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 02-Jul-2021 16:04:12 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H4Z2/2_msa/Q9H4Z2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H4Z2/3_mltree/Q9H4Z2 --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/Q9H4Z2/2_msa/Q9H4Z2_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1000 taxa and 284 sites

WARNING: Sequences tr_A0A0R4IIL1_A0A0R4IIL1_DANRE_7955 and tr_H0WF13_H0WF13_DANRE_7955 are exactly identical!
WARNING: Sequences tr_M3YKR6_M3YKR6_MUSPF_9669 and tr_J9P0Y6_J9P0Y6_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3YKR6_M3YKR6_MUSPF_9669 and tr_F6TRH0_F6TRH0_HORSE_9796 are exactly identical!
WARNING: Sequences tr_M3YKR6_M3YKR6_MUSPF_9669 and tr_I3N0W6_I3N0W6_ICTTR_43179 are exactly identical!
WARNING: Sequences tr_M3YKR6_M3YKR6_MUSPF_9669 and tr_F1RG79_F1RG79_PIG_9823 are exactly identical!
WARNING: Sequences tr_M3YKR6_M3YKR6_MUSPF_9669 and tr_M3X1R2_M3X1R2_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3YKR6_M3YKR6_MUSPF_9669 and tr_A0A2Y9LF49_A0A2Y9LF49_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YKR6_M3YKR6_MUSPF_9669 and tr_A0A2Y9ERQ4_A0A2Y9ERQ4_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_O61360_O61360_DROME_7227 and tr_B4HX81_B4HX81_DROSE_7238 are exactly identical!
WARNING: Sequences tr_O61360_O61360_DROME_7227 and tr_B4G871_B4G871_DROPE_7234 are exactly identical!
WARNING: Sequences tr_O61360_O61360_DROME_7227 and tr_A0A1W4WDA0_A0A1W4WDA0_DROFC_30025 are exactly identical!
WARNING: Sequences tr_A0A2I2YVE2_A0A2I2YVE2_GORGO_9595 and tr_A0A2J8WXH0_A0A2J8WXH0_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3R395_G3R395_GORGO_9595 and tr_A0A2J8S1E3_A0A2J8S1E3_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3R395_G3R395_GORGO_9595 and tr_H2R1F3_H2R1F3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3R395_G3R395_GORGO_9595 and sp_P58317_ZN121_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3R395_G3R395_GORGO_9595 and tr_A0A0A0MWU7_A0A0A0MWU7_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3R395_G3R395_GORGO_9595 and tr_A0A0D9R5P1_A0A0D9R5P1_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3R395_G3R395_GORGO_9595 and tr_A0A2K5LXQ7_A0A2K5LXQ7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3R395_G3R395_GORGO_9595 and tr_A0A2K6BYT6_A0A2K6BYT6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3R395_G3R395_GORGO_9595 and tr_A0A2K5XMF9_A0A2K5XMF9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3R395_G3R395_GORGO_9595 and tr_A0A2R8ZJP8_A0A2R8ZJP8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RCJ8_G3RCJ8_GORGO_9595 and tr_K7CQ46_K7CQ46_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RCJ8_G3RCJ8_GORGO_9595 and sp_Q9H4Z2_ZN335_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RCJ8_G3RCJ8_GORGO_9595 and tr_F7I5H1_F7I5H1_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3RCJ8_G3RCJ8_GORGO_9595 and tr_A0A0D9RQ48_A0A0D9RQ48_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3RCJ8_G3RCJ8_GORGO_9595 and tr_A0A2R9CBC3_A0A2R9CBC3_PANPA_9597 are exactly identical!
