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 15:53:40 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H9B1/2_msa/Q9H9B1_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H9B1/3_mltree/Q9H9B1 --seed 2 --threads 8 --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 (8 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H9B1/2_msa/Q9H9B1_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 676 sites

WARNING: Sequences tr_M3YH69_M3YH69_MUSPF_9669 and tr_A0A2Y9KA49_A0A2Y9KA49_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3YQD6_M3YQD6_MUSPF_9669 and tr_E2R289_E2R289_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3YQD6_M3YQD6_MUSPF_9669 and tr_G3X6G5_G3X6G5_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_M3YQD6_M3YQD6_MUSPF_9669 and tr_A0A2U3VP04_A0A2U3VP04_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YQD6_M3YQD6_MUSPF_9669 and tr_A0A2U3Y3Y8_A0A2U3Y3Y8_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3YQD6_M3YQD6_MUSPF_9669 and tr_A0A2Y9JRS3_A0A2Y9JRS3_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G1R8Q1_G1R8Q1_NOMLE_61853 and tr_G3S5S8_G3S5S8_GORGO_9595 are exactly identical!
WARNING: Sequences tr_G1R8Q1_G1R8Q1_NOMLE_61853 and tr_H2QYK0_H2QYK0_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G1R8Q1_G1R8Q1_NOMLE_61853 and tr_F7APZ4_F7APZ4_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G1R8Q1_G1R8Q1_NOMLE_61853 and tr_A0A2I3LCB2_A0A2I3LCB2_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G1R8Q1_G1R8Q1_NOMLE_61853 and tr_A0A2K5MJN8_A0A2K5MJN8_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G1R8Q1_G1R8Q1_NOMLE_61853 and tr_A0A2K6AUY4_A0A2K6AUY4_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G1R8Q1_G1R8Q1_NOMLE_61853 and tr_A0A2K5Z7Y0_A0A2K5Z7Y0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I2ZS57_A0A2I2ZS57_GORGO_9595 and tr_H2PIL1_H2PIL1_PONAB_9601 are exactly identical!
WARNING: Sequences tr_A0A2I2ZS57_A0A2I2ZS57_GORGO_9595 and tr_H2R7G9_H2R7G9_PANTR_9598 are exactly identical!
WARNING: Sequences sp_Q5RB81_SUV91_PONAB_9601 and sp_O43463_SUV91_HUMAN_9606 are exactly identical!
WARNING: Sequences sp_Q5RB81_SUV91_PONAB_9601 and tr_A0A0D9RLA0_A0A0D9RLA0_CHLSB_60711 are exactly identical!
WARNING: Sequences sp_Q5RB81_SUV91_PONAB_9601 and tr_A0A2R9AA50_A0A2R9AA50_PANPA_9597 are exactly identical!
WARNING: Sequences tr_K7AU49_K7AU49_PANTR_9598 and sp_Q9H5I1_SUV92_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_K7AU49_K7AU49_PANTR_9598 and tr_A0A2R9AKX9_A0A2R9AKX9_PANPA_9597 are exactly identical!
WARNING: Sequences tr_W5NZR1_W5NZR1_SHEEP_9940 and tr_F1N413_F1N413_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A088AK17_A0A088AK17_APIME_7460 and tr_A0A2A3EFT4_A0A2A3EFT4_APICC_94128 are exactly identical!
WARNING: Sequences tr_A0A0E0J3Y4_A0A0E0J3Y4_ORYNI_4536 and tr_A0A0E0RAL9_A0A0E0RAL9_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0J3Y4_A0A0E0J3Y4_ORYNI_4536 and tr_A0A0E0BKY4_A0A0E0BKY4_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_A0A1D5R4M1_A0A1D5R4M1_MACMU_9544 and tr_A0A096NWL9_A0A096NWL9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5R4M1_A0A1D5R4M1_MACMU_9544 and tr_A0A0D9RWC2_A0A0D9RWC2_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5R4M1_A0A1D5R4M1_MACMU_9544 and tr_A0A2K5NVN5_A0A2K5NVN5_CERAT_9531 are exactly identical!
WARNING: Sequences tr_I1R1G3_I1R1G3_ORYGL_4538 and tr_A0A0D3HNR5_A0A0D3HNR5_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1R1G3_I1R1G3_ORYGL_4538 and tr_Q2R1K5_Q2R1K5_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0N3X6_A0A0E0N3X6_ORYRU_4529 and tr_Q8RUS3_Q8RUS3_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0QIP5_A0A0E0QIP5_ORYRU_4529 and tr_Q6Z2A2_Q6Z2A2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_U3JSN1_U3JSN1_FICAL_59894 and tr_A0A218UDV4_A0A218UDV4_9PASE_299123 are exactly identical!
WARNING: Sequences tr_A0A096NH96_A0A096NH96_PAPAN_9555 and tr_A0A2K6CNV9_A0A2K6CNV9_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NH96_A0A096NH96_PAPAN_9555 and tr_A0A2K6A613_A0A2K6A613_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A0V1MCB2_A0A0V1MCB2_9BILA_268474 and tr_A0A0V1H9A4_A0A0V1H9A4_9BILA_268475 are exactly identical!
WARNING: Sequences tr_A0A1S4D209_A0A1S4D209_TOBAC_4097 and tr_A0A1U7X7C6_A0A1U7X7C6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4DJM8_A0A1S4DJM8_TOBAC_4097 and tr_A0A1U7XM12_A0A1U7XM12_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S4DQX0_A0A1S4DQX0_TOBAC_4097 and tr_A0A1U7Y9I9_A0A1U7Y9I9_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A226NG00_A0A226NG00_CALSU_9009 and tr_A0A226PMU1_A0A226PMU1_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2U3X024_A0A2U3X024_ODORO_9708 and tr_A0A2U3Y459_A0A2U3Y459_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_A0A2Y9EWL2_A0A2Y9EWL2_PHYCD_9755 and tr_A0A384B369_A0A384B369_BALAS_310752 are exactly identical!
WARNING: Duplicate sequences found: 41

