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 07-Jul-2021 03:14:30 as follows:

raxml-ng --msa /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q99590/2_msa/Q99590_trimmed_msa.fasta --data-type AA --model LG4X --prefix /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q99590/3_mltree/Q99590 --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: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q99590/2_msa/Q99590_trimmed_msa.fasta
[00:00:00] Loaded alignment with 367 taxa and 128 sites

WARNING: Sequences tr_M3XMT2_M3XMT2_MUSPF_9669 and tr_E2RKG5_E2RKG5_CANLF_9615 are exactly identical!
WARNING: Sequences tr_M3XMT2_M3XMT2_MUSPF_9669 and tr_A0A2I2U7G6_A0A2I2U7G6_FELCA_9685 are exactly identical!
WARNING: Sequences tr_M3XMT2_M3XMT2_MUSPF_9669 and tr_A0A1U7TGE7_A0A1U7TGE7_TARSY_1868482 are exactly identical!
WARNING: Sequences tr_M3XMT2_M3XMT2_MUSPF_9669 and tr_A0A2U3VLZ1_A0A2U3VLZ1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_M3XMT2_M3XMT2_MUSPF_9669 and tr_A0A2U3Y573_A0A2U3Y573_LEPWE_9713 are exactly identical!
WARNING: Sequences tr_M3XMT2_M3XMT2_MUSPF_9669 and tr_A0A2Y9KV79_A0A2Y9KV79_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_M3XMT2_M3XMT2_MUSPF_9669 and tr_A0A384D7F1_A0A384D7F1_URSMA_29073 are exactly identical!
WARNING: Sequences tr_G1PSC5_G1PSC5_MYOLU_59463 and tr_W5QE32_W5QE32_SHEEP_9940 are exactly identical!
WARNING: Sequences tr_G1PSC5_G1PSC5_MYOLU_59463 and tr_A0A2U4BAL5_A0A2U4BAL5_TURTR_9739 are exactly identical!
WARNING: Sequences tr_G1PSC5_G1PSC5_MYOLU_59463 and tr_A0A2Y9E1G5_A0A2Y9E1G5_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_G1PSC5_G1PSC5_MYOLU_59463 and tr_A0A2Y9N9H3_A0A2Y9N9H3_DELLE_9749 are exactly identical!
WARNING: Sequences tr_G1PSC5_G1PSC5_MYOLU_59463 and tr_A0A2Y9SJK1_A0A2Y9SJK1_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_G1PSC5_G1PSC5_MYOLU_59463 and tr_A0A383ZVY6_A0A383ZVY6_BALAS_310752 are exactly identical!
WARNING: Sequences tr_G3I804_G3I804_CRIGR_10029 and tr_A0A1U7QJ75_A0A1U7QJ75_MESAU_10036 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_H2QGV9_H2QGV9_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_H0XMF3_H0XMF3_OTOGA_30611 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_H0VZQ5_H0VZQ5_CAVPO_10141 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and sp_Q9H7N4_SFR19_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_F6RK87_F6RK87_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_F7DYL4_F7DYL4_CALJA_9483 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_F1MEK3_F1MEK3_BOVIN_9913 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_A0A0A0MUI3_A0A0A0MUI3_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_A0A0D9S3X4_A0A0D9S3X4_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_A0A2K5M301_A0A2K5M301_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_A0A2K6DK15_A0A2K6DK15_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_A0A2U3WLV5_A0A2U3WLV5_ODORO_9708 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_A0A2Y9R9K3_A0A2Y9R9K3_TRIMA_127582 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_A0A2Y9L7V0_A0A2Y9L7V0_ENHLU_391180 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_A0A2Y9P3P0_A0A2Y9P3P0_DELLE_9749 are exactly identical!
