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 07-Jul-2021 23:54:35 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UDY2/2_msa/Q9UDY2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UDY2/3_mltree/Q9UDY2 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UDY2/2_msa/Q9UDY2_trimmed_msa.fasta [00:00:00] Loaded alignment with 670 taxa and 125 sites WARNING: Sequences tr_B4QWP1_B4QWP1_DROSI_7240 and sp_Q7KRY7_LAP4_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QWP1_B4QWP1_DROSI_7240 and tr_B4ICM6_B4ICM6_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4QWP1_B4QWP1_DROSI_7240 and tr_A0A1W4VKS1_A0A1W4VKS1_DROFC_30025 are exactly identical! WARNING: Sequences tr_B4QXW5_B4QXW5_DROSI_7240 and tr_A0A0B4K6Y7_A0A0B4K6Y7_DROME_7227 are exactly identical! WARNING: Sequences tr_B4QXW5_B4QXW5_DROSI_7240 and tr_A0A0P9ANW5_A0A0P9ANW5_DROAN_7217 are exactly identical! WARNING: Sequences tr_E2AM50_E2AM50_CAMFO_104421 and tr_A0A026W6I5_A0A026W6I5_OOCBI_2015173 are exactly identical! WARNING: Sequences tr_E2AT58_E2AT58_CAMFO_104421 and tr_E2B5H8_E2B5H8_HARSA_610380 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_H2V503_H2V503_TAKRU_31033 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_H3CVI0_H3CVI0_TETNG_99883 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_G3PSF9_G3PSF9_GASAC_69293 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A3B1JNQ3_A0A3B1JNQ3_ASTMX_7994 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_W5LIK8_W5LIK8_ASTMX_7994 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_W5N8F1_W5N8F1_LEPOC_7918 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A0P7ZEX9_A0A0P7ZEX9_9TELE_113540 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A2D0SE10_A0A2D0SE10_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A2D0SE11_A0A2D0SE11_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A2D0SE15_A0A2D0SE15_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A2D0SE16_A0A2D0SE16_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A2D0SE19_A0A2D0SE19_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A2D0SE24_A0A2D0SE24_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A2D0SER9_A0A2D0SER9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A2D0SES4_A0A2D0SES4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A2D0SFE4_A0A2D0SFE4_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2R8QMK9_A0A2R8QMK9_DANRE_7955 and tr_A0A2U9BC10_A0A2U9BC10_SCOMX_52904 are exactly identical! WARNING: Sequences tr_A0A1D5P943_A0A1D5P943_CHICK_9031 and tr_A0A093HJX2_A0A093HJX2_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_H0Z5K7_H0Z5K7_TAEGU_59729 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_F7AQ54_F7AQ54_XENTR_8364 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_U3KDE6_U3KDE6_FICAL_59894 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_U3IK57_U3IK57_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A151MA54_A0A151MA54_ALLMI_8496 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A0Q3QCU0_A0A0Q3QCU0_AMAAE_12930 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A091EUN7_A0A091EUN7_CORBR_85066 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A093Q5R7_A0A093Q5R7_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A091WKN8_A0A091WKN8_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A087R451_A0A087R451_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A099YTR7_A0A099YTR7_TINGU_94827 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A091FR21_A0A091FR21_9AVES_55661 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A0A0AK82_A0A0A0AK82_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A2I0M6P3_A0A2I0M6P3_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A093I9S4_A0A093I9S4_DRYPU_118200 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A091ITP3_A0A091ITP3_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A3Q0G6E8_A0A3Q0G6E8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A1V4JDC2_A0A1V4JDC2_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A218UP11_A0A218UP11_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A226MGK6_A0A226MGK6_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PF09_A0A1D5PF09_CHICK_9031 and tr_A0A226PRC9_A0A226PRC9_COLVI_9014 are exactly identical! WARNING: Sequences tr_F1N8X8_F1N8X8_CHICK_9031 and tr_A0A226MXX3_A0A226MXX3_CALSU_9009 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_M3YHZ6_M3YHZ6_MUSPF_9669 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_G1P3E9_G1P3E9_MYOLU_59463 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_G3SBW7_G3SBW7_GORGO_9595 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_H2NMM8_H2NMM8_PONAB_9601 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_H9G3I0_H9G3I0_ANOCA_28377 