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 03-Jul-2021 19:47:43 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UKA2/2_msa/Q9UKA2_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UKA2/3_mltree/Q9UKA2 --seed 2 --threads 3 --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 (3 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UKA2/2_msa/Q9UKA2_trimmed_msa.fasta
[00:00:00] Loaded alignment with 432 taxa and 143 sites

WARNING: Sequences sp_Q91W61_FXL15_MOUSE_10090 and tr_A0A3Q0D4F2_A0A3Q0D4F2_MESAU_10036 are exactly identical!
WARNING: Sequences tr_M3YZK7_M3YZK7_MUSPF_9669 and sp_E2RKN7_FXL15_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3YZK7_M3YZK7_MUSPF_9669 and tr_L5K3F5_L5K3F5_PTEAL_9402 are exactly identical!
WARNING: Sequences tr_M3YZK7_M3YZK7_MUSPF_9669 and tr_A0A2U3W263_A0A2U3W263_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3YZK7_M3YZK7_MUSPF_9669 and tr_A0A2U3XI20_A0A2U3XI20_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3YZK7_M3YZK7_MUSPF_9669 and tr_A0A2Y9J2Y2_A0A2Y9J2Y2_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_A0A0B4KF28_A0A0B4KF28_DROME_7227 and tr_B4I893_B4I893_DROSE_7238 are exactly identical!
WARNING: Sequences tr_A0A0B4KF28_A0A0B4KF28_DROME_7227 and tr_B4MQC2_B4MQC2_DROWI_7260 are exactly identical!
WARNING: Sequences tr_A0A0B4KF28_A0A0B4KF28_DROME_7227 and tr_B3MIW7_B3MIW7_DROAN_7217 are exactly identical!
WARNING: Sequences tr_A0A0B4KF28_A0A0B4KF28_DROME_7227 and tr_A0A1W4VQR6_A0A1W4VQR6_DROFC_30025 are exactly identical!
WARNING: Sequences tr_D8QPI6_D8QPI6_SELML_88036 and tr_D8SKY7_D8SKY7_SELML_88036 are exactly identical!
WARNING: Sequences tr_G3QFU1_G3QFU1_GORGO_9595 and sp_Q9UKA2_FBXL4_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QFU1_G3QFU1_GORGO_9595 and tr_G7P432_G7P432_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3QFU1_G3QFU1_GORGO_9595 and tr_A0A2K6A7P0_A0A2K6A7P0_MANLE_9568 are exactly identical!
WARNING: Sequences tr_Q291P6_Q291P6_DROPS_46245 and tr_B4GAF9_B4GAF9_DROPE_7234 are exactly identical!
WARNING: Sequences tr_E2R1T6_E2R1T6_CANLF_9615 and tr_A0A2Y9KS75_A0A2Y9KS75_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_H2QTF8_H2QTF8_PANTR_9598 and tr_A0A2R9AMQ8_A0A2R9AMQ8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_F7CBT2_F7CBT2_HORSE_9796 and tr_M3VWA4_M3VWA4_FELCA_9685 are exactly identical!
WARNING: Sequences tr_W5PQS8_W5PQS8_SHEEP_9940 and sp_Q0VD31_FBXL4_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_A0A158NH63_A0A158NH63_ATTCE_12957 and tr_A0A195B7W1_A0A195B7W1_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NH95_A0A158NH95_ATTCE_12957 and tr_A0A195B7H1_A0A195B7H1_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A0E0HER4_A0A0E0HER4_ORYNI_4536 and tr_A2Y4V4_A2Y4V4_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_A0A0E0HER4_A0A0E0HER4_ORYNI_4536 and tr_I1PVT5_I1PVT5_ORYGL_4538 are exactly identical!
