RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab. Developed by: Alexey M. Kozlov and Alexandros Stamatakis. Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth. Latest version: https://github.com/amkozlov/raxml-ng Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM RAxML-NG was called at 01-Jul-2021 17:06:20 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/2_msa/P51610_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/3_mltree/P51610 --seed 2 --threads 6 --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 (6 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/2_msa/P51610_trimmed_msa.fasta [00:00:00] Loaded alignment with 895 taxa and 289 sites WARNING: Sequences tr_E1BSD7_E1BSD7_CHICK_9031 and tr_A0A091G886_A0A091G886_9AVES_55661 are exactly identical! WARNING: Sequences sp_Q61191_HCFC1_MOUSE_10090 and tr_D3ZN95_D3ZN95_RAT_10116 are exactly identical! WARNING: Sequences sp_Q61191_HCFC1_MOUSE_10090 and tr_A0A1U7Q220_A0A1U7Q220_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q61191_HCFC1_MOUSE_10090 and sp_P51611_HCFC1_MESAU_10036 are exactly identical! WARNING: Sequences sp_Q8VEM9_KLDC3_MOUSE_10090 and tr_G3HR72_G3HR72_CRIGR_10029 are exactly identical! WARNING: Sequences sp_Q8VEM9_KLDC3_MOUSE_10090 and sp_Q6AYI2_KLDC3_RAT_10116 are exactly identical! WARNING: Sequences sp_Q8VEM9_KLDC3_MOUSE_10090 and tr_A0A1U7QES9_A0A1U7QES9_MESAU_10036 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_G3R2W8_G3R2W8_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_H2PX72_H2PX72_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_H2QZT7_H2QZT7_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and sp_P51610_HCFC1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_F7GKR6_F7GKR6_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_A0A096NAF2_A0A096NAF2_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_A0A0D9R3A5_A0A0D9R3A5_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_A0A2K5L3M5_A0A2K5L3M5_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_A0A2K6C8M3_A0A2K6C8M3_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_A0A2K6A9N8_A0A2K6A9N8_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_A0A2R9CM34_A0A2R9CM34_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3YCA0_M3YCA0_MUSPF_9669 and tr_A0A2Y9IM09_A0A2Y9IM09_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YKV3_M3YKV3_MUSPF_9669 and tr_I3M5R8_I3M5R8_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3YKV3_M3YKV3_MUSPF_9669 and tr_D2H1T2_D2H1T2_AILME_9646 are exactly identical! WARNING: Sequences tr_M3YKV3_M3YKV3_MUSPF_9669 and tr_E1BEJ7_E1BEJ7_BOVIN_9913 are exactly identical! WARNING: Sequences tr_M3YKV3_M3YKV3_MUSPF_9669 and tr_M3WK15_M3WK15_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3YKV3_M3YKV3_MUSPF_9669 and tr_A0A2Y9IRC9_A0A2Y9IRC9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3YNX7_M3YNX7_MUSPF_9669 and tr_A0A2Y9JJA8_A0A2Y9JJA8_ENHLU_391180 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_G1SES4_G1SES4_RABIT_9986 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_E2QXV1_E2QXV1_CANLF_9615 