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_G1U8Y2_G1U8Y2_RABIT_9986 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_J9PAE7_J9PAE7_CANLF_9615 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and sp_O97758_ZO1_CANLF_9615 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_H2Q923_H2Q923_PANTR_9598 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_F6VAF4_F6VAF4_HORSE_9796 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_W5Q4W6_W5Q4W6_SHEEP_9940 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and sp_A0A0G2K2P5_ZO1_RAT_10116 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_I3MGS3_I3MGS3_ICTTR_43179 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_H0WRQ0_H0WRQ0_OTOGA_30611 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_H0VI14_H0VI14_CAVPO_10141 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and sp_Q07157_ZO1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_F6V6C5_F6V6C5_MACMU_9544 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_K7FD61_K7FD61_PELSI_13735 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_G3SQ25_G3SQ25_LOXAF_9785 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_G3WFU6_G3WFU6_SARHA_9305 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2R8NBR9_A0A2R8NBR9_CALJA_9483 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A287BF71_A0A287BF71_PIG_9823 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_G1L8X7_G1L8X7_AILME_9646 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_G7PAM0_G7PAM0_MACFA_9541 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2I2U4E0_A0A2I2U4E0_FELCA_9685 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2I3LKS6_A0A2I3LKS6_PAPAN_9555 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A091DA16_A0A091DA16_FUKDA_885580 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A0D9R350_A0A0D9R350_CHLSB_60711 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A1S2ZJR7_A0A1S2ZJR7_ERIEU_9365 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A1S3ESH9_A0A1S3ESH9_DIPOR_10020 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A3Q0DZT0_A0A3Q0DZT0_TARSY_1868482 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A1U8CIZ4_A0A1U8CIZ4_MESAU_10036 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2K5ME38_A0A2K5ME38_CERAT_9531 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2K6BPQ1_A0A2K6BPQ1_MACNE_9545 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2K5XTQ1_A0A2K5XTQ1_MANLE_9568 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2R9C179_A0A2R9C179_PANPA_9597 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2U4C785_A0A2U4C785_TURTR_9739 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2U3ZTJ1_A0A2U3ZTJ1_ODORO_9708 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2U3XF36_A0A2U3XF36_LEPWE_9713 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2Y9QNM2_A0A2Y9QNM2_TRIMA_127582 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2Y9K0Z2_A0A2Y9K0Z2_ENHLU_391180 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2Y9LKM7_A0A2Y9LKM7_DELLE_9749 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A2Y9TBS5_A0A2Y9TBS5_PHYCD_9755 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A384BUG2_A0A384BUG2_URSMA_29073 are exactly identical! WARNING: Sequences sp_P39447_ZO1_MOUSE_10090 and tr_A0A383YY11_A0A383YY11_BALAS_310752 are exactly identical! WARNING: Sequences sp_Q9Z0U1_ZO2_MOUSE_10090 and tr_Q3ZB99_Q3ZB99_RAT_10116 are exactly identical! WARNING: Sequences sp_Q9Z0U1_ZO2_MOUSE_10090 and tr_A0A1D5QPT5_A0A1D5QPT5_MACMU_9544 are exactly identical! WARNING: Sequences sp_Q9Z0U1_ZO2_MOUSE_10090 and tr_A0A2I3MZG9_A0A2I3MZG9_PAPAN_9555 are exactly identical! WARNING: Sequences sp_Q9Z0U1_ZO2_MOUSE_10090 and tr_A0A0D9R7W9_A0A0D9R7W9_CHLSB_60711 are exactly identical! WARNING: Sequences sp_Q9Z0U1_ZO2_MOUSE_10090 and tr_A0A1S3WIR8_A0A1S3WIR8_ERIEU_9365 are exactly identical! WARNING: Sequences sp_Q9Z0U1_ZO2_MOUSE_10090 and tr_A0A3Q0E6Z5_A0A3Q0E6Z5_TARSY_1868482 are exactly identical! WARNING: Sequences sp_Q9Z0U1_ZO2_MOUSE_10090 and tr_A0A2K5KJY0_A0A2K5KJY0_CERAT_9531 are exactly identical! WARNING: Sequences sp_Q9Z0U1_ZO2_MOUSE_10090 and tr_A0A2K6CP92_A0A2K6CP92_MACNE_9545 are exactly identical! WARNING: Sequences sp_Q9Z0U1_ZO2_MOUSE_10090 and tr_A0A2K5XJJ1_A0A2K5XJJ1_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A3B3H6Q7_A0A3B3H6Q7_ORYLA_8090 and tr_A0A3B5PYU7_A0A3B5PYU7_XIPMA_8083 are exactly identical! WARNING: Sequences tr_A0A3B3H6Q7_A0A3B3H6Q7_ORYLA_8090 and tr_H2TFF5_H2TFF5_TAKRU_31033 are exactly identical! WARNING: Sequences tr_A0A3B3H6Q7_A0A3B3H6Q7_ORYLA_8090 and tr_G3NS97_G3NS97_GASAC_69293 are exactly identical! WARNING: Sequences tr_A0A3B3H6Q7_A0A3B3H6Q7_ORYLA_8090 and