WARNING: Sequences tr_A0A0E0HER4_A0A0E0HER4_ORYNI_4536 and tr_A0A0E0PMR5_A0A0E0PMR5_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0HER4_A0A0E0HER4_ORYNI_4536 and tr_A0A0D3G7V2_A0A0D3G7V2_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_A0A0E0HER4_A0A0E0HER4_ORYNI_4536 and tr_Q60EC4_Q60EC4_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0I3T4_A0A0E0I3T4_ORYNI_4536 and tr_A0A0E0FD10_A0A0E0FD10_9ORYZ_40149 are exactly identical!
WARNING: Sequences tr_A0A0E0I3T4_A0A0E0I3T4_ORYNI_4536 and tr_A0A0E0RIJ9_A0A0E0RIJ9_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_A0A0E0I3T4_A0A0E0I3T4_ORYNI_4536 and tr_A0A0E0BTW4_A0A0E0BTW4_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_F7G6N0_F7G6N0_MACMU_9544 and tr_A0A096NDT8_A0A096NDT8_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_I1R731_I1R731_ORYGL_4538 and tr_A0A0D3HVJ2_A0A0D3HVJ2_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_H0ZPX5_H0ZPX5_TAEGU_59729 and tr_U3K4U4_U3K4U4_FICAL_59894 are exactly identical!
WARNING: Sequences tr_H0ZPX5_H0ZPX5_TAEGU_59729 and tr_A0A091F126_A0A091F126_CORBR_85066 are exactly identical!
WARNING: Sequences tr_H0ZPX5_H0ZPX5_TAEGU_59729 and tr_A0A087QUK7_A0A087QUK7_APTFO_9233 are exactly identical!
WARNING: Sequences tr_H0ZPX5_H0ZPX5_TAEGU_59729 and tr_A0A0A0APP0_A0A0A0APP0_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_H0ZPX5_H0ZPX5_TAEGU_59729 and tr_A0A2I0MUY1_A0A2I0MUY1_COLLI_8932 are exactly identical!
WARNING: Sequences tr_H0ZPX5_H0ZPX5_TAEGU_59729 and tr_A0A091ID40_A0A091ID40_CALAN_9244 are exactly identical!
WARNING: Sequences tr_H0ZPX5_H0ZPX5_TAEGU_59729 and tr_A0A1V4JM30_A0A1V4JM30_PATFA_372326 are exactly identical!
WARNING: Sequences tr_H0ZPX5_H0ZPX5_TAEGU_59729 and tr_A0A218VCJ5_A0A218VCJ5_9PASE_299123 are exactly identical!
WARNING: Sequences tr_B4LIS9_B4LIS9_DROVI_7244 and tr_B4KP95_B4KP95_DROMO_7230 are exactly identical!
WARNING: Sequences tr_M7ZZF8_M7ZZF8_TRIUA_4572 and tr_A0A3B6EMI6_A0A3B6EMI6_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A3B6LI15_A0A3B6LI15_WHEAT_4565 and tr_A0A3B6MNU5_A0A3B6MNU5_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A067H7J3_A0A067H7J3_CITSI_2711 and tr_V4V6A4_V4V6A4_9ROSI_85681 are exactly identical!
WARNING: Sequences tr_A0A067H7J3_A0A067H7J3_CITSI_2711 and tr_A0A2H5PI45_A0A2H5PI45_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0A2VIJ1_A0A0A2VIJ1_BEABA_1245745 and tr_A0A2N6NUP4_A0A2N6NUP4_BEABA_176275 are exactly identical!
WARNING: Sequences tr_A0A0D2RHN1_A0A0D2RHN1_GOSRA_29730 and tr_A0A1U8JU07_A0A1U8JU07_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A1U8FAI8_A0A1U8FAI8_CAPAN_4072 and tr_A0A2G3BY54_A0A2G3BY54_CAPCH_80379 are exactly identical!
WARNING: Sequences tr_A0A2U4AVP6_A0A2U4AVP6_TURTR_9739 and tr_A0A2Y9LIY4_A0A2Y9LIY4_DELLE_9749 are exactly identical!
WARNING: Sequences tr_A0A2U4AVP6_A0A2U4AVP6_TURTR_9739 and tr_A0A2Y9F4B9_A0A2Y9F4B9_PHYCD_9755 are exactly identical!
WARNING: Duplicate sequences found: 49

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/Q9UKA2/3_mltree/Q9UKA2.raxml.reduced.phy

