RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, 36 cores, 251 GB RAM

RAxML-NG was called at 17-Jun-2021 23:45:27 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q9NPF4/2_msa/Q9NPF4_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q9NPF4/3_mltree/Q9NPF4 --seed 2 --threads 5 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q9NPF4/2_msa/Q9NPF4_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 303 sites

WARNING: Sequences sp_Q1E406_KAE1_COCIM_246410 and tr_E9D8L0_E9D8L0_COCPS_443226 are exactly identical!
WARNING: Sequences sp_Q1E406_KAE1_COCIM_246410 and tr_A0A0J6Y3C5_A0A0J6Y3C5_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B2VS34_B2VS34_PYRTR_426418 and tr_A0A2W1H346_A0A2W1H346_9PLEO_45151 are exactly identical!
WARNING: Sequences tr_C0NZW4_C0NZW4_AJECG_447093 and tr_A6RF13_A6RF13_AJECN_339724 are exactly identical!
WARNING: Sequences sp_Q7S745_KAE1_NEUCR_367110 and tr_G4UDQ5_G4UDQ5_NEUT9_510952 are exactly identical!
WARNING: Sequences tr_B8NDR0_B8NDR0_ASPFN_332952 and sp_Q2U9B5_KAE1_ASPOR_510516 are exactly identical!
WARNING: Sequences tr_B8NDR0_B8NDR0_ASPFN_332952 and tr_A0A1S9D9U1_A0A1S9D9U1_ASPOZ_5062 are exactly identical!
WARNING: Sequences tr_A0A179UWG8_A0A179UWG8_BLAGS_559298 and tr_C5GLM1_C5GLM1_AJEDR_559297 are exactly identical!
WARNING: Sequences tr_H2Q7W2_H2Q7W2_PANTR_9598 and sp_Q9NPF4_OSGEP_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_H2Q7W2_H2Q7W2_PANTR_9598 and tr_A0A2R8ZJ76_A0A2R8ZJ76_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F9FLH5_F9FLH5_FUSOF_660025 and tr_X0D8C5_X0D8C5_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_F9FLH5_F9FLH5_FUSOF_660025 and tr_A0A2H3T8I7_A0A2H3T8I7_FUSOX_5507 are exactly identical!
WARNING: Sequences tr_E9F4Z3_E9F4Z3_METRA_655844 and tr_A0A0B4HGG1_A0A0B4HGG1_METMF_1276143 are exactly identical!
WARNING: Sequences tr_E9F4Z3_E9F4Z3_METRA_655844 and tr_A0A0D9NVP3_A0A0D9NVP3_METAN_1291518 are exactly identical!
WARNING: Sequences tr_A0A0E0HAQ1_A0A0E0HAQ1_ORYNI_4536 and tr_A2Y190_A2Y190_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HAQ1_A0A0E0HAQ1_ORYNI_4536 and tr_I1PT54_I1PT54_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0HAQ1_A0A0E0HAQ1_ORYNI_4536 and tr_A0A0E0PIL0_A0A0E0PIL0_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HAQ1_A0A0E0HAQ1_ORYNI_4536 and tr_Q6L4N8_Q6L4N8_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A1DLT8_A1DLT8_NEOFI_331117 and tr_A0A2I1CDZ4_A0A2I1CDZ4_9EURO_1392255 are exactly identical!
WARNING: Sequences tr_A2R4M2_A2R4M2_ASPNC_425011 and tr_G3XXJ3_G3XXJ3_ASPNA_380704 are exactly identical!
WARNING: Sequences tr_A2R4M2_A2R4M2_ASPNC_425011 and tr_A0A319AAB1_A0A319AAB1_9EURO_1450533 are exactly identical!
WARNING: Sequences tr_F7FCR0_F7FCR0_MACMU_9544 and tr_G8F5P9_G8F5P9_MACFA_9541 are exactly identical!
WARNING: Sequences tr_F7FCR0_F7FCR0_MACMU_9544 and tr_A0A096NNK8_A0A096NNK8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_F7FCR0_F7FCR0_MACMU_9544 and tr_A0A2K5LDL9_A0A2K5LDL9_CERAT_9531 are exactly identical!
WARNING: Sequences tr_F7FCR0_F7FCR0_MACMU_9544 and tr_A0A2K6CM06_A0A2K6CM06_MACNE_9545 are exactly identical!