tr_A0A087XIG3_A0A087XIG3_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A3B3H6Q7_A0A3B3H6Q7_ORYLA_8090 and tr_A0A2I4CAF3_A0A2I4CAF3_9TELE_52670 are exactly identical! WARNING: Sequences tr_A0A3B3H6Q7_A0A3B3H6Q7_ORYLA_8090 and tr_A0A2U9BWQ5_A0A2U9BWQ5_SCOMX_52904 are exactly identical! WARNING: Sequences tr_G1NY63_G1NY63_MYOLU_59463 and tr_G3GYA3_G3GYA3_CRIGR_10029 are exactly identical! WARNING: Sequences tr_G1NY63_G1NY63_MYOLU_59463 and tr_F1PYW1_F1PYW1_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1NY63_G1NY63_MYOLU_59463 and tr_A0A384BUP0_A0A384BUP0_URSMA_29073 are exactly identical! WARNING: Sequences tr_G1PG03_G1PG03_MYOLU_59463 and tr_F6RTU4_F6RTU4_MONDO_13616 are exactly identical! WARNING: Sequences tr_G1PG03_G1PG03_MYOLU_59463 and tr_G1LQ13_G1LQ13_AILME_9646 are exactly identical! WARNING: Sequences tr_G1PG03_G1PG03_MYOLU_59463 and tr_A0A3Q0EAK8_A0A3Q0EAK8_TARSY_1868482 are exactly identical! WARNING: Sequences tr_G1PG03_G1PG03_MYOLU_59463 and tr_A0A226MI07_A0A226MI07_CALSU_9009 are exactly identical! WARNING: Sequences tr_G3IMK2_G3IMK2_CRIGR_10029 and tr_A0A1U8C7K3_A0A1U8C7K3_MESAU_10036 are exactly identical! WARNING: Sequences tr_G1NK59_G1NK59_MELGA_9103 and tr_U3IRW2_U3IRW2_ANAPL_8839 are exactly identical! WARNING: Sequences tr_A0A0R3NJD9_A0A0R3NJD9_DROPS_46245 and tr_B4GFV4_B4GFV4_DROPE_7234 are exactly identical! WARNING: Sequences tr_F1PEE3_F1PEE3_CANLF_9615 and tr_W5PU47_W5PU47_SHEEP_9940 are exactly identical! WARNING: Sequences tr_F1PEE3_F1PEE3_CANLF_9615 and tr_A0A287AZ07_A0A287AZ07_PIG_9823 are exactly identical! WARNING: Sequences tr_F1PEE3_F1PEE3_CANLF_9615 and tr_A0A2U3VQV2_A0A2U3VQV2_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PEE3_F1PEE3_CANLF_9615 and tr_A0A2U3XS61_A0A2U3XS61_LEPWE_9713 are exactly identical! WARNING: Sequences tr_F1PMK1_F1PMK1_CANLF_9615 and tr_F6V0G4_F6V0G4_HORSE_9796 are exactly identical! WARNING: Sequences tr_F1PMK1_F1PMK1_CANLF_9615 and tr_A0A2I2UND9_A0A2I2UND9_FELCA_9685 are exactly identical! WARNING: Sequences tr_F1PMK1_F1PMK1_CANLF_9615 and tr_A0A2U3VAW0_A0A2U3VAW0_ODORO_9708 are exactly identical! WARNING: Sequences tr_F1PMK1_F1PMK1_CANLF_9615 and tr_A0A384DC62_A0A384DC62_URSMA_29073 are exactly identical! WARNING: Sequences tr_F1Q080_F1Q080_CANLF_9615 and sp_O62683_ZO3_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3RIL3_A0A2I3RIL3_PANTR_9598 and sp_Q9UDY2_ZO2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3RIL3_A0A2I3RIL3_PANTR_9598 and tr_A0A2R9BLT3_A0A2R9BLT3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2QEZ5_H2QEZ5_PANTR_9598 and sp_O95049_ZO3_HUMAN_9606 are exactly identical! WARNING: Sequences tr_H2QEZ5_H2QEZ5_PANTR_9598 and tr_A0A2R9CBY6_A0A2R9CBY6_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A3B5Q5S1_A0A3B5Q5S1_XIPMA_8083 and tr_A0A087XD80_A0A087XD80_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A087ZPH4_A0A087ZPH4_APIME_7460 and tr_A0A0M8ZWT8_A0A0M8ZWT8_9HYME_166423 are exactly identical! WARNING: Sequences tr_A0A087ZPH4_A0A087ZPH4_APIME_7460 and tr_A0A154P021_A0A154P021_9HYME_178035 are exactly identical! WARNING: Sequences tr_A0A158NPX8_A0A158NPX8_ATTCE_12957 and tr_A0A195AT68_A0A195AT68_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158P3U0_A0A158P3U0_ATTCE_12957 and tr_F4WKY6_F4WKY6_ACREC_103372 are exactly identical! WARNING: Sequences tr_A0A158P3U0_A0A158P3U0_ATTCE_12957 and tr_A0A151WF88_A0A151WF88_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158P3U0_A0A158P3U0_ATTCE_12957 and tr_A0A195FIM9_A0A195FIM9_9HYME_34720 are exactly identical! WARNING: Sequences tr_F6S1D8_F6S1D8_MACMU_9544 and tr_G7P5U8_G7P5U8_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6S1D8_F6S1D8_MACMU_9544 and tr_A0A096N3B6_A0A096N3B6_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6S1D8_F6S1D8_MACMU_9544 and tr_A0A0D9QWE5_A0A0D9QWE5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6S1D8_F6S1D8_MACMU_9544 and tr_A0A2K5KXH0_A0A2K5KXH0_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6S1D8_F6S1D8_MACMU_9544 and tr_A0A2K6BPC7_A0A2K6BPC7_MACNE_9545 are exactly identical! WARNING: Sequences tr_E5SJF2_E5SJF2_TRISP_6334 and tr_A0A0V0UUM6_A0A0V0UUM6_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5STG8_E5STG8_TRISP_6334 and tr_A0A0V0RSV4_A0A0V0RSV4_9BILA_6336 are exactly identical! WARNING: Sequences tr_E5STG8_E5STG8_TRISP_6334 and tr_A0A0V1CP20_A0A0V1CP20_TRIBR_45882 are exactly identical! WARNING: Sequences tr_E5STG8_E5STG8_TRISP_6334 and tr_A0A0V0VJY8_A0A0V0VJY8_9BILA_181606 are exactly identical! WARNING: Sequences tr_E5STG8_E5STG8_TRISP_6334 and tr_A0A0V1LFP1_A0A0V1LFP1_9BILA_6335 are exactly identical! WARNING: Sequences tr_E5STG8_E5STG8_TRISP_6334 and tr_A0A0V0ZXM9_A0A0V0ZXM9_9BILA_990121 are