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 04-Jul-2021 00:25:46 as follows: raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q2KHN1/2_msa/Q2KHN1_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q2KHN1/3_mltree/Q2KHN1 --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/Q2KHN1/2_msa/Q2KHN1_trimmed_msa.fasta [00:00:00] Loaded alignment with 835 taxa and 243 sites WARNING: Sequences tr_B4QSG2_B4QSG2_DROSI_7240 and tr_Q9VCD3_Q9VCD3_DROME_7227 are exactly identical! WARNING: Sequences tr_A0A1D5PDU4_A0A1D5PDU4_CHICK_9031 and tr_H9H138_H9H138_MELGA_9103 are exactly identical! WARNING: Sequences tr_A0A1D5PDU4_A0A1D5PDU4_CHICK_9031 and tr_G1KGY0_G1KGY0_ANOCA_28377 are exactly identical! WARNING: Sequences tr_A0A1D5PDU4_A0A1D5PDU4_CHICK_9031 and tr_A0A2I0LK86_A0A2I0LK86_COLLI_8932 are exactly identical! WARNING: Sequences tr_A0A1D5PDU4_A0A1D5PDU4_CHICK_9031 and tr_A0A226MEA7_A0A226MEA7_CALSU_9009 are exactly identical! WARNING: Sequences tr_A0A1D5PVI0_A0A1D5PVI0_CHICK_9031 and tr_A0A226PIH0_A0A226PIH0_COLVI_9014 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_G1RJI8_G1RJI8_NOMLE_61853 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_G3HRQ1_G3HRQ1_CRIGR_10029 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_G3R697_G3R697_GORGO_9595 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and sp_Q5R7T5_RNF41_PONAB_9601 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_E2QVC5_E2QVC5_CANLF_9615 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_H2Q681_H2Q681_PANTR_9598 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_F7ACG1_F7ACG1_HORSE_9796 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_I3M2E9_I3M2E9_ICTTR_43179 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_H0WIS7_H0WIS7_OTOGA_30611 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A286XAC3_A0A286XAC3_CAVPO_10141 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and sp_Q9H4P4_RNF41_HUMAN_9606 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_F6RSF7_F6RSF7_MACMU_9544 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_U3ENC8_U3ENC8_CALJA_9483 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_D2H347_D2H347_AILME_9646 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_G7PIG9_G7PIG9_MACFA_9541 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_M3WYQ0_M3WYQ0_FELCA_9685 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A2I3MFA3_A0A2I3MFA3_PAPAN_9555 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A0D9QYS9_A0A0D9QYS9_CHLSB_60711 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A1U7T917_A0A1U7T917_TARSY_1868482 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A2K5KUH1_A0A2K5KUH1_CERAT_9531 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A2K6BF72_A0A2K6BF72_MACNE_9545 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A2K5ZNP8_A0A2K5ZNP8_MANLE_9568 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A2R9A9W7_A0A2R9A9W7_PANPA_9597 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A2U3W1B1_A0A2U3W1B1_ODORO_9708 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A2U3Z7C9_A0A2U3Z7C9_LEPWE_9713 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A2Y9KYM9_A0A2Y9KYM9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_M3XQD5_M3XQD5_MUSPF_9669 