WARNING: Sequences tr_G3RZF7_G3RZF7_GORGO_9595 and tr_H2NWL2_H2NWL2_PONAB_9601 are exactly identical!
WARNING: Sequences tr_G3RZF7_G3RZF7_GORGO_9595 and tr_H2QEQ2_H2QEQ2_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RZF7_G3RZF7_GORGO_9595 and sp_Q9C0G0_ZN407_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_E2RCJ4_E2RCJ4_CANLF_9615 and tr_G1M279_G1M279_AILME_9646 are exactly identical!
WARNING: Sequences tr_E2RCJ4_E2RCJ4_CANLF_9615 and tr_A0A2U3WAD5_A0A2U3WAD5_ODORO_9708 are exactly identical!
WARNING: Sequences tr_E2RCJ4_E2RCJ4_CANLF_9615 and tr_A0A384CPN1_A0A384CPN1_URSMA_29073 are exactly identical!
WARNING: Sequences tr_K7APN7_K7APN7_PANTR_9598 and tr_A0A2R8ZEJ1_A0A2R8ZEJ1_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5P3G2_W5P3G2_SHEEP_9940 and tr_E1BF46_E1BF46_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A3B5PP11_A0A3B5PP11_XIPMA_8083 and tr_A0A3B5QXI2_A0A3B5QXI2_XIPMA_8083 are exactly identical!
WARNING: Sequences tr_M3ZRW5_M3ZRW5_XIPMA_8083 and tr_A0A087XJU1_A0A087XJU1_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A088AQW3_A0A088AQW3_APIME_7460 and tr_A0A0N0BKL8_A0A0N0BKL8_9HYME_166423 are exactly identical!
WARNING: Sequences tr_A0A088AQW3_A0A088AQW3_APIME_7460 and tr_A0A195CY15_A0A195CY15_9HYME_456900 are exactly identical!
WARNING: Sequences tr_A0A158P2W0_A0A158P2W0_ATTCE_12957 and tr_F4W5X7_F4W5X7_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A158P2W0_A0A158P2W0_ATTCE_12957 and tr_A0A0L7R540_A0A0L7R540_9HYME_597456 are exactly identical!
WARNING: Sequences tr_A0A158P2W0_A0A158P2W0_ATTCE_12957 and tr_A0A151XH71_A0A151XH71_9HYME_64791 are exactly identical!
WARNING: Sequences tr_F6S565_F6S565_MACMU_9544 and tr_G7PG42_G7PG42_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6S565_F6S565_MACMU_9544 and tr_A0A096NX24_A0A096NX24_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6S565_F6S565_MACMU_9544 and tr_A0A2K5N3E7_A0A2K5N3E7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6S565_F6S565_MACMU_9544 and tr_A0A2K6CSE2_A0A2K6CSE2_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F6S565_F6S565_MACMU_9544 and tr_A0A2K5YZC4_A0A2K5YZC4_MANLE_9568 are exactly identical!
WARNING: Sequences tr_F6WJT3_F6WJT3_MACMU_9544 and tr_G8F2T8_G8F2T8_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F6WJT3_F6WJT3_MACMU_9544 and tr_A0A096NDF2_A0A096NDF2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F6WJT3_F6WJT3_MACMU_9544 and tr_A0A2K5L4M7_A0A2K5L4M7_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F6WJT3_F6WJT3_MACMU_9544 and tr_A0A2K5ZXT3_A0A2K5ZXT3_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H9H338_H9H338_MACMU_9544 and tr_G7PZ53_G7PZ53_MACFA_9541 are exactly identical!