exactly identical! WARNING: Sequences tr_E5STG8_E5STG8_TRISP_6334 and tr_A0A0V1NJW1_A0A0V1NJW1_9BILA_92180 are exactly identical! WARNING: Sequences tr_E5STG8_E5STG8_TRISP_6334 and tr_A0A0V0TWZ6_A0A0V0TWZ6_9BILA_144512 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_U3KHH7_U3KHH7_FICAL_59894 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_U3I7P8_U3I7P8_ANAPL_8839 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_A0A091EPR0_A0A091EPR0_CORBR_85066 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_A0A091JPV8_A0A091JPV8_EGRGA_188379 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_A0A093QDE2_A0A093QDE2_9PASS_328815 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_A0A091VAR5_A0A091VAR5_NIPNI_128390 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_A0A087RFY4_A0A087RFY4_APTFO_9233 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_A0A091W9T0_A0A091W9T0_OPIHO_30419 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_A0A091GCP6_A0A091GCP6_9AVES_55661 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_A0A2I0M0X0_A0A2I0M0X0_COLLI_8932 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_A0A093FU54_A0A093FU54_DRYPU_118200 are exactly identical! WARNING: Sequences tr_H0ZCH5_H0ZCH5_TAEGU_59729 and tr_A0A1V4KSC8_A0A1V4KSC8_PATFA_372326 are exactly identical! WARNING: Sequences tr_F4W7K0_F4W7K0_ACREC_103372 and tr_A0A151X8K9_A0A151X8K9_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A0P8Y0Q5_A0A0P8Y0Q5_DROAN_7217 and tr_A0A0M3QXL6_A0A0M3QXL6_DROBS_30019 are exactly identical! WARNING: Sequences tr_E3N1N6_E3N1N6_CAERE_31234 and tr_A8XWB2_A8XWB2_CAEBR_6238 are exactly identical! WARNING: Sequences tr_E3N1N6_E3N1N6_CAERE_31234 and tr_A0A2G5VT46_A0A2G5VT46_9PELO_1611254 are exactly identical! WARNING: Sequences tr_A8XKG7_A8XKG7_CAEBR_6238 and tr_A0A2G5SU12_A0A2G5SU12_9PELO_1611254 are exactly identical! WARNING: Sequences tr_A0A337S9E6_A0A337S9E6_FELCA_9685 and tr_A0A384C4C9_A0A384C4C9_URSMA_29073 are exactly identical! WARNING: Sequences tr_U3JKH1_U3JKH1_FICAL_59894 and tr_A0A091EK28_A0A091EK28_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3JKH1_U3JKH1_FICAL_59894 and tr_A0A093PIA8_A0A093PIA8_9PASS_328815 are exactly identical! WARNING: Sequences tr_A0A0K0FNW6_A0A0K0FNW6_STRVS_75913 and tr_A0A0N5BJU7_A0A0N5BJU7_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A151N1P3_A0A151N1P3_ALLMI_8496 and tr_A0A1U7SP87_A0A1U7SP87_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A0Q3TQZ8_A0A0Q3TQZ8_AMAAE_12930 and tr_A0A226MK34_A0A226MK34_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A194RMI3_A0A194RMI3_PAPMA_76193 and tr_A0A194PLT3_A0A194PLT3_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A0A0AR04_A0A0A0AR04_CHAVO_50402 and tr_A0A091HR54_A0A091HR54_CALAN_9244 are exactly identical! WARNING: Sequences tr_A0A2I0LL77_A0A2I0LL77_COLLI_8932 and tr_A0A1V4KG53_A0A1V4KG53_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A0V0XXB4_A0A0V0XXB4_TRIPS_6337 and tr_A0A0V1HCV7_A0A0V1HCV7_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A1S3ISC5_A0A1S3ISC5_LINUN_7574 and tr_A0A1S3IT50_A0A1S3IT50_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3KS05_A0A1S3KS05_SALSA_8030 and tr_A0A1S3PDQ0_A0A1S3PDQ0_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3KUJ6_A0A1S3KUJ6_SALSA_8030 and tr_A0A1S3PTA7_A0A1S3PTA7_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3KUJ6_A0A1S3KUJ6_SALSA_8030 and tr_A0A060WGJ7_A0A060WGJ7_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1I7TJU6_A0A1I7TJU6_9PELO_1561998 and tr_A0A1I7TJU7_A0A1I7TJU7_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1I7TJU6_A0A1I7TJU6_9PELO_1561998 and tr_A0A1I7TJU8_A0A1I7TJU8_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A1I7USX2_A0A1I7USX2_9PELO_1561998 and tr_A0A1I7USX3_A0A1I7USX3_9PELO_1561998 are exactly identical! WARNING: Sequences tr_A0A2D0PU68_A0A2D0PU68_ICTPU_7998 and tr_A0A2D0PVM0_A0A2D0PVM0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PU68_A0A2D0PU68_ICTPU_7998 and tr_A0A2D0PVN7_A0A2D0PVN7_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0PU68_A0A2D0PU68_ICTPU_7998 and tr_A0A2D0PXC3_A0A2D0PXC3_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QZ11_A0A2D0QZ11_ICTPU_7998 and tr_A0A2D0QZ14_A0A2D0QZ14_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0RTZ7_A0A2D0RTZ7_ICTPU_7998 and tr_A0A2D0RTZ8_A0A2D0RTZ8_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0SPJ5_A0A2D0SPJ5_ICTPU_7998 and tr_A0A2D0SQ56_A0A2D0SQ56_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2U4BAQ2_A0A2U4BAQ2_TURTR_9739 and tr_A0A2U4BAQ3_A0A2U4BAQ3_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4BAQ2_A0A2U4BAQ2_TURTR_9739 and tr_A0A2U4BAQ6_A0A2U4BAQ6_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4BAQ2_A0A2U4BAQ2_TURTR_9739 