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 03:23:28 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y6X6/2_msa/Q9Y6X6_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y6X6/3_mltree/Q9Y6X6 --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/Q9Y6X6/2_msa/Q9Y6X6_trimmed_msa.fasta
[00:00:00] Loaded alignment with 997 taxa and 522 sites

WARNING: Sequences tr_A0A2R8QRQ3_A0A2R8QRQ3_DANRE_7955 and tr_F1Q777_F1Q777_DANRE_7955 are exactly identical!
WARNING: Sequences tr_M3YI26_M3YI26_MUSPF_9669 and tr_A0A2Y9K4P2_A0A2Y9K4P2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A2I2ZY45_A0A2I2ZY45_GORGO_9595 and tr_A0A2I3RRT3_A0A2I3RRT3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_A0A2I2ZY45_A0A2I2ZY45_GORGO_9595 and tr_A0A2R9AJD2_A0A2R9AJD2_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2P7S5_H2P7S5_PONAB_9601 and tr_A0A2R8ZZR5_A0A2R8ZZR5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2PF80_H2PF80_PONAB_9601 and tr_H2QQP3_H2QQP3_PANTR_9598 are exactly identical!
WARNING: Sequences tr_H2PF80_H2PF80_PONAB_9601 and sp_Q9HD67_MYO10_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_B8NSE3_B8NSE3_ASPFN_332952 and tr_Q2UTJ6_Q2UTJ6_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NSE3_B8NSE3_ASPFN_332952 and tr_A0A1S9D4F4_A0A1S9D4F4_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A2I3SHH5_A0A2I3SHH5_PANTR_9598 and tr_A0A2R9B373_A0A2R9B373_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A2J8M1K6_A0A2J8M1K6_PANTR_9598 and tr_A0A2R9AJ57_A0A2R9AJ57_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2QCE0_H2QCE0_PANTR_9598 and sp_Q9UKN7_MYO15_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_A0A158NLQ2_A0A158NLQ2_ATTCE_12957 and tr_F4X2U1_F4X2U1_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A158NLQ2_A0A158NLQ2_ATTCE_12957 and tr_A0A151WK06_A0A151WK06_9HYME_64791 are exactly identical!
WARNING: Sequences tr_A0A158NLQ2_A0A158NLQ2_ATTCE_12957 and tr_A0A151IUA1_A0A151IUA1_9HYME_471704 are exactly identical!
WARNING: Sequences tr_A0A158NLQ2_A0A158NLQ2_ATTCE_12957 and tr_A0A195BLG5_A0A195BLG5_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NLQ2_A0A158NLQ2_ATTCE_12957 and tr_A0A195FVR3_A0A195FVR3_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A158NSE1_A0A158NSE1_ATTCE_12957 and tr_A0A195AXX9_A0A195AXX9_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A1D5Q0C1_A0A1D5Q0C1_MACMU_9544 and tr_A0A096P329_A0A096P329_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5Q0C1_A0A1D5Q0C1_MACMU_9544 and tr_A0A2K5LNK1_A0A2K5LNK1_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A1D5Q0C1_A0A1D5Q0C1_MACMU_9544 and tr_A0A2K6DH67_A0A2K6DH67_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A1D5Q0C1_A0A1D5Q0C1_MACMU_9544 and tr_A0A2K5XDY5_A0A2K5XDY5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_H0YSD2_H0YSD2_TAEGU_59729 and tr_U3JXQ8_U3JXQ8_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0ZB81_H0ZB81_TAEGU_59729 and tr_A0A218UCT2_A0A218UCT2_9PASE_299123 are exactly identical!
WARNING: Sequences tr_F4W8A1_F4W8A1_ACREC_103372 and tr_A0A151HY88_A0A151HY88_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F4W8A1_F4W8A1_ACREC_103372 and tr_A0A195EXJ5_A0A195EXJ5_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A8WVP7_A8WVP7_CAEBR_6238 and tr_A0A2G5VEZ0_A0A2G5VEZ0_9PELO_1611254 are exactly identical!
WARNING: Sequences tr_M4F6H8_M4F6H8_BRARP_51351 and tr_A0A078HQ64_A0A078HQ64_BRANA_3708 are exactly identical!
