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 6258R CPU @ 2.70GHz, 56 cores, 187 GB RAM RAxML-NG was called at 04-Jun-2021 03:53:15 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/2_msa/P69892_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/3_mltree/P69892 --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/020621_run/phylogeny-snakemake/results/P69892/2_msa/P69892_trimmed_msa.fasta [00:00:00] Loaded alignment with 901 taxa and 139 sites WARNING: Sequences tr_F6P731_F6P731_DANRE_7955 and tr_Q7ZT21_Q7ZT21_DANRE_7955 are exactly identical! WARNING: Sequences tr_M3YFG8_M3YFG8_MUSPF_9669 and sp_P68044_HBB_MUSPF_9669 are exactly identical! WARNING: Sequences tr_G1S6C6_G1S6C6_NOMLE_61853 and sp_P61773_HBD_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1S6C6_G1S6C6_NOMLE_61853 and sp_P61772_HBD_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1S6C6_G1S6C6_NOMLE_61853 and tr_A0A2R9AC19_A0A2R9AC19_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QY87_G3QY87_GORGO_9595 and tr_H2NPI6_H2NPI6_PONAB_9601 are exactly identical! WARNING: Sequences sp_P62742_HBG2_GORGO_9595 and sp_P61921_HBG2_PANTR_9598 are exactly identical! WARNING: Sequences sp_P62742_HBG2_GORGO_9595 and sp_P69892_HBG2_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q6LDH0_HBE_GORGO_9595 and sp_Q6LDH1_HBE_PANTR_9598 are exactly identical! WARNING: Sequences sp_Q6LDH0_HBE_GORGO_9595 and sp_P02100_HBE_HUMAN_9606 are exactly identical! WARNING: Sequences sp_Q6LDH0_HBE_GORGO_9595 and tr_A0A2R9BP35_A0A2R9BP35_PANPA_9597 are exactly identical! WARNING: Sequences tr_G1U9Q8_G1U9Q8_MELGA_9103 and tr_A0A226MDR3_A0A226MDR3_CALSU_9009 are exactly identical! WARNING: Sequences tr_G1U9Q8_G1U9Q8_MELGA_9103 and tr_A0A226P0J4_A0A226P0J4_COLVI_9014 are exactly identical! WARNING: Sequences tr_G1TPE2_G1TPE2_RABIT_9986 and sp_P02103_HBE_RABIT_9986 are exactly identical! WARNING: Sequences tr_J9JHW7_J9JHW7_CANLF_9615 and tr_J9P710_J9P710_CANLF_9615 are exactly identical! WARNING: Sequences tr_J9NXL3_J9NXL3_CANLF_9615 and sp_P60529_HBA_CANLF_9615 are exactly identical! WARNING: Sequences tr_A0A2I3SN30_A0A2I3SN30_PANTR_9598 and sp_P09105_HBAT_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I3SN30_A0A2I3SN30_PANTR_9598 and tr_A0A2R9BK37_A0A2R9BK37_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R1M1_H2R1M1_PANTR_9598 and tr_A0A2R8ZJR3_A0A2R8ZJR3_PANPA_9597 are exactly identical! WARNING: Sequences tr_H2R5L8_H2R5L8_PANTR_9598 and sp_Q28779_HBG1_PANPA_9597 are exactly identical! WARNING: Sequences sp_P06347_HBAZ_PANTR_9598 and tr_A0A2R8ZJQ4_A0A2R8ZJQ4_PANPA_9597 are exactly identical! WARNING: Sequences sp_P61920_HBG1_PANTR_9598 and sp_P69891_HBG1_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P68873_HBB_PANTR_9598 and sp_P68871_HBB_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P68873_HBB_PANTR_9598 and sp_P68872_HBB_PANPA_9597 are exactly identical! WARNING: Sequences sp_P69907_HBA_PANTR_9598 and sp_P69905_HBA_HUMAN_9606 are exactly identical! WARNING: Sequences sp_P69907_HBA_PANTR_9598 and sp_P69906_HBA_PANPA_9597 are exactly identical! WARNING: Sequences tr_F6RDD3_F6RDD3_HORSE_9796 and sp_P02062_HBB_HORSE_9796 are exactly identical! WARNING: Sequences tr_F7AV81_F7AV81_MACMU_9544 and tr_G7PQY3_G7PQY3_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7AV81_F7AV81_MACMU_9544 and sp_P68225_HBB_MACNE_9545 are exactly identical! WARNING: Sequences sp_P68077_HBG_MACMU_9544 and tr_A9L8Y0_A9L8Y0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_D3U1H2_D3U1H2_LOXAF_9785 and sp_P01955_HBA_LOXAF_9785 are exactly identical! WARNING: Sequences sp_P02085_HBB_LOXAF_9785 and sp_Q45XJ0_HBD_LOXAF_9785 are exactly identical! WARNING: Sequences tr_F6WIM6_F6WIM6_CALJA_9483 and sp_Q9GJS7_HBG_CALJA_9483 are exactly identical! WARNING: Sequences tr_F1RGX4_F1RGX4_PIG_9823 and sp_P01965_HBA_PIG_9823 are exactly identical! WARNING: Sequences tr_F1RII6_F1RII6_PIG_9823 and sp_P04246_HBT_PIG_9823 are exactly identical! WARNING: Sequences tr_H3AAE3_H3AAE3_LATCH_7897 and sp_P23740_HBA_LATCH_7897 are exactly identical! WARNING: Sequences tr_A0A0A0MQ02_A0A0A0MQ02_FELCA_9685 and sp_P07405_HBA_FELCA_9685 are exactly identical! WARNING: Sequences tr_A9L8U0_A9L8