and tr_A0A2U4BB34_A0A2U4BB34_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4BAQ2_A0A2U4BAQ2_TURTR_9739 and tr_A0A2Y9NCU1_A0A2Y9NCU1_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2Y9EQ36_A0A2Y9EQ36_PHYCD_9755 and tr_A0A383ZNE7_A0A383ZNE7_BALAS_310752 are exactly identical! WARNING: Duplicate sequences found: 195 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UDY2/3_mltree/Q9UDY2.raxml.reduced.phy Alignment comprises 1 partitions and 125 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 125 / 125 Gaps: 6.55 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UDY2/3_mltree/Q9UDY2.raxml.rba Parallelization scheme autoconfig: 3 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 670 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 125 / 10000 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -139554.405586] Initial branch length optimization [00:00:01 -107831.952581] Model parameter optimization (eps = 10.000000) [00:00:21 -106902.395825] AUTODETECT spr round 1 (radius: 5) [00:01:12 -74948.773190] AUTODETECT spr round 2 (radius: 10) [00:02:07 -56136.209790] AUTODETECT spr round 3 (radius: 15) [00:03:08 -44666.200939] AUTODETECT spr round 4 (radius: 20) [00:04:15 -38050.662124] AUTODETECT spr round 5 (radius: 25) [00:05:31 -36207.469600] SPR radius for FAST iterations: 25 (autodetect) [00:05:31 -36207.469600] Model parameter optimization (eps = 3.000000) [00:05:48 -36075.693574] FAST spr round 1 (radius: 25) [00:06:49 -29565.789992] FAST spr round 2 (radius: 25) [00:07:38 -28409.154896] FAST spr round 3 (radius: 25) [00:08:22 -28328.198723] FAST spr round 4 (radius: 25) [00:09:03 -28325.668767] FAST spr round 5 (radius: 25) [00:09:44 -28323.945164] FAST spr round 6 (radius: 25) [00:10:22 -28323.944680] Model parameter optimization (eps = 1.000000) [00:10:31 -28320.904903] SLOW spr round 1 (radius: 5) [00:11:18 -28295.960244] SLOW spr round 2 (radius: 5) [00:12:05 -28295.561571] SLOW spr round 3 (radius: 5) [00:12:50 -28295.560919] SLOW spr round 4 (radius: 10) [00:13:39 -28294.963159] SLOW spr round 5 (radius: 5) [00:14:38 -28294.962484] SLOW spr round 6 (radius: 10) [00:15:35 -28293.351544] SLOW spr round 7 (radius: 5) [00:16:35 -28292.362853] SLOW spr round 8 (radius: 5) [00:17:26 -28292.362559] SLOW spr round 9 (radius: 10) [00:18:19 -28291.136109] SLOW spr round 10 (radius: 5) [00:19:17 -28291.135064] SLOW spr round 11 (radius: 10) [00:19:22] [worker #2] ML tree search #3, logLikelihood: -28280.563780 [00:20:13 -28291.134767] SLOW spr round 12 (radius: 15) [00:21:22 -28291.134483] SLOW spr round 13 (radius: 20) [00:22:59 -28288.763579] SLOW spr round 14 (radius: 5) [00:24:06 -28283.223963] SLOW spr round 15 (radius: 5) [00:25:04 -28282.990484] SLOW spr round 16 (radius: 5) [00:25:54 -28282.359737] SLOW spr round 17 (radius: 5) [00:26:44 -28281.762157] SLOW spr round 18 (radius: 5) [00:27:30 -28281.759212] SLOW spr round 19 (radius: 10) [00:28:19 -28281.724658] SLOW spr round 20 (radius: 15) [00:29:32 -28281.724608] SLOW spr round 21 (radius: 20) [00:31:11 -28281.724576] SLOW spr round 22 (radius: 25) [00:33:18 -28278.804311] SLOW spr round 23 (radius: 5) [00:34:23 -28278.804275] SLOW spr round 24 (radius: 10) [00:35:22 -28278.804272] SLOW spr round 25 (radius: 15) [00:36:31 -28278.804270] SLOW spr round 26 (radius: 20) [00:36:46] [worker #1] ML tree search #2, logLikelihood: -28572.471265 [00:38:12 -28278.804270] SLOW spr round 27 (radius: 25) [00:40:17 -28278.804269] Model parameter optimization (eps = 0.100000) [00:40:23] [worker #0] ML tree search #1, logLikelihood: -28278.492757 [00:40:24 -138262.006411] Initial branch length optimization [00:40:25 -107318.244823] Model parameter optimization (eps = 10.000000) [00:40:44 -106458.136373] AUTODETECT spr round 1 (radius: 5) [00:41:34 -71318.955608] AUTODETECT spr round 2 (radius: 10) [00:42:29 -51034.384430] AUTODETECT spr round 3 (radius: 15) [00:43:32 -42229.855374] AUTODETECT spr round 4 (radius: 20) [00:44:33 -38253.503164] AUTODETECT spr round 5 (radius: 25) [00:45:45 -36071.113843] SPR radius for FAST iterations: 25 (autodetect) [00:45:45 -36071.113843] Model parameter optimization (eps = 3.000000) [00:45:58 -35940.287231] FAST spr round 1 (radius: 25) [00:47:01 -28748.350669] FAST spr round 2 (radius: 25) [00:47:54 -28354.890605] FAST spr round 3 (radius: 25) [00:48:25] [worker #2] ML tree search #6, logLikelihood: -28271.920855 [00:48:40 -28298.632017] FAST spr round 4 (radius: 25) [00:49:21 -28297.512925] FAST spr round 5 (radius: 25) [00:50:00 -28297.511634] Model parameter optimization (eps = 1.000000) [00:50:07 -28295.602476] SLOW spr round 1 (radius: 5) [00:50:54 -28285.337375] SLOW spr