and tr_A0A384BGD1_A0A384BGD1_URSMA_29073 are exactly identical! WARNING: Sequences tr_M3YK34_M3YK34_MUSPF_9669 and tr_A0A2Y9JQV9_A0A2Y9JQV9_ENHLU_391180 are exactly identical! WARNING: Sequences tr_B4HIK9_B4HIK9_DROSE_7238 and tr_A0A1W4VBA8_A0A1W4VBA8_DROFC_30025 are exactly identical! WARNING: Sequences tr_G3QST5_G3QST5_GORGO_9595 and tr_H2NDP0_H2NDP0_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3QST5_G3QST5_GORGO_9595 and tr_H2Q3F3_H2Q3F3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3QST5_G3QST5_GORGO_9595 and tr_A0A2R9CI00_A0A2R9CI00_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3R6G0_G3R6G0_GORGO_9595 and tr_H2QDK8_H2QDK8_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3R6G0_G3R6G0_GORGO_9595 and sp_Q5M7Z0_RNFT1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_G3R6G0_G3R6G0_GORGO_9595 and tr_A0A2R9ASA9_A0A2R9ASA9_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2NV93_H2NV93_PONAB_9601 and tr_W5PZ53_W5PZ53_SHEEP_9940 are exactly identical! WARNING: Sequences tr_H2NV93_H2NV93_PONAB_9601 and tr_H0WX41_H0WX41_OTOGA_30611 are exactly identical! WARNING: Sequences tr_H2NV93_H2NV93_PONAB_9601 and tr_G3TCX3_G3TCX3_LOXAF_9785 are exactly identical! WARNING: Sequences tr_H2NV93_H2NV93_PONAB_9601 and tr_F1MDV4_F1MDV4_BOVIN_9913 are exactly identical! WARNING: Sequences tr_H2NV93_H2NV93_PONAB_9601 and tr_A0A2Y9QYP3_A0A2Y9QYP3_TRIMA_127582 are exactly identical! WARNING: Sequences tr_Q298K3_Q298K3_DROPS_46245 and tr_B4G423_B4G423_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q2M0J1_Q2M0J1_DROPS_46245 and tr_B4GRK0_B4GRK0_DROPE_7234 are exactly identical! WARNING: Sequences tr_H2Q131_H2Q131_PANTR_9598 and tr_A0A2R9AKW0_A0A2R9AKW0_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6W4Q5_F6W4Q5_MONDO_13616 and tr_G3WTZ3_G3WTZ3_SARHA_9305 are exactly identical! WARNING: Sequences tr_W5PJ70_W5PJ70_SHEEP_9940 and tr_G5BB83_G5BB83_HETGA_10181 are exactly identical! WARNING: Sequences tr_W5PJ70_W5PJ70_SHEEP_9940 and tr_G3TDZ4_G3TDZ4_LOXAF_9785 are exactly identical! WARNING: Sequences tr_W5PJ70_W5PJ70_SHEEP_9940 and tr_F1SLZ9_F1SLZ9_PIG_9823 are exactly identical! WARNING: Sequences tr_W5PJ70_W5PJ70_SHEEP_9940 and tr_A0A1S3FPD0_A0A1S3FPD0_DIPOR_10020 are exactly identical! WARNING: Sequences tr_W5PJ70_W5PJ70_SHEEP_9940 and tr_A0A2U3ZYY6_A0A2U3ZYY6_TURTR_9739 are exactly identical! WARNING: Sequences tr_W5PJ70_W5PJ70_SHEEP_9940 and tr_A0A2Y9FRT7_A0A2Y9FRT7_PHYCD_9755 are exactly identical! WARNING: Sequences tr_W5PJ70_W5PJ70_SHEEP_9940 and tr_A0A383ZWZ9_A0A383ZWZ9_BALAS_310752 are exactly identical! WARNING: Sequences tr_M3ZJS7_M3ZJS7_XIPMA_8083 and tr_A0A096M5C7_A0A096M5C7_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A087ZPQ6_A0A087ZPQ6_APIME_7460 and tr_A0A2A3EKU9_A0A2A3EKU9_APICC_94128 are exactly identical! WARNING: Sequences tr_A0A158NWK0_A0A158NWK0_ATTCE_12957 and tr_A0A151WYQ3_A0A151WYQ3_9HYME_64791 are exactly identical! WARNING: Sequences tr_A0A158NWK0_A0A158NWK0_ATTCE_12957 and tr_A0A195EC94_A0A195EC94_9HYME_471704 are exactly identical! WARNING: Sequences tr_A0A158NWK0_A0A158NWK0_ATTCE_12957 and tr_A0A151I536_A0A151I536_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158NWK0_A0A158NWK0_ATTCE_12957 and