WARNING: Sequences tr_A0A044TB68_A0A044TB68_ONCVO_6282 and tr_A0A182E4H8_A0A182E4H8_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A096NFD1_A0A096NFD1_PAPAN_9555 and tr_A0A2K5YEN7_A0A2K5YEN7_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A096NZG0_A0A096NZG0_PAPAN_9555 and tr_A0A2K5N8B6_A0A2K5N8B6_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A096NZG0_A0A096NZG0_PAPAN_9555 and tr_A0A2K6CRD6_A0A2K6CRD6_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A096NZG0_A0A096NZG0_PAPAN_9555 and tr_A0A2K5YYK9_A0A2K5YYK9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3MCK3_A0A2I3MCK3_PAPAN_9555 and tr_A0A0D9QV07_A0A0D9QV07_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A2I3MCK3_A0A2I3MCK3_PAPAN_9555 and tr_A0A2K5MWX4_A0A2K5MWX4_CERAT_9531 are exactly identical!
WARNING: Sequences tr_A0A2I3MCK3_A0A2I3MCK3_PAPAN_9555 and tr_A0A2K6BQ77_A0A2K6BQ77_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A078GGV9_A0A078GGV9_BRANA_3708 and tr_A0A0D3CI85_A0A0D3CI85_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A078HXQ8_A0A078HXQ8_BRANA_3708 and tr_A0A0D3CPQ4_A0A0D3CPQ4_BRAOL_109376 are exactly identical!
WARNING: Sequences tr_A0A0D2VA85_A0A0D2VA85_GOSRA_29730 and tr_A0A1U8KQN3_A0A1U8KQN3_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0F0I4N6_A0A0F0I4N6_ASPPU_1403190 and tr_A0A2G7FXZ6_A0A2G7FXZ6_9EURO_656916 are exactly identical!
WARNING: Sequences tr_A0A0A1P9D4_A0A0A1P9D4_9FUNG_58291 and tr_A0A367JQQ7_A0A367JQQ7_9FUNG_86630 are exactly identical!
WARNING: Sequences tr_A0A151P424_A0A151P424_ALLMI_8496 and tr_A0A3Q0GLR9_A0A3Q0GLR9_ALLSI_38654 are exactly identical!
WARNING: Sequences tr_A0A091J1T7_A0A091J1T7_EGRGA_188379 and tr_A0A091UQB4_A0A091UQB4_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A091J1T7_A0A091J1T7_EGRGA_188379 and tr_A0A087RFB5_A0A087RFB5_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091J1T7_A0A091J1T7_EGRGA_188379 and tr_A0A0A0A8I6_A0A0A0A8I6_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A0V1CTS5_A0A0V1CTS5_TRIBR_45882 and tr_A0A0V0VQ09_A0A0V0VQ09_9BILA_181606 are exactly identical!
WARNING: Sequences tr_A0A0V1CTS5_A0A0V1CTS5_TRIBR_45882 and tr_A0A0V1PCY5_A0A0V1PCY5_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A195DB37_A0A195DB37_9HYME_471704 and tr_A0A151K0S2_A0A151K0S2_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A1S4BD30_A0A1S4BD30_TOBAC_4097 and tr_A0A1U7X8C6_A0A1U7X8C6_NICSY_4096 are exactly identical!
WARNING: Sequences tr_A0A1S3H515_A0A1S3H515_LINUN_7574 and tr_A0A2R2MNA5_A0A2R2MNA5_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3HW14_A0A1S3HW14_LINUN_7574 and tr_A0A1S3JXD0_A0A1S3JXD0_LINUN_7574 are exactly identical!
WARNING: Sequences tr_A0A1S3W079_A0A1S3W079_VIGRR_3916 and tr_A0A3Q0ER19_A0A3Q0ER19_VIGRR_3916 are exactly identical!
WARNING: Sequences tr_A0A1I7TBZ6_A0A1I7TBZ6_9PELO_1561998 and tr_A0A1I7TBZ7_A0A1I7TBZ7_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1I7TEC1_A0A1I7TEC1_9PELO_1561998 and tr_A0A1I7TEC2_A0A1I7TEC2_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A1I7TEC1_A0A1I7TEC1_9PELO_1561998 and tr_A0A1I7TEC3_A0A1I7TEC3_9PELO_1561998 are exactly identical!
WARNING: Sequences tr_A0A2D0SQR3_A0A2D0SQR3_ICTPU_7998 and tr_A0A2D0SRB1_A0A2D0SRB1_ICTPU_7998 are exactly identical!
WARNING: Sequences tr_A0A2U4CMD7_A0A2U4CMD7_TURTR_9739 and tr_A0A2Y9NSW1_A0A2Y9NSW1_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A319CMC1_A0A319CMC1_9EURO_1448315 and tr_A0A2V5HR05_A0A2V5HR05_9EURO_1450541 are exactly identical!
WARNING: Sequences tr_A0A319CMC1_A0A319CMC1_9EURO_1448315 and tr_A0A2V5HKY6_A0A2V5HKY6_9EURO_1450538 are exactly identical!
WARNING: Duplicate sequences found: 59