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/Q9H9B1/3_mltree/Q9H9B1.raxml.reduced.phy

Alignment comprises 1 partitions and 676 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 676 / 676
Gaps: 29.28 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H9B1/3_mltree/Q9H9B1.raxml.rba

Parallelization scheme autoconfig: 2 worker(s) x 4 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 169 / 13520
[00:00:00] Data distribution: max. searches per worker: 10

Starting ML tree search with 20 distinct starting trees

[00:00:00 -1063708.629070] Initial branch length optimization
[00:00:08 -898858.957016] Model parameter optimization (eps = 10.000000)
[00:00:50 -897577.278253] AUTODETECT spr round 1 (radius: 5)
[00:03:39 -661922.813731] AUTODETECT spr round 2 (radius: 10)
[00:06:46 -486638.104872] AUTODETECT spr round 3 (radius: 15)
[00:10:02 -394026.997357] AUTODETECT spr round 4 (radius: 20)
[00:13:37 -366057.521477] AUTODETECT spr round 5 (radius: 25)
[00:18:52 -360707.901087] SPR radius for FAST iterations: 25 (autodetect)
[00:18:52 -360707.901087] Model parameter optimization (eps = 3.000000)
[00:19:16 -360559.543081] FAST spr round 1 (radius: 25)
[00:23:17 -318555.062359] FAST spr round 2 (radius: 25)
[00:26:12 -317034.806179] FAST spr round 3 (radius: 25)
[00:28:37 -316953.674830] FAST spr round 4 (radius: 25)
[00:30:49 -316916.697377] FAST spr round 5 (radius: 25)
[00:32:51 -316906.825600] FAST spr round 6 (radius: 25)
[00:34:49 -316901.808884] FAST spr round 7 (radius: 25)
[00:36:44 -316899.334444] FAST spr round 8 (radius: 25)
[00:38:40 -316899.333119] Model parameter optimization (eps = 1.000000)
[00:38:59 -316890.853884] SLOW spr round 1 (radius: 5)
[00:41:40 -316826.919420] SLOW spr round 2 (radius: 5)
[00:44:18 -316815.238690] SLOW spr round 3 (radius: 5)
[00:46:50 -316813.814974] SLOW spr round 4 (radius: 5)
[00:49:19 -316813.814852] SLOW spr round 5 (radius: 10)
[00:51:57 -316813.814781] SLOW spr round 6 (radius: 15)
[00:57:19 -316813.412125] SLOW spr round 7 (radius: 5)
[01:00:38 -316811.717305] SLOW spr round 8 (radius: 5)
[01:03:31 -316811.717214] SLOW spr round 9 (radius: 10)
[01:06:20 -316810.569838] SLOW spr round 10 (radius: 5)
[01:09:24 -316810.569767] SLOW spr round 11 (radius: 10)
[01:12:21 -316810.569697] SLOW spr round 12 (radius: 15)
[01:17:20 -316810.569626] SLOW spr round 13 (radius: 20)
[01:25:57 -316808.731182] SLOW spr round 14 (radius: 5)
[01:29:21 -316808.731081] SLOW spr round 15 (radius: 10)
[01:32:46 -316808.731010] SLOW spr round 16 (radius: 15)
[01:37:41 -316808.730940] SLOW spr round 17 (radius: 20)
[01:46:19 -316808.730869] SLOW spr round 18 (radius: 25)
[01:56:33 -316808.730799] Model parameter optimization (eps = 0.100000)