tr_A0A151JUP5_A0A151JUP5_9HYME_34720 are exactly identical! WARNING: Sequences tr_H2UR29_H2UR29_TAKRU_31033 and tr_H3D4Q0_H3D4Q0_TETNG_99883 are exactly identical! WARNING: Sequences sp_B6CJY5_TRAF6_MACMU_9544 and tr_A0A096MX12_A0A096MX12_PAPAN_9555 are exactly identical! WARNING: Sequences sp_B6CJY5_TRAF6_MACMU_9544 and tr_A0A0D9QZK2_A0A0D9QZK2_CHLSB_60711 are exactly identical! WARNING: Sequences sp_B6CJY5_TRAF6_MACMU_9544 and sp_B6CJY4_TRAF6_CERAT_9531 are exactly identical! WARNING: Sequences sp_B6CJY5_TRAF6_MACMU_9544 and tr_A0A2K6DR01_A0A2K6DR01_MACNE_9545 are exactly identical! WARNING: Sequences sp_B6CJY5_TRAF6_MACMU_9544 and tr_A0A2K5XGP2_A0A2K5XGP2_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7E732_F7E732_MACMU_9544 and tr_A0A2K5KPQ3_A0A2K5KPQ3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7E732_F7E732_MACMU_9544 and tr_A0A2K6CFY4_A0A2K6CFY4_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FNK1_F7FNK1_MACMU_9544 and tr_A0A2K6D6P5_A0A2K6D6P5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7HSW3_F7HSW3_MACMU_9544 and tr_A0A096NKZ0_A0A096NKZ0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7HSW3_F7HSW3_MACMU_9544 and tr_A0A2K5LCL1_A0A2K5LCL1_CERAT_9531 are exactly identical! WARNING: Sequences tr_H0ZBG8_H0ZBG8_TAEGU_59729 and tr_A0A218UUP9_A0A218UUP9_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0E0QLH0_A0A0E0QLH0_ORYRU_4529 and tr_A0A0N7KQ64_A0A0N7KQ64_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_G7PUH7_G7PUH7_MACFA_9541 and tr_A0A096P4X9_A0A096P4X9_PAPAN_9555 are exactly identical! WARNING: Sequences tr_G7PUH7_G7PUH7_MACFA_9541 and tr_A0A2K5MZ03_A0A2K5MZ03_CERAT_9531 are exactly identical! WARNING: Sequences tr_G7PUH7_G7PUH7_MACFA_9541 and tr_A0A2K6C707_A0A2K6C707_MACNE_9545 are exactly identical! WARNING: Sequences tr_G7PUH7_G7PUH7_MACFA_9541 and tr_A0A2K5ZNX7_A0A2K5ZNX7_MANLE_9568 are exactly identical! WARNING: Sequences tr_F2PVY8_F2PVY8_TRIEC_559882 and tr_A0A059J788_A0A059J788_9EURO_1215338 are exactly identical! WARNING: Sequences tr_U3JSJ3_U3JSJ3_FICAL_59894 and tr_A0A091F5L4_A0A091F5L4_CORBR_85066 are exactly identical! WARNING: Sequences tr_U3JSJ3_U3JSJ3_FICAL_59894 and tr_A0A091ULF9_A0A091ULF9_NIPNI_128390 are exactly identical! WARNING: Sequences tr_U3JSJ3_U3JSJ3_FICAL_59894 and tr_A0A087R030_A0A087R030_APTFO_9233 are exactly identical! WARNING: Sequences tr_U3JSJ3_U3JSJ3_FICAL_59894 and tr_A0A091VS21_A0A091VS21_OPIHO_30419 are exactly identical! WARNING: Sequences tr_U3JSJ3_U3JSJ3_FICAL_59894 and tr_A0A099ZLM1_A0A099ZLM1_TINGU_94827 are exactly identical! WARNING: Sequences tr_W2PM85_W2PM85_PHYPN_761204 and tr_A0A0W8D8V5_A0A0W8D8V5_PHYNI_4790 are exactly identical! WARNING: Sequences tr_A0A096NY00_A0A096NY00_PAPAN_9555 and tr_A0A0D9RS18_A0A0D9RS18_CHLSB_60711 are exactly identical! WARNING: Sequences tr_A0A096NY00_A0A096NY00_PAPAN_9555 and tr_A0A2K5NJM3_A0A2K5NJM3_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NY00_A0A096NY00_PAPAN_9555 and tr_A0A2K6A0Y5_A0A2K6A0Y5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A0K0G4I4_A0A0K0G4I4_STRVS_75913 and tr_A0A0N5B4I0_A0A0N5B4I0_STREA_174720 are exactly identical! WARNING: Sequences tr_A0A091IWV8_A0A091IWV8_EGRGA_188379 and tr_A0A091V3P6_A0A091V3P6_NIPNI_128390 