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_I3N3V9_I3N3V9_ICTTR_43179 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_G3TTQ4_G3TTQ4_LOXAF_9785 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_G1MJG9_G1MJG9_AILME_9646 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_L5KGT9_L5KGT9_PTEAL_9402 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_A0A2I2U583_A0A2I2U583_FELCA_9685 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_A0A1S3AHC1_A0A1S3AHC1_ERIEU_9365 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_A0A1S3GQ84_A0A1S3GQ84_DIPOR_10020 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_A0A2U3WK97_A0A2U3WK97_ODORO_9708 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_A0A2Y9EC60_A0A2Y9EC60_TRIMA_127582 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_A0A2Y9MKL8_A0A2Y9MKL8_DELLE_9749 are exactly identical! WARNING: Sequences tr_G1PPP6_G1PPP6_MYOLU_59463 and tr_A0A2Y9S1M4_A0A2Y9S1M4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_B6QQV5_B6QQV5_TALMQ_441960 and tr_A0A093XE30_A0A093XE30_TALMA_1077442 are exactly identical! WARNING: Sequences tr_A0A2I2YK61_A0A2I2YK61_GORGO_9595 and sp_Q9Y5Z7_HCFC2_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2YK61_A0A2I2YK61_GORGO_9595 and tr_F7HUQ6_F7HUQ6_CALJA_9483 are exactly identical! WARNING: Sequences tr_A0A2I2YK61_A0A2I2YK61_GORGO_9595 and tr_A0A0D9S2E0_A0A0D9S2E0_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_H2PJ37_H2PJ37_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_G2HIN0_G2HIN0_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_G7P3Z0_G7P3Z0_MACFA_9541 are exactly identical! WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_A0A096NI88_A0A096NI88_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_A0A0D9RGK8_A0A0D9RGK8_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_A0A2K5MK54_A0A2K5MK54_CERAT_9531 are exactly identical! WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_A0A2K6B6Q7_A0A2K6B6Q7_MACNE_9545 are exactly identical! WARNING: Sequences tr_G3S6N3_G3S6N3_GORGO_9595 and tr_A0A2R9BC63_A0A2R9BC63_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A179U7M8_A0A179U7M8_BLAGS_559298 and tr_C5GX79_C5GX79_AJEDR_559297 are exactly identical! WARNING: Sequences tr_A0A3B5RE01_A0A3B5RE01_XIPMA_8083 and tr_A0A087YJA9_A0A087YJA9_POEFO_48698 are exactly identical! WARNING: Sequences tr_M4A542_M4A542_XIPMA_8083 and tr_A0A087YBP1_A0A087YBP1_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A088ALI5_A0A088ALI5_APIME_7460 and tr_A0A2A3EAK3_A0A2A3EAK3_APICC_94128 are exactly identical! WARNING: Sequences tr_H2U647_H2U647_TAKRU_31033 and tr_H3C6E6_H3C6E6_TETNG_99883 are exactly identical! WARNING: Sequences tr_A0A0E0FKN0_A0A0E0FKN0_ORYNI_4536 and tr_I1NMH2_I1NMH2_ORYGL_4538 are exactly identical! WARNING: Sequences tr_A0A0E0FKN0_A0A0E0FKN0_ORYNI_4536 and tr_A0A0E0MV54_A0A0E0MV54_ORYRU_4529 are exactly identical! WARNING: Sequences tr_A0A0E0FKN0_A0A0E0FKN0_ORYNI_4536 and tr_Q94D04_Q94D04_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_I1QMA2_I1QMA2_ORYGL_4538 and tr_Q6ZXK6_Q6ZXK6_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G3P7C9_G3P7C9_GASAC_69293 