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 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM RAxML-NG was called at 05-Jul-2021 16:43:01 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P43405/2_msa/P43405_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P43405/3_mltree/P43405 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P43405/2_msa/P43405_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 349 sites WARNING: Sequences tr_B4QCQ4_B4QCQ4_DROSI_7240 and sp_Q9V9J3_SRC42_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QCQ4_B4QCQ4_DROSI_7240 and tr_B4II23_B4II23_DROSE_7238 are exactly identical! WARNING: Sequences tr_A0A1D5PKH0_A0A1D5PKH0_CHICK_9031 and tr_G1NIB9_G1NIB9_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5PKH0_A0A1D5PKH0_CHICK_9031 and tr_U3I5P3_U3I5P3_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5PKH0_A0A1D5PKH0_CHICK_9031 and tr_A0A091V095_A0A091V095_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1L1S0Q6_A0A1L1S0Q6_CHICK_9031 and tr_H0ZMM7_H0ZMM7_TAEGU_59729 are exactly identical! WARNING: Sequences tr_A0A1L1S0Q6_A0A1L1S0Q6_CHICK_9031 and tr_U3KEW3_U3KEW3_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A1L1S0Q6_A0A1L1S0Q6_CHICK_9031 and tr_R0LH93_R0LH93_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1L1S0Q6_A0A1L1S0Q6_CHICK_9031 and tr_A0A151N9I4_A0A151N9I4_ALLMI_8496 are exactly identical! WARNING: Sequences tr_A0A1L1S0Q6_A0A1L1S0Q6_CHICK_9031 and tr_A0A087R5J3_A0A087R5J3_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1L1S0Q6_A0A1L1S0Q6_CHICK_9031 and tr_A0A091GP40_A0A091GP40_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1L1S0Q6_A0A1L1S0Q6_CHICK_9031 and tr_A0A2I0MIN8_A0A2I0MIN8_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1L1S0Q6_A0A1L1S0Q6_CHICK_9031 and tr_A0A091HM34_A0A091HM34_CALAN_9244 are exactly identical! WARNING: Sequences tr_F1NCD9_F1NCD9_CHICK_9031 and tr_G1N1M4_G1N1M4_MELGA_9103 are exactly identical! WARNING: Sequences tr_F1NCD9_F1NCD9_CHICK_9031 and tr_U3IYV8_U3IYV8_ANAPL_8839 are exactly identical! WARNING: Sequences sp_P00520_ABL1_MOUSE_10090 and tr_E9PT20_E9PT20_RAT_10116 are exactly identical! WARNING: Sequences sp_P00520_ABL1_MOUSE_10090 and tr_A0A1U7R1K5_A0A1U7R1K5_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q61527_ERBB4_MOUSE_10090 and tr_G1SXY0_G1SXY0_RABIT_9986 are exactly identical! WARNING: Sequences sp_Q61527_ERBB4_MOUSE_10090 and tr_A0A1S3ERE6_A0A1S3ERE6_DIPOR_10020 are exactly identical! WARNING: Sequences sp_Q61527_ERBB4_MOUSE_10090 and tr_A0A1U7T888_A0A1U7T888_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q61527_ERBB4_MOUSE_10090 and tr_A0A1U7QBV4_A0A1U7QBV4_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3Y1H1_M3Y1H1_MUSPF_9669 and tr_F1PPK2_F1PPK2_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3Y1H1_M3Y1H1_MUSPF_9669 and tr_F1M0N1_F1M0N1_RAT_10116 are exactly identical! WARNING: Sequences tr_M3Y1H1_M3Y1H1_MUSPF_9669 and tr_D2H3L6_D2H3L6_AILME_9646 are exactly identical! WARNING: Sequences tr_M3Y1H1_M3Y1H1_MUSPF_9669 and tr_L5KXU8_L5KXU8_PTEAL_9402 are exactly identical! WARNING: Sequences tr_M3Y1H1_M3Y1H1_MUSPF_9669 and tr_A0A2U3VSL4_A0A2U3VSL4_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3Y1H1_M3Y1H1_MUSPF_9669 and tr_A0A2U3XRU8_A0A2U3XRU8_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3Y1H1_M3Y1H1_MUSPF_9669 and tr_A0A2Y9JSJ0_A0A2Y9JSJ0_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3Y1H1_M3Y1H1_MUSPF_9669 and tr_A0A384CJV3_A0A384CJV3_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and tr_A0A2I2Z1W9_A0A2I2Z1W9_GORGO_9595 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and tr_A0A2I3RYF9_A0A2I3RYF9_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and tr_A0A1D5RE09_A0A1D5RE09_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and sp_P55245_EGFR_MACMU_9544 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and tr_G7P1R4_G7P1R4_MACFA_9541 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and