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/Q9Y6X6/3_mltree/Q9Y6X6.raxml.reduced.phy

Alignment comprises 1 partitions and 522 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 522 / 522
Gaps: 1.56 %
Invariant sites: 2.30 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y6X6/3_mltree/Q9Y6X6.raxml.rba

Parallelization scheme autoconfig: 3 worker(s) x 2 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 997 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 261 / 20880
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -854119.724302] Initial branch length optimization
[00:00:11 -726643.214906] Model parameter optimization (eps = 10.000000)
[00:01:04 -724782.334308] AUTODETECT spr round 1 (radius: 5)
[00:04:43 -451358.086798] AUTODETECT spr round 2 (radius: 10)
[00:08:53 -319230.210112] AUTODETECT spr round 3 (radius: 15)
[00:13:06 -265398.289206] AUTODETECT spr round 4 (radius: 20)
[00:17:33 -229982.689960] AUTODETECT spr round 5 (radius: 25)
[00:23:25 -223829.882226] SPR radius for FAST iterations: 25 (autodetect)
[00:23:25 -223829.882226] Model parameter optimization (eps = 3.000000)
[00:23:49 -223786.523124] FAST spr round 1 (radius: 25)
[00:27:35 -194789.123824] FAST spr round 2 (radius: 25)
[00:30:08 -193279.087432] FAST spr round 3 (radius: 25)
[00:32:32 -193172.993176] FAST spr round 4 (radius: 25)
[00:34:39 -193150.402642] FAST spr round 5 (radius: 25)
[00:36:40 -193150.402567] Model parameter optimization (eps = 1.000000)
[00:36:57 -193147.065674] SLOW spr round 1 (radius: 5)
[00:39:58 -193103.292645] SLOW spr round 2 (radius: 5)
[00:42:50 -193100.531121] SLOW spr round 3 (radius: 5)
[00:45:33 -193100.529518] SLOW spr round 4 (radius: 10)
[00:48:14 -193100.528723] SLOW spr round 5 (radius: 15)
[00:52:55 -193099.613564] SLOW spr round 6 (radius: 5)
[00:56:42 -193099.612764] SLOW spr round 7 (radius: 10)
[00:59:55 -193097.595001] SLOW spr round 8 (radius: 5)
[01:03:26 -193094.665518] SLOW spr round 9 (radius: 5)
[01:06:28 -193094.665271] SLOW spr round 10 (radius: 10)
[01:09:13 -193094.665270] SLOW spr round 11 (radius: 15)
[01:13:47 -193094.665270] SLOW spr round 12 (radius: 20)
[01:15:02] [worker #2] ML tree search #3, logLikelihood: -193096.540355
[01:18:57] [worker #1] ML tree search #2, logLikelihood: -193082.622379
[01:22:09 -193094.665270] SLOW spr round 13 (radius: 25)
[01:32:59 -193094.665270] Model parameter optimization (eps = 0.100000)