round 2 (radius: 5) [00:51:40 -28284.352078] SLOW spr round 3 (radius: 5) [00:52:26 -28284.244354] SLOW spr round 4 (radius: 5) [00:53:11 -28284.244098] SLOW spr round 5 (radius: 10) [00:54:01 -28281.105672] SLOW spr round 6 (radius: 5) [00:55:01 -28281.104654] SLOW spr round 7 (radius: 10) [00:55:58 -28280.400333] SLOW spr round 8 (radius: 5) [00:56:55 -28280.400256] SLOW spr round 9 (radius: 10) [00:57:50 -28280.400217] SLOW spr round 10 (radius: 15) [00:59:03 -28280.400196] SLOW spr round 11 (radius: 20) [01:00:47 -28280.295713] SLOW spr round 12 (radius: 5) [01:01:52 -28280.064878] SLOW spr round 13 (radius: 5) [01:02:48 -28280.064872] SLOW spr round 14 (radius: 10) [01:03:42 -28280.064867] SLOW spr round 15 (radius: 15) [01:04:01] [worker #1] ML tree search #5, logLikelihood: -28267.017047 [01:04:55 -28280.064863] SLOW spr round 16 (radius: 20) [01:06:40 -28280.064859] SLOW spr round 17 (radius: 25) [01:08:51 -28279.687242] SLOW spr round 18 (radius: 5) [01:09:57 -28271.158402] SLOW spr round 19 (radius: 5) [01:10:55 -28266.413420] SLOW spr round 20 (radius: 5) [01:11:45 -28266.411235] SLOW spr round 21 (radius: 10) [01:12:36 -28266.410289] SLOW spr round 22 (radius: 15) [01:13:47 -28266.409843] SLOW spr round 23 (radius: 20) [01:15:27 -28266.409635] SLOW spr round 24 (radius: 25) [01:15:48] [worker #2] ML tree search #9, logLikelihood: -28268.534866 [01:17:34 -28266.409538] Model parameter optimization (eps = 0.100000) [01:17:38] [worker #0] ML tree search #4, logLikelihood: -28266.352367 [01:17:38 -137970.034203] Initial branch length optimization [01:17:39 -106934.823369] Model parameter optimization (eps = 10.000000) [01:17:57 -106135.784342] AUTODETECT spr round 1 (radius: 5) [01:18:45 -74021.869473] AUTODETECT spr round 2 (radius: 10) [01:19:38 -53093.071610] AUTODETECT spr round 3 (radius: 15) [01:20:37 -38943.015067] AUTODETECT spr round 4 (radius: 20) [01:21:40 -34963.231764] AUTODETECT spr round 5 (radius: 25) [01:22:45 -33501.791624] SPR radius for FAST iterations: 25 (autodetect) [01:22:45 -33501.791624] Model parameter optimization (eps = 3.000000) [01:22:59 -33413.246407] FAST spr round 1 (radius: 25) [01:23:59 -28994.477498] FAST spr round 2 (radius: 25) [01:24:08] [worker #1] ML tree search #8, logLikelihood: -28268.327050 [01:24:51 -28373.127249] FAST spr round 3 (radius: 25) [01:25:37 -28300.701575] FAST spr round 4 (radius: 25) [01:26:16 -28295.671170] FAST spr round 5 (radius: 25) [01:26:53 -28295.392558] FAST spr round 6 (radius: 25) [01:27:31 -28295.392315] Model parameter optimization (eps = 1.000000) [01:27:38 -28292.821148] SLOW spr round 1 (radius: 5) [01:28:27 -28276.128443] SLOW spr round 2 (radius: 5) [01:29:14 -28276.050169] SLOW spr round 3 (radius: 10) [01:30:06 -28274.510787] SLOW spr round 4 (radius: 5) [01:31:09 -28274.510045] SLOW spr round 5 (radius: 10) [01:32:09 -28273.824700] SLOW spr round 6 (radius: 5) [01:33:09 -28273.824313] SLOW spr round 7 (radius: 10) [01:34:07 -28273.824166] SLOW spr round 8 (radius: 15) [01:35:28 -28272.523248] SLOW spr round 9 (radius: 5) [01:36:26] [worker #2] ML tree search #12, logLikelihood: -28283.795957 [01:36:34 -28272.168459] SLOW spr round 10 (radius: 5) [01:37:31 -28272.168103] SLOW spr round 11 (radius: 10) [01:38:28 -28272.167954] SLOW spr round 12 (radius: 15) [01:39:48 -28272.167819] SLOW spr round 13 (radius: 20) [01:41:46 -28269.635873] SLOW spr round 14 (radius: 5) [01:42:54 -28269.633884] SLOW spr round 15 (radius: 10) [01:43:58 -28269.633192] SLOW spr round 16 (radius: 15) [01:45:17 -28269.632891] SLOW spr round 17 (radius: 20) [01:47:15 -28269.632711] SLOW spr round 18 (radius: 25) [01:48:49] [worker #1] ML tree search #11, logLikelihood: -28280.972808 [01:49:41 -28269.632567] Model parameter optimization (eps = 0.100000) [01:49:47] [worker #0] ML tree search #7, logLikelihood: -28269.317132 [01:49:47 -138651.793894] Initial branch length optimization [01:49:49 -107723.773568] Model parameter optimization (eps = 10.000000) [01:50:21 -106908.183022] AUTODETECT spr round 1 (radius: 5) [01:51:16 -74346.019112] AUTODETECT spr round 2 (radius: 10) [01:52:13 -53782.470408] AUTODETECT spr round 3 (radius: 15) [01:53:17 -44821.224415] AUTODETECT spr round 4 (radius: 20) [01:54:39 -36135.237331] AUTODETECT spr round 5 (radius: 25) [01:56:03 -34537.235077] SPR radius for FAST iterations: 25 (autodetect) [01:56:03 -34537.235077] Model parameter optimization (eps = 3.000000) [01:56:16 -34434.630856] FAST spr round 1 (radius: 25) [01:57:13 -28960.900863] FAST spr round 2 (radius: 25) [01:58:05 -28393.070994] FAST spr round 3 (radius: 25) [01:58:48 -28283.370702] FAST spr round 4 (radius: 25) [01:59:28 -28279.409658] FAST spr round 5 (radius: 