search #4, logLikelihood: -69130.171198 [01:07:09 -69111.836526] SLOW spr round 12 (radius: 20) [01:09:13] [worker #2] ML tree search #3, logLikelihood: -69148.634581 [01:12:52 -69111.836525] SLOW spr round 13 (radius: 25) [01:19:41 -69111.836525] Model parameter optimization (eps = 0.100000) [01:20:00] [worker #0] ML tree search #1, logLikelihood: -69110.947743 [01:20:01 -231894.284992] Initial branch length optimization [01:20:08 -192891.639296] Model parameter optimization (eps = 10.000000) [01:20:59 -192515.324813] AUTODETECT spr round 1 (radius: 5) [01:23:51 -134392.669645] AUTODETECT spr round 2 (radius: 10) [01:27:01 -107338.234422] AUTODETECT spr round 3 (radius: 15) [01:30:22 -91772.900428] AUTODETECT spr round 4 (radius: 20) [01:34:17 -80699.592086] AUTODETECT spr round 5 (radius: 25) [01:38:17 -78981.061795] SPR radius for FAST iterations: 25 (autodetect) [01:38:17 -78981.061795] Model parameter optimization (eps = 3.000000) [01:38:47 -78915.665727] FAST spr round 1 (radius: 25) [01:42:51 -69644.304303] FAST spr round 2 (radius: 25) [01:45:50 -69224.034280] FAST spr round 3 (radius: 25) [01:48:25 -69189.855426] FAST spr round 4 (radius: 25) [01:50:34 -69187.068119] FAST spr round 5 (radius: 25) [01:52:40 -69184.082590] FAST spr round 6 (radius: 25) [01:54:42 -69183.729042] FAST spr round 7 (radius: 25) [01:56:43 -69183.728804] Model parameter optimization (eps = 1.000000) [01:56:59 -69183.130141] SLOW spr round 1 (radius: 5) [01:59:56 -69139.812964] SLOW spr round 2 (radius: 5) [02:02:48 -69132.500626] SLOW spr round 3 (radius: 5) [02:05:07] [worker #1] ML tree search #6, logLikelihood: -69127.201452 [02:05:35 -69129.573305] SLOW spr round 4 (radius: 5) [02:08:19 -69129.572368] SLOW spr round 5 (radius: 10) [02:11:05 -69123.203020] SLOW spr round 6 (radius: 5) [02:14:34 -69123.202468] SLOW spr round 7 (radius: 10) [02:17:39 -69123.202267] SLOW spr round 8 (radius: 15) [02:21:53 -69123.202232] SLOW spr round 9 (radius: 20) [02:27:56 -69123.202215] SLOW spr round 10 (radius: 25) [02:29:04] [worker #3] ML tree search #8, logLikelihood: -69151.678449 [02:29:49] [worker #2] ML tree search #7, logLikelihood: -69136.485030 [02:35:03 -69123.202206] Model parameter optimization (eps = 0.100000) [02:35:21] [worker #0] ML tree search #5, logLikelihood: -69122.615229 [02:35:21 -231718.842183] Initial branch length optimization [02:35:26 -195170.889260] Model parameter optimization (eps = 10.000000) [02:36:54 -193973.443403] AUTODETECT spr round 1 (radius: 5) [02:39:45 -133189.746498] AUTODETECT spr round 2 (radius: 10) [02:42:51 -105329.444643] AUTODETECT spr round 3 (radius: 15) [02:46:20 -91792.184976] AUTODETECT spr round 4 (radius: 20) [02:50:23 -78604.814176] AUTODETECT spr round 5 (radius: 25) [02:54:44 -77117.730738] SPR radius for FAST iterations: 25 (autodetect) [02:54:44 -77117.730738] Model parameter optimization (eps = 3.000000) [02:55:19 -76965.785463] FAST spr round 1 (radius: 25) [02:58:59 -69528.695382] FAST spr round 2 (radius: 25) [03:01:39 -69239.584187] FAST spr round 3 (radius: 25) [03:04:00 -69201.760844] FAST spr round 4 (radius: 