WARNING: Sequences tr_G3QE05_G3QE05_GORGO_9595 and tr_A0A2Y9TIJ0_A0A2Y9TIJ0_PHYCD_9755 are exactly identical!
WARNING: Sequences tr_G3QZ45_G3QZ45_GORGO_9595 and sp_Q9P1Y6_PHRF1_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RFZ5_G3RFZ5_GORGO_9595 and tr_H2R3I6_H2R3I6_PANTR_9598 are exactly identical!
WARNING: Sequences tr_G3RFZ5_G3RFZ5_GORGO_9595 and sp_Q99590_SCAFB_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_G3RFZ5_G3RFZ5_GORGO_9595 and tr_F7HT89_F7HT89_MACMU_9544 are exactly identical!
WARNING: Sequences tr_G3RFZ5_G3RFZ5_GORGO_9595 and tr_G7PHN3_G7PHN3_MACFA_9541 are exactly identical!
WARNING: Sequences tr_G3RFZ5_G3RFZ5_GORGO_9595 and tr_A0A096N5J9_A0A096N5J9_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_G3RFZ5_G3RFZ5_GORGO_9595 and tr_A0A0D9R337_A0A0D9R337_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_G3RFZ5_G3RFZ5_GORGO_9595 and tr_A0A2K5LVV0_A0A2K5LVV0_CERAT_9531 are exactly identical!
WARNING: Sequences tr_G3RFZ5_G3RFZ5_GORGO_9595 and tr_A0A2K6B937_A0A2K6B937_MACNE_9545 are exactly identical!
WARNING: Sequences tr_G3RFZ5_G3RFZ5_GORGO_9595 and tr_A0A2K6A1K5_A0A2K6A1K5_MANLE_9568 are exactly identical!
WARNING: Sequences tr_G3RFZ5_G3RFZ5_GORGO_9595 and tr_A0A2R9B7M6_A0A2R9B7M6_PANPA_9597 are exactly identical!
WARNING: Sequences tr_H2R5P2_H2R5P2_PANTR_9598 and tr_A0A2R9CIV5_A0A2R9CIV5_PANPA_9597 are exactly identical!
WARNING: Sequences tr_A0A3B5PYH3_A0A3B5PYH3_XIPMA_8083 and tr_A0A087YFF6_A0A087YFF6_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A158NK66_A0A158NK66_ATTCE_12957 and tr_F4W8G0_F4W8G0_ACREC_103372 are exactly identical!
WARNING: Sequences tr_A0A158NK66_A0A158NK66_ATTCE_12957 and tr_A0A195BAX2_A0A195BAX2_9HYME_520822 are exactly identical!
WARNING: Sequences tr_A0A158NK66_A0A158NK66_ATTCE_12957 and tr_A0A195FB73_A0A195FB73_9HYME_34720 are exactly identical!
WARNING: Sequences tr_A0A1D5QF78_A0A1D5QF78_MACMU_9544 and tr_A0A2I3M3R6_A0A2I3M3R6_PAPAN_9555 are exactly identical!
WARNING: Sequences tr_A0A1D5QF78_A0A1D5QF78_MACMU_9544 and tr_A0A0D9RES9_A0A0D9RES9_CHLSB_60711 are exactly identical!
WARNING: Sequences tr_A0A1D5QF78_A0A1D5QF78_MACMU_9544 and tr_A0A2K5YNM9_A0A2K5YNM9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A091V3C7_A0A091V3C7_NIPNI_128390 and tr_A0A087RFG6_A0A087RFG6_APTFO_9233 are exactly identical!
WARNING: Sequences tr_A0A091V3C7_A0A091V3C7_NIPNI_128390 and tr_A0A091WRW8_A0A091WRW8_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A091V3C7_A0A091V3C7_NIPNI_128390 and tr_A0A0A0A5L6_A0A0A0A5L6_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A091VJ24_A0A091VJ24_OPIHO_30419 and tr_A0A091WMG8_A0A091WMG8_OPIHO_30419 are exactly identical!
WARNING: Sequences tr_A0A2I0MJ55_A0A2I0MJ55_COLLI_8932 and tr_A0A1V4J9B3_A0A1V4J9B3_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1S3MKQ8_A0A1S3MKQ8_SALSA_8030 and tr_A0A060WGG6_A0A060WGG6_ONCMY_8022 are exactly identical!
WARNING: Sequences tr_A0A226N360_A0A226N360_CALSU_9009 and tr_A0A226P9K5_A0A226P9K5_COLVI_9014 are exactly identical!
WARNING: Sequences tr_A0A2D0SEW4_A0A2D0SEW4_ICTPU_7998 and tr_A0A2D0SEX6_A0A2D0SEX6_ICTPU_7998 are exactly identical!
WARNING: Duplicate sequences found: 57