and tr_A0A2U9BH34_A0A2U9BH34_SCOMX_52904 are exactly identical! WARNING: Sequences tr_F2SEM9_F2SEM9_TRIRC_559305 and tr_F2PIU8_F2PIU8_TRIEC_559882 are exactly identical! WARNING: Sequences tr_F2SEM9_F2SEM9_TRIRC_559305 and tr_A0A059J2S2_A0A059J2S2_9EURO_1215338 are exactly identical! WARNING: Sequences tr_F2SEM9_F2SEM9_TRIRC_559305 and tr_A0A178ETG7_A0A178ETG7_TRIRU_5551 are exactly identical! WARNING: Sequences tr_W7LAC6_W7LAC6_GIBM7_334819 and tr_S0DQJ4_S0DQJ4_GIBF5_1279085 are exactly identical! WARNING: Sequences tr_W7LAC6_W7LAC6_GIBM7_334819 and tr_X0CZA5_X0CZA5_FUSOX_1089458 are exactly identical! WARNING: Sequences tr_W7LAC6_W7LAC6_GIBM7_334819 and tr_A0A2H3T0C9_A0A2H3T0C9_FUSOX_5507 are exactly identical! WARNING: Sequences tr_W7LAC6_W7LAC6_GIBM7_334819 and tr_A0A2H3HV43_A0A2H3HV43_FUSOX_327505 are exactly identical! WARNING: Sequences tr_W7LAC6_W7LAC6_GIBM7_334819 and tr_A0A2K0VUH4_A0A2K0VUH4_GIBNY_42673 are exactly identical! WARNING: Sequences tr_W7LAC6_W7LAC6_GIBM7_334819 and tr_A0A365MUQ7_A0A365MUQ7_GIBIN_948311 are exactly identical! WARNING: Sequences tr_M4EA65_M4EA65_BRARP_51351 and tr_A0A078GJM9_A0A078GJM9_BRANA_3708 are exactly identical! WARNING: Sequences tr_U3JDH3_U3JDH3_FICAL_59894 and tr_A0A093PRB6_A0A093PRB6_9PASS_328815 are exactly identical! WARNING: Sequences tr_U3JDH3_U3JDH3_FICAL_59894 and tr_A0A0A0A320_A0A0A0A320_CHAVO_50402 are exactly identical! WARNING: Sequences tr_U3JDH3_U3JDH3_FICAL_59894 and tr_A0A2I0LV87_A0A2I0LV87_COLLI_8932 are exactly identical! WARNING: Sequences tr_U3JDH3_U3JDH3_FICAL_59894 and tr_A0A1V4KBD3_A0A1V4KBD3_PATFA_372326 are exactly identical! WARNING: Sequences tr_W2RAS5_W2RAS5_PHYPN_761204 and tr_A0A0W8CFI4_A0A0W8CFI4_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A015JNQ8_A0A015JNQ8_9GLOM_1432141 and tr_A0A2H5RP79_A0A2H5RP79_RHIID_747089 are exactly identical! WARNING: Sequences tr_A0A044T6V2_A0A044T6V2_ONCVO_6282 and tr_A0A182E772_A0A182E772_ONCOC_42157 are exactly identical! WARNING: Sequences tr_A0A096NGK6_A0A096NGK6_PAPAN_9555 and tr_A0A2K6D2L4_A0A2K6D2L4_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A0D2R286_A0A0D2R286_GOSRA_29730 and tr_A0A1U8LJS1_A0A1U8LJS1_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0D2R9I4_A0A0D2R9I4_GOSRA_29730 and tr_A0A1U8M3Z8_A0A1U8M3Z8_GOSHI_3635 are exactly identical! WARNING: Sequences tr_A0A0M9EXI9_A0A0M9EXI9_FUSLA_179993 and tr_I1RWM7_I1RWM7_GIBZE_229533 are exactly identical! WARNING: Sequences tr_A0A0A1MML8_A0A0A1MML8_9FUNG_58291 and tr_A0A367JJD2_A0A367JJD2_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1N2L6_A0A0A1N2L6_9FUNG_58291 and tr_A0A367JMY5_A0A367JMY5_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0A1P7M5_A0A0A1P7M5_9FUNG_58291 and tr_A0A367JYL3_A0A367JYL3_9FUNG_86630 are exactly identical! WARNING: Sequences tr_A0A0N0PE86_A0A0N0PE86_PAPMA_76193 and tr_A0A194PKM0_A0A194PKM0_PAPXU_66420 are exactly identical! WARNING: Sequences tr_A0A0V1CUR9_A0A0V1CUR9_TRIBR_45882 and tr_A0A0V1PA35_A0A0V1PA35_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D308_A0A0V1D308_TRIBR_45882 