25) [03:06:13 -69191.142388] FAST spr round 5 (radius: 25) [03:07:29] [worker #1] ML tree search #10, logLikelihood: -69120.412447 [03:08:20 -69184.048095] FAST spr round 6 (radius: 25) [03:10:20 -69184.048014] Model parameter optimization (eps = 1.000000) [03:10:47 -69176.189553] SLOW spr round 1 (radius: 5) [03:13:36 -69155.053084] SLOW spr round 2 (radius: 5) [03:16:25 -69154.072264] SLOW spr round 3 (radius: 5) [03:19:13 -69154.071006] SLOW spr round 4 (radius: 10) [03:21:59 -69154.070406] SLOW spr round 5 (radius: 15) [03:26:13 -69151.693561] SLOW spr round 6 (radius: 5) [03:29:51 -69149.751053] SLOW spr round 7 (radius: 5) [03:31:25] [worker #3] ML tree search #12, logLikelihood: -69149.933903 [03:32:58 -69149.750476] SLOW spr round 8 (radius: 10) [03:35:50 -69149.750303] SLOW spr round 9 (radius: 15) [03:39:51 -69149.750248] SLOW spr round 10 (radius: 20) [03:45:05 -69149.750225] SLOW spr round 11 (radius: 25) [03:46:53] [worker #2] ML tree search #11, logLikelihood: -69152.444652 [03:51:23 -69149.750216] Model parameter optimization (eps = 0.100000) [03:51:33] [worker #0] ML tree search #9, logLikelihood: -69149.709481 [03:51:33 -233786.488793] Initial branch length optimization [03:51:44 -196117.958206] Model parameter optimization (eps = 10.000000) [03:52:38 -195686.066067] AUTODETECT spr round 1 (radius: 5) [03:55:35 -128200.433353] AUTODETECT spr round 2 (radius: 10) [03:58:42 -99983.099508] AUTODETECT spr round 3 (radius: 15) [04:02:22 -87774.300337] AUTODETECT spr round 4 (radius: 20) [04:06:08 -81514.580238] AUTODETECT spr round 5 (radius: 25) [04:07:12] [worker #1] ML tree search #14, logLikelihood: -69118.116620 [04:09:50 -80028.977894] SPR radius for FAST iterations: 25 (autodetect) [04:09:50 -80028.977894] Model parameter optimization (eps = 3.000000) [04:10:20 -79941.151922] FAST spr round 1 (radius: 25) [04:14:17 -69819.029037] FAST spr round 2 (radius: 25) [04:17:20 -69275.574005] FAST spr round 3 (radius: 25) [04:19:56 -69193.825714] FAST spr round 4 (radius: 25) [04:22:13 -69183.512197] FAST spr round 5 (radius: 25) [04:24:18 -69182.878716] FAST spr round 6 (radius: 25) [04:26:19 -69182.862956] Model parameter optimization (eps = 1.000000) [04:26:46 -69177.113723] SLOW spr round 1 (radius: 5) [04:29:38 -69150.537438] SLOW spr round 2 (radius: 5) [04:32:24 -69148.734716] SLOW spr round 3 (radius: 5) [04:33:56] [worker #3] ML tree search #16, logLikelihood: -69132.266628 [04:35:09 -69146.412404] SLOW spr round 4 (radius: 5) [04:37:48 -69146.412335] SLOW spr round 5 (radius: 10) [04:40:36 -69138.270144] SLOW spr round 6 (radius: 5) [04:44:11 -69129.036990] SLOW spr round 7 (radius: 5) [04:47:12 -69129.036468] SLOW spr round 8 (radius: 10) [04:50:01 -69129.036243] SLOW spr round 9 (radius: 15) [04:51:23] [worker #2] ML tree search #15, logLikelihood: -69141.399845 [04:54:13 -69129.036141] SLOW spr round 10 (radius: 20) [04:59:35 -69129.036088] SLOW spr round 11 (radius: 25) [05:06:02 -69129.036060] Model parameter optimization (eps = 0.100000) [05:06:12] [worker #0] ML tree search #13, logLikelihood: -69128.994606 [05:06:12 -230896.142848] Initial