WARNING: Sequences tr_H0Z1H7_H0Z1H7_TAEGU_59729 and tr_A0A218UUQ2_A0A218UUQ2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_H0Z6H0_H0Z6H0_TAEGU_59729 and tr_A0A091EU49_A0A091EU49_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0Z6H0_H0Z6H0_TAEGU_59729 and tr_A0A218U9Z5_A0A218U9Z5_9PASE_299123 are exactly identical!
WARNING: Sequences tr_B4MVY6_B4MVY6_DROWI_7260 and tr_A0A0Q9WMP8_A0A0Q9WMP8_DROVI_7244 are exactly identical!
WARNING: Sequences tr_B4MVY6_B4MVY6_DROWI_7260 and tr_A0A0Q9XEP2_A0A0Q9XEP2_DROMO_7230 are exactly identical!
WARNING: Sequences tr_G7PW94_G7PW94_MACFA_9541 and tr_A0A096MWZ9_A0A096MWZ9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G7PW94_G7PW94_MACFA_9541 and tr_A0A0D9S057_A0A0D9S057_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G7PW94_G7PW94_MACFA_9541 and tr_A0A2K5KH64_A0A2K5KH64_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G7PW94_G7PW94_MACFA_9541 and tr_A0A2K6C0N3_A0A2K6C0N3_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G7PW94_G7PW94_MACFA_9541 and tr_A0A2K5ZDD6_A0A2K5ZDD6_MANLE_9568 are exactly identical!
WARNING: Sequences tr_U3IJE7_U3IJE7_ANAPL_8839 and tr_A0A091EIR0_A0A091EIR0_CORBR_85066 are exactly identical!
WARNING: Sequences tr_U3IJE7_U3IJE7_ANAPL_8839 and tr_A0A091IZD3_A0A091IZD3_EGRGA_188379 are exactly identical!
WARNING: Sequences tr_U3IJE7_U3IJE7_ANAPL_8839 and tr_A0A091XCA1_A0A091XCA1_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_U3IJE7_U3IJE7_ANAPL_8839 and tr_A0A0A0AG63_A0A0A0AG63_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A087X4H3_A0A087X4H3_POEFO_48698 and tr_A0A096MG47_A0A096MG47_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A151NZA9_A0A151NZA9_ALLMI_8496 and tr_A0A3Q0G0W8_A0A3Q0G0W8_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A151P1Z6_A0A151P1Z6_ALLMI_8496 and tr_A0A3Q0H849_A0A3Q0H849_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A1S3NEA3_A0A1S3NEA3_SALSA_8030 and tr_A0A060W2U8_A0A060W2U8_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A1V4JDM5_A0A1V4JDM5_PATFA_372326 and tr_A0A226N674_A0A226N674_CALSU_9009 are exactly identical!
WARNING: Sequences tr_A0A1V4JDM5_A0A1V4JDM5_PATFA_372326 and tr_A0A226PDK3_A0A226PDK3_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0QYR8_A0A2D0QYR8_ICTPU_7998 and tr_A0A2D0QZ01_A0A2D0QZ01_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4C1Q2_A0A2U4C1Q2_TURTR_9739 and tr_A0A2Y9F5E1_A0A2Y9F5E1_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_A0A2U3VQ47_A0A2U3VQ47_ODORO_9708 and tr_A0A2U3Y2S6_A0A2U3Y2S6_LEPWE_9713 are exactly identical!
WARNING: Duplicate sequences found: 74