and tr_A0A0V0WEK7_A0A0V0WEK7_9BILA_92179 are exactly identical! WARNING: Sequences tr_A0A0V1D308_A0A0V1D308_TRIBR_45882 and tr_A0A0V0UVR8_A0A0V0UVR8_9BILA_181606 are exactly identical! WARNING: Sequences tr_A0A0V1D308_A0A0V1D308_TRIBR_45882 and tr_A0A0V1LES6_A0A0V1LES6_9BILA_6335 are exactly identical! WARNING: Sequences tr_A0A0V1D308_A0A0V1D308_TRIBR_45882 and tr_A0A0V1NLP2_A0A0V1NLP2_9BILA_92180 are exactly identical! WARNING: Sequences tr_A0A0V1D308_A0A0V1D308_TRIBR_45882 and tr_A0A0V0TQU9_A0A0V0TQU9_9BILA_144512 are exactly identical! WARNING: Sequences tr_A0A0V1MJ13_A0A0V1MJ13_9BILA_268474 and tr_A0A0V1HEH0_A0A0V1HEH0_9BILA_268475 are exactly identical! WARNING: Sequences tr_A0A0V1MVF4_A0A0V1MVF4_9BILA_268474 and tr_A0A0V1I4S5_A0A0V1I4S5_9BILA_268475 are exactly identical! WARNING: Sequences tr_I1RAW8_I1RAW8_GIBZE_229533 and tr_A0A2T4H8Q0_A0A2T4H8Q0_FUSCU_5516 are exactly identical! WARNING: Sequences tr_A0A151J7W9_A0A151J7W9_9HYME_471704 and tr_A0A195BVP0_A0A195BVP0_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A151J7W9_A0A151J7W9_9HYME_471704 and tr_A0A151I726_A0A151I726_9HYME_456900 are exactly identical! WARNING: Sequences tr_A0A1S3P314_A0A1S3P314_SALSA_8030 and tr_A0A060W8B6_A0A060W8B6_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3UXI3_A0A1S3UXI3_VIGRR_3916 and tr_A0A3Q0F611_A0A3Q0F611_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A1S3UXI3_A0A1S3UXI3_VIGRR_3916 and tr_A0A3Q0F9R4_A0A3Q0F9R4_VIGRR_3916 are exactly identical! WARNING: Sequences tr_A0A2D0QZ81_A0A2D0QZ81_ICTPU_7998 and tr_A0A2D0QZ84_A0A2D0QZ84_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QZ81_A0A2D0QZ81_ICTPU_7998 and tr_A0A2D0QZH0_A0A2D0QZH0_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0QZ81_A0A2D0QZ81_ICTPU_7998 and tr_A0A2D0R0Z9_A0A2D0R0Z9_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2D0T4I9_A0A2D0T4I9_ICTPU_7998 and tr_A0A2D0T549_A0A2D0T549_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G2Y0F7_A0A2G2Y0F7_CAPAN_4072 and tr_A0A2G3AWY2_A0A2G3AWY2_CAPCH_80379 are exactly identical! WARNING: Sequences tr_A0A2K5MV84_A0A2K5MV84_CERAT_9531 and tr_A0A2K6AEL8_A0A2K6AEL8_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2U4CRC8_A0A2U4CRC8_TURTR_9739 and tr_A0A2U4CRD2_A0A2U4CRD2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4CRC8_A0A2U4CRC8_TURTR_9739 and tr_A0A2U4CRD6_A0A2U4CRD6_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4CRC8_A0A2U4CRC8_TURTR_9739 and tr_A0A2U4CRE2_A0A2U4CRE2_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4CRC8_A0A2U4CRC8_TURTR_9739 and tr_A0A2U4CRN9_A0A2U4CRN9_TURTR_9739 are exactly identical! WARNING: Sequences tr_A0A2U4CRC8_A0A2U4CRC8_TURTR_9739 and tr_A0A2Y9QKG9_A0A2Y9QKG9_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CRC8_A0A2U4CRC8_TURTR_9739 and tr_A0A2Y9FEG0_A0A2Y9FEG0_PHYCD_9755 are exactly identical! WARNING: Duplicate sequences found: 111 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/P51610/3_mltree/P51610.raxml.reduced.phy Alignment comprises 1 partitions and 289 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 289 / 289 Gaps: 14.84 