WARNING: Sequences tr_F7FCR0_F7FCR0_MACMU_9544 and tr_A0A2K5XY89_A0A2K5XY89_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G7XH89_G7XH89_ASPKW_1033177 and tr_A0A146G0R6_A0A146G0R6_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_A0A1D6JRU0_A0A1D6JRU0_MAIZE_4577 and tr_A0A1D6L6I0_A0A1D6L6I0_MAIZE_4577 are exactly identical!
WARNING: Sequences tr_A0A1X7YHX4_A0A1X7YHX4_MAIZE_4577 and tr_A0A1X7YID1_A0A1X7YID1_MAIZE_4577 are exactly identical!
WARNING: Sequences tr_G2YID4_G2YID4_BOTF4_999810 and tr_M7UDL8_M7UDL8_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_F2SVJ8_F2SVJ8_TRIRC_559305 and tr_A0A178EYU5_A0A178EYU5_TRIRU_5551 are exactly identical!
WARNING: Sequences tr_C4V8X0_C4V8X0_NOSCE_578460 and tr_A0A0F9WCS2_A0A0F9WCS2_9MICR_40302 are exactly identical!
WARNING: Sequences tr_W7M8E1_W7M8E1_GIBM7_334819 and tr_A0A0D2XC64_A0A0D2XC64_FUSO4_426428 are exactly identical!
WARNING: Sequences tr_W7M8E1_W7M8E1_GIBM7_334819 and tr_S0DT03_S0DT03_GIBF5_1279085 are exactly identical!
WARNING: Sequences tr_W7M8E1_W7M8E1_GIBM7_334819 and tr_A0A2H3H5B6_A0A2H3H5B6_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_W7M8E1_W7M8E1_GIBM7_334819 and tr_A0A2K0UNA1_A0A2K0UNA1_GIBNY_42673 are exactly identical!
WARNING: Sequences tr_W7M8E1_W7M8E1_GIBM7_334819 and tr_A0A365MQI5_A0A365MQI5_GIBIN_948311 are exactly identical!
WARNING: Sequences tr_M3W6S4_M3W6S4_FELCA_9685 and tr_A0A2U3XIY6_A0A2U3XIY6_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_V2Z2Y0_V2Z2Y0_MONRO_1381753 and tr_A0A0W0G2S0_A0A0W0G2S0_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_W2QVT9_W2QVT9_PHYPN_761204 and tr_W2HY92_W2HY92_PHYPR_4792 are exactly identical!
WARNING: Sequences tr_A0A015JGV5_A0A015JGV5_9GLOM_1432141 and tr_A0A2I1H5K1_A0A2I1H5K1_9GLOM_588596 are exactly identical!
WARNING: Sequences tr_A0A067DQP4_A0A067DQP4_CITSI_2711 and tr_V4SV63_V4SV63_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A094E3M8_A0A094E3M8_9PEZI_1420912 and tr_A0A1B8GNR3_A0A1B8GNR3_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_W6QKZ4_W6QKZ4_PENRF_1365484 and tr_A0A0G4P6C7_A0A0G4P6C7_PENCA_1429867 are exactly identical!
WARNING: Sequences tr_W6QKZ4_W6QKZ4_PENRF_1365484 and tr_A0A1V6NA19_A0A1V6NA19_9EURO_60169 are exactly identical!
WARNING: Sequences tr_W6QKZ4_W6QKZ4_PENRF_1365484 and tr_A0A1V6RB42_A0A1V6RB42_9EURO_60172 are exactly identical!
WARNING: Sequences tr_A0A0G4P685_A0A0G4P685_PENCA_1429867 and tr_A0A1V6RAB1_A0A1V6RAB1_9EURO_60172 are exactly identical!
WARNING: Sequences tr_A0A0V0S988_A0A0V0S988_9BILA_6336 and tr_A0A0V1DCL6_A0A0V1DCL6_TRIBR_45882 are exactly identical!
WARNING: Sequences tr_A0A0V0S988_A0A0V0S988_9BILA_6336 and tr_A0A0V0W761_A0A0V0W761_9BILA_92179 are exactly identical!
WARNING: Sequences tr_A0A0V0S988_A0A0V0S988_9BILA_6336 and tr_A0A0V1KVN9_A0A0V1KVN9_9BILA_6335 are exactly identical!
WARNING: Sequences sp_Q4I5V2_KAE1_GIBZE_229533 and tr_A0A1B8ADW7_A0A1B8ADW7_FUSPO_36050 are exactly identical!
WARNING: Sequences sp_Q4I5V2_KAE1_GIBZE_229533 and tr_A0A2T4H4K5_A0A2T4H4K5_FUSCU_5516 are exactly identical!
WARNING: Sequences sp_Q4I5V2_KAE1_GIBZE_229533 and tr_A0A2L2T2W6_A0A2L2T2W6_9HYPO_56646 are exactly identical!
WARNING: Sequences tr_A0A164UEV4_A0A164UEV4_9HOMO_1314777 and tr_A0A166HDA3_A0A166HDA3_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A2I1G7I6_A0A2I1G7I6_9GLOM_588596 and tr_A0A2H5UB77_A0A2H5UB77_RHIID_747089 are exactly identical!
WARNING: Duplicate sequences found: 55