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q99590/3_mltree/Q99590.raxml.reduced.phy

Alignment comprises 1 partitions and 128 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 128 / 128
Gaps: 9.94 %
Invariant sites: 0.00 %


NOTE: Binary MSA file created: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q99590/3_mltree/Q99590.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 367 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 128 / 10240
[00:00:00] Data distribution: max. searches per worker: 7

Starting ML tree search with 20 distinct starting trees

[00:00:00 -62929.524048] Initial branch length optimization
[00:00:01 -51662.269927] Model parameter optimization (eps = 10.000000)
[00:00:21 -51350.775364] AUTODETECT spr round 1 (radius: 5)
[00:00:40 -34322.395068] AUTODETECT spr round 2 (radius: 10)
[00:01:04 -28257.509489] AUTODETECT spr round 3 (radius: 15)
[00:01:34 -25198.727794] AUTODETECT spr round 4 (radius: 20)
[00:02:08 -24303.992377] AUTODETECT spr round 5 (radius: 25)
[00:02:51 -23259.252793] SPR radius for FAST iterations: 25 (autodetect)
[00:02:51 -23259.252793] Model parameter optimization (eps = 3.000000)
[00:03:00 -23114.449938] FAST spr round 1 (radius: 25)
[00:03:31 -20297.067107] FAST spr round 2 (radius: 25)
[00:03:57 -19998.380994] FAST spr round 3 (radius: 25)
[00:04:17 -19984.760693] FAST spr round 4 (radius: 25)
[00:04:34 -19984.424324] FAST spr round 5 (radius: 25)
[00:04:50 -19984.423524] Model parameter optimization (eps = 1.000000)
[00:04:56 -19981.462686] SLOW spr round 1 (radius: 5)
[00:05:20 -19978.318555] SLOW spr round 2 (radius: 5)
[00:05:43 -19978.243524] SLOW spr round 3 (radius: 10)
[00:06:11 -19978.225466] SLOW spr round 4 (radius: 15)
[00:06:59 -19978.224215] SLOW spr round 5 (radius: 20)
[00:08:01 -19978.057756] SLOW spr round 6 (radius: 5)
[00:08:39 -19976.548485] SLOW spr round 7 (radius: 5)
[00:09:10 -19976.548182] SLOW spr round 8 (radius: 10)
[00:09:40 -19976.548091] SLOW spr round 9 (radius: 15)
[00:09:55] [worker #2] ML tree search #3, logLikelihood: -19951.431109
[00:10:28 -19976.548036] SLOW spr round 10 (radius: 20)
[00:11:31 -19976.547997] SLOW spr round 11 (radius: 25)
[00:12:28 -19976.547968] Model parameter optimization (eps = 0.100000)