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/3_mltree/P51610.raxml.rba Parallelization scheme autoconfig: 6 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 895 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 289 / 23120 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -464733.518733] Initial branch length optimization [00:00:06 -370647.791733] Model parameter optimization (eps = 10.000000) [00:01:23 -366831.059517] AUTODETECT spr round 1 (radius: 5) [00:04:23 -282440.163405] AUTODETECT spr round 2 (radius: 10) [00:07:39 -211061.405622] AUTODETECT spr round 3 (radius: 15) [00:11:08 -172977.377327] AUTODETECT spr round 4 (radius: 20) [00:15:30 -147707.091691] AUTODETECT spr round 5 (radius: 25) [00:20:08 -143690.978229] SPR radius for FAST iterations: 25 (autodetect) [00:20:08 -143690.978229] Model parameter optimization (eps = 3.000000) [00:20:44 -143495.523345] FAST spr round 1 (radius: 25) [00:24:54 -124910.876633] FAST spr round 2 (radius: 25) [00:27:58 -124043.215172] FAST spr round 3 (radius: 25) [00:30:31 -123922.624713] FAST spr round 4 (radius: 25) [00:32:51 -123911.627137] FAST spr round 5 (radius: 25) [00:35:02 -123898.862278] FAST spr round 6 (radius: 25) [00:37:05 -123894.547938] FAST spr round 7 (radius: 25) [00:39:15 -123722.898238] FAST spr round 8 (radius: 25) [00:41:19 -123720.895552] FAST spr round 9 (radius: 25) [00:43:14 -123720.894919] Model parameter optimization (eps = 1.000000) [00:43:41 -123650.950435] SLOW spr round 1 (radius: 5) [00:46:21 -123622.921245] SLOW spr round 2 (radius: 5) [00:48:58 -123617.492641] SLOW spr round 3 (radius: 5) [00:51:37 -123617.199454] SLOW spr round 4 (radius: 5) [00:54:13 -123617.197325] SLOW spr round 5 (radius: 10) [00:57:14 -123604.959972] SLOW spr round 6 (radius: 5) [01:00:28 -123602.854576] SLOW spr round 7 (radius: 5) [01:03:19 -123602.421942] SLOW spr round 8 (radius: 5) [01:06:00 -123602.421705] SLOW spr round 9 (radius: 10) [01:08:56 -123602.421658] SLOW spr round 10 (radius: 15) [01:13:55 -123601.731432] SLOW spr round 11 (radius: 5) [01:17:16 -123601.033021] SLOW spr round 12 (radius: 5) [01:20:11 -123601.032100] SLOW spr round 13 (radius: 10) [01:23:17 -123601.032040] SLOW spr round 14 (radius: 15) [01:28:02 -123601.032032] SLOW spr round 15 (radius: 20) [01:34:59 -123601.032030] SLOW spr round 16 (radius: 25) [01:37:36] [worker #5] ML tree search #6, logLikelihood: -123625.443759 [01:43:28 -123600.572473] SLOW spr round 17 (radius: 5) [01:46:56 -123600.572390] SLOW spr round 18 (radius: 10) [01:50:38 -123600.572388] SLOW spr round 19 (radius: 15) [01:51:39] [worker #3] ML tree search #4, logLikelihood: -123599.387360 [01:55:18 -123600.572387] SLOW spr round 20 (radius: 20) [02:01:20] [worker #2] ML tree search #3, logLikelihood: -123623.317796 [02:02:15 -123600.572387] SLOW spr round 21 (radius: 25) [02:02:43] [worker #1] ML tree search #2, logLikelihood: -123644.840472 [02:06:11] [worker #4] ML tree search #5, logLikelihood: -123600.967966 [02:10:44 -123600.572386] Model parameter optimization (eps = 0.100000) [02:10:56] [worker #0] ML tree