[01:56:40] [worker #0] ML tree search #1, logLikelihood: -316808.639458

[01:56:40 -1062251.176287] Initial branch length optimization
[01:56:48 -892157.882161] Model parameter optimization (eps = 10.000000)
[01:57:36 -890959.322058] AUTODETECT spr round 1 (radius: 5)
[01:58:06] [worker #1] ML tree search #2, logLikelihood: -316819.445514
[02:00:27 -660995.510345] AUTODETECT spr round 2 (radius: 10)
[02:03:36 -495895.301861] AUTODETECT spr round 3 (radius: 15)
[02:07:07 -384266.992788] AUTODETECT spr round 4 (radius: 20)
[02:11:00 -364924.684051] AUTODETECT spr round 5 (radius: 25)
[02:16:03 -362061.319329] SPR radius for FAST iterations: 25 (autodetect)
[02:16:03 -362061.319329] Model parameter optimization (eps = 3.000000)
[02:16:31 -361901.146706] FAST spr round 1 (radius: 25)
[02:20:38 -318484.416975] FAST spr round 2 (radius: 25)
[02:23:25 -317085.674908] FAST spr round 3 (radius: 25)
[02:25:58 -316935.111791] FAST spr round 4 (radius: 25)
[02:28:07 -316927.659089] FAST spr round 5 (radius: 25)
[02:30:06 -316927.649095] Model parameter optimization (eps = 1.000000)
[02:30:26 -316911.203537] SLOW spr round 1 (radius: 5)
[02:33:06 -316826.759591] SLOW spr round 2 (radius: 5)
[02:35:45 -316816.883717] SLOW spr round 3 (radius: 5)
[02:38:16 -316816.882738] SLOW spr round 4 (radius: 10)
[02:40:54 -316816.882591] SLOW spr round 5 (radius: 15)
[02:46:17 -316814.949992] SLOW spr round 6 (radius: 5)
[02:49:36 -316814.949983] SLOW spr round 7 (radius: 10)
[02:52:52 -316814.539091] SLOW spr round 8 (radius: 5)
[02:55:53 -316814.539090] SLOW spr round 9 (radius: 10)
[02:58:47 -316814.539090] SLOW spr round 10 (radius: 15)
[03:03:49 -316814.539090] SLOW spr round 11 (radius: 20)
[03:12:28 -316814.539090] SLOW spr round 12 (radius: 25)
[03:21:26] [worker #1] ML tree search #4, logLikelihood: -316820.518018
[03:22:52 -316814.539090] Model parameter optimization (eps = 0.100000)