Alignment comprises 1 partitions and 143 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 143 / 143
Gaps: 5.98 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UKA2/3_mltree/Q9UKA2.raxml.rba

Parallelization scheme autoconfig: 3 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 432 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 143 / 11440
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -126552.693617] Initial branch length optimization
[00:00:01 -100879.246820] Model parameter optimization (eps = 10.000000)
[00:00:22 -100443.669791] AUTODETECT spr round 1 (radius: 5)
[00:00:47 -70147.201358] AUTODETECT spr round 2 (radius: 10)
[00:01:15 -54085.001393] AUTODETECT spr round 3 (radius: 15)
[00:01:48 -44679.420052] AUTODETECT spr round 4 (radius: 20)
[00:02:26 -42835.565429] AUTODETECT spr round 5 (radius: 25)
[00:03:06 -42540.110026] SPR radius for FAST iterations: 25 (autodetect)
[00:03:06 -42540.110026] Model parameter optimization (eps = 3.000000)
[00:03:14 -42442.928527] FAST spr round 1 (radius: 25)
[00:03:46 -38185.204828] FAST spr round 2 (radius: 25)
[00:04:09 -38016.166182] FAST spr round 3 (radius: 25)
[00:04:31 -38005.760560] FAST spr round 4 (radius: 25)
[00:04:50 -38005.422356] FAST spr round 5 (radius: 25)
[00:05:09 -38005.422057] Model parameter optimization (eps = 1.000000)
[00:05:15 -38003.748124] SLOW spr round 1 (radius: 5)
[00:05:46 -37998.368429] SLOW spr round 2 (radius: 5)
[00:06:15 -37997.061234] SLOW spr round 3 (radius: 5)
[00:06:42 -37997.059796] SLOW spr round 4 (radius: 10)
[00:07:11 -37993.111625] SLOW spr round 5 (radius: 5)
[00:07:49 -37992.797603] SLOW spr round 6 (radius: 5)
[00:08:21 -37992.797166] SLOW spr round 7 (radius: 10)
[00:08:51 -37992.797129] SLOW spr round 8 (radius: 15)
[00:09:38 -37992.797124] SLOW spr round 9 (radius: 20)
[00:10:37 -37992.797123] SLOW spr round 10 (radius: 25)
[00:11:43 -37992.384541] SLOW spr round 11 (radius: 5)
[00:12:23 -37992.384397] SLOW spr round 12 (radius: 10)
[00:13:00 -37992.384375] SLOW spr round 13 (radius: 15)
[00:13:44 -37992.384366] SLOW spr round 14 (radius: 20)
[00:14:44 -37992.384361] SLOW spr round 15 (radius: 25)
[00:14:50] [worker #1] ML tree search #2, logLikelihood: -38000.308835
[00:15:49 -37992.384357] Model parameter optimization (eps = 0.100000)