search #1, logLikelihood: -123600.405219 [02:10:56 -467066.378967] Initial branch length optimization [02:11:00 -374559.811917] Model parameter optimization (eps = 10.000000) [02:12:13 -370610.728136] AUTODETECT spr round 1 (radius: 5) [02:15:09 -276043.665094] AUTODETECT spr round 2 (radius: 10) [02:18:22 -211256.161781] AUTODETECT spr round 3 (radius: 15) [02:21:42 -172273.128226] AUTODETECT spr round 4 (radius: 20) [02:25:41 -160819.480253] AUTODETECT spr round 5 (radius: 25) [02:30:35 -148165.813932] SPR radius for FAST iterations: 25 (autodetect) [02:30:35 -148165.813932] Model parameter optimization (eps = 3.000000) [02:31:16 -147901.858484] FAST spr round 1 (radius: 25) [02:35:14 -125017.228610] FAST spr round 2 (radius: 25) [02:38:02 -123797.675800] FAST spr round 3 (radius: 25) [02:40:33 -123692.893021] FAST spr round 4 (radius: 25) [02:42:50 -123667.064096] FAST spr round 5 (radius: 25) [02:44:55 -123664.333046] FAST spr round 6 (radius: 25) [02:46:58 -123658.691490] FAST spr round 7 (radius: 25) [02:48:59 -123652.506051] FAST spr round 8 (radius: 25) [02:50:57 -123651.181215] FAST spr round 9 (radius: 25) [02:52:53 -123651.180966] Model parameter optimization (eps = 1.000000) [02:53:13 -123648.322645] SLOW spr round 1 (radius: 5) [02:55:51 -123619.487376] SLOW spr round 2 (radius: 5) [02:58:32 -123611.277531] SLOW spr round 3 (radius: 5) [03:01:07 -123610.478137] SLOW spr round 4 (radius: 5) [03:03:40 -123610.477993] SLOW spr round 5 (radius: 10) [03:06:33 -123610.477954] SLOW spr round 6 (radius: 15) [03:11:48 -123610.477952] SLOW spr round 7 (radius: 20) [03:19:06 -123610.235645] SLOW spr round 8 (radius: 5) [03:22:31 -123610.234719] SLOW spr round 9 (radius: 10) [03:26:07 -123610.234710] SLOW spr round 10 (radius: 15) [03:31:07 -123610.234710] SLOW spr round 11 (radius: 20) [03:36:08] [worker #3] ML tree search #10, logLikelihood: -123596.126547 [03:38:28 -123610.234710] SLOW spr round 12 (radius: 25) [03:39:33] [worker #4] ML tree search #11, logLikelihood: -123611.992450 [03:47:11 -123609.788150] SLOW spr round 13 (radius: 5) [03:50:39 -123609.788149] SLOW spr round 14 (radius: 10) [03:53:32] [worker #1] ML tree search #8, logLikelihood: -123603.394334 [03:54:20 -123609.788149] SLOW spr round 15 (radius: 15) [03:59:20 -123609.788149] SLOW spr round 16 (radius: 20) [04:02:28] [worker #2] ML tree search #9, logLikelihood: -123631.494658 [04:06:42 -123609.788149] SLOW spr round 17 (radius: 25) [04:06:46] [worker #5] ML tree search #12, logLikelihood: -123609.389355 [04:15:25 -123609.788149] Model parameter optimization (eps = 0.100000) [04:15:37] [worker #0] ML tree search #7, logLikelihood: -123609.671028 [04:15:37 -463416.164108] Initial branch length optimization [04:15:43 -372686.803370] Model parameter optimization (eps = 10.000000) [04:16:40 -368661.341484] AUTODETECT spr round 1 (radius: 5) [04:19:39 -273847.321890] AUTODETECT spr round 2 (radius: 10) [04:22:54 -210084.477566] AUTODETECT spr round 3 (radius: 15) [04:26:30 -170430.766099] AUTODETECT spr round 4 (radius: 20) [04:31:05 -147792.656224] AUTODETECT spr