[00:12:31] [worker #0] ML tree search #1, logLikelihood: -19976.534501

[00:12:31 -63483.435772] Initial branch length optimization
[00:12:31 -51635.239913] Model parameter optimization (eps = 10.000000)
[00:12:47 -51380.853364] AUTODETECT spr round 1 (radius: 5)
[00:13:06 -35695.464729] AUTODETECT spr round 2 (radius: 10)
[00:13:30 -27842.317904] AUTODETECT spr round 3 (radius: 15)
[00:14:00 -25396.462953] AUTODETECT spr round 4 (radius: 20)
[00:14:37 -23210.819344] AUTODETECT spr round 5 (radius: 25)
[00:15:12 -22391.206475] SPR radius for FAST iterations: 25 (autodetect)
[00:15:12 -22391.206475] Model parameter optimization (eps = 3.000000)
[00:15:23 -22258.023175] FAST spr round 1 (radius: 25)
[00:15:54 -20156.208334] FAST spr round 2 (radius: 25)
[00:16:18 -19988.386017] FAST spr round 3 (radius: 25)
[00:16:40 -19976.230760] FAST spr round 4 (radius: 25)
[00:16:57 -19971.825861] FAST spr round 5 (radius: 25)
[00:17:14 -19970.274123] FAST spr round 6 (radius: 25)
[00:17:22] [worker #1] ML tree search #2, logLikelihood: -19962.598914
[00:17:33 -19966.049516] FAST spr round 7 (radius: 25)
[00:17:49 -19964.725033] FAST spr round 8 (radius: 25)
[00:18:06 -19964.724413] Model parameter optimization (eps = 1.000000)
[00:18:08 -19964.226854] SLOW spr round 1 (radius: 5)
[00:18:32 -19961.377874] SLOW spr round 2 (radius: 5)
[00:18:56 -19960.009488] SLOW spr round 3 (radius: 5)
[00:19:19 -19959.871866] SLOW spr round 4 (radius: 5)
[00:19:41 -19959.871687] SLOW spr round 5 (radius: 10)
[00:20:06 -19959.462467] SLOW spr round 6 (radius: 5)
[00:20:40 -19959.433786] SLOW spr round 7 (radius: 10)
[00:21:11 -19959.431175] SLOW spr round 8 (radius: 15)
[00:21:58 -19959.430119] SLOW spr round 9 (radius: 20)
[00:23:00 -19959.429671] SLOW spr round 10 (radius: 25)
[00:23:58 -19959.429476] Model parameter optimization (eps = 0.100000)

[00:24:01] [worker #0] ML tree search #4, logLikelihood: -19959.411680

[00:24:01 -63160.768355] Initial branch length optimization
[00:24:02 -51288.924647] Model parameter optimization (eps = 10.000000)
[00:24:15 -51007.737249] AUTODETECT spr round 1 (radius: 5)
[00:24:35 -34278.040938] AUTODETECT spr round 2 (radius: 10)
[00:25:00 -27714.336531] AUTODETECT spr round 3 (radius: 15)
[00:25:25] [worker #2] ML tree search #6, logLikelihood: -19962.800494
[00:25:31 -24650.855735] AUTODETECT spr round 4 (radius: 20)
[00:26:08 -23074.749937] AUTODETECT spr round 5 (radius: 25)
[00:26:53 -22514.892092] SPR radius for FAST iterations: 25 (autodetect)
[00:26:53 -22514.892092] Model parameter optimization (eps = 3.000000)
[00:27:03 -22382.759515] FAST spr round 1 (radius: 25)
[00:27:31 -20070.049452] FAST spr round 2 (radius: 25)
[00:27:53 -19980.314954] FAST spr round 3 (radius: 25)
[00:28:13 -19973.872957] FAST spr round 4 (radius: 25)
[00:28:30 -19973.324680] FAST spr round 5 (radius: 25)
[00:28:47 -19973.323555] Model parameter optimization (eps = 1.000000)
[00:28:51 -19972.956654] SLOW spr round 1 (radius: 5)
[00:29:15 -19962.509415] SLOW spr round 2 (radius: 5)
[00:29:38 -19962.505671] SLOW spr round 3 (radius: 10)
[00:30:05 -19961.604680] SLOW spr round 4 (radius: 5)
[00:30:35] [worker #1] ML tree search #5, logLikelihood: -19960.105066
[00:30:39 -19961.603416] SLOW spr round 5 (radius: 10)
[00:31:13 -19959.514599] SLOW spr round 6 (radius: 5)
[00:31:45 -19959.022419] SLOW spr round 7 (radius: 5)
[00:32:12 -19959.020760] SLOW spr round 8 (radius: 10)
[00:32:41 -19959.020583] SLOW spr round 9 (radius: 15)
[00:33:29 -19959.020562] SLOW spr round 10 (radius: 20)
[00:34:33 -19958.971875] SLOW spr round 11 (radius: 25)
[00:35:31 -19958.971809] Model parameter optimization (eps = 0.100000)