are exactly identical! WARNING: Sequences tr_A0A091IWV8_A0A091IWV8_EGRGA_188379 and tr_A0A087R3I7_A0A087R3I7_APTFO_9233 are exactly identical! WARNING: Sequences tr_A0A091IWV8_A0A091IWV8_EGRGA_188379 and tr_A0A093K020_A0A093K020_STRCA_441894 are exactly identical! WARNING: Sequences tr_A0A091IWV8_A0A091IWV8_EGRGA_188379 and tr_A0A0A0AW75_A0A0A0AW75_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A091WH96_A0A091WH96_OPIHO_30419 and tr_A0A091FVD2_A0A091FVD2_9AVES_55661 are exactly identical! WARNING: Sequences tr_W6YIU5_W6YIU5_COCCA_930089 and tr_W6ZRU7_W6ZRU7_COCMI_930090 are exactly identical! WARNING: Sequences tr_A0A1S3IZM8_A0A1S3IZM8_LINUN_7574 and tr_A0A1S3J0Y2_A0A1S3J0Y2_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3LJ97_A0A1S3LJ97_SALSA_8030 and tr_B5XCQ0_B5XCQ0_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3LJ97_A0A1S3LJ97_SALSA_8030 and tr_A0A060VYX4_A0A060VYX4_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A1S3S1U1_A0A1S3S1U1_SALSA_8030 and tr_B5X7W6_B5X7W6_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A1S3S219_A0A1S3S219_SALSA_8030 and tr_A0A1S3S229_A0A1S3S229_SALSA_8030 are exactly identical! WARNING: Sequences tr_A0A226MFH5_A0A226MFH5_CALSU_9009 and tr_A0A226PPY3_A0A226PPY3_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0S028_A0A2D0S028_ICTPU_7998 and tr_A0A2D0S0Q2_A0A2D0S0Q2_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2G8JHQ6_A0A2G8JHQ6_STIJA_307972 and tr_A0A2G8LB09_A0A2G8LB09_STIJA_307972 are exactly identical! WARNING: Sequences tr_A0A2U4CF07_A0A2U4CF07_TURTR_9739 and tr_A0A2Y9PAB2_A0A2Y9PAB2_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4CF07_A0A2U4CF07_TURTR_9739 and tr_A0A2Y9ERK4_A0A2Y9ERK4_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U4CF07_A0A2U4CF07_TURTR_9739 and tr_A0A384A1C9_A0A384A1C9_BALAS_310752 are exactly identical! WARNING: Sequences tr_A0A2U3VR71_A0A2U3VR71_ODORO_9708 and tr_A0A2U3Y9H4_A0A2U3Y9H4_LEPWE_9713 are exactly identical! WARNING: Duplicate sequences found: 109 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/Q2KHN1/3_mltree/Q2KHN1.raxml.reduced.phy Alignment comprises 1 partitions and 243 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 243 / 243 Gaps: 25.99 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q2KHN1/3_mltree/Q2KHN1.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 835 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 243 / 19440 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -363283.018398] Initial branch length optimization [00:00:05 -296888.374423] Model parameter optimization (eps = 10.000000) [00:00:52 -296756.393521] AUTODETECT spr round 1 (radius: 5) [00:03:33 -220183.308402] AUTODETECT spr round 2 (radius: 10) [00:06:34 -171351.160540] AUTODETECT spr round 3 (radius: 15) [00:09:50 -136132.652743] AUTODETECT spr round 4 (radius: 20) [00:13:34 -122970.750930] AUTODETECT spr round 5 (radius: 25) [00:17:54 -120372.363111] SPR radius for FAST iterations: 25 (autodetect) [00:17:54 -120372.363111] Model parameter optimization (eps = 3.000000) [00:18:25 -120335.527859] FAST spr round 1 (radius: 25) [00:22:51 -111037.664289] FAST spr round 2 (radius: 25) [00:25:39 -110526.149659] FAST spr round 3 (radius: 25) [00:27:54 -110476.128922] FAST spr round 4 (radius: 25) [00:29:50 -110474.020966] FAST spr round 5 (radius: 25) [00:31:41 -110462.199670] FAST spr round 6 (radius: 25) [00:33:26 -110461.743341] FAST spr round 7 (radius: 25) [00:35:10 -110461.743278] Model parameter optimization (eps = 1.000000) [00:35:28 -110448.352318] SLOW spr round 1 (radius: 5) [00:37:54 -110429.605659] SLOW spr round 2 (radius: 5) [00:40:17 -110428.742332] SLOW spr round 3 (radius: 5) [00:42:38 -110427.039451] SLOW spr round 4 (radius: 5) [00:44:56 -110427.038138] SLOW spr round 5 (radius: 10) [00:47:22 -110422.342586] SLOW spr round 6 (radius: 5) [00:50:21 -110422.219032] SLOW spr round 7 (radius: 5) [00:52:57 -110422.217491] SLOW spr round 8 (radius: 10) [00:55:30 -110422.217315] SLOW spr round 9 (radius: 15) [01:00:30 -110422.217289] SLOW spr round 10 (radius: 20) [01:07:49 -110422.217284] SLOW spr round 11 (radius: 25) [01:16:46 -110422.217282] Model parameter optimization (eps = 0.100000) [01:16:52] [worker #0] ML tree search #1, logLikelihood: -110422.198041 [01:16:52 -359274.015154] Initial branch length optimization [01:16:58 -295013.768797] Model parameter optimization (eps = 10.000000) [01:17:39 -294901.583523] AUTODETECT spr round 1 (radius: 5) [01:20:17 -212776.127563] AUTODETECT spr round 2 (radius: 10) [01:22:36] [worker #1] ML tree search #2, logLikelihood: -110438.246593 [01:23:05] [worker #3] ML tree search #4, logLikelihood: -110436.494388 [01:23:09 -165564.930520] AUTODETECT spr round 3 (radius: 15) [01:26:18] [worker #2] ML tree search #3, logLikelihood: -110416.081158 [01:26:39 -138016.324074] AUTODETECT spr round 4 (radius: 20) [01:30:13 -124871.867131] AUTODETECT spr round 5 (radius: 25) [01:34:04 -123908.285390] SPR radius for FAST iterations: 25 (autodetect) [01:34:04 -123908.285390] Model parameter optimization (eps = 3.000000) [01:34:39 -123852.849774] FAST spr round 1 (radius: 25) [01:38:56 -111089.480845] FAST spr round 2 (radius: 25) [01:41:57 -110515.206527] FAST spr round 3 (radius: 25) [01:44:13 -110482.272873] FAST spr round 4 (radius: 25) [01:46:13 -110474.234413] FAST spr round 5 (radius: 25) [01:48:02 -110472.591231] FAST spr round 6 (radius: 25) [01:49:46 -110472.591208] Model parameter optimization (eps = 1.000000) [01:50:00 -110460.556667] SLOW spr round 1 (radius: 5) [01:52:29 -110436.081517] SLOW spr round 2 (radius: 5) [01:54:55 -110432.815536] SLOW spr round 3 (radius: 5) [01:57:15 -110432.529618] SLOW spr round 4 (radius: 5) [01:59:33 -110432.526882] SLOW spr round 5 (radius: 10) [02:02:03 -110427.697908] SLOW spr round 6 (radius: 5) [02:05:04 -110425.967443] SLOW spr round 7 (radius: 5) [02:07:43 -110424.901513] SLOW spr round 8 (radius: 5) [02:10:09 -110424.511189] SLOW spr round 9 (radius: 5) [02:11:11] [worker #4] ML tree search #5, logLikelihood: -110444.780117 [02:12:30 -110424.511141] SLOW spr round 10 (radius: 10) [02:14:56 -110424.511137] SLOW spr round 11 (radius: 15) [02:20:01 -110424.301144] SLOW spr round 12 (radius: 5) [02:23:02 -110424.301144] SLOW spr round 13 (radius: 10) [02:26:02 -110424.301144] SLOW spr round 14 (radius: 15) [02:30:34 -110424.301144] SLOW spr round 15 (radius: 20) [02:37:45 -110424.301144] SLOW spr round 16 (radius: 25) [02:37:47] [worker #2] ML tree search #8, logLikelihood: -110431.711814 [02:46:10 -110424.301144] Model parameter optimization (eps = 0.100000) [02:46:15] [worker #0] ML tree search #6, logLikelihood: -110424.265481 [02:46:16 -356494.280040] Initial branch length optimization [02:46:21 -290343.041960] Model parameter optimization (eps = 10.000000) [02:47:07 -290253.957262] AUTODETECT spr round 1 (radius: 5) [02:49:43 -215594.117042] AUTODETECT spr round 2 (radius: 10) [02:50:56] [worker #3] ML tree search #9, logLikelihood: -110417.766205 [02:52:43 -161682.199857] AUTODETECT spr round 3 (radius: 15) [02:56:14 -133732.510067] AUTODETECT spr round 4 (radius: 20) [02:58:19] [worker #1] ML tree search #7, logLikelihood: -110415.452713 [03:00:02 -122223.934557] AUTODETECT spr round 5 (radius: 25) [03:05:19 -120533.329770] SPR radius for FAST iterations: 25 (autodetect) [03:05:19 -120533.329770] Model parameter optimization (eps = 3.000000) [03:05:44 -120487.149348] FAST spr round 1 (radius: 25) [03:10:22 -111053.444952] FAST spr round 2 (radius: 25) [03:13:26 -110524.617715] FAST spr round 3 (radius: 25) [03:15:48 -110489.839872] FAST spr round 4 (radius: 25) [03:17:47 -110484.003652] FAST spr round 5 (radius: 25) [03:19:35 -110483.411685] FAST spr round 6 (radius: 25) [03:21:19 -110483.407274] Model parameter optimization (eps = 1.000000) [03:21:37 -110475.519570] SLOW spr round 1 (radius: 5) [03:24:09 -110452.593060] SLOW spr round 2 (radius: 5) [03:26:38 -110446.729304] SLOW spr round 3 (radius: 5) [03:28:55 -110446.538392] SLOW spr round 4 (radius: 5) [03:31:10 -110446.538176] SLOW spr round 5 (radius: 10) [03:33:33 -110446.538158] SLOW spr round 6 (radius: 15) [03:38:39 -110443.718320] SLOW spr round 7 (radius: 5) [03:41:39 -110443.718240] SLOW spr round 8 (radius: 10) [03:44:40 -110443.718239] SLOW spr round 9 (radius: 15) [03:49:10 -110443.718239] SLOW spr round 10 (radius: 20) [03:56:30 -110441.241797] SLOW spr round 11 (radius: 5) [03:58:06] [worker #2] ML tree search #13, logLikelihood: -110428.183448 [03:59:37 -110440.952910] SLOW spr round 12 (radius: 5) [04:01:27] [worker #4] ML tree search #10, logLikelihood: -110419.872073 [04:02:17 -110440.952646] SLOW spr round 13 (radius: 10) [04:04:57 -110437.729777] SLOW spr round 14 (radius: 5) [04:08:00 -110430.323766] SLOW spr round 15 (radius: 5) [04:10:32 -110429.928045] SLOW spr round 16 (radius: 5) [04:12:55 -110429.927562] SLOW spr round 17 (radius: 10) [04:15:21 -110428.013823] SLOW spr round 18 (radius: 5) [04:18:17 -110426.890866] SLOW spr round 19 (radius: 5) [04:20:50 -110426.805954] SLOW spr round 20 (radius: 10) [04:23:21 -110426.805456] SLOW spr round 21 (radius: 15) [04:28:22 -110426.805339] SLOW spr round 22 (radius: 20) [04:28:51] [worker #3] ML tree search #14, logLikelihood: -110420.137526 [04:31:48] [worker #1] ML tree search #12, logLikelihood: -110422.773825 [04:35:45 -110426.805291] SLOW spr round 23 (radius: 25) [04:44:50 -110426.805269] Model parameter optimization (eps = 0.100000) [04:45:00] [worker #0] ML tree search #11, logLikelihood: -110426.537217 [04:45:00 -362871.461785] Initial branch length optimization [04:45:06 -297957.530266] Model parameter optimization (eps = 10.000000) [04:45:49 -297786.030061] AUTODETECT spr round 1 (radius: 5) [04:48:27 -214986.620367] AUTODETECT spr round 2 (radius: 10) [04:51:26 -168587.173473] AUTODETECT spr round 3 (radius: 15) [04:54:42 -141660.918607] AUTODETECT spr round 4 (radius: 20) [04:58:35 -124624.702163] AUTODETECT spr round 5 (radius: 25) [05:03:02 -122471.843419] SPR radius for FAST iterations: 25 (autodetect) [05:03:02 -122471.843419] Model parameter optimization (eps = 3.000000) [05:03:28 -122409.736336] FAST spr round 1 (radius: 25) [05:07:52 -111262.819257] FAST spr round 2 (radius: 25) [05:10:39 -110591.095772] FAST spr round 3 (radius: 25) [05:12:54 -110469.497124] FAST spr round 4 (radius: 25) [05:14:53 -110458.245969] FAST spr round 5 (radius: 25) [05:16:40 -110456.134234] FAST spr round 6 (radius: 25) [05:18:23 -110456.133491] Model parameter optimization (eps = 1.000000) [05:18:35 -110453.440287] SLOW spr round 1 (radius: 5) [05:21:03 -110425.207532] SLOW spr round 2 (radius: 5) [05:23:28 -110422.907752] SLOW spr round 3 (radius: 5) [05:25:51 -110420.075685] SLOW spr round 4 (radius: 5) [05:28:08 -110418.801704] SLOW spr round 5 (radius: 5) [05:30:24 -110418.801693] SLOW spr round 6 (radius: 10) [05:32:46 -110418.589391] SLOW spr round 7 (radius: 5) [05:35:42 -110418.589390] SLOW spr round 8 (radius: 10) [05:38:12] [worker #4] ML tree search #15, logLikelihood: -110423.219039 [05:38:33 -110418.589389] SLOW spr round 9 (radius: 15) [05:42:50] [worker #2] ML tree search #18, logLikelihood: -110430.478122 [05:43:12 -110418.524339] SLOW spr round 10 (radius: 20) [05:49:12] [worker #1] ML tree search #17, logLikelihood: -110410.990439 [05:50:15 -110418.422548] SLOW spr round 11 (radius: 5) [05:53:23 -110418.422425] SLOW spr round 12 (radius: 10) [05:56:32 -110418.422425] SLOW spr round 13 (radius: 15) [05:59:34] [worker #3] ML tree search #19, logLikelihood: -110575.568080 [06:01:04 -110418.422424] SLOW spr round 14 (radius: 20) [06:08:07 -110418.422424] SLOW spr round 15 (radius: 25) [06:16:25 -110418.422424] Model parameter optimization (eps = 0.100000) [06:16:31] [worker #0] ML tree search #16, logLikelihood: -110418.407795 [07:07:14] [worker #4] ML tree search #20, logLikelihood: -110426.428769 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.086794,0.150187) (0.074081,0.378566) (0.440923,0.811474) (0.398202,1.509593) 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: -110410.990439 AIC score: 224167.980878 / AICc score: 5825371.980878 / BIC score: 230011.872673 Free parameters (model + branch lengths): 1673 WARNING: Number of free parameters (K=1673) is larger than alignment size (n=243). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 183 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q2KHN1/3_mltree/Q2KHN1.raxml.bestTreeCollapsed Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q2KHN1/3_mltree/Q2KHN1.raxml.bestTree All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q2KHN1/3_mltree/Q2KHN1.raxml.mlTrees Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q2KHN1/3_mltree/Q2KHN1.raxml.bestModel Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q2KHN1/3_mltree/Q2KHN1.raxml.log Analysis started: 04-Jul-2021 00:25:46 / finished: 04-Jul-2021 07:33:01 Elapsed time: 25635.125 seconds