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/Q9H4Z2/3_mltree/Q9H4Z2.raxml.reduced.phy

Alignment comprises 1 partitions and 284 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 284 / 284
Gaps: 8.76 %
Invariant sites: 1.06 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H4Z2/3_mltree/Q9H4Z2.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 1000 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 284 / 22720
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -490089.551711] Initial branch length optimization
[00:00:07 -428907.072555] Model parameter optimization (eps = 10.000000)
[00:01:20 -426267.118734] AUTODETECT spr round 1 (radius: 5)
[00:05:24 -346422.182992] AUTODETECT spr round 2 (radius: 10)
[00:10:09 -285890.727129] AUTODETECT spr round 3 (radius: 15)
[00:15:36 -260771.763901] AUTODETECT spr round 4 (radius: 20)
[00:22:41 -248587.943971] AUTODETECT spr round 5 (radius: 25)
[00:29:39 -242855.439830] SPR radius for FAST iterations: 25 (autodetect)
[00:29:39 -242855.439830] Model parameter optimization (eps = 3.000000)
[00:30:14 -242060.699419] FAST spr round 1 (radius: 25)
[00:40:00 -228259.410818] FAST spr round 2 (radius: 25)
[00:47:36 -223093.105327] FAST spr round 3 (radius: 25)
[00:53:45 -221504.734354] FAST spr round 4 (radius: 25)
[00:59:04 -221453.426320] FAST spr round 5 (radius: 25)
[01:03:40 -221443.585375] FAST spr round 6 (radius: 25)
[01:07:52 -221443.584862] Model parameter optimization (eps = 1.000000)
[01:08:21 -221438.173375] SLOW spr round 1 (radius: 5)
[01:13:31 -221366.233281] SLOW spr round 2 (radius: 5)
[01:18:31 -221360.324719] SLOW spr round 3 (radius: 5)
[01:23:14 -221360.057595] SLOW spr round 4 (radius: 5)
[01:27:51 -221360.057527] SLOW spr round 5 (radius: 10)
[01:33:14 -221344.520848] SLOW spr round 6 (radius: 5)
[01:39:03 -221332.115803] SLOW spr round 7 (radius: 5)
[01:44:24 -221318.810858] SLOW spr round 8 (radius: 5)
[01:49:30 -221316.137848] SLOW spr round 9 (radius: 5)
[01:54:22 -221309.682265] SLOW spr round 10 (radius: 5)
[01:59:09 -221309.682243] SLOW spr round 11 (radius: 10)
[02:04:12 -221305.863401] SLOW spr round 12 (radius: 5)
[02:09:59 -221301.827128] SLOW spr round 13 (radius: 5)
[02:15:07 -221301.825593] SLOW spr round 14 (radius: 10)
[02:20:32 -221298.806990] SLOW spr round 15 (radius: 5)
[02:26:16 -221294.247282] SLOW spr round 16 (radius: 5)
[02:31:23 -221294.245665] SLOW spr round 17 (radius: 10)
[02:36:42 -221294.245609] SLOW spr round 18 (radius: 15)
[02:45:56 -221291.428034] SLOW spr round 19 (radius: 5)
[02:51:46 -221289.946010] SLOW spr round 20 (radius: 5)
[02:56:57 -221289.945589] SLOW spr round 21 (radius: 10)
[03:02:22 -221289.945513] SLOW spr round 22 (radius: 15)
[03:11:40 -221289.945499] SLOW spr round 23 (radius: 20)
[03:24:29 -221284.576971] SLOW spr round 24 (radius: 5)
[03:30:31 -221276.882021] SLOW spr round 25 (radius: 5)
[03:32:13] [worker #1] ML tree search #2, logLikelihood: -221314.892425
[03:35:55 -221272.270550] SLOW spr round 26 (radius: 5)
[03:40:51 -221272.270216] SLOW spr round 27 (radius: 10)
[03:46:09 -221270.098286] SLOW spr round 28 (radius: 5)
[03:51:57 -221262.625478] SLOW spr round 29 (radius: 5)
[03:57:04 -221262.625356] SLOW spr round 30 (radius: 10)
[04:02:24 -221262.625356] SLOW spr round 31 (radius: 15)
[04:11:47 -221262.625356] SLOW spr round 32 (radius: 20)
[04:24:39 -221261.630704] SLOW spr round 33 (radius: 5)
[04:30:44 -221260.538748] SLOW spr round 34 (radius: 5)
[04:36:15 -221259.390021] SLOW spr round 35 (radius: 5)
[04:41:20 -221259.389924] SLOW spr round 36 (radius: 10)
[04:46:40 -221257.915097] SLOW spr round 37 (radius: 5)
[04:49:33] [worker #3] ML tree search #4, logLikelihood: -221467.104844
[04:52:31 -221254.557251] SLOW spr round 38 (radius: 5)
[04:53:47] [worker #4] ML tree search #5, logLikelihood: -221249.927800
[04:57:49 -221253.543026] SLOW spr round 39 (radius: 5)
[05:02:54 -221250.921809] SLOW spr round 40 (radius: 5)
[05:07:49 -221250.921714] SLOW spr round 41 (radius: 10)
[05:13:00 -221250.921714] SLOW spr round 42 (radius: 15)
[05:22:52 -221250.921714] SLOW spr round 43 (radius: 20)
[05:35:49 -221250.921714] SLOW spr round 44 (radius: 25)
[05:42:00] [worker #2] ML tree search #3, logLikelihood: -223184.353770
[05:50:56 -221250.921714] Model parameter optimization (eps = 0.100000)