[00:15:53] [worker #0] ML tree search #1, logLikelihood: -37992.162415

[00:15:53 -126675.091945] Initial branch length optimization
[00:15:54 -99828.781154] Model parameter optimization (eps = 10.000000)
[00:16:10 -99468.129228] AUTODETECT spr round 1 (radius: 5)
[00:16:35 -71127.297732] AUTODETECT spr round 2 (radius: 10)
[00:17:03 -54678.173422] AUTODETECT spr round 3 (radius: 15)
[00:17:23] [worker #2] ML tree search #3, logLikelihood: -37989.119429
[00:17:36 -46872.494106] AUTODETECT spr round 4 (radius: 20)
[00:18:14 -44486.405145] AUTODETECT spr round 5 (radius: 25)
[00:18:59 -44368.977375] SPR radius for FAST iterations: 25 (autodetect)
[00:18:59 -44368.977375] Model parameter optimization (eps = 3.000000)
[00:19:08 -44221.235183] FAST spr round 1 (radius: 25)
[00:19:39 -38533.981742] FAST spr round 2 (radius: 25)
[00:20:03 -38052.832377] FAST spr round 3 (radius: 25)
[00:20:25 -38040.585916] FAST spr round 4 (radius: 25)
[00:20:45 -38038.707846] FAST spr round 5 (radius: 25)
[00:21:04 -38038.707579] Model parameter optimization (eps = 1.000000)
[00:21:10 -38036.095177] SLOW spr round 1 (radius: 5)
[00:21:40 -38023.729093] SLOW spr round 2 (radius: 5)
[00:22:10 -38017.750324] SLOW spr round 3 (radius: 5)
[00:22:38 -38017.683607] SLOW spr round 4 (radius: 10)
[00:23:07 -38016.725251] SLOW spr round 5 (radius: 5)
[00:23:44 -38016.487475] SLOW spr round 6 (radius: 5)
[00:24:16 -38016.485046] SLOW spr round 7 (radius: 10)
[00:24:46 -38016.484412] SLOW spr round 8 (radius: 15)
[00:25:32 -38015.036769] SLOW spr round 9 (radius: 5)
[00:26:11 -38013.711200] SLOW spr round 10 (radius: 5)
[00:26:44 -38013.710955] SLOW spr round 11 (radius: 10)
[00:27:15 -38013.221745] SLOW spr round 12 (radius: 5)
[00:27:50 -38013.221741] SLOW spr round 13 (radius: 10)
[00:28:23 -38013.221739] SLOW spr round 14 (radius: 15)
[00:29:07 -38013.221739] SLOW spr round 15 (radius: 20)
[00:30:01 -38013.221738] SLOW spr round 16 (radius: 25)
[00:30:59 -38013.221738] Model parameter optimization (eps = 0.100000)

[00:31:03] [worker #0] ML tree search #4, logLikelihood: -38013.088320

[00:31:03 -127503.608182] Initial branch length optimization
[00:31:04 -100823.418285] Model parameter optimization (eps = 10.000000)
[00:31:20 -100442.763095] AUTODETECT spr round 1 (radius: 5)
[00:31:28] [worker #2] ML tree search #6, logLikelihood: -37988.252662
[00:31:45 -69251.165471] AUTODETECT spr round 2 (radius: 10)
[00:32:06] [worker #1] ML tree search #5, logLikelihood: -38000.386701
[00:32:13 -53666.394278] AUTODETECT spr round 3 (radius: 15)
[00:32:46 -47059.203067] AUTODETECT spr round 4 (radius: 20)
[00:33:23 -45746.484019] AUTODETECT spr round 5 (radius: 25)
[00:34:00 -44962.605877] SPR radius for FAST iterations: 25 (autodetect)
[00:34:00 -44962.605877] Model parameter optimization (eps = 3.000000)
[00:34:11 -44851.448301] FAST spr round 1 (radius: 25)
[00:34:47 -38623.074674] FAST spr round 2 (radius: 25)
[00:35:15 -38072.414164] FAST spr round 3 (radius: 25)
[00:35:38 -38033.009772] FAST spr round 4 (radius: 25)
[00:36:00 -38018.149671] FAST spr round 5 (radius: 25)
[00:36:20 -38010.719719] FAST spr round 6 (radius: 25)
[00:36:38 -38010.718603] Model parameter optimization (eps = 1.000000)
[00:36:43 -38009.658002] SLOW spr round 1 (radius: 5)
[00:37:13 -37996.199213] SLOW spr round 2 (radius: 5)
[00:37:41 -37995.554745] SLOW spr round 3 (radius: 5)
[00:38:09 -37995.554633] SLOW spr round 4 (radius: 10)
[00:38:36 -37995.206028] SLOW spr round 5 (radius: 5)
[00:39:12 -37995.206004] SLOW spr round 6 (radius: 10)
[00:39:46 -37995.206003] SLOW spr round 7 (radius: 15)
[00:40:10] [worker #2] ML tree search #9, logLikelihood: -43024.093761
[00:40:30 -37995.206003] SLOW spr round 8 (radius: 20)
[00:41:27 -37995.206002] SLOW spr round 9 (radius: 25)
[00:42:30 -37995.206002] Model parameter optimization (eps = 0.100000)