[00:35:35] [worker #0] ML tree search #7, logLikelihood: -19958.757516

[00:35:35 -63316.383181] Initial branch length optimization
[00:35:36 -51339.097560] Model parameter optimization (eps = 10.000000)
[00:35:48 -51093.431706] AUTODETECT spr round 1 (radius: 5)
[00:36:07 -34672.163332] AUTODETECT spr round 2 (radius: 10)
[00:36:31 -26238.732461] AUTODETECT spr round 3 (radius: 15)
[00:37:01 -22922.620352] AUTODETECT spr round 4 (radius: 20)
[00:37:37 -22392.183434] AUTODETECT spr round 5 (radius: 25)
[00:38:03] [worker #2] ML tree search #9, logLikelihood: -19970.922120
[00:38:16 -21921.730284] SPR radius for FAST iterations: 25 (autodetect)
[00:38:16 -21921.730284] Model parameter optimization (eps = 3.000000)
[00:38:29 -21848.416050] FAST spr round 1 (radius: 25)
[00:38:59 -20268.789979] FAST spr round 2 (radius: 25)
[00:39:24 -20038.651013] FAST spr round 3 (radius: 25)
[00:39:44 -20029.948977] FAST spr round 4 (radius: 25)
[00:40:01 -20029.737293] FAST spr round 5 (radius: 25)
[00:40:17 -20029.735946] Model parameter optimization (eps = 1.000000)
[00:40:26 -20025.154871] SLOW spr round 1 (radius: 5)
[00:40:49 -20021.482117] SLOW spr round 2 (radius: 5)
[00:41:12 -20021.463940] SLOW spr round 3 (radius: 10)
[00:41:40 -20021.463506] SLOW spr round 4 (radius: 15)
[00:42:32] [worker #1] ML tree search #8, logLikelihood: -19968.570151
[00:42:33 -20019.837736] SLOW spr round 5 (radius: 5)
[00:43:11 -20018.611104] SLOW spr round 6 (radius: 5)
[00:43:42 -20017.041361] SLOW spr round 7 (radius: 5)
[00:44:09 -20017.033456] SLOW spr round 8 (radius: 10)
[00:44:36 -20017.032740] SLOW spr round 9 (radius: 15)
[00:45:24 -20017.032461] SLOW spr round 10 (radius: 20)
[00:46:27 -20017.032273] SLOW spr round 11 (radius: 25)
[00:47:24 -20017.032138] Model parameter optimization (eps = 0.100000)