[01:33:13] [worker #0] ML tree search #1, logLikelihood: -193094.357582

[01:33:13 -852756.228907] Initial branch length optimization
[01:33:22 -727015.157318] Model parameter optimization (eps = 10.000000)
[01:34:12 -725145.601197] AUTODETECT spr round 1 (radius: 5)
[01:37:50 -472340.553503] AUTODETECT spr round 2 (radius: 10)
[01:42:12 -313162.028873] AUTODETECT spr round 3 (radius: 15)
[01:46:19 -264097.387717] AUTODETECT spr round 4 (radius: 20)
[01:51:36 -239674.153723] AUTODETECT spr round 5 (radius: 25)
[01:57:47 -222876.570136] SPR radius for FAST iterations: 25 (autodetect)
[01:57:47 -222876.570136] Model parameter optimization (eps = 3.000000)
[01:58:26 -222814.816038] FAST spr round 1 (radius: 25)
[02:01:58 -194429.551588] FAST spr round 2 (radius: 25)
[02:04:28 -193299.067771] FAST spr round 3 (radius: 25)
[02:06:50 -193203.665016] FAST spr round 4 (radius: 25)
[02:08:52 -193194.094629] FAST spr round 5 (radius: 25)
[02:10:51 -193194.094619] Model parameter optimization (eps = 1.000000)
[02:11:02 -193193.249358] SLOW spr round 1 (radius: 5)
[02:14:09 -193131.486762] SLOW spr round 2 (radius: 5)
[02:17:06 -193105.180488] SLOW spr round 3 (radius: 5)
[02:19:53 -193105.169015] SLOW spr round 4 (radius: 10)
[02:22:38 -193104.709772] SLOW spr round 5 (radius: 5)
[02:26:19 -193104.698853] SLOW spr round 6 (radius: 10)
[02:29:25 -193104.698071] SLOW spr round 7 (radius: 15)
[02:30:33] [worker #1] ML tree search #5, logLikelihood: -193096.720178
[02:33:58 -193104.697289] SLOW spr round 8 (radius: 20)
[02:38:50] [worker #2] ML tree search #6, logLikelihood: -193092.655646
[02:43:01 -193104.696506] SLOW spr round 9 (radius: 25)
[02:54:22 -193104.695722] Model parameter optimization (eps = 0.100000)