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q9NPF4/3_mltree/Q9NPF4.raxml.reduced.phy

Alignment comprises 1 partitions and 303 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 303 / 303
Gaps: 4.95 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q9NPF4/3_mltree/Q9NPF4.raxml.rba

Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s)

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

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 303 / 24240
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -289910.872975] Initial branch length optimization
[00:00:08 -243371.892892] Model parameter optimization (eps = 10.000000)
[00:01:15 -242954.854778] AUTODETECT spr round 1 (radius: 5)
[00:05:11 -185681.009073] AUTODETECT spr round 2 (radius: 10)
[00:09:54 -146449.702633] AUTODETECT spr round 3 (radius: 15)
[00:15:17 -128031.661182] AUTODETECT spr round 4 (radius: 20)
[00:21:34 -118040.996053] AUTODETECT spr round 5 (radius: 25)
[00:30:26 -113033.910929] SPR radius for FAST iterations: 25 (autodetect)
[00:30:26 -113033.910929] Model parameter optimization (eps = 3.000000)
[00:31:05 -112897.710389] FAST spr round 1 (radius: 25)
[00:36:56 -98904.607415] FAST spr round 2 (radius: 25)
[00:40:48 -98427.438493] FAST spr round 3 (radius: 25)
[00:44:02 -98354.881478] FAST spr round 4 (radius: 25)
[00:47:01 -98325.997244] FAST spr round 5 (radius: 25)
[00:49:39 -98325.216990] FAST spr round 6 (radius: 25)
[00:52:10 -98325.216227] Model parameter optimization (eps = 1.000000)
[00:52:35 -98318.858726] SLOW spr round 1 (radius: 5)
[00:56:28 -98286.990351] SLOW spr round 2 (radius: 5)
[01:00:11 -98282.358314] SLOW spr round 3 (radius: 5)
[01:03:40 -98279.046292] SLOW spr round 4 (radius: 5)
[01:07:06 -98278.996390] SLOW spr round 5 (radius: 10)
[01:10:41 -98278.861956] SLOW spr round 6 (radius: 5)
[01:15:17 -98278.235111] SLOW spr round 7 (radius: 5)
[01:19:15 -98278.234997] SLOW spr round 8 (radius: 10)
[01:23:02 -98278.234997] SLOW spr round 9 (radius: 15)
[01:29:41 -98276.668466] SLOW spr round 10 (radius: 5)
[01:34:25 -98276.668249] SLOW spr round 11 (radius: 10)
[01:38:47 -98276.668249] SLOW spr round 12 (radius: 15)
[01:45:02 -98276.668249] SLOW spr round 13 (radius: 20)
[01:49:29] [worker #1] ML tree search #2, logLikelihood: -98313.215663
[01:55:27 -98276.668249] SLOW spr round 14 (radius: 25)
[02:07:38] [worker #2] ML tree search #3, logLikelihood: -98357.345649
[02:09:02 -98276.668249] Model parameter optimization (eps = 0.100000)