[03:23:01] [worker #0] ML tree search #3, logLikelihood: -316814.353849

[03:23:01 -1062629.919067] Initial branch length optimization
[03:23:09 -896835.441715] Model parameter optimization (eps = 10.000000)
[03:23:49 -895452.745328] AUTODETECT spr round 1 (radius: 5)
[03:26:40 -656234.873537] AUTODETECT spr round 2 (radius: 10)
[03:29:45 -481102.208935] AUTODETECT spr round 3 (radius: 15)
[03:33:07 -395678.041625] AUTODETECT spr round 4 (radius: 20)
[03:36:58 -374542.437969] AUTODETECT spr round 5 (radius: 25)
[03:43:21 -370789.499358] SPR radius for FAST iterations: 25 (autodetect)
[03:43:21 -370789.499358] Model parameter optimization (eps = 3.000000)
[03:43:47 -370664.891685] FAST spr round 1 (radius: 25)
[03:47:58 -319100.450501] FAST spr round 2 (radius: 25)
[03:50:51 -317028.139749] FAST spr round 3 (radius: 25)
[03:53:17 -316914.980155] FAST spr round 4 (radius: 25)
[03:55:26 -316910.296120] FAST spr round 5 (radius: 25)
[03:57:29 -316898.955299] FAST spr round 6 (radius: 25)
[03:59:27 -316898.954849] Model parameter optimization (eps = 1.000000)
[03:59:45 -316892.499015] SLOW spr round 1 (radius: 5)
[04:02:27 -316809.668590] SLOW spr round 2 (radius: 5)
[04:05:04 -316809.128684] SLOW spr round 3 (radius: 5)
[04:07:37 -316807.835077] SLOW spr round 4 (radius: 5)
[04:10:13 -316806.881359] SLOW spr round 5 (radius: 5)
[04:12:44 -316806.881257] SLOW spr round 6 (radius: 10)
[04:15:24 -316806.881187] SLOW spr round 7 (radius: 15)
[04:20:48 -316806.881117] SLOW spr round 8 (radius: 20)
[04:29:04 -316806.881048] SLOW spr round 9 (radius: 25)
[04:39:09 -316806.880978] Model parameter optimization (eps = 0.100000)

[04:39:16] [worker #0] ML tree search #5, logLikelihood: -316806.790047

[04:39:16 -1061493.129330] Initial branch length optimization
[04:39:22 -895432.445202] Model parameter optimization (eps = 10.000000)
[04:40:00 -894073.173905] AUTODETECT spr round 1 (radius: 5)
[04:42:46 -653689.044632] AUTODETECT spr round 2 (radius: 10)
[04:45:46 -492945.659763] AUTODETECT spr round 3 (radius: 15)
[04:45:49] [worker #1] ML tree search #6, logLikelihood: -316800.702754
[04:49:08 -411848.545806] AUTODETECT spr round 4 (radius: 20)
[04:52:47 -388630.312623] AUTODETECT spr round 5 (radius: 25)
[04:57:33 -374513.547770] SPR radius for FAST iterations: 25 (autodetect)
[04:57:33 -374513.547770] Model parameter optimization (eps = 3.000000)
[04:57:58 -374395.466965] FAST spr round 1 (radius: 25)
[05:02:34 -319728.382735] FAST spr round 2 (radius: 25)
[05:05:32 -317086.245660] FAST spr round 3 (radius: 25)
[05:07:58 -316926.343223] FAST spr round 4 (radius: 25)
[05:10:06 -316908.474719] FAST spr round 5 (radius: 25)
[05:12:07 -316908.474182] Model parameter optimization (eps = 1.000000)
[05:12:27 -316897.924069] SLOW spr round 1 (radius: 5)
[05:15:11 -316819.033105] SLOW spr round 2 (radius: 5)
[05:17:51 -316816.254285] SLOW spr round 3 (radius: 5)
[05:20:25 -316816.251351] SLOW spr round 4 (radius: 10)
[05:23:04 -316816.250650] SLOW spr round 5 (radius: 15)
[05:28:28 -316815.988277] SLOW spr round 6 (radius: 5)
[05:31:48 -316815.988156] SLOW spr round 7 (radius: 10)
[05:35:02 -316815.988081] SLOW spr round 8 (radius: 15)
[05:39:57 -316815.988011] SLOW spr round 9 (radius: 20)
[05:48:35 -316815.987942] SLOW spr round 10 (radius: 25)
[05:58:50 -316815.987874] Model parameter optimization (eps = 0.100000)