tr_A0A0D9RU37_A0A0D9RU37_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and tr_A0A2K6B1P2_A0A2K6B1P2_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2I3GX32_A0A2I3GX32_NOMLE_61853 and tr_A0A2R9CTL6_A0A2R9CTL6_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_A0A2I2Z667_A0A2I2Z667_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_I3LW46_I3LW46_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and sp_Q15303_ERBB4_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_F7G3H1_F7G3H1_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_F7HB76_F7HB76_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_G7PLC3_G7PLC3_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_A0A2K5NV86_A0A2K5NV86_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_A0A2K6DNJ0_A0A2K6DNJ0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1R6F8_G1R6F8_NOMLE_61853 and tr_A0A2K5XRB5_A0A2K5XRB5_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_G3QJK0_G3QJK0_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_A0A2I3TWE6_A0A2I3TWE6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and sp_P42684_ABL2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_F7AU70_F7AU70_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_G5C7J7_G5C7J7_HETGA_10181 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_A0A2R8MYN3_A0A2R8MYN3_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_A0A2I3MIM0_A0A2I3MIM0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_A0A0D9RI41_A0A0D9RI41_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_A0A1U7TZR0_A0A1U7TZR0_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_A0A2K5MCB1_A0A2K5MCB1_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_A0A2K6CR83_A0A2K6CR83_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_A0A2K5XUV6_A0A2K5XUV6_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1S0A6_G1S0A6_NOMLE_61853 and tr_A0A2R9CMZ1_A0A2R9CMZ1_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_G3HW12_G3HW12_CRIGR_10029 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_H2N4J6_H2N4J6_PONAB_9601 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_F7B6Q9_F7B6Q9_HORSE_9796 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_W5Q539_W5Q539_SHEEP_9940 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_I3N8T1_I3N8T1_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_I3LP68_I3LP68_PIG_9823 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_F1MWH8_F1MWH8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_A0A091DK86_A0A091DK86_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_A0A1U8C216_A0A1U8C216_MESAU_10036 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_A0A2U4CQS2_A0A2U4CQS2_TURTR_9739 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_A0A2Y9LZ58_A0A2Y9LZ58_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_A0A2Y9TJX0_A0A2Y9TJX0_PHYCD_9755 are exactly identical! WARNING: Sequences tr_G1P8R6_G1P8R6_MYOLU_59463 and tr_A0A384AMB6_A0A384AMB6_BALAS_310752 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_G3R4W2_G3R4W2_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_F1PEX6_F1PEX6_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A2I3RAJ1_A0A2I3RAJ1_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A2I3S7G9_A0A2I3S7G9_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_H0WWK4_H0WWK4_OTOGA_30611 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and sp_P00519_ABL1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_H9YUX8_H9YUX8_MACMU_9544 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_G3SZ92_G3SZ92_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_U3CVZ7_U3CVZ7_CALJA_9483 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A287BB27_A0A287BB27_PIG_9823 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_D2H177_D2H177_AILME_9646 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_G7PRB8_G7PRB8_MACFA_9541 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_L5K6Z7_L5K6Z7_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_M3W3H7_M3W3H7_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A0D9RQJ3_A0A0D9RQJ3_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A2K5LX70_A0A2K5LX70_CERAT_9531 