[05:51:15] [worker #0] ML tree search #1, logLikelihood: -221250.316052

[05:51:15 -493090.314419] Initial branch length optimization
[05:51:22 -430723.546299] Model parameter optimization (eps = 10.000000)
[05:52:26 -428069.536417] AUTODETECT spr round 1 (radius: 5)
[05:56:37 -347200.328549] AUTODETECT spr round 2 (radius: 10)
[06:01:35 -284112.487001] AUTODETECT spr round 3 (radius: 15)
[06:07:04 -257963.723047] AUTODETECT spr round 4 (radius: 20)
[06:13:32 -245637.593026] AUTODETECT spr round 5 (radius: 25)
[06:20:02 -242068.928339] SPR radius for FAST iterations: 25 (autodetect)
[06:20:02 -242068.928339] Model parameter optimization (eps = 3.000000)
[06:20:45 -241237.100449] FAST spr round 1 (radius: 25)
[06:30:08 -226980.747972] FAST spr round 2 (radius: 25)
[06:38:04 -224477.509841] FAST spr round 3 (radius: 25)
[06:44:43 -222877.932789] FAST spr round 4 (radius: 25)
[06:48:14] [worker #5] ML tree search #6, logLikelihood: -221206.121394
[06:50:40 -222015.409902] FAST spr round 5 (radius: 25)
[06:56:03 -221795.518024] FAST spr round 6 (radius: 25)
[07:00:32 -221703.362676] FAST spr round 7 (radius: 25)
[07:04:42 -221703.361606] Model parameter optimization (eps = 1.000000)
[07:05:01 -221696.878978] SLOW spr round 1 (radius: 5)
[07:10:23 -221628.145996] SLOW spr round 2 (radius: 5)
[07:15:33 -221605.639174] SLOW spr round 3 (radius: 5)
[07:20:27 -221605.492985] SLOW spr round 4 (radius: 5)
[07:25:15 -221605.492326] SLOW spr round 5 (radius: 10)
[07:30:17 -221600.759983] SLOW spr round 6 (radius: 5)
[07:36:00 -221595.214566] SLOW spr round 7 (radius: 5)
[07:41:09 -221590.836171] SLOW spr round 8 (radius: 5)
[07:46:00 -221590.836166] SLOW spr round 9 (radius: 10)
[07:51:15 -221589.748900] SLOW spr round 10 (radius: 5)
[07:56:51 -221587.025468] SLOW spr round 11 (radius: 5)
[08:02:02 -221584.619972] SLOW spr round 12 (radius: 5)
[08:06:52 -221584.619929] SLOW spr round 13 (radius: 10)
[08:12:02 -221584.619926] SLOW spr round 14 (radius: 15)
[08:22:04 -221558.252836] SLOW spr round 15 (radius: 5)
[08:28:09 -221452.550756] SLOW spr round 16 (radius: 5)
[08:33:37 -221437.550909] SLOW spr round 17 (radius: 5)
[08:38:38 -221435.680198] SLOW spr round 18 (radius: 5)
[08:43:21 -221435.680121] SLOW spr round 19 (radius: 10)
[08:48:29 -221294.664860] SLOW spr round 20 (radius: 5)
[08:51:39] [worker #1] ML tree search #8, logLikelihood: -221300.861256
[08:54:05 -221294.096377] SLOW spr round 21 (radius: 5)
[08:59:13 -221293.509359] SLOW spr round 22 (radius: 5)
[09:04:07 -221293.509345] SLOW spr round 23 (radius: 10)
[09:09:16 -221293.509344] SLOW spr round 24 (radius: 15)
[09:19:17 -221293.421293] SLOW spr round 25 (radius: 20)
[09:31:37 -221293.421205] SLOW spr round 26 (radius: 25)
[09:45:44 -221293.421203] Model parameter optimization (eps = 0.100000)