round 5 (radius: 25) [04:36:41 -144547.795113] SPR radius for FAST iterations: 25 (autodetect) [04:36:41 -144547.795113] Model parameter optimization (eps = 3.000000) [04:37:15 -144415.165468] FAST spr round 1 (radius: 25) [04:41:42 -124743.815155] FAST spr round 2 (radius: 25) [04:44:50 -123923.458988] FAST spr round 3 (radius: 25) [04:47:20 -123880.269586] FAST spr round 4 (radius: 25) [04:49:37 -123866.492021] FAST spr round 5 (radius: 25) [04:51:42 -123863.584276] FAST spr round 6 (radius: 25) [04:53:43 -123862.070452] FAST spr round 7 (radius: 25) [04:55:41 -123859.139283] FAST spr round 8 (radius: 25) [04:57:37 -123859.138951] Model parameter optimization (eps = 1.000000) [04:58:18 -123828.941439] SLOW spr round 1 (radius: 5) [05:01:00 -123620.596121] SLOW spr round 2 (radius: 5) [05:03:41 -123616.085896] SLOW spr round 3 (radius: 5) [05:06:21 -123613.359232] SLOW spr round 4 (radius: 5) [05:08:56 -123613.357330] SLOW spr round 5 (radius: 10) [05:11:52 -123604.417826] SLOW spr round 6 (radius: 5) [05:15:05 -123602.241069] SLOW spr round 7 (radius: 5) [05:17:57 -123601.136499] SLOW spr round 8 (radius: 5) [05:20:36 -123601.130381] SLOW spr round 9 (radius: 10) [05:23:33 -123600.083183] SLOW spr round 10 (radius: 5) [05:26:44 -123598.995545] SLOW spr round 11 (radius: 5) [05:28:08] [worker #4] ML tree search #17, logLikelihood: -123609.030868 [05:29:32 -123598.989243] SLOW spr round 12 (radius: 10) [05:31:07] [worker #3] ML tree search #16, logLikelihood: -123616.418812 [05:32:32 -123598.989050] SLOW spr round 13 (radius: 15) [05:37:38 -123596.767921] SLOW spr round 14 (radius: 5) [05:41:02 -123595.705165] SLOW spr round 15 (radius: 5) [05:43:59 -123595.454893] SLOW spr round 16 (radius: 5) [05:46:39 -123595.454637] SLOW spr round 17 (radius: 10) [05:49:35 -123595.454597] SLOW spr round 18 (radius: 15) [05:54:42 -123595.454577] SLOW spr round 19 (radius: 20) [06:03:03 -123595.241689] SLOW spr round 20 (radius: 5) [06:06:29 -123595.241061] SLOW spr round 21 (radius: 10) [06:10:08 -123595.241037] SLOW spr round 22 (radius: 15) [06:15:05 -123595.241021] SLOW spr round 23 (radius: 20) [06:23:32 -123595.241004] SLOW spr round 24 (radius: 25) [06:25:16] [worker #1] ML tree search #14, logLikelihood: -123613.755811 [06:33:51 -123595.240988] Model parameter optimization (eps = 0.100000) [06:34:07] [worker #0] ML tree search #13, logLikelihood: -123594.617933 [06:34:07 -465441.663714] Initial branch length optimization [06:34:13 -372219.272250] Model parameter optimization (eps = 10.000000) [06:35:10 -368224.243010] AUTODETECT spr round 1 (radius: 5) [06:38:12 -278813.337584] AUTODETECT spr round 2 (radius: 10) [06:39:03] [worker #2] ML tree search #15, logLikelihood: -123594.299840 [06:40:15] [worker #5] ML tree search #18, logLikelihood: -123596.845490 [06:41:25 -212097.935132] AUTODETECT spr round 3 (radius: 15) [06:44:51 -178279.073701] AUTODETECT spr round 4 (radius: 20) [06:48:24 -153385.019906] AUTODETECT spr round 5 (radius: 25) [06:53:01 -148754.587132] SPR radius for FAST iterations: 25 (autodetect) [06:53:01 -148754.587132] Model