[05:59:06] [worker #0] ML tree search #7, logLikelihood: -316814.507599

[05:59:06 -1066734.593147] Initial branch length optimization
[05:59:12 -900000.175817] Model parameter optimization (eps = 10.000000)
[05:59:54 -898526.188656] AUTODETECT spr round 1 (radius: 5)
[06:02:46 -658142.934701] AUTODETECT spr round 2 (radius: 10)
[06:05:57 -494068.893453] AUTODETECT spr round 3 (radius: 15)
[06:09:17 -424500.941798] AUTODETECT spr round 4 (radius: 20)
[06:13:25 -383119.364401] AUTODETECT spr round 5 (radius: 25)
[06:18:16 -374765.236742] SPR radius for FAST iterations: 25 (autodetect)
[06:18:16 -374765.236742] Model parameter optimization (eps = 3.000000)
[06:18:40 -374533.847659] FAST spr round 1 (radius: 25)
[06:23:24 -319089.062406] FAST spr round 2 (radius: 25)
[06:26:27 -317023.662689] FAST spr round 3 (radius: 25)
[06:29:00 -316946.957646] FAST spr round 4 (radius: 25)
[06:31:16 -316933.486164] FAST spr round 5 (radius: 25)
[06:33:16 -316933.485952] Model parameter optimization (eps = 1.000000)
[06:33:45 -316927.116431] SLOW spr round 1 (radius: 5)
[06:33:51] [worker #1] ML tree search #8, logLikelihood: -316826.037575
[06:36:39 -316824.308893] SLOW spr round 2 (radius: 5)
[06:39:26 -316810.328394] SLOW spr round 3 (radius: 5)
[06:42:02 -316809.295028] SLOW spr round 4 (radius: 5)
[06:44:37 -316807.566835] SLOW spr round 5 (radius: 5)
[06:47:09 -316807.565473] SLOW spr round 6 (radius: 10)
[06:49:48 -316807.565333] SLOW spr round 7 (radius: 15)
[06:55:22 -316807.309182] SLOW spr round 8 (radius: 5)
[06:58:41 -316807.309108] SLOW spr round 9 (radius: 10)
[07:01:57 -316807.309039] SLOW spr round 10 (radius: 15)
[07:07:00 -316807.308970] SLOW spr round 11 (radius: 20)
[07:15:42 -316807.308901] SLOW spr round 12 (radius: 25)
[07:26:08 -316807.308832] Model parameter optimization (eps = 0.100000)

[07:26:25] [worker #0] ML tree search #9, logLikelihood: -316805.373969

[07:26:25 -1060546.500980] Initial branch length optimization
[07:26:31 -895715.484501] Model parameter optimization (eps = 10.000000)
[07:27:27 -894369.511816] AUTODETECT spr round 1 (radius: 5)
[07:30:16 -664141.335596] AUTODETECT spr round 2 (radius: 10)
[07:33:20 -479674.945655] AUTODETECT spr round 3 (radius: 15)
[07:36:46 -410764.386260] AUTODETECT spr round 4 (radius: 20)
[07:40:46 -373779.620789] AUTODETECT spr round 5 (radius: 25)
[07:47:05 -368167.303237] SPR radius for FAST iterations: 25 (autodetect)
[07:47:05 -368167.303237] Model parameter optimization (eps = 3.000000)
[07:47:31 -368054.915671] FAST spr round 1 (radius: 25)
[07:51:44 -318806.162718] FAST spr round 2 (radius: 25)
[07:54:39 -317012.675021] FAST spr round 3 (radius: 25)
[07:57:11 -316902.578443] FAST spr round 4 (radius: 25)
[07:59:18 -316896.214084] FAST spr round 5 (radius: 25)
[08:00:45] [worker #1] ML tree search #10, logLikelihood: -316806.285753
[08:01:15 -316896.213029] Model parameter optimization (eps = 1.000000)
[08:01:36 -316879.477353] SLOW spr round 1 (radius: 5)
[08:04:18 -316808.846542] SLOW spr round 2 (radius: 5)
[08:06:59 -316800.868477] SLOW spr round 3 (radius: 5)
[08:09:30 -316800.262162] SLOW spr round 4 (radius: 5)
[08:11:59 -316799.983502] SLOW spr round 5 (radius: 5)
[08:14:27 -316799.983370] SLOW spr round 6 (radius: 10)
[08:17:03 -316799.983287] SLOW spr round 7 (radius: 15)
[08:22:27 -316799.515664] SLOW spr round 8 (radius: 5)
[08:25:43 -316799.515053] SLOW spr round 9 (radius: 10)
[08:28:57 -316799.514946] SLOW spr round 10 (radius: 15)
[08:33:54 -316799.514873] SLOW spr round 11 (radius: 20)
[08:42:27 -316799.514803] SLOW spr round 12 (radius: 25)
[08:52:43 -316799.514733] Model parameter optimization (eps = 0.100000)