[09:46:00] [worker #0] ML tree search #7, logLikelihood: -221293.322595

[09:46:00 -491238.686511] Initial branch length optimization
[09:46:07 -429435.866503] Model parameter optimization (eps = 10.000000)
[09:47:23 -427850.613158] AUTODETECT spr round 1 (radius: 5)
[09:51:25 -345841.875933] AUTODETECT spr round 2 (radius: 10)
[09:56:28 -281937.876608] AUTODETECT spr round 3 (radius: 15)
[10:01:58 -255208.506775] AUTODETECT spr round 4 (radius: 20)
[10:08:13 -241902.548247] AUTODETECT spr round 5 (radius: 25)
[10:15:12 -237886.534891] SPR radius for FAST iterations: 25 (autodetect)
[10:15:12 -237886.534891] Model parameter optimization (eps = 3.000000)
[10:15:48 -237648.920669] FAST spr round 1 (radius: 25)
[10:21:40] [worker #2] ML tree search #9, logLikelihood: -221160.287545
[10:26:18 -223413.499048] FAST spr round 2 (radius: 25)
[10:35:11 -221870.374048] FAST spr round 3 (radius: 25)
[10:41:53 -221576.961973] FAST spr round 4 (radius: 25)
[10:47:35 -221521.591270] FAST spr round 5 (radius: 25)
[10:52:28 -221512.665287] FAST spr round 6 (radius: 25)
[10:57:04 -221508.714822] FAST spr round 7 (radius: 25)
[11:01:17 -221508.714505] Model parameter optimization (eps = 1.000000)
[11:01:38 -221485.438534] SLOW spr round 1 (radius: 5)
[11:07:06 -221406.253463] SLOW spr round 2 (radius: 5)
[11:12:13 -221391.677060] SLOW spr round 3 (radius: 5)
[11:17:00 -221390.836470] SLOW spr round 4 (radius: 5)
[11:21:45 -221389.561476] SLOW spr round 5 (radius: 5)
[11:26:27 -221389.561318] SLOW spr round 6 (radius: 10)
[11:31:41 -221378.002387] SLOW spr round 7 (radius: 5)
[11:37:21 -221375.022987] SLOW spr round 8 (radius: 5)
[11:42:21 -221375.022780] SLOW spr round 9 (radius: 10)
[11:47:41 -221371.528410] SLOW spr round 10 (radius: 5)
[11:53:11 -221370.387227] SLOW spr round 11 (radius: 5)
[11:58:11 -221370.387206] SLOW spr round 12 (radius: 10)
[12:03:27 -221370.387206] SLOW spr round 13 (radius: 15)
[12:13:04 -221364.119725] SLOW spr round 14 (radius: 5)
[12:13:11] [worker #3] ML tree search #10, logLikelihood: -221311.610453
[12:18:42 -221362.953011] SLOW spr round 15 (radius: 5)
[12:23:47 -221362.952898] SLOW spr round 16 (radius: 10)
[12:29:08 -221361.281168] SLOW spr round 17 (radius: 5)
[12:34:39 -221356.642706] SLOW spr round 18 (radius: 5)
[12:38:35] [worker #4] ML tree search #11, logLikelihood: -221230.937775
[12:39:33 -221356.642656] SLOW spr round 19 (radius: 10)
[12:44:49 -221356.642655] SLOW spr round 20 (radius: 15)
[12:54:10 -221354.140693] SLOW spr round 21 (radius: 5)
[12:59:55 -221347.423049] SLOW spr round 22 (radius: 5)
[13:04:59 -221347.260249] SLOW spr round 23 (radius: 5)
[13:09:42 -221347.260228] SLOW spr round 24 (radius: 10)
[13:14:47 -221346.550785] SLOW spr round 25 (radius: 5)
[13:20:12 -221346.524407] SLOW spr round 26 (radius: 10)
[13:25:57 -221346.523974] SLOW spr round 27 (radius: 15)
[13:34:47 -221346.523967] SLOW spr round 28 (radius: 20)
[13:46:47 -221343.103589] SLOW spr round 29 (radius: 5)
[13:52:39 -221328.475782] SLOW spr round 30 (radius: 5)
[13:57:47 -221328.475319] SLOW spr round 31 (radius: 10)
[14:03:13 -221327.261414] SLOW spr round 32 (radius: 5)
[14:08:41 -221327.261253] SLOW spr round 33 (radius: 10)
[14:14:27 -221327.261250] SLOW spr round 34 (radius: 15)
[14:23:26 -221327.261250] SLOW spr round 35 (radius: 20)
[14:35:32 -221326.686145] SLOW spr round 36 (radius: 5)
[14:41:17 -221326.685363] SLOW spr round 37 (radius: 10)
[14:47:39 -221326.685215] SLOW spr round 38 (radius: 15)
[14:56:26 -221326.685179] SLOW spr round 39 (radius: 20)
[14:57:17] [worker #1] ML tree search #14, logLikelihood: -221315.298662
[15:08:32 -221326.685170] SLOW spr round 40 (radius: 25)
[15:23:16 -221326.225475] SLOW spr round 41 (radius: 5)
[15:29:03 -221326.225355] SLOW spr round 42 (radius: 10)
[15:35:36 -221326.225354] SLOW spr round 43 (radius: 15)
[15:37:20] [worker #5] ML tree search #12, logLikelihood: -221227.875047
[15:44:26 -221326.225354] SLOW spr round 44 (radius: 20)
[15:56:35 -221326.225354] SLOW spr round 45 (radius: 25)
[16:11:22 -221326.225354] Model parameter optimization (eps = 0.100000)