[02:09:10] [worker #0] ML tree search #1, logLikelihood: -98276.645360

[02:09:10 -290928.716505] Initial branch length optimization
[02:09:18 -244651.671982] Model parameter optimization (eps = 10.000000)
[02:10:37 -244188.027167] AUTODETECT spr round 1 (radius: 5)
[02:14:37 -184466.274703] AUTODETECT spr round 2 (radius: 10)
[02:18:26] [worker #4] ML tree search #5, logLikelihood: -98324.935478
[02:19:18 -145227.414498] AUTODETECT spr round 3 (radius: 15)
[02:24:33 -128047.358231] AUTODETECT spr round 4 (radius: 20)
[02:30:43 -121954.753177] AUTODETECT spr round 5 (radius: 25)
[02:37:42 -116605.014472] SPR radius for FAST iterations: 25 (autodetect)
[02:37:42 -116605.014472] Model parameter optimization (eps = 3.000000)
[02:38:16 -116468.626892] FAST spr round 1 (radius: 25)
[02:39:08] [worker #3] ML tree search #4, logLikelihood: -98308.090458
[02:44:17 -99057.105486] FAST spr round 2 (radius: 25)
[02:48:17 -98435.204614] FAST spr round 3 (radius: 25)
[02:51:32 -98367.348831] FAST spr round 4 (radius: 25)
[02:54:22 -98358.669448] FAST spr round 5 (radius: 25)
[02:56:59 -98358.669422] Model parameter optimization (eps = 1.000000)
[02:57:24 -98350.088927] SLOW spr round 1 (radius: 5)
[03:01:30 -98313.610260] SLOW spr round 2 (radius: 5)
[03:05:20 -98308.288811] SLOW spr round 3 (radius: 5)
[03:08:53 -98307.928260] SLOW spr round 4 (radius: 5)
[03:12:21 -98307.928078] SLOW spr round 5 (radius: 10)
[03:16:00 -98299.279154] SLOW spr round 6 (radius: 5)
[03:20:40 -98298.445487] SLOW spr round 7 (radius: 5)
[03:24:42 -98297.864273] SLOW spr round 8 (radius: 5)
[03:28:23 -98297.864222] SLOW spr round 9 (radius: 10)
[03:32:01 -98297.864221] SLOW spr round 10 (radius: 15)
[03:38:36 -98297.864221] SLOW spr round 11 (radius: 20)
[03:48:33 -98297.864221] SLOW spr round 12 (radius: 25)
[04:02:17 -98297.864221] Model parameter optimization (eps = 0.100000)

[04:02:24] [worker #0] ML tree search #6, logLikelihood: -98297.844344

[04:02:25 -288823.216692] Initial branch length optimization
[04:02:31 -242825.715152] Model parameter optimization (eps = 10.000000)
[04:03:42 -242378.683158] AUTODETECT spr round 1 (radius: 5)
[04:07:41 -189352.420468] AUTODETECT spr round 2 (radius: 10)
[04:12:29 -143321.764116] AUTODETECT spr round 3 (radius: 15)
[04:12:55] [worker #4] ML tree search #10, logLikelihood: -98311.454915
[04:17:49 -129449.724829] AUTODETECT spr round 4 (radius: 20)
[04:21:55] [worker #2] ML tree search #8, logLikelihood: -98302.997543
[04:24:25] [worker #3] ML tree search #9, logLikelihood: -98301.025818
[04:25:05 -119516.850620] AUTODETECT spr round 5 (radius: 25)
[04:34:40 -112274.178416] SPR radius for FAST iterations: 25 (autodetect)
[04:34:40 -112274.178416] Model parameter optimization (eps = 3.000000)
[04:35:11 -112183.856384] FAST spr round 1 (radius: 25)
[04:41:01] [worker #1] ML tree search #7, logLikelihood: -98293.752728
[04:41:23 -98960.903926] FAST spr round 2 (radius: 25)
[04:45:18 -98451.198939] FAST spr round 3 (radius: 25)
[04:48:38 -98390.928544] FAST spr round 4 (radius: 25)
[04:51:27 -98371.699455] FAST spr round 5 (radius: 25)
[04:54:04 -98369.052892] FAST spr round 6 (radius: 25)
[04:56:38 -98367.883423] FAST spr round 7 (radius: 25)
[04:59:08 -98367.883211] Model parameter optimization (eps = 1.000000)
[04:59:27 -98360.655898] SLOW spr round 1 (radius: 5)
[05:03:18 -98335.387642] SLOW spr round 2 (radius: 5)
[05:07:04 -98329.531048] SLOW spr round 3 (radius: 5)
[05:10:34 -98329.530488] SLOW spr round 4 (radius: 10)
[05:14:07 -98329.251769] SLOW spr round 5 (radius: 5)
[05:18:42 -98329.251740] SLOW spr round 6 (radius: 10)
[05:22:48 -98329.251732] SLOW spr round 7 (radius: 15)
[05:28:49 -98329.251726] SLOW spr round 8 (radius: 20)
[05:38:33 -98329.251722] SLOW spr round 9 (radius: 25)
[05:51:33 -98329.251719] Model parameter optimization (eps = 0.100000)