[00:47:28] [worker #0] ML tree search #10, logLikelihood: -20016.898107

[00:47:28 -63679.504948] Initial branch length optimization
[00:47:29 -52001.129099] Model parameter optimization (eps = 10.000000)
[00:47:45 -51708.293647] AUTODETECT spr round 1 (radius: 5)
[00:48:05 -33874.510824] AUTODETECT spr round 2 (radius: 10)
[00:48:30 -26922.821359] AUTODETECT spr round 3 (radius: 15)
[00:49:00 -23634.801837] AUTODETECT spr round 4 (radius: 20)
[00:49:34 -22963.724232] AUTODETECT spr round 5 (radius: 25)
[00:50:13 -22484.820443] SPR radius for FAST iterations: 25 (autodetect)
[00:50:13 -22484.820443] Model parameter optimization (eps = 3.000000)
[00:50:24 -22391.497269] FAST spr round 1 (radius: 25)
[00:50:53 -20201.396619] FAST spr round 2 (radius: 25)
[00:51:16 -19991.617509] FAST spr round 3 (radius: 25)
[00:51:37 -19980.554512] FAST spr round 4 (radius: 25)
[00:51:54 -19973.577417] FAST spr round 5 (radius: 25)
[00:52:11 -19973.565109] Model parameter optimization (eps = 1.000000)
[00:52:18 -19970.970887] SLOW spr round 1 (radius: 5)
[00:52:29] [worker #1] ML tree search #11, logLikelihood: -19956.651967
[00:52:34] [worker #2] ML tree search #12, logLikelihood: -19958.879578
[00:52:42 -19968.497641] SLOW spr round 2 (radius: 5)
[00:53:04 -19968.494993] SLOW spr round 3 (radius: 10)
[00:53:30 -19968.494707] SLOW spr round 4 (radius: 15)
[00:54:18 -19967.831801] SLOW spr round 5 (radius: 5)
[00:54:54 -19967.830941] SLOW spr round 6 (radius: 10)
[00:55:30 -19963.835255] SLOW spr round 7 (radius: 5)
[00:56:04 -19960.321205] SLOW spr round 8 (radius: 5)
[00:56:32 -19960.150530] SLOW spr round 9 (radius: 5)
[00:56:57 -19960.149461] SLOW spr round 10 (radius: 10)
[00:57:24 -19960.149417] SLOW spr round 11 (radius: 15)
[00:58:12 -19959.792930] SLOW spr round 12 (radius: 5)
[00:58:49 -19959.792691] SLOW spr round 13 (radius: 10)
[00:59:23 -19959.792669] SLOW spr round 14 (radius: 15)
[01:00:10 -19959.792664] SLOW spr round 15 (radius: 20)
[01:01:11 -19959.792663] SLOW spr round 16 (radius: 25)
[01:02:09 -19959.792663] Model parameter optimization (eps = 0.100000)

[01:02:12] [worker #0] ML tree search #13, logLikelihood: -19959.700812

[01:02:12 -64082.006747] Initial branch length optimization
[01:02:13 -52019.162964] Model parameter optimization (eps = 10.000000)
[01:02:26 -51749.646246] AUTODETECT spr round 1 (radius: 5)
[01:02:46 -34987.185723] AUTODETECT spr round 2 (radius: 10)
[01:03:11 -27242.445795] AUTODETECT spr round 3 (radius: 15)
[01:03:41 -24292.256269] AUTODETECT spr round 4 (radius: 20)
[01:04:17 -21913.278713] AUTODETECT spr round 5 (radius: 25)
[01:04:52 -21858.021729] SPR radius for FAST iterations: 25 (autodetect)
[01:04:52 -21858.021729] Model parameter optimization (eps = 3.000000)
[01:05:03 -21725.033116] FAST spr round 1 (radius: 25)
[01:05:35 -20070.769587] FAST spr round 2 (radius: 25)
[01:05:59 -19976.433803] FAST spr round 3 (radius: 25)
[01:06:17 -19972.297351] FAST spr round 4 (radius: 25)
[01:06:34 -19970.392117] FAST spr round 5 (radius: 25)
[01:06:50 -19970.392059] Model parameter optimization (eps = 1.000000)
[01:06:57 -19967.451869] SLOW spr round 1 (radius: 5)
[01:07:19 -19964.840095] SLOW spr round 2 (radius: 5)
[01:07:25] [worker #1] ML tree search #14, logLikelihood: -19961.186066
[01:07:43 -19964.837117] SLOW spr round 3 (radius: 10)
[01:08:10 -19964.818757] SLOW spr round 4 (radius: 15)
[01:08:59 -19958.844605] SLOW spr round 5 (radius: 5)
[01:09:16] [worker #2] ML tree search #15, logLikelihood: -19962.308372
[01:09:37 -19957.685592] SLOW spr round 6 (radius: 5)
[01:10:06 -19957.685176] SLOW spr round 7 (radius: 10)
[01:10:36 -19957.685047] SLOW spr round 8 (radius: 15)
[01:11:23 -19957.495273] SLOW spr round 9 (radius: 5)
[01:12:00 -19957.495238] SLOW spr round 10 (radius: 10)
[01:12:34 -19957.495225] SLOW spr round 11 (radius: 15)
[01:13:21 -19957.495219] SLOW spr round 12 (radius: 20)
[01:14:21 -19957.495215] SLOW spr round 13 (radius: 25)
[01:15:18 -19957.495212] Model parameter optimization (eps = 0.100000)