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A2K6B7I9_A0A2K6B7I9_MACNE_9545 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A2K5XNT4_A0A2K5XNT4_MANLE_9568 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A2R9BA11_A0A2R9BA11_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A2U3VD43_A0A2U3VD43_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A2Y9DJL9_A0A2Y9DJL9_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A2Y9NX24_A0A2Y9NX24_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1PC86_G1PC86_MYOLU_59463 and tr_A0A384CRH9_A0A384CRH9_URSMA_29073 are exactly identical! WARNING: Sequences tr_G3R4D0_G3R4D0_GORGO_9595 and tr_A0A2J8KTF6_A0A2J8KTF6_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R4D0_G3R4D0_GORGO_9595 and sp_P43405_KSYK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R4D0_G3R4D0_GORGO_9595 and tr_A0A2R9BI29_A0A2R9BI29_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3S1C3_G3S1C3_GORGO_9595 and sp_Q05397_FAK1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3S1C3_G3S1C3_GORGO_9595 and tr_A0A2I3N5G5_A0A2I3N5G5_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S1C3_G3S1C3_GORGO_9595 and tr_A0A2K5YHF7_A0A2K5YHF7_MANLE_9568 are exactly identical! WARNING: Sequences tr_H2PRA3_H2PRA3_PONAB_9601 and tr_A0A1D5QGC6_A0A1D5QGC6_MACMU_9544 are exactly identical! WARNING: Sequences tr_H2PRA3_H2PRA3_PONAB_9601 and tr_G7PD12_G7PD12_MACFA_9541 are exactly identical! WARNING: Sequences tr_H2PRA3_H2PRA3_PONAB_9601 and tr_A0A0D9RB32_A0A0D9RB32_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_H1A456_H1A456_TAEGU_59729 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_U3K0H4_U3K0H4_FICAL_59894 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A091EWN1_A0A091EWN1_CORBR_85066 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A091IJE8_A0A091IJE8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A093PWB2_A0A093PWB2_9PASS_328815 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A091UYW5_A0A091UYW5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A087QVI0_A0A087QVI0_APTFO_9233 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A093HBT4_A0A093HBT4_STRCA_441894 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A2I0MBR5_A0A2I0MBR5_COLLI_8932 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A091I2G2_A0A091I2G2_CALAN_9244 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A1V4JYW4_A0A1V4JYW4_PATFA_372326 are exactly identical! WARNING: Sequences tr_G1MUH1_G1MUH1_MELGA_9103 and tr_A0A218V4Y8_A0A218V4Y8_9PASE_299123 are exactly identical! WARNING: Sequences tr_Q29D50_Q29D50_DROPS_46245 and tr_B4MXF9_B4MXF9_DROWI_7260 are exactly identical! WARNING: Sequences tr_Q29D50_Q29D50_DROPS_46245 and tr_B4LCY8_B4LCY8_DROVI_7244 are exactly identical! WARNING: Sequences tr_Q29D50_Q29D50_DROPS_46245 and tr_A0A1W4UV97_A0A1W4UV97_DROFC_30025 are exactly identical! WARNING: Sequences tr_E2RGQ1_E2RGQ1_CANLF_9615 and tr_A0A2U3WB52_A0A2U3WB52_ODORO_9708 are exactly identical! WARNING: Sequences tr_E2RGQ1_E2RGQ1_CANLF_9615 and tr_A0A384CR38_A0A384CR38_URSMA_29073 are exactly identical! WARNING: Sequences tr_F1PQ05_F1PQ05_CANLF_9615 and tr_F6ZSZ9_F6ZSZ9_MONDO_13616 are exactly identical! WARNING: Sequences tr_F1PQ05_F1PQ05_CANLF_9615 and tr_F1SSQ9_F1SSQ9_PIG_9823 are exactly identical! WARNING: Sequences tr_F1PQ05_F1PQ05_CANLF_9615 and tr_A0A337S8Z7_A0A337S8Z7_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1PQ05_F1PQ05_CANLF_9615 and tr_A0A2U4BML0_A0A2U4BML0_TURTR_9739 are exactly identical! WARNING: Sequences tr_F1PQ05_F1PQ05_CANLF_9615 and tr_A0A2Y9MQV3_A0A2Y9MQV3_DELLE_9749 are exactly identical! WARNING: Sequences tr_F1PQ05_F1PQ05_CANLF_9615 and tr_A0A2Y9SV06_A0A2Y9SV06_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2I3RF60_A0A2I3RF60_PANTR_9598 and tr_A0A096MT35_A0A096MT35_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A2I3RF60_A0A2I3RF60_PANTR_9598 