[02:54:35] [worker #0] ML tree search #4, logLikelihood: -193104.586456

[02:54:35 -855536.240732] Initial branch length optimization
[02:54:43 -729625.211203] Model parameter optimization (eps = 10.000000)
[02:55:40 -727775.853541] AUTODETECT spr round 1 (radius: 5)
[02:59:17 -460703.703434] AUTODETECT spr round 2 (radius: 10)
[03:03:22 -321361.537104] AUTODETECT spr round 3 (radius: 15)
[03:07:30 -261688.206684] AUTODETECT spr round 4 (radius: 20)
[03:12:21 -233293.197814] AUTODETECT spr round 5 (radius: 25)
[03:18:23 -226933.909377] SPR radius for FAST iterations: 25 (autodetect)
[03:18:23 -226933.909377] Model parameter optimization (eps = 3.000000)
[03:18:49 -226898.635199] FAST spr round 1 (radius: 25)
[03:22:33 -195067.530100] FAST spr round 2 (radius: 25)
[03:25:22 -193312.304169] FAST spr round 3 (radius: 25)
[03:27:51 -193141.236206] FAST spr round 4 (radius: 25)
[03:29:57 -193132.802042] FAST spr round 5 (radius: 25)
[03:31:57 -193131.507150] FAST spr round 6 (radius: 25)
[03:33:54 -193131.506835] Model parameter optimization (eps = 1.000000)
[03:34:09 -193129.001329] SLOW spr round 1 (radius: 5)
[03:37:02 -193095.518670] SLOW spr round 2 (radius: 5)
[03:39:49 -193095.063811] SLOW spr round 3 (radius: 5)
[03:42:32 -193095.062984] SLOW spr round 4 (radius: 10)
[03:45:17 -193095.062187] SLOW spr round 5 (radius: 15)
[03:45:54] [worker #1] ML tree search #8, logLikelihood: -193099.712681
[03:50:00 -193095.061390] SLOW spr round 6 (radius: 20)
[03:51:11] [worker #2] ML tree search #9, logLikelihood: -193086.684643
[03:58:01 -193095.060593] SLOW spr round 7 (radius: 25)
[04:08:38 -193095.059795] Model parameter optimization (eps = 0.100000)

[04:08:47] [worker #0] ML tree search #7, logLikelihood: -193094.963509

[04:08:47 -855154.719433] Initial branch length optimization
[04:09:00 -732956.203064] Model parameter optimization (eps = 10.000000)
[04:09:44 -731001.776352] AUTODETECT spr round 1 (radius: 5)
[04:13:20 -472567.833911] AUTODETECT spr round 2 (radius: 10)
[04:17:30 -331390.821345] AUTODETECT spr round 3 (radius: 15)
[04:21:55 -266317.004579] AUTODETECT spr round 4 (radius: 20)
[04:26:36 -234434.712231] AUTODETECT spr round 5 (radius: 25)
[04:31:28 -225016.903873] SPR radius for FAST iterations: 25 (autodetect)
[04:31:28 -225016.903873] Model parameter optimization (eps = 3.000000)
[04:31:51 -224960.485793] FAST spr round 1 (radius: 25)
[04:35:35 -194640.505641] FAST spr round 2 (radius: 25)
[04:38:13 -193320.524531] FAST spr round 3 (radius: 25)
[04:40:40 -193164.717587] FAST spr round 4 (radius: 25)
[04:42:50 -193149.778663] FAST spr round 5 (radius: 25)
[04:44:51 -193147.755597] FAST spr round 6 (radius: 25)
[04:46:49 -193147.755571] Model parameter optimization (eps = 1.000000)
[04:47:08 -193139.962510] SLOW spr round 1 (radius: 5)
[04:50:04 -193083.930707] SLOW spr round 2 (radius: 5)
[04:52:58 -193077.347524] SLOW spr round 3 (radius: 5)
[04:55:44 -193077.335642] SLOW spr round 4 (radius: 10)
[04:57:50] [worker #1] ML tree search #11, logLikelihood: -193085.178117
[04:58:29 -193077.334848] SLOW spr round 5 (radius: 15)
[05:03:13 -193077.334054] SLOW spr round 6 (radius: 20)
[05:11:21 -193077.333260] SLOW spr round 7 (radius: 25)
[05:16:24] [worker #2] ML tree search #12, logLikelihood: -193084.037640
[05:22:06 -193077.332465] Model parameter optimization (eps = 0.100000)