parameter optimization (eps = 3.000000) [06:53:49 -148530.357856] FAST spr round 1 (radius: 25) [06:57:56 -130140.888508] FAST spr round 2 (radius: 25) [07:01:00 -125324.999108] FAST spr round 3 (radius: 25) [07:03:45 -124085.310422] FAST spr round 4 (radius: 25) [07:06:03 -123968.380911] FAST spr round 5 (radius: 25) [07:08:05 -123964.311631] FAST spr round 6 (radius: 25) [07:10:02 -123962.609184] FAST spr round 7 (radius: 25) [07:11:59 -123667.045616] FAST spr round 8 (radius: 25) [07:13:54 -123667.045561] Model parameter optimization (eps = 1.000000) [07:14:09 -123662.721773] SLOW spr round 1 (radius: 5) [07:16:47 -123629.068145] SLOW spr round 2 (radius: 5) [07:19:29 -123607.232385] SLOW spr round 3 (radius: 5) [07:22:07 -123603.768039] SLOW spr round 4 (radius: 5) [07:24:44 -123598.183016] SLOW spr round 5 (radius: 5) [07:27:16 -123597.842575] SLOW spr round 6 (radius: 5) [07:29:47 -123597.841583] SLOW spr round 7 (radius: 10) [07:32:36 -123592.989891] SLOW spr round 8 (radius: 5) [07:35:45 -123586.581602] SLOW spr round 9 (radius: 5) [07:38:31 -123586.493701] SLOW spr round 10 (radius: 10) [07:41:27 -123586.492601] SLOW spr round 11 (radius: 15) [07:46:29 -123585.728231] SLOW spr round 12 (radius: 5) [07:49:46 -123585.477471] SLOW spr round 13 (radius: 5) [07:52:39 -123584.028998] SLOW spr round 14 (radius: 5) [07:55:18 -123584.027884] SLOW spr round 15 (radius: 10) [07:58:10 -123584.027833] SLOW spr round 16 (radius: 15) [08:03:13 -123584.027831] SLOW spr round 17 (radius: 20) [08:10:24 -123584.027828] SLOW spr round 18 (radius: 25) [08:13:31] [worker #1] ML tree search #20, logLikelihood: -123607.169859 [08:19:35 -123583.782188] SLOW spr round 19 (radius: 5) [08:23:00 -123583.781463] SLOW spr round 20 (radius: 10) [08:26:36 -123583.781452] SLOW spr round 21 (radius: 15) [08:31:29 -123583.781452] SLOW spr round 22 (radius: 20) [08:38:41 -123583.781452] SLOW spr round 23 (radius: 25) [08:47:44 -123583.781452] Model parameter optimization (eps = 0.100000) [08:47:57] [worker #0] ML tree search #19, logLikelihood: -123583.399504 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.098785,1.243662) (0.208640,0.611229) (0.499215,0.862862) (0.193361,1.649070) 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: -123583.399504 AIC score: 250752.799008 / AICc score: 6684036.799008 / BIC score: 257326.702060 Free parameters (model + branch lengths): 1793 WARNING: Number of free parameters (K=1793) is larger than alignment size (n=289). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 4 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/3_mltree/P51610.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/3_mltree/P51610.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/3_mltree/P51610.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/3_mltree/P51610.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P51610/3_mltree/P51610.raxml.log Analysis started: 01-Jul-2021 17:06:20 / finished: 02-Jul-2021 01:54:17 Elapsed time: 31677.421 seconds Consumed energy: 2713.810 Wh (= 14 km in an electric car, or 68 km with an e-scooter!)