[08:52:49] [worker #0] ML tree search #11, logLikelihood: -316799.422285

[08:52:49 -1064809.875982] Initial branch length optimization
[08:52:55 -896870.898676] Model parameter optimization (eps = 10.000000)
[08:53:51 -895414.933164] AUTODETECT spr round 1 (radius: 5)
[08:56:41 -665111.240787] AUTODETECT spr round 2 (radius: 10)
[08:59:43 -509002.409500] AUTODETECT spr round 3 (radius: 15)
[09:03:36 -407161.657282] AUTODETECT spr round 4 (radius: 20)
[09:07:20 -374981.479563] AUTODETECT spr round 5 (radius: 25)
[09:12:26 -369313.579084] SPR radius for FAST iterations: 25 (autodetect)
[09:12:26 -369313.579084] Model parameter optimization (eps = 3.000000)
[09:12:53 -369170.939391] FAST spr round 1 (radius: 25)
[09:16:58 -319083.033209] FAST spr round 2 (radius: 25)
[09:19:53 -317047.359569] FAST spr round 3 (radius: 25)
[09:21:49] [worker #1] ML tree search #12, logLikelihood: -316821.522961
[09:22:20 -316913.604481] FAST spr round 4 (radius: 25)
[09:24:24 -316912.020408] FAST spr round 5 (radius: 25)
[09:26:23 -316912.020388] Model parameter optimization (eps = 1.000000)
[09:26:44 -316909.333642] SLOW spr round 1 (radius: 5)
[09:29:27 -316827.557817] SLOW spr round 2 (radius: 5)
[09:32:06 -316814.665304] SLOW spr round 3 (radius: 5)
[09:34:39 -316811.597397] SLOW spr round 4 (radius: 5)
[09:37:08 -316811.597020] SLOW spr round 5 (radius: 10)
[09:39:46 -316811.293905] SLOW spr round 6 (radius: 5)
[09:42:52 -316811.293748] SLOW spr round 7 (radius: 10)
[09:45:53 -316811.293678] SLOW spr round 8 (radius: 15)
[09:50:58 -316811.293608] SLOW spr round 9 (radius: 20)
[09:59:32 -316811.293539] SLOW spr round 10 (radius: 25)
[10:09:39 -316811.293469] Model parameter optimization (eps = 0.100000)