[16:11:33] [worker #0] ML tree search #13, logLikelihood: -221326.158489

[16:11:33 -491987.375544] Initial branch length optimization
[16:11:41 -430815.396282] Model parameter optimization (eps = 10.000000)
[16:12:55 -429258.752971] AUTODETECT spr round 1 (radius: 5)
[16:17:00 -345407.757883] AUTODETECT spr round 2 (radius: 10)
[16:21:55 -283779.045013] AUTODETECT spr round 3 (radius: 15)
[16:27:10 -258292.524662] AUTODETECT spr round 4 (radius: 20)
[16:33:45 -247166.723962] AUTODETECT spr round 5 (radius: 25)
[16:41:27 -241529.183010] SPR radius for FAST iterations: 25 (autodetect)
[16:41:27 -241529.183010] Model parameter optimization (eps = 3.000000)
[16:42:11 -241354.699689] FAST spr round 1 (radius: 25)
[16:53:05 -223662.910953] FAST spr round 2 (radius: 25)
[17:01:55 -221823.924454] FAST spr round 3 (radius: 25)
[17:08:43 -221496.057843] FAST spr round 4 (radius: 25)
[17:14:16 -221478.219861] FAST spr round 5 (radius: 25)
[17:19:09 -221469.117649] FAST spr round 6 (radius: 25)
[17:19:54] [worker #2] ML tree search #15, logLikelihood: -221311.728222
[17:23:36 -221469.116562] Model parameter optimization (eps = 1.000000)
[17:23:57 -221459.383507] SLOW spr round 1 (radius: 5)
[17:29:45 -221387.565931] SLOW spr round 2 (radius: 5)
[17:35:11 -221340.923002] SLOW spr round 3 (radius: 5)
[17:40:25 -221325.764418] SLOW spr round 4 (radius: 5)
[17:45:20 -221325.763496] SLOW spr round 5 (radius: 10)
[17:50:50 -221306.114501] SLOW spr round 6 (radius: 5)
[17:56:53 -221287.520644] SLOW spr round 7 (radius: 5)
[18:02:30 -221281.754607] SLOW spr round 8 (radius: 5)
[18:07:46 -221280.940432] SLOW spr round 9 (radius: 5)
[18:12:46 -221280.940363] SLOW spr round 10 (radius: 10)
[18:17:57 -221279.069623] SLOW spr round 11 (radius: 5)
[18:23:50 -221278.405487] SLOW spr round 12 (radius: 5)
[18:29:13 -221278.405473] SLOW spr round 13 (radius: 10)
[18:34:39 -221278.405473] SLOW spr round 14 (radius: 15)
[18:45:08 -221261.805381] SLOW spr round 15 (radius: 5)
[18:51:25 -221255.599331] SLOW spr round 16 (radius: 5)
[18:56:59 -221252.549335] SLOW spr round 17 (radius: 5)
[19:02:08 -221252.549165] SLOW spr round 18 (radius: 10)
[19:07:38 -221240.474750] SLOW spr round 19 (radius: 5)
[19:13:50 -221233.238078] SLOW spr round 20 (radius: 5)