[05:51:45] [worker #0] ML tree search #11, logLikelihood: -98329.197288

[05:51:45 -291663.325753] Initial branch length optimization
[05:51:51 -244582.599172] Model parameter optimization (eps = 10.000000)
[05:52:54 -244187.623956] AUTODETECT spr round 1 (radius: 5)
[05:56:52 -188321.289221] AUTODETECT spr round 2 (radius: 10)
[06:01:39 -145772.801408] AUTODETECT spr round 3 (radius: 15)
[06:06:46 -127009.497456] AUTODETECT spr round 4 (radius: 20)
[06:12:11 -116069.595034] AUTODETECT spr round 5 (radius: 25)
[06:16:38] [worker #4] ML tree search #15, logLikelihood: -98479.645800
[06:18:26 -113978.673701] SPR radius for FAST iterations: 25 (autodetect)
[06:18:26 -113978.673701] Model parameter optimization (eps = 3.000000)
[06:19:03 -113831.861875] FAST spr round 1 (radius: 25)
[06:20:58] [worker #2] ML tree search #13, logLikelihood: -98291.992137
[06:25:01 -101509.571637] FAST spr round 2 (radius: 25)
[06:28:55 -100764.898920] FAST spr round 3 (radius: 25)
[06:32:06 -100674.570535] FAST spr round 4 (radius: 25)
[06:34:47] [worker #3] ML tree search #14, logLikelihood: -98269.767584
[06:35:08 -98589.948762] FAST spr round 5 (radius: 25)
[06:38:04 -98406.944268] FAST spr round 6 (radius: 25)
[06:40:37 -98400.790062] FAST spr round 7 (radius: 25)
[06:43:05 -98400.789922] Model parameter optimization (eps = 1.000000)
[06:43:32 -98384.992214] SLOW spr round 1 (radius: 5)
[06:47:18 -98344.871134] SLOW spr round 2 (radius: 5)
[06:47:19] [worker #1] ML tree search #12, logLikelihood: -98292.214669
[06:51:02 -98333.416207] SLOW spr round 3 (radius: 5)
[06:54:36 -98332.466406] SLOW spr round 4 (radius: 5)
[06:58:02 -98332.466365] SLOW spr round 5 (radius: 10)
[07:01:36 -98332.466361] SLOW spr round 6 (radius: 15)
[07:08:21 -98331.845546] SLOW spr round 7 (radius: 5)
[07:13:10 -98326.825353] SLOW spr round 8 (radius: 5)
[07:17:14 -98326.823089] SLOW spr round 9 (radius: 10)
[07:21:04 -98321.677178] SLOW spr round 10 (radius: 5)
[07:25:40 -98314.123785] SLOW spr round 11 (radius: 5)
[07:29:40 -98314.110340] SLOW spr round 12 (radius: 10)
[07:33:28 -98314.109105] SLOW spr round 13 (radius: 15)
[07:40:00 -98314.108723] SLOW spr round 14 (radius: 20)
[07:50:17 -98314.108567] SLOW spr round 15 (radius: 25)
[08:04:07 -98314.108498] Model parameter optimization (eps = 0.100000)

[08:04:16] [worker #0] ML tree search #16, logLikelihood: -98314.062372

[08:17:32] [worker #2] ML tree search #18, logLikelihood: -98327.155243
[08:33:06] [worker #4] ML tree search #20, logLikelihood: -98297.252724
[08:41:06] [worker #3] ML tree search #19, logLikelihood: -98325.706942
[08:56:24] [worker #1] ML tree search #17, logLikelihood: -98278.318497

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.344282,0.398064) (0.357438,0.660010) (0.192681,1.194912) (0.105598,3.757683) 
   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: -98269.767584

AIC score: 200549.535168 / AICc score: 8244609.535168 / BIC score: 207995.569443
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=303).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 123 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q9NPF4/3_mltree/Q9NPF4.raxml.bestTreeCollapsed
Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q9NPF4/3_mltree/Q9NPF4.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q9NPF4/3_mltree/Q9NPF4.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q9NPF4/3_mltree/Q9NPF4.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_040621/phylogeny-snakemake/results/Q9NPF4/3_mltree/Q9NPF4.raxml.log

Analysis started: 17-Jun-2021 23:45:27 / finished: 18-Jun-2021 08:41:52

Elapsed time: 32184.772 seconds