[05:22:19] [worker #0] ML tree search #10, logLikelihood: -193077.278132

[05:22:20 -857543.794716] Initial branch length optimization
[05:22:28 -734557.346155] Model parameter optimization (eps = 10.000000)
[05:23:23 -732510.803548] AUTODETECT spr round 1 (radius: 5)
[05:27:04 -459223.024964] AUTODETECT spr round 2 (radius: 10)
[05:31:09 -316693.648361] AUTODETECT spr round 3 (radius: 15)
[05:35:06 -252798.522097] AUTODETECT spr round 4 (radius: 20)
[05:39:50 -230136.085947] AUTODETECT spr round 5 (radius: 25)
[05:45:01 -227465.769999] SPR radius for FAST iterations: 25 (autodetect)
[05:45:01 -227465.769999] Model parameter optimization (eps = 3.000000)
[05:45:25 -227406.338607] FAST spr round 1 (radius: 25)
[05:49:11 -194942.756458] FAST spr round 2 (radius: 25)
[05:52:04 -193392.693510] FAST spr round 3 (radius: 25)
[05:54:30 -193174.846860] FAST spr round 4 (radius: 25)
[05:56:40 -193140.354054] FAST spr round 5 (radius: 25)
[05:58:42 -193136.912617] FAST spr round 6 (radius: 25)
[06:00:40 -193136.912577] Model parameter optimization (eps = 1.000000)
[06:00:58 -193132.580382] SLOW spr round 1 (radius: 5)
[06:03:56 -193106.748535] SLOW spr round 2 (radius: 5)
[06:06:45 -193101.566876] SLOW spr round 3 (radius: 5)
[06:09:27 -193101.071789] SLOW spr round 4 (radius: 5)
[06:12:09 -193100.836607] SLOW spr round 5 (radius: 5)
[06:14:49 -193100.835769] SLOW spr round 6 (radius: 10)
[06:17:37 -193097.175327] SLOW spr round 7 (radius: 5)
[06:20:27] [worker #1] ML tree search #14, logLikelihood: -193088.546857
[06:21:15 -193093.088295] SLOW spr round 8 (radius: 5)
[06:24:21 -193093.087291] SLOW spr round 9 (radius: 10)
[06:27:13 -193093.086472] SLOW spr round 10 (radius: 15)
[06:29:04] [worker #2] ML tree search #15, logLikelihood: -193099.787773
[06:31:48 -193093.085652] SLOW spr round 11 (radius: 20)
[06:40:16 -193093.084831] SLOW spr round 12 (radius: 25)
[06:51:13 -193093.084010] Model parameter optimization (eps = 0.100000)

[06:51:25] [worker #0] ML tree search #13, logLikelihood: -193092.970532

[06:51:25 -856314.079299] Initial branch length optimization
[06:51:37 -729180.989704] Model parameter optimization (eps = 10.000000)
[06:52:47 -727270.042190] AUTODETECT spr round 1 (radius: 5)
[06:56:29 -458914.809574] AUTODETECT spr round 2 (radius: 10)
[07:00:42 -325901.618144] AUTODETECT spr round 3 (radius: 15)
[07:04:48 -288454.040714] AUTODETECT spr round 4 (radius: 20)
[07:10:04 -250325.747671] AUTODETECT spr round 5 (radius: 25)
[07:16:28 -235298.673124] SPR radius for FAST iterations: 25 (autodetect)
[07:16:28 -235298.673124] Model parameter optimization (eps = 3.000000)
[07:16:51 -235230.177400] FAST spr round 1 (radius: 25)
[07:20:45 -195264.795818] FAST spr round 2 (radius: 25)
[07:23:29 -193226.816129] FAST spr round 3 (radius: 25)
[07:25:55 -193152.380154] FAST spr round 4 (radius: 25)
[07:28:02 -193142.979204] FAST spr round 5 (radius: 25)
[07:30:00 -193142.978694] Model parameter optimization (eps = 1.000000)
[07:30:16 -193141.079677] SLOW spr round 1 (radius: 5)
[07:33:15 -193108.582474] SLOW spr round 2 (radius: 5)
[07:36:00 -193108.582354] SLOW spr round 3 (radius: 10)
[07:38:48 -193105.881966] SLOW spr round 4 (radius: 5)
[07:42:28 -193100.481702] SLOW spr round 5 (radius: 5)
[07:42:50] [worker #1] ML tree search #17, logLikelihood: -193118.312134
[07:45:36 -193100.480881] SLOW spr round 6 (radius: 10)
[07:48:30 -193098.557881] SLOW spr round 7 (radius: 5)
[07:51:30] [worker #2] ML tree search #18, logLikelihood: -193099.992426
[07:52:05 -193098.557049] SLOW spr round 8 (radius: 10)
[07:55:12 -193098.556229] SLOW spr round 9 (radius: 15)
[07:59:40 -193098.555409] SLOW spr round 10 (radius: 20)
[08:08:52 -193098.554589] SLOW spr round 11 (radius: 25)
[08:20:23 -193098.553769] Model parameter optimization (eps = 0.100000)