25) [02:00:10 -28277.411095] FAST spr round 6 (radius: 25) [02:00:51 -28277.410648] Model parameter optimization (eps = 1.000000) [02:01:02 -28275.695994] SLOW spr round 1 (radius: 5) [02:01:51 -28268.886228] SLOW spr round 2 (radius: 5) [02:01:59] [worker #2] ML tree search #15, logLikelihood: -28277.372282 [02:02:39 -28268.808121] SLOW spr round 3 (radius: 10) [02:03:32 -28268.567692] SLOW spr round 4 (radius: 5) [02:04:35 -28268.565843] SLOW spr round 5 (radius: 10) [02:05:35 -28268.007901] SLOW spr round 6 (radius: 5) [02:06:36 -28266.659986] SLOW spr round 7 (radius: 5) [02:07:30 -28266.659047] SLOW spr round 8 (radius: 10) [02:08:24 -28266.658672] SLOW spr round 9 (radius: 15) [02:09:43 -28265.681921] SLOW spr round 10 (radius: 5) [02:10:50 -28265.681762] SLOW spr round 11 (radius: 10) [02:11:51 -28265.681646] SLOW spr round 12 (radius: 15) [02:13:08 -28265.681545] SLOW spr round 13 (radius: 20) [02:14:50 -28265.554231] SLOW spr round 14 (radius: 5) [02:15:52 -28265.553947] SLOW spr round 15 (radius: 10) [02:16:53 -28265.553802] SLOW spr round 16 (radius: 15) [02:17:35] [worker #1] ML tree search #14, logLikelihood: -28270.041152 [02:18:09 -28265.553689] SLOW spr round 17 (radius: 20) [02:20:00 -28265.553590] SLOW spr round 18 (radius: 25) [02:22:19 -28265.553496] Model parameter optimization (eps = 0.100000) [02:22:25] [worker #0] ML tree search #10, logLikelihood: -28265.382265 [02:22:25 -138952.185906] Initial branch length optimization [02:22:27 -107546.183433] Model parameter optimization (eps = 10.000000) [02:22:45 -106675.175687] AUTODETECT spr round 1 (radius: 5) [02:23:39 -72777.396326] AUTODETECT spr round 2 (radius: 10) [02:24:36 -53085.863250] AUTODETECT spr round 3 (radius: 15) [02:25:42 -40100.853762] AUTODETECT spr round 4 (radius: 20) [02:27:06 -35362.292831] AUTODETECT spr round 5 (radius: 25) [02:28:41 -34895.195335] SPR radius for FAST iterations: 25 (autodetect) [02:28:41 -34895.195335] Model parameter optimization (eps = 3.000000) [02:28:56 -34767.214207] FAST spr round 1 (radius: 25) [02:29:53 -29121.637984] FAST spr round 2 (radius: 25) [02:30:43 -28373.895364] FAST spr round 3 (radius: 25) [02:31:27 -28312.194702] FAST spr round 4 (radius: 25) [02:31:58] [worker #2] ML tree search #18, logLikelihood: -28269.540497 [02:32:05 -28304.525721] FAST spr round 5 (radius: 25) [02:32:40 -28304.525053] Model parameter optimization (eps = 1.000000) [02:32:49 -28300.011515] SLOW spr round 1 (radius: 5) [02:33:33 -28288.955834] SLOW spr round 2 (radius: 5) [02:34:17 -28287.063020] SLOW spr round 3 (radius: 5) [02:34:59 -28287.061688] SLOW spr round 4 (radius: 10) [02:35:47 -28286.219779] SLOW spr round 5 (radius: 5) [02:36:42 -28286.218652] SLOW spr round 6 (radius: 10) [02:37:36 -28286.218178] SLOW spr round 7 (radius: 15) [02:38:43 -28283.513374] SLOW spr round 8 (radius: 5) [02:39:43 -28283.511966] SLOW spr round 9 (radius: 10) [02:40:40 -28282.528662] SLOW spr round 10 (radius: 5) [02:41:33 -28282.527763] SLOW spr round 11 (radius: 10) [02:42:26 -28281.197881] SLOW spr round 12 (radius: 5) [02:43:21 -28274.229899] SLOW spr round 13 (radius: 5) [02:44:11 -28270.858298] SLOW spr round 14 (radius: 5) [02:44:57 -28270.857184] SLOW spr round 15 (radius: 10) [02:45:44 -28270.088163] SLOW spr round 16 (radius: 5) [02:46:40 -28269.118122] SLOW spr round 17 (radius: 5) [02:47:29 -28269.117370] SLOW spr round 18 (radius: 10) [02:48:20 -28269.117181] SLOW spr round 19 (radius: 15) [02:49:29 -28269.117041] SLOW spr round 20 (radius: 20) [02:51:07 -28269.116925] SLOW spr round 21 (radius: 25) [02:53:06 -28269.116834] Model parameter optimization (eps = 0.100000) [02:53:09] [worker #0] ML tree search #13, logLikelihood: -28269.098942 [02:53:09 -138401.412885] Initial branch length optimization [02:53:11 -106575.153417] Model parameter optimization (eps = 10.000000) [02:53:34 -105769.145278] AUTODETECT spr round 1 (radius: 5) [02:54:32 -73869.142423] AUTODETECT spr round 2 (radius: 10) [02:55:33 -51907.808908] AUTODETECT spr round 3 (radius: 15) [02:56:43 -42746.072827] AUTODETECT spr round 4 (radius: 20) [02:58:10 -34851.976698] AUTODETECT spr round 5 (radius: 25) [02:59:46 -33167.625512] SPR radius for FAST iterations: 25 (autodetect) [02:59:46 -33167.625512] Model parameter optimization (eps = 3.000000) [03:00:15 -33007.843996] FAST spr round 1 (radius: 25) [03:01:18 -29085.838436] FAST spr round 2 (radius: 25) [03:02:12 -28556.918981] FAST spr round 3 (radius: 25) [03:03:04 -28486.798975] FAST spr round 4 (radius: 25) [03:03:51 -28376.591120] FAST spr round 5 (radius: 25) [03:04:36 -28309.792530] FAST spr round 6 (radius: 25) [03:04:52] [worker #1] ML tree search #17, logLikelihood: -28283.125139 [03:05:19 -28307.842783] FAST spr round 7 (radius: 25) [03:06:01 -28307.842508] Model parameter optimization (eps = 1.000000) [03:06:14 -28298.586679] SLOW spr round 1 (radius: 5) [03:07:08 -28288.233305] SLOW spr round 2 (radius: 5) [03:07:59 -28288.017518] SLOW spr round 3 (radius: 5) [03:08:50 -28288.017481] SLOW spr round 4 (radius: 10) [03:09:46 -28287.812720] SLOW spr round 5 (radius: 5) [03:10:55 -28287.671612] SLOW spr round 6 (radius: 5) [03:11:55 -28287.671506] SLOW spr round 7 (radius: 10) [03:12:55 -28287.671505] SLOW spr round 8 (radius: 15) [03:14:15 -28287.671505] SLOW spr round 9 (radius: 20) [03:16:08 -28287.671505] SLOW spr round 10 (radius: 25) [03:18:22 -28287.460219] SLOW spr round 11 (radius: 5) [03:19:37 -28287.460212] SLOW spr round 12 (radius: 10) [03:20:47 -28287.460211] SLOW spr round 13 (radius: 15) [03:22:05 -28287.460211] SLOW spr round 14 (radius: 20) [03:23:57 -28287.460211] SLOW spr round 15 (radius: 25) [03:26:11 -28287.460211] Model parameter optimization (eps = 0.100000) [03:26:20] [worker #0] ML tree search #16, logLikelihood: -28286.520498 [03:26:20 -138671.924455] Initial branch length optimization [03:26:22 -107211.725882] Model parameter optimization (eps = 10.000000) [03:26:47 -106290.793496] AUTODETECT spr round 1 (radius: 5) [03:27:46 -72634.989915] AUTODETECT spr round 2 (radius: 10) [03:28:48 -54126.846616] AUTODETECT spr round 3 (radius: 15) [03:29:58 -43809.043913] AUTODETECT spr round 4 (radius: 20) [03:31:22 -39484.054416] AUTODETECT spr round 5 (radius: 25) [03:33:06 -37476.941961] SPR radius for FAST iterations: 25 (autodetect) [03:33:07 -37476.941961] Model parameter optimization (eps = 3.000000) [03:33:26 -37299.673130] FAST spr round 1 (radius: 25) [03:34:21] [worker #1] ML tree search #20, logLikelihood: -28294.641122 [03:34:39 -29429.972550] FAST spr round 2 (radius: 25) [03:35:39 -28833.727283] FAST spr round 3 (radius: 25) [03:36:34 -28557.605261] FAST spr round 4 (radius: 25) [03:37:27 -28390.917920] FAST spr round 5 (radius: 25) [03:38:15 -28324.558177] FAST spr round 6 (radius: 25) [03:38:58 -28324.557364] Model parameter optimization (eps = 1.000000) [03:39:05 -28322.786781] SLOW spr round 1 (radius: 5) [03:39:59 -28305.835883] SLOW spr round 2 (radius: 5) [03:40:51 -28302.312976] SLOW spr round 3 (radius: 5) [03:41:42 -28302.310906] SLOW spr round 4 (radius: 10) [03:42:41 -28298.637460] SLOW spr round 5 (radius: 5) [03:43:51 -28295.933110] SLOW spr round 6 (radius: 5) [03:44:52 -28295.468848] SLOW spr round 7 (radius: 5) [03:45:48 -28295.466385] SLOW spr round 8 (radius: 10) [03:46:45 -28295.465447] SLOW spr round 9 (radius: 15) [03:48:12 -28295.241232] SLOW spr round 10 (radius: 5) [03:49:23 -28295.237553] SLOW spr round 11 (radius: 10) [03:50:29 -28295.237412] SLOW spr round 12 (radius: 15) [03:51:51 -28295.237294] SLOW spr round 13 (radius: 20) [03:53:50 -28294.995494] SLOW spr round 14 (radius: 5) [03:55:03 -28294.995392] SLOW spr round 15 (radius: 10) [03:56:11 -28294.995293] SLOW spr round 16 (radius: 15) [03:57:32 -28294.995193] SLOW spr round 17 (radius: 20) [03:59:31 -28294.995094] SLOW spr round 18 (radius: 25) [04:01:58 -28294.720415] SLOW spr round 19 (radius: 5) [04:03:11 -28294.625204] SLOW spr round 20 (radius: 10) [04:04:21 -28293.083898] SLOW spr round 21 (radius: 5) [04:05:25 -28293.083554] SLOW spr round 22 (radius: 10) [04:06:28 -28293.083442] SLOW spr round 23 (radius: 15) [04:07:50 -28293.083338] SLOW spr round 24 (radius: 20) [04:09:49 -28293.083234] SLOW spr round 25 (radius: 25) [04:12:16 -28293.083130] Model parameter optimization (eps = 0.100000) [04:12:20] [worker #0] ML tree search #19, logLikelihood: -28293.029126 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.207702,0.523702) (0.193698,0.532203) (0.463917,1.149949) (0.134683,1.890796) 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: -28265.382265 AIC score: 59216.764531 / AICc score: 3669200.764531 / BIC score: 63015.189880 Free parameters (model + branch lengths): 1343 WARNING: Number of free parameters (K=1343) is larger than alignment size (n=125). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 264 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UDY2/3_mltree/Q9UDY2.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UDY2/3_mltree/Q9UDY2.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UDY2/3_mltree/Q9UDY2.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UDY2/3_mltree/Q9UDY2.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UDY2/3_mltree/Q9UDY2.raxml.log Analysis started: 07-Jul-2021 23:54:35 / finished: 08-Jul-2021 04:06:55 Elapsed time: 15140.413 seconds Consumed energy: 845.922 Wh (= 4 km in an electric car, or 21 km with an e-scooter!)