[19:19:12 -221233.238041] SLOW spr round 21 (radius: 10)
[19:24:39 -221232.532785] SLOW spr round 22 (radius: 5)
[19:30:36 -221232.532755] SLOW spr round 23 (radius: 10)
[19:36:42 -221232.504261] SLOW spr round 24 (radius: 15)
[19:46:36 -221230.993973] SLOW spr round 25 (radius: 5)
[19:52:52 -221225.285791] SLOW spr round 26 (radius: 5)
[19:58:22 -221225.285041] SLOW spr round 27 (radius: 10)
[20:04:03 -221219.780918] SLOW spr round 28 (radius: 5)
[20:09:57 -221219.780799] SLOW spr round 29 (radius: 10)
[20:12:06] [worker #4] ML tree search #17, logLikelihood: -221215.857900
[20:16:03 -221219.780799] SLOW spr round 30 (radius: 15)
[20:26:04 -221219.436813] SLOW spr round 31 (radius: 5)
[20:32:17 -221219.270873] SLOW spr round 32 (radius: 5)
[20:37:46 -221219.270484] SLOW spr round 33 (radius: 10)
[20:43:24 -221219.270481] SLOW spr round 34 (radius: 15)
[20:50:36] [worker #5] ML tree search #18, logLikelihood: -221269.245978
[20:53:40 -221219.270481] SLOW spr round 35 (radius: 20)
[21:08:03 -221219.270481] SLOW spr round 36 (radius: 25)
[21:24:47 -221219.270481] Model parameter optimization (eps = 0.100000)

[21:25:00] [worker #0] ML tree search #19, logLikelihood: -221217.459069

[21:48:13] [worker #3] ML tree search #16, logLikelihood: -221185.324423
[22:38:13] [worker #1] ML tree search #20, logLikelihood: -221289.923485

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.258392,0.266337) (0.112762,0.474176) (0.558285,1.244880) (0.070560,2.589458) 
   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: -221160.287545

AIC score: 446326.575089 / AICc score: 8474350.575089 / BIC score: 453635.470488
Free parameters (model + branch lengths): 2003

WARNING: Number of free parameters (K=2003) is larger than alignment size (n=284).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H4Z2/3_mltree/Q9H4Z2.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H4Z2/3_mltree/Q9H4Z2.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H4Z2/3_mltree/Q9H4Z2.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H4Z2/3_mltree/Q9H4Z2.raxml.log

Analysis started: 02-Jul-2021 16:04:12 / finished: 03-Jul-2021 14:42:26

Elapsed time: 81493.984 seconds

Consumed energy: 6916.270 Wh (= 35 km in an electric car, or 173 km with an e-scooter!)