[00:42:32] [worker #0] ML tree search #7, logLikelihood: -37995.200001

[00:42:32 -126818.298182] Initial branch length optimization
[00:42:33 -100766.846471] Model parameter optimization (eps = 10.000000)
[00:42:52 -100376.730780] AUTODETECT spr round 1 (radius: 5)
[00:43:17 -72314.385622] AUTODETECT spr round 2 (radius: 10)
[00:43:46 -56624.957636] AUTODETECT spr round 3 (radius: 15)
[00:44:17 -44766.329116] AUTODETECT spr round 4 (radius: 20)
[00:44:45] [worker #1] ML tree search #8, logLikelihood: -37991.511155
[00:44:53 -43320.739826] AUTODETECT spr round 5 (radius: 25)
[00:45:35 -43127.232407] SPR radius for FAST iterations: 25 (autodetect)
[00:45:35 -43127.232407] Model parameter optimization (eps = 3.000000)
[00:45:47 -43030.233654] FAST spr round 1 (radius: 25)
[00:46:17 -38387.313701] FAST spr round 2 (radius: 25)
[00:46:41 -38074.164861] FAST spr round 3 (radius: 25)
[00:47:03 -38020.805775] FAST spr round 4 (radius: 25)
[00:47:23 -38015.337570] FAST spr round 5 (radius: 25)
[00:47:42 -38015.099985] FAST spr round 6 (radius: 25)
[00:48:01 -38015.099446] Model parameter optimization (eps = 1.000000)
[00:48:08 -38012.953217] SLOW spr round 1 (radius: 5)
[00:48:38 -38003.214858] SLOW spr round 2 (radius: 5)
[00:49:07 -37999.712958] SLOW spr round 3 (radius: 5)
[00:49:35 -37999.240418] SLOW spr round 4 (radius: 5)
[00:50:02 -37999.186145] SLOW spr round 5 (radius: 10)
[00:50:30 -37997.909051] SLOW spr round 6 (radius: 5)
[00:51:08 -37997.908966] SLOW spr round 7 (radius: 10)
[00:51:41 -37997.908966] SLOW spr round 8 (radius: 15)
[00:52:28 -37997.908966] SLOW spr round 9 (radius: 20)
[00:53:29 -37997.640564] SLOW spr round 10 (radius: 5)
[00:54:10 -37994.386828] SLOW spr round 11 (radius: 5)
[00:54:44 -37994.382190] SLOW spr round 12 (radius: 10)
[00:55:16 -37994.382186] SLOW spr round 13 (radius: 15)
[00:56:03 -37994.382185] SLOW spr round 14 (radius: 20)
[00:56:16] [worker #2] ML tree search #12, logLikelihood: -38001.420817
[00:57:03 -37994.382183] SLOW spr round 15 (radius: 25)
[00:58:06 -37994.285216] Model parameter optimization (eps = 0.100000)

[00:58:09] [worker #0] ML tree search #10, logLikelihood: -37994.103513

[00:58:09 -126050.114746] Initial branch length optimization
[00:58:11 -99735.747317] Model parameter optimization (eps = 10.000000)
[00:58:26 -99403.786357] AUTODETECT spr round 1 (radius: 5)
[00:58:51 -71634.419889] AUTODETECT spr round 2 (radius: 10)
[00:59:20 -53502.064442] AUTODETECT spr round 3 (radius: 15)
[00:59:54 -48007.226295] AUTODETECT spr round 4 (radius: 20)
[01:00:02] [worker #1] ML tree search #11, logLikelihood: -37995.245939
[01:00:31 -47615.631242] AUTODETECT spr round 5 (radius: 25)
[01:01:13 -44071.600942] SPR radius for FAST iterations: 25 (autodetect)
[01:01:13 -44071.600942] Model parameter optimization (eps = 3.000000)
[01:01:24 -43980.373774] FAST spr round 1 (radius: 25)
[01:01:54 -38546.620007] FAST spr round 2 (radius: 25)
[01:02:19 -38067.321383] FAST spr round 3 (radius: 25)
[01:02:41 -38015.444033] FAST spr round 4 (radius: 25)
[01:03:01 -38012.743080] FAST spr round 5 (radius: 25)
[01:03:19 -38012.742389] Model parameter optimization (eps = 1.000000)
[01:03:23 -38012.117620] SLOW spr round 1 (radius: 5)
[01:03:54 -38003.082845] SLOW spr round 2 (radius: 5)
[01:04:23 -38002.639952] SLOW spr round 3 (radius: 5)
[01:04:51 -38002.639488] SLOW spr round 4 (radius: 10)
[01:05:19 -38000.404470] SLOW spr round 5 (radius: 5)
[01:05:55 -38000.403275] SLOW spr round 6 (radius: 10)
[01:06:28 -38000.402890] SLOW spr round 7 (radius: 15)
[01:07:11 -38000.402730] SLOW spr round 8 (radius: 20)
[01:08:06 -38000.402658] SLOW spr round 9 (radius: 25)
[01:09:06 -38000.402625] Model parameter optimization (eps = 0.100000)