and tr_A0A2R9C6L4_A0A2R9C6L4_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I3T3L8_A0A2I3T3L8_PANTR_9598 and tr_A0A2R9CGB2_A0A2R9CGB2_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QIE3_H2QIE3_PANTR_9598 and sp_P43403_ZAP70_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QTL3_H2QTL3_PANTR_9598 and sp_P42685_FRK_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QTL3_H2QTL3_PANTR_9598 and tr_A0A2R9BRU0_A0A2R9BRU0_PANPA_9597 are exactly identical! WARNING: Sequences tr_F7FU48_F7FU48_MONDO_13616 and tr_G3WV25_G3WV25_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5PBZ8_W5PBZ8_SHEEP_9940 and tr_F1MXG8_F1MXG8_BOVIN_9913 are exactly identical! WARNING: Sequences tr_A0A087ZQN7_A0A087ZQN7_APIME_7460 and tr_A0A0L7QY19_A0A0L7QY19_9HYME_597456 are exactly identical! WARNING: Sequences tr_A0A087ZQN7_A0A087ZQN7_APIME_7460 and tr_A0A2A3E5Z4_A0A2A3E5Z4_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A088AT87_A0A088AT87_APIME_7460 and tr_A0A026W235_A0A026W235_OOCBI_2015173 are exactly identical! WARNING: Sequences tr_A0A088AT87_A0A088AT87_APIME_7460 and tr_A0A0L7R834_A0A0L7R834_9HYME_597456 are exactly identical! WARNING: Sequences tr_A0A088AT87_A0A088AT87_APIME_7460 and tr_A0A2A3EUP4_A0A2A3EUP4_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NHS2_A0A158NHS2_ATTCE_12957 and tr_F4WY89_F4WY89_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NHS2_A0A158NHS2_ATTCE_12957 and tr_A0A151X6R4_A0A151X6R4_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NHS2_A0A158NHS2_ATTCE_12957 and tr_A0A195EHE4_A0A195EHE4_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NHS2_A0A158NHS2_ATTCE_12957 and tr_A0A195AWS6_A0A195AWS6_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NHS2_A0A158NHS2_ATTCE_12957 and tr_A0A195FER6_A0A195FER6_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A158NHS2_A0A158NHS2_ATTCE_12957 and tr_A0A195CB93_A0A195CB93_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_F4WV60_F4WV60_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_A0A151WUC9_A0A151WUC9_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_A0A195DS06_A0A195DS06_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_A0A195BS54_A0A195BS54_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_A0A195EXC2_A0A195EXC2_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A158NUM9_A0A158NUM9_ATTCE_12957 and tr_A0A195C704_A0A195C704_9HYME_456900 are exactly identical! WARNING: Sequences tr_H0V6K4_H0V6K4_CAVPO_10141 and tr_G5AT60_G5AT60_HETGA_10181 are exactly identical! WARNING: Sequences tr_A0A158Q054_A0A158Q054_BRUMA_6279 and tr_A0A044SXD4_A0A044SXD4_ONCVO_6282 are exactly identical! WARNING: Sequences tr_F7FAI7_F7FAI7_MACMU_9544 and tr_A0A096NGT8_A0A096NGT8_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FAI7_F7FAI7_MACMU_9544 and tr_A0A0D9RXH6_A0A0D9RXH6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7FAI7_F7FAI7_MACMU_9544 and tr_A0A2K5MYN1_A0A2K5MYN1_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FAI7_F7FAI7_MACMU_9544 and tr_A0A2K6CVN0_A0A2K6CVN0_MACNE_9545 are exactly identical! WARNING: Sequences tr_G5C8Y8_G5C8Y8_HETGA_10181 and tr_A0A091D8K0_A0A091D8K0_FUKDA_885580 are exactly identical! WARNING: Sequences tr_G5C8Y8_G5C8Y8_HETGA_10181 and tr_A0A1S3FW28_A0A1S3FW28_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G5C8Y8_G5C8Y8_HETGA_10181 and tr_A0A1U7SLU4_A0A1U7SLU4_TARSY_1868482 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_H0Z2V6_H0Z2V6_TAEGU_59729 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_U3JFF5_U3JFF5_FICAL_59894 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A151MFN4_A0A151MFN4_ALLMI_8496 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A091FAS5_A0A091FAS5_CORBR_85066 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A091JHP5_A0A091JHP5_EGRGA_188379 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A093PK85_A0A093PK85_9PASS_328815 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A091URD2_A0A091URD2_NIPNI_128390 