[10:09:51] [worker #0] ML tree search #13, logLikelihood: -316810.158431

[10:09:52 -1067250.111025] Initial branch length optimization
[10:10:01 -899973.414278] Model parameter optimization (eps = 10.000000)
[10:10:46 -898775.676307] AUTODETECT spr round 1 (radius: 5)
[10:13:35 -660838.119309] AUTODETECT spr round 2 (radius: 10)
[10:16:38 -503185.387622] AUTODETECT spr round 3 (radius: 15)
[10:20:09 -406255.392450] AUTODETECT spr round 4 (radius: 20)
[10:23:31 -366005.362728] AUTODETECT spr round 5 (radius: 25)
[10:28:25 -358649.792975] SPR radius for FAST iterations: 25 (autodetect)
[10:28:25 -358649.792975] Model parameter optimization (eps = 3.000000)
[10:28:48 -358464.363761] FAST spr round 1 (radius: 25)
[10:32:49 -318843.477586] FAST spr round 2 (radius: 25)
[10:35:32 -317002.889624] FAST spr round 3 (radius: 25)
[10:38:04 -316927.693008] FAST spr round 4 (radius: 25)
[10:40:10 -316910.759509] FAST spr round 5 (radius: 25)
[10:41:18] [worker #1] ML tree search #14, logLikelihood: -316824.979605
[10:42:08 -316908.646352] FAST spr round 6 (radius: 25)
[10:44:01 -316908.645946] Model parameter optimization (eps = 1.000000)
[10:44:22 -316897.312080] SLOW spr round 1 (radius: 5)
[10:46:48 -316830.306046] SLOW spr round 2 (radius: 5)
[10:49:18 -316819.967212] SLOW spr round 3 (radius: 5)
[10:51:51 -316819.966599] SLOW spr round 4 (radius: 10)
[10:54:32 -316815.429853] SLOW spr round 5 (radius: 5)
[10:57:45 -316809.744871] SLOW spr round 6 (radius: 5)
[11:00:32 -316809.494115] SLOW spr round 7 (radius: 5)
[11:03:09 -316809.493313] SLOW spr round 8 (radius: 10)
[11:05:48 -316809.493167] SLOW spr round 9 (radius: 15)
[11:11:00 -316809.240388] SLOW spr round 10 (radius: 5)
[11:14:17 -316809.240319] SLOW spr round 11 (radius: 10)
[11:17:32 -316809.240251] SLOW spr round 12 (radius: 15)
[11:22:21 -316809.240183] SLOW spr round 13 (radius: 20)
[11:30:44 -316809.240115] SLOW spr round 14 (radius: 25)
[11:40:53 -316809.240047] Model parameter optimization (eps = 0.100000)

[11:41:05] [worker #0] ML tree search #15, logLikelihood: -316808.703314

[11:41:05 -1067618.921025] Initial branch length optimization
[11:41:14 -897963.297487] Model parameter optimization (eps = 10.000000)
[11:42:06 -896763.905146] AUTODETECT spr round 1 (radius: 5)
[11:44:55 -665125.095632] AUTODETECT spr round 2 (radius: 10)
[11:47:59 -492719.092544] AUTODETECT spr round 3 (radius: 15)
[11:51:25 -403078.552655] AUTODETECT spr round 4 (radius: 20)
[11:54:56 -364091.412811] AUTODETECT spr round 5 (radius: 25)
[11:55:54] [worker #1] ML tree search #16, logLikelihood: -316807.549614
[11:59:54 -360304.999298] SPR radius for FAST iterations: 25 (autodetect)
[11:59:54 -360304.999298] Model parameter optimization (eps = 3.000000)
[12:00:21 -360154.976253] FAST spr round 1 (radius: 25)
[12:04:19 -318476.052167] FAST spr round 2 (radius: 25)
[12:07:04 -316956.846930] FAST spr round 3 (radius: 25)
[12:09:28 -316894.632084] FAST spr round 4 (radius: 25)
[12:11:32 -316890.228443] FAST spr round 5 (radius: 25)
[12:13:29 -316890.228001] Model parameter optimization (eps = 1.000000)
[12:13:47 -316886.785381] SLOW spr round 1 (radius: 5)
[12:16:27 -316829.964149] SLOW spr round 2 (radius: 5)
[12:19:04 -316822.787853] SLOW spr round 3 (radius: 5)
[12:21:42 -316818.944179] SLOW spr round 4 (radius: 5)
[12:24:13 -316818.944048] SLOW spr round 5 (radius: 10)
[12:26:54 -316813.788418] SLOW spr round 6 (radius: 5)
[12:30:04 -316813.749439] SLOW spr round 7 (radius: 10)
[12:33:05 -316813.749053] SLOW spr round 8 (radius: 15)
[12:38:05 -316813.500722] SLOW spr round 9 (radius: 5)
[12:41:23 -316813.500651] SLOW spr round 10 (radius: 10)
[12:44:37 -316813.500583] SLOW spr round 11 (radius: 15)
[12:49:29 -316813.500514] SLOW spr round 12 (radius: 20)
[12:57:56 -316811.762819] SLOW spr round 13 (radius: 5)
[13:01:19 -316811.762734] SLOW spr round 14 (radius: 10)
[13:04:43 -316811.762666] SLOW spr round 15 (radius: 15)
[13:05:25] [worker #1] ML tree search #18, logLikelihood: -316802.016547
[13:09:38 -316811.762598] SLOW spr round 16 (radius: 20)
[13:18:09 -316811.762529] SLOW spr round 17 (radius: 25)
[13:28:26 -316811.762461] Model parameter optimization (eps = 0.100000)