[01:09:11] [worker #0] ML tree search #13, logLikelihood: -38000.221988

[01:09:11 -126710.807702] Initial branch length optimization
[01:09:12 -100314.277487] Model parameter optimization (eps = 10.000000)
[01:09:26 -99905.223826] AUTODETECT spr round 1 (radius: 5)
[01:09:51 -71248.319437] AUTODETECT spr round 2 (radius: 10)
[01:09:51] [worker #2] ML tree search #15, logLikelihood: -37998.746678
[01:10:19 -56426.962866] AUTODETECT spr round 3 (radius: 15)
[01:10:52 -48503.367360] AUTODETECT spr round 4 (radius: 20)
[01:11:31 -47768.714852] AUTODETECT spr round 5 (radius: 25)
[01:12:08 -45459.234857] SPR radius for FAST iterations: 25 (autodetect)
[01:12:08 -45459.234857] Model parameter optimization (eps = 3.000000)
[01:12:19 -45336.456021] FAST spr round 1 (radius: 25)
[01:12:55 -38501.340658] FAST spr round 2 (radius: 25)
[01:13:24 -38062.353394] FAST spr round 3 (radius: 25)
[01:13:49 -38032.759526] FAST spr round 4 (radius: 25)
[01:14:10 -38010.217135] FAST spr round 5 (radius: 25)
[01:14:30 -38009.381187] FAST spr round 6 (radius: 25)
[01:14:49 -38009.381161] Model parameter optimization (eps = 1.000000)
[01:14:54 -38005.947605] SLOW spr round 1 (radius: 5)
[01:15:02] [worker #1] ML tree search #14, logLikelihood: -37996.212478
[01:15:24 -37998.627913] SLOW spr round 2 (radius: 5)
[01:15:54 -37995.352847] SLOW spr round 3 (radius: 5)
[01:16:21 -37995.352660] SLOW spr round 4 (radius: 10)
[01:16:49 -37995.352610] SLOW spr round 5 (radius: 15)
[01:17:38 -37995.352608] SLOW spr round 6 (radius: 20)
[01:18:35 -37995.352608] SLOW spr round 7 (radius: 25)
[01:19:37 -37995.352608] Model parameter optimization (eps = 0.100000)