branch length optimization [05:06:22 -193989.055011] Model parameter optimization (eps = 10.000000) [05:08:08] [worker #1] ML tree search #18, logLikelihood: -69130.621137 [05:08:11 -193466.750721] AUTODETECT spr round 1 (radius: 5) [05:11:05 -131636.554296] AUTODETECT spr round 2 (radius: 10) [05:14:16 -105795.184028] AUTODETECT spr round 3 (radius: 15) [05:17:53 -90352.626544] AUTODETECT spr round 4 (radius: 20) [05:21:46 -85518.185532] AUTODETECT spr round 5 (radius: 25) [05:26:01 -82640.367164] SPR radius for FAST iterations: 25 (autodetect) [05:26:01 -82640.367164] Model parameter optimization (eps = 3.000000) [05:26:35 -82568.399618] FAST spr round 1 (radius: 25) [05:30:25 -69953.752865] FAST spr round 2 (radius: 25) [05:33:18 -69250.283056] FAST spr round 3 (radius: 25) [05:35:45 -69183.506989] FAST spr round 4 (radius: 25) [05:38:00 -69179.167173] FAST spr round 5 (radius: 25) [05:40:08 -69173.010733] FAST spr round 6 (radius: 25) [05:42:07 -69172.808651] FAST spr round 7 (radius: 25) [05:44:06 -69169.917732] FAST spr round 8 (radius: 25) [05:46:08 -69164.074700] FAST spr round 9 (radius: 25) [05:48:05 -69161.786713] FAST spr round 10 (radius: 25) [05:49:59 -69161.786420] Model parameter optimization (eps = 1.000000) [05:50:25 -69156.069533] SLOW spr round 1 (radius: 5) [05:51:20] [worker #3] ML tree search #20, logLikelihood: -69119.582392 [05:53:06 -69136.832564] SLOW spr round 2 (radius: 5) [05:55:47 -69134.154665] SLOW spr round 3 (radius: 5) [05:56:58] [worker #2] ML tree search #19, logLikelihood: -69151.832699 [05:58:28 -69134.153886] SLOW spr round 4 (radius: 10) [06:01:11 -69133.679009] SLOW spr round 5 (radius: 5) [06:04:41 -69133.678347] SLOW spr round 6 (radius: 10) [06:07:50 -69133.678262] SLOW spr round 7 (radius: 15) [06:12:04 -69133.678255] SLOW spr round 8 (radius: 20) [06:17:43 -69133.678255] SLOW spr round 9 (radius: 25) [06:24:33 -69133.678254] Model parameter optimization (eps = 0.100000) [06:24:53] [worker #0] ML tree search #17, logLikelihood: -69133.416810 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.171834,0.288816) (0.246676,0.401421) (0.317360,0.919730) (0.264130,2.118142) 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: -69110.947743 AIC score: 141163.895486 / AICc score: 4471787.895486 / BIC score: 145844.299088 Free parameters (model + branch lengths): 1471 WARNING: Number of free parameters (K=1471) is larger than alignment size (n=178). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 4 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8K979/3_mltree/A8K979.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8K979/3_mltree/A8K979.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8K979/3_mltree/A8K979.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8K979/3_mltree/A8K979.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/250721_run/phylogeny-snakemake/results/A8K979/3_mltree/A8K979.raxml.log Analysis started: 26-Jul-2021 00:10:20 / finished: 26-Jul-2021 06:35:14 Elapsed time: 23093.772 seconds Consumed energy: 809.267 Wh (= 4 km in an electric car, or 20 km with an e-scooter!)