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A087RGY7_A0A087RGY7_APTFO_9233 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A093HB20_A0A093HB20_STRCA_441894 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A091V7N8_A0A091V7N8_OPIHO_30419 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A091GMR3_A0A091GMR3_9AVES_55661 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A093GBE1_A0A093GBE1_DRYPU_118200 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A091IH79_A0A091IH79_CALAN_9244 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A1U7S4W8_A0A1U7S4W8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A1V4J6M5_A0A1V4J6M5_PATFA_372326 are exactly identical! WARNING: Sequences tr_K7FHZ2_K7FHZ2_PELSI_13735 and tr_A0A218V5K2_A0A218V5K2_9PASE_299123 are exactly identical! WARNING: Sequences tr_H3DDH2_H3DDH2_TETNG_99883 and tr_A0A2U9C7V6_A0A2U9C7V6_SCOMX_52904 are exactly identical! WARNING: Sequences tr_H0YPY8_H0YPY8_TAEGU_59729 and tr_A0A218UCB5_A0A218UCB5_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZR18_H0ZR18_TAEGU_59729 and tr_U3JJM0_U3JJM0_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZR18_H0ZR18_TAEGU_59729 and tr_A0A093PND3_A0A093PND3_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZR18_H0ZR18_TAEGU_59729 and tr_A0A218UMU6_A0A218UMU6_9PASE_299123 are exactly identical! WARNING: Sequences tr_F7BKF3_F7BKF3_XENTR_8364 and tr_A0A1L8GGA5_A0A1L8GGA5_XENLA_8355 are exactly identical! WARNING: Sequences tr_F7BKF3_F7BKF3_XENTR_8364 and tr_A0A1L8GML3_A0A1L8GML3_XENLA_8355 are exactly identical! WARNING: Sequences tr_G7P3L9_G7P3L9_MACFA_9541 and tr_A0A096NGV3_A0A096NGV3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PSP1_G7PSP1_MACFA_9541 and tr_A0A096P223_A0A096P223_PAPAN_9555 are exactly identical! WARNING: Sequences tr_A0A096MVJ9_A0A096MVJ9_PAPAN_9555 and tr_A0A2K5N7J8_A0A2K5N7J8_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A0K0FZX4_A0A0K0FZX4_STRVS_75913 and tr_A0A0N5BRC9_A0A0N5BRC9_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A151MIR6_A0A151MIR6_ALLMI_8496 and tr_A0A1U7SM91_A0A1U7SM91_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151NWA6_A0A151NWA6_ALLMI_8496 and tr_A0A3Q0FMM4_A0A3Q0FMM4_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A151P831_A0A151P831_ALLMI_8496 and tr_A0A3Q0HEE0_A0A3Q0HEE0_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A091IVD5_A0A091IVD5_EGRGA_188379 and tr_A0A091VW16_A0A091VW16_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IVD5_A0A091IVD5_EGRGA_188379 and tr_A0A091W908_A0A091W908_OPIHO_30419 are exactly identical! WARNING: Sequences tr_A0A091IVD5_A0A091IVD5_EGRGA_188379 and tr_A0A099YVS8_A0A099YVS8_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A091IVD5_A0A091IVD5_EGRGA_188379 and tr_A0A091GCH0_A0A091GCH0_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091IVD5_A0A091IVD5_EGRGA_188379 and tr_A0A091IJF5_A0A091IJF5_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A091JHY2_A0A091JHY2_EGRGA_188379 and tr_A0A091UWV7_A0A091UWV7_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091JHY2_A0A091JHY2_EGRGA_188379 and tr_A0A087RD36_A0A087RD36_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091JHY2_A0A091JHY2_EGRGA_188379 and tr_A0A093H843_A0A093H843_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091JHY2_A0A091JHY2_EGRGA_188379 and tr_A0A091G8V1_A0A091G8V1_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A091JHY2_A0A091JHY2_EGRGA_188379 and tr_A0A091IG63_A0A091IG63_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A2I0M4T2_A0A2I0M4T2_COLLI_8932 and tr_A0A1V4JVA3_A0A1V4JVA3_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0XMU8_A0A0V0XMU8_TRIPS_6337 and tr_A0A0V1I0Q3_A0A0V1I0Q3_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A151WIK7_A0A151WIK7_9HYME_64791 and tr_A0A151IX42_A0A151IX42_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A151I609_A0A151I609_9HYME_520822 and tr_A0A195FUN6_A0A195FUN6_9HYME_34720 are exactly identical! WARNING: Sequences