[08:20:37] [worker #0] ML tree search #16, logLikelihood: -193098.306214

[08:20:37 -856169.090859] Initial branch length optimization
[08:20:47 -730173.663800] Model parameter optimization (eps = 10.000000)
[08:21:41 -728291.059728] AUTODETECT spr round 1 (radius: 5)
[08:25:22 -464898.622252] AUTODETECT spr round 2 (radius: 10)
[08:29:38 -310129.053857] AUTODETECT spr round 3 (radius: 15)
[08:33:49 -267892.827003] AUTODETECT spr round 4 (radius: 20)
[08:38:50 -235434.889610] AUTODETECT spr round 5 (radius: 25)
[08:43:52 -227762.820851] SPR radius for FAST iterations: 25 (autodetect)
[08:43:52 -227762.820851] Model parameter optimization (eps = 3.000000)
[08:44:16 -227686.005639] FAST spr round 1 (radius: 25)
[08:47:48 -194485.719459] FAST spr round 2 (radius: 25)
[08:50:35 -193230.228349] FAST spr round 3 (radius: 25)
[08:53:02 -193152.125587] FAST spr round 4 (radius: 25)
[08:55:05 -193148.205159] FAST spr round 5 (radius: 25)
[08:57:01 -193148.205152] Model parameter optimization (eps = 1.000000)
[08:57:12 -193147.581958] SLOW spr round 1 (radius: 5)
[09:00:11 -193102.688205] SLOW spr round 2 (radius: 5)
[09:02:56 -193096.585717] SLOW spr round 3 (radius: 5)
[09:03:04] [worker #1] ML tree search #20, logLikelihood: -193093.550946
[09:05:36 -193096.584903] SLOW spr round 4 (radius: 10)
[09:08:21 -193089.397893] SLOW spr round 5 (radius: 5)
[09:11:58 -193085.469592] SLOW spr round 6 (radius: 5)
[09:14:49 -193085.468758] SLOW spr round 7 (radius: 10)
[09:17:13 -193085.467944] SLOW spr round 8 (radius: 15)
[09:21:02 -193085.467130] SLOW spr round 9 (radius: 20)
[09:28:38 -193085.466315] SLOW spr round 10 (radius: 25)
[09:39:11 -193085.465500] Model parameter optimization (eps = 0.100000)

[09:39:24] [worker #0] ML tree search #19, logLikelihood: -193084.987850


Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.200465,0.284760) (0.369081,0.428627) (0.252220,1.242236) (0.178233,2.644850) 
   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: -193077.278132

AIC score: 390148.556264 / AICc score: 8370160.556264 / BIC score: 398651.118437
Free parameters (model + branch lengths): 1997

WARNING: Number of free parameters (K=1997) is larger than alignment size (n=522).
         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/Q9Y6X6/3_mltree/Q9Y6X6.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y6X6/3_mltree/Q9Y6X6.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y6X6/3_mltree/Q9Y6X6.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9Y6X6/3_mltree/Q9Y6X6.raxml.log

Analysis started: 01-Jul-2021 03:23:28 / finished: 01-Jul-2021 13:02:52

Elapsed time: 34764.547 seconds

Consumed energy: 3215.566 Wh (= 16 km in an electric car, or 80 km with an e-scooter!)