[01:19:40] [worker #0] ML tree search #16, logLikelihood: -37995.298662

[01:19:40 -125525.204987] Initial branch length optimization
[01:19:41 -100891.070410] Model parameter optimization (eps = 10.000000)
[01:19:59 -100509.646184] AUTODETECT spr round 1 (radius: 5)
[01:20:24 -72326.169567] AUTODETECT spr round 2 (radius: 10)
[01:20:53 -55610.707169] AUTODETECT spr round 3 (radius: 15)
[01:21:24 -48018.839063] AUTODETECT spr round 4 (radius: 20)
[01:22:07 -45559.281829] AUTODETECT spr round 5 (radius: 25)
[01:22:54 -43483.984661] SPR radius for FAST iterations: 25 (autodetect)
[01:22:54 -43483.984661] Model parameter optimization (eps = 3.000000)
[01:23:03 -43345.327777] FAST spr round 1 (radius: 25)
[01:23:35 -38646.436341] FAST spr round 2 (radius: 25)
[01:24:02 -38084.566453] FAST spr round 3 (radius: 25)
[01:24:25 -38048.663945] FAST spr round 4 (radius: 25)
[01:24:46 -38042.254329] FAST spr round 5 (radius: 25)
[01:25:05 -38036.082589] FAST spr round 6 (radius: 25)
[01:25:24 -38036.080804] Model parameter optimization (eps = 1.000000)
[01:25:27 -38035.405374] SLOW spr round 1 (radius: 5)
[01:25:58 -38021.494136] SLOW spr round 2 (radius: 5)
[01:26:27 -38019.932650] SLOW spr round 3 (radius: 5)
[01:26:55 -38019.931283] SLOW spr round 4 (radius: 10)
[01:27:24 -38016.464815] SLOW spr round 5 (radius: 5)
[01:28:01 -38015.218329] SLOW spr round 6 (radius: 5)
[01:28:34 -38013.851226] SLOW spr round 7 (radius: 5)
[01:28:35] [worker #2] ML tree search #18, logLikelihood: -38000.238809
[01:29:04 -38012.864799] SLOW spr round 8 (radius: 5)
[01:29:34 -38008.209938] SLOW spr round 9 (radius: 5)
[01:30:02 -38008.201979] SLOW spr round 10 (radius: 10)
[01:30:30 -38006.003344] SLOW spr round 11 (radius: 5)
[01:31:07 -38005.633415] SLOW spr round 12 (radius: 5)
[01:31:39 -38005.632628] SLOW spr round 13 (radius: 10)
[01:32:09 -38005.632627] SLOW spr round 14 (radius: 15)
[01:32:55 -38004.854598] SLOW spr round 15 (radius: 5)
[01:33:35 -38003.793591] SLOW spr round 16 (radius: 5)
[01:34:08 -38003.793255] SLOW spr round 17 (radius: 10)
[01:34:38 -38002.997763] SLOW spr round 18 (radius: 5)
[01:35:14 -38002.488504] SLOW spr round 19 (radius: 5)
[01:35:45 -38002.488504] SLOW spr round 20 (radius: 10)
[01:36:15 -38002.488502] SLOW spr round 21 (radius: 15)
[01:36:50] [worker #1] ML tree search #17, logLikelihood: -37988.716820
[01:37:02 -38002.488502] SLOW spr round 22 (radius: 20)
[01:37:59 -38001.443376] SLOW spr round 23 (radius: 5)
[01:38:39 -38001.441811] SLOW spr round 24 (radius: 10)
[01:39:16 -38001.440901] SLOW spr round 25 (radius: 15)
[01:40:01 -38001.440346] SLOW spr round 26 (radius: 20)
[01:41:00 -38001.028569] SLOW spr round 27 (radius: 5)
[01:41:42 -38001.028370] SLOW spr round 28 (radius: 10)
[01:42:20 -38001.028307] SLOW spr round 29 (radius: 15)
[01:43:06 -38001.028268] SLOW spr round 30 (radius: 20)
[01:44:08 -38001.028244] SLOW spr round 31 (radius: 25)
[01:45:14 -38001.028229] Model parameter optimization (eps = 0.100000)

[01:45:17] [worker #0] ML tree search #19, logLikelihood: -38000.923415

[01:59:20] [worker #1] ML tree search #20, logLikelihood: -38003.048231

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.177205,0.593626) (0.234121,0.432813) (0.395972,1.009183) (0.192701,2.043928) 
   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: -37988.252662

AIC score: 77710.505323 / AICc score: 1582822.505323 / BIC score: 80279.291618
Free parameters (model + branch lengths): 867

WARNING: Number of free parameters (K=867) is larger than alignment size (n=143).
         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/Q9UKA2/3_mltree/Q9UKA2.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UKA2/3_mltree/Q9UKA2.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UKA2/3_mltree/Q9UKA2.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UKA2/3_mltree/Q9UKA2.raxml.log

Analysis started: 03-Jul-2021 19:47:43 / finished: 03-Jul-2021 21:47:04

Elapsed time: 7160.908 seconds

Consumed energy: 435.554 Wh (= 2 km in an electric car, or 11 km with an e-scooter!)