[13:28:43] [worker #0] ML tree search #17, logLikelihood: -316811.118497

[13:28:43 -1056202.925158] Initial branch length optimization
[13:28:50 -893034.178813] Model parameter optimization (eps = 10.000000)
[13:29:47 -891812.705153] AUTODETECT spr round 1 (radius: 5)
[13:32:35 -655253.999312] AUTODETECT spr round 2 (radius: 10)
[13:35:38 -493662.625244] AUTODETECT spr round 3 (radius: 15)
[13:39:18 -395080.523594] AUTODETECT spr round 4 (radius: 20)
[13:43:05 -367180.169268] AUTODETECT spr round 5 (radius: 25)
[13:47:58 -363035.737774] SPR radius for FAST iterations: 25 (autodetect)
[13:47:58 -363035.737774] Model parameter optimization (eps = 3.000000)
[13:48:20 -362844.258974] FAST spr round 1 (radius: 25)
[13:52:32 -318433.296830] FAST spr round 2 (radius: 25)
[13:55:28 -317063.476975] FAST spr round 3 (radius: 25)
[13:57:54 -316977.075910] FAST spr round 4 (radius: 25)
[14:00:04 -316908.293086] FAST spr round 5 (radius: 25)
[14:02:03 -316908.292928] Model parameter optimization (eps = 1.000000)
[14:02:20 -316904.785226] SLOW spr round 1 (radius: 5)
[14:05:09 -316817.028864] SLOW spr round 2 (radius: 5)
[14:07:46 -316808.924626] SLOW spr round 3 (radius: 5)
[14:10:21 -316808.659613] SLOW spr round 4 (radius: 5)
[14:12:50 -316808.659397] SLOW spr round 5 (radius: 10)
[14:15:28 -316803.694647] SLOW spr round 6 (radius: 5)
[14:18:33 -316803.694318] SLOW spr round 7 (radius: 10)
[14:21:33 -316803.694245] SLOW spr round 8 (radius: 15)
[14:26:32 -316803.428658] SLOW spr round 9 (radius: 5)
[14:29:51 -316803.428582] SLOW spr round 10 (radius: 10)
[14:33:06 -316803.428510] SLOW spr round 11 (radius: 15)
[14:38:03 -316803.428439] SLOW spr round 12 (radius: 20)
[14:46:30 -316803.428368] SLOW spr round 13 (radius: 25)
[14:56:34 -316803.428297] Model parameter optimization (eps = 0.100000)

[14:56:44] [worker #0] ML tree search #19, logLikelihood: -316803.138301

[15:02:29] [worker #1] ML tree search #20, logLikelihood: -316808.164051

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.094723,0.311457) (0.082177,0.415851) (0.371891,0.748178) (0.451209,1.458489) 
   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: -316799.422285

AIC score: 637608.844570 / AICc score: 8681668.844570 / BIC score: 646663.811687
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=676).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 100 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H9B1/3_mltree/Q9H9B1.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H9B1/3_mltree/Q9H9B1.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H9B1/3_mltree/Q9H9B1.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H9B1/3_mltree/Q9H9B1.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9H9B1/3_mltree/Q9H9B1.raxml.log

Analysis started: 01-Jul-2021 15:53:40 / finished: 02-Jul-2021 06:56:10

Elapsed time: 54149.755 seconds

Consumed energy: 4443.506 Wh (= 22 km in an electric car, or 111 km with an e-scooter!)