tr_A0A1S3M4G8_A0A1S3M4G8_SALSA_8030 and tr_A0A1S3Q299_A0A1S3Q299_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3MBP8_A0A1S3MBP8_SALSA_8030 and tr_C0HA59_C0HA59_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1V4K778_A0A1V4K778_PATFA_372326 and tr_A0A218UCB9_A0A218UCB9_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A2A2KF13_A0A2A2KF13_9BILA_2018661 and tr_A0A2A2KJJ3_A0A2A2KJJ3_9BILA_2018661 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PSY2_A0A2D0PSY2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PUF6_A0A2D0PUF6_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PUH5_A0A2D0PUH5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PW58_A0A2D0PW58_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PW63_A0A2D0PW63_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PX14_A0A2D0PX14_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PSX8_A0A2D0PSX8_ICTPU_7998 and tr_A0A2D0PX19_A0A2D0PX19_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QAM3_A0A2D0QAM3_ICTPU_7998 and tr_A0A2D0QAN0_A0A2D0QAN0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R3A6_A0A2D0R3A6_ICTPU_7998 and tr_A0A2D0R4V7_A0A2D0R4V7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0R3A6_A0A2D0R3A6_ICTPU_7998 and tr_A0A2D0R5J2_A0A2D0R5J2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RBL1_A0A2D0RBL1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RBP7_A0A2D0RBP7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RBR4_A0A2D0RBR4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RBS3_A0A2D0RBS3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RBT5_A0A2D0RBT5_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RBT8_A0A2D0RBT8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RBU8_A0A2D0RBU8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RCT4_A0A2D0RCT4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RCU1_A0A2D0RCU1_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RBJ8_A0A2D0RBJ8_ICTPU_7998 and tr_A0A2D0RCV2_A0A2D0RCV2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SR71_A0A2D0SR71_ICTPU_7998 and tr_A0A2D0SR82_A0A2D0SR82_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SR71_A0A2D0SR71_ICTPU_7998 and tr_A0A2D0SSC0_A0A2D0SSC0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4B0F7_A0A2U4B0F7_TURTR_9739 and tr_A0A2Y9Q6T4_A0A2Y9Q6T4_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B2R3_A0A2U4B2R3_TURTR_9739 and tr_A0A2Y9M0P3_A0A2Y9M0P3_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4B2R3_A0A2U4B2R3_TURTR_9739 and tr_A0A2Y9T6F6_A0A2Y9T6F6_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2Y9IH64_A0A2Y9IH64_ENHLU_391180 and tr_A0A384AKS3_A0A384AKS3_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2Y9MGM5_A0A2Y9MGM5_DELLE_9749 and tr_A0A384B1B1_A0A384B1B1_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 236 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P43405/3_mltree/P43405.raxml.reduced.phy Alignment comprises 1 partitions and 348 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 349 / 348 Gaps: 3.16 % Invariant sites: 2.29 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P43405/3_mltree/P43405.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 / 348 / 27840 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -622948.065077] Initial branch length optimization [00:00:07 -501722.043966] Model parameter optimization (eps = 10.000000) [00:01:14 -500753.835969] AUTODETECT spr round 1 (radius: 5) [00:05:59 -282787.339354] AUTODETECT spr round 2 (radius: 10) [00:10:57 -192683.526822] AUTODETECT spr round 3 (radius: 15) [00:15:51 -158185.283333] AUTODETECT spr round 4 (radius: 20) [00:22:05 -130281.984722] AUTODETECT spr round 5 (radius: 25) [00:27:50 -119248.523285] SPR radius for FAST iterations: 25 (autodetect) [00:27:50 -119248.523285] Model parameter optimization (eps = 3.000000) [00:28:26 -119144.008174] FAST spr round 1 (radius: 25) [00:32:51 -97508.099555] FAST spr round 2 (radius: 25) [00:36:16 -95411.739304] FAST spr round 3 (radius: 25) [00:39:01 -95200.224977] FAST spr round 4 (radius: 25) [00:41:34 -95196.151462] FAST spr round 5 (radius: 25) [00:43:56 -95196.149734] Model parameter optimization (eps = 1.000000) [00:44:15 -95191.758522] SLOW spr round 1 (radius: 5) [00:47:34 -95156.627810] SLOW spr round 2 (radius: 5) [00:50:48 -95149.807914] SLOW spr round 3 (radius: 5) [00:53:51 -95149.807645] SLOW spr round 4 (radius: 10) [00:57:10 -95149.807497] SLOW spr round 5 (radius: 15) [01:02:32 -95149.807477] SLOW spr round 6 (radius: 20) [01:10:25 -95149.807468] SLOW spr round 7 (radius: 25) [01:20:43 -95149.807464] Model parameter optimization (eps = 0.100000) [01:20:56] [worker #0] ML tree search #1, logLikelihood: -95149.680817 [01:20:57 -621529.512852] Initial branch length optimization [01:21:05 -498866.193031] Model parameter optimization (eps = 10.000000) [01:22:09 -498026.335798] AUTODETECT spr round 1 (radius: 5) [01:27:03 -292655.318032] AUTODETECT spr round 2 (radius: 10) [01:27:43] [worker #3] ML tree search #4, logLikelihood: -95158.300002 [01:31:54 -187988.939843] AUTODETECT spr round 3 (radius: 15) [01:33:25] [worker #4] ML tree search #5, logLikelihood: -95158.518441 [01:36:50 -146786.173925] AUTODETECT spr round 4 (radius: 20) [01:37:01] [worker #1] ML tree search #2, logLikelihood: -95154.316655 [01:40:55] [worker #2] ML tree search #3, logLikelihood: -95158.899960 [01:42:26 -129567.005428] AUTODETECT spr round 5 (radius: 25) [01:48:36 -117250.122440] SPR radius for FAST iterations: 25 (autodetect) [01:48:36 -117250.122440] Model parameter optimization (eps = 3.000000) [01:49:03 -117170.155440] FAST spr round 1 (radius: 25) [01:53:38 -97815.851869] FAST spr round 2 (radius: 25) [01:56:56 -95362.665488] FAST spr round 3 (radius: 25) [01:59:52 -95276.517054] FAST spr round 4 (radius: 25) [02:02:28 -95221.571227] FAST spr round 5 (radius: 25) [02:05:01 -95218.243850] FAST spr round 6 (radius: 25) [02:07:18 -95218.243771] Model parameter optimization (eps = 1.000000) [02:07:42 -95200.658130] SLOW spr round 1 (radius: 5) [02:11:03 -95175.830176] SLOW spr round 2 (radius: 5) [02:14:13 -95165.376062] SLOW spr round 3 (radius: 5) [02:17:22 -95160.528891] SLOW spr round 4 (radius: 5) [02:20:24 -95159.685458] SLOW spr round 5 (radius: 5) [02:23:27 -95159.685424] SLOW spr round 6 (radius: 10) [02:26:49 -95158.662711] SLOW spr round 7 (radius: 5) [02:30:58 -95158.662688] SLOW spr round 8 (radius: 10) [02:34:46 -95158.662675] SLOW spr round 9 (radius: 15) [02:40:01 -95158.662663] SLOW spr round 10 (radius: 20) [02:48:39 -95158.662651] SLOW spr round 11 (radius: 25) [02:48:47] [worker #3] ML tree search #9, logLikelihood: -95166.556764 [02:59:37 -95158.662638] Model parameter optimization (eps = 0.100000) [02:59:45] [worker #0] ML tree search #6, logLikelihood: -95158.582817 [02:59:46 -622905.591782] Initial branch length optimization [02:59:54 -503005.110412] Model parameter optimization (eps = 10.000000) [03:01:10 -502135.448785] AUTODETECT spr round 1 (radius: 5) [03:06:01 -288623.933537] AUTODETECT spr round 2 (radius: 10) [03:09:57] [worker #4] ML tree search #10, logLikelihood: -95152.105763 [03:10:27] [worker #1] ML tree search #7, logLikelihood: -95150.414635 [03:11:07 -201183.995573] AUTODETECT spr round 3 (radius: 15) [03:16:12 -157970.620964] AUTODETECT spr round 4 (radius: 20) [03:21:31 -137594.831858] AUTODETECT spr round 5 (radius: 25) [03:27:29 -120827.194767] SPR radius for FAST iterations: 25 (autodetect) [03:27:29 -120827.194767] Model parameter optimization (eps = 3.000000) [03:28:05 -120722.654250] FAST spr round 1 (radius: 25) [03:28:31] [worker #2] ML tree search #8, logLikelihood: -95170.237780 [03:32:26 -98707.132186] FAST spr round 2 (radius: 25) [03:35:31 -95699.578181] FAST spr round 3 (radius: 25) [03:38:19 -95222.155828] FAST spr round 4 (radius: 25) [03:41:02 -95193.125525] FAST spr round 5 (radius: 25) [03:43:34 -95190.266859] FAST spr round 6 (radius: 25) [03:46:00 -95183.161298] FAST spr round 7 (radius: 25) [03:48:19 -95183.161149] Model parameter optimization (eps = 1.000000) [03:48:32 -95181.162522] SLOW spr round 1 (radius: 5) [03:51:48 -95162.147486] SLOW spr round 2 (radius: 5) [03:55:03 -95156.875881] SLOW spr round 3 (radius: 5) [03:58:09 -95156.875650] SLOW spr round 4 (radius: 10) [04:01:29 -95149.742523] SLOW spr round 5 (radius: 5) [04:05:40 -95148.740268] SLOW spr round 6 (radius: 5) [04:09:17 -95148.740038] SLOW spr round 7 (radius: 10) [04:12:45 -95148.740030] SLOW spr round 8 (radius: 15) [04:17:58 -95148.740024] SLOW spr round 9 (radius: 20) [04:25:52 -95148.740017] SLOW spr round 10 (radius: 25) [04:36:31 -95148.740011] Model parameter optimization (eps = 0.100000) [04:36:42] [worker #0] ML tree search #11, logLikelihood: -95148.682486 [04:36:42 -616664.268892] Initial branch length optimization [04:36:50 -497731.793828] Model parameter optimization (eps = 10.000000) [04:37:56 -496850.053611] AUTODETECT spr round 1 (radius: 5) [04:39:49] [worker #1] ML tree search #12, logLikelihood: -95148.073639 [04:42:43 -289665.251261] AUTODETECT spr round 2 (radius: 10) [04:47:51 -201834.548937] AUTODETECT spr round 3 (radius: 15) [04:49:19] [worker #4] ML tree search #15, logLikelihood: -95144.116793 [04:50:45] [worker #3] ML tree search #14, logLikelihood: -95153.337755 [04:53:02 -160734.562611] AUTODETECT spr round 4 (radius: 20) [04:58:43 -131064.793490] AUTODETECT spr round 5 (radius: 25) [05:05:01 -118241.114431] SPR radius for FAST iterations: 25 (autodetect) [05:05:01 -118241.114431] Model parameter optimization (eps = 3.000000) [05:05:31 -118141.780672] FAST spr round 1 (radius: 25) [05:07:38] [worker #2] ML tree search #13, logLikelihood: -95153.713174 [05:09:51 -97875.036566] FAST spr round 2 (radius: 25) [05:13:15 -95455.367971] FAST spr round 3 (radius: 25) [05:16:11 -95262.831049] FAST spr round 4 (radius: 25) [05:18:51 -95205.698642] FAST spr round 5 (radius: 25) [05:21:17 -95202.951938] FAST spr round 6 (radius: 25) [05:23:36 -95202.951785] Model parameter optimization (eps = 1.000000) [05:23:55 -95198.894809] SLOW spr round 1 (radius: 5) [05:27:18 -95169.095878] SLOW spr round 2 (radius: 5) [05:30:30 -95164.786630] SLOW spr round 3 (radius: 5) [05:33:38 -95163.269978] SLOW spr round 4 (radius: 5) [05:36:42 -95163.269959] SLOW spr round 5 (radius: 10) [05:40:04 -95161.226488] SLOW spr round 6 (radius: 5) [05:44:12 -95160.681531] SLOW spr round 7 (radius: 5) [05:47:47 -95160.680989] SLOW spr round 8 (radius: 10) [05:51:15 -95160.680961] SLOW spr round 9 (radius: 15) [05:56:34 -95160.680951] SLOW spr round 10 (radius: 20) [06:02:15] [worker #1] ML tree search #17, logLikelihood: -95159.890655 [06:04:46 -95160.680943] SLOW spr round 11 (radius: 25) [06:15:33 -95160.680934] Model parameter optimization (eps = 0.100000) [06:15:39] [worker #0] ML tree search #16, logLikelihood: -95160.605525 [06:21:26] [worker #4] ML tree search #20, logLikelihood: -95161.085129 [06:29:19] [worker #3] ML tree search #19, logLikelihood: -95158.066694 [06:54:01] [worker #2] ML tree search #18, logLikelihood: -95169.156091 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.178422,0.288048) (0.243638,0.365868) (0.313514,0.953262) (0.264426,2.120087) 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: -95144.116793 AIC score: 194298.233586 / AICc score: 8238358.233586 / BIC score: 202027.652790 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=349). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 286 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P43405/3_mltree/P43405.raxml.bestTreeCollapsed Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P43405/3_mltree/P43405.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P43405/3_mltree/P43405.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P43405/3_mltree/P43405.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/P43405/3_mltree/P43405.raxml.log Analysis started: 05-Jul-2021 16:43:01 / finished: 05-Jul-2021 23:37:03 Elapsed time: 24841.785 seconds