[01:15:22] [worker #0] ML tree search #16, logLikelihood: -19957.121573

[01:15:22 -64131.260234] Initial branch length optimization
[01:15:23 -51970.836640] Model parameter optimization (eps = 10.000000)
[01:15:46 -51698.548308] AUTODETECT spr round 1 (radius: 5)
[01:16:06 -33771.840720] AUTODETECT spr round 2 (radius: 10)
[01:16:31 -27439.558460] AUTODETECT spr round 3 (radius: 15)
[01:16:59 -24719.869087] AUTODETECT spr round 4 (radius: 20)
[01:17:33 -22555.873087] AUTODETECT spr round 5 (radius: 25)
[01:18:15 -22434.040334] SPR radius for FAST iterations: 25 (autodetect)
[01:18:15 -22434.040334] Model parameter optimization (eps = 3.000000)
[01:18:28 -22311.748191] FAST spr round 1 (radius: 25)
[01:18:56 -20092.974507] FAST spr round 2 (radius: 25)
[01:19:20 -19985.355370] FAST spr round 3 (radius: 25)
[01:19:42 -19976.861285] FAST spr round 4 (radius: 25)
[01:19:53] [worker #1] ML tree search #17, logLikelihood: -19965.074332
[01:19:59 -19974.686985] FAST spr round 5 (radius: 25)
[01:20:17 -19973.788915] FAST spr round 6 (radius: 25)
[01:20:34 -19973.787328] Model parameter optimization (eps = 1.000000)
[01:20:39 -19972.493514] SLOW spr round 1 (radius: 5)
[01:21:04 -19969.277325] SLOW spr round 2 (radius: 5)
[01:21:27 -19964.844166] SLOW spr round 3 (radius: 5)
[01:21:51 -19963.266492] SLOW spr round 4 (radius: 5)
[01:22:13 -19963.266429] SLOW spr round 5 (radius: 10)
[01:22:18] [worker #2] ML tree search #18, logLikelihood: -19953.463066
[01:22:39 -19963.248688] SLOW spr round 6 (radius: 15)
[01:23:26 -19963.069391] SLOW spr round 7 (radius: 5)
[01:24:01 -19963.069381] SLOW spr round 8 (radius: 10)
[01:24:34 -19963.069376] SLOW spr round 9 (radius: 15)
[01:25:18 -19963.069370] SLOW spr round 10 (radius: 20)
[01:26:17 -19963.069365] SLOW spr round 11 (radius: 25)
[01:27:16 -19963.069360] Model parameter optimization (eps = 0.100000)

[01:27:18] [worker #0] ML tree search #19, logLikelihood: -19963.029555

[01:34:35] [worker #1] ML tree search #20, logLikelihood: -19958.817907

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.188467,0.465354) (0.110871,1.532152) (0.286362,0.603953) (0.414300,1.374548) 
   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: -19951.431109

AIC score: 41376.862218 / AICc score: 1129188.862218 / BIC score: 43478.808522
Free parameters (model + branch lengths): 737

WARNING: Number of free parameters (K=737) is larger than alignment size (n=128).
         This might lead to overfitting and compromise tree inference results!


Best ML tree saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q99590/3_mltree/Q99590.raxml.bestTree
All ML trees saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q99590/3_mltree/Q99590.raxml.mlTrees
Optimized model saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q99590/3_mltree/Q99590.raxml.bestModel

Execution log saved to: /cta/users/eakkoyun/WORKFOLDER/PROD/run_300621/phylogeny-snakemake/results/Q99590/3_mltree/Q99590.raxml.log

Analysis started: 07-Jul-2021 03:14:30 / finished: 07-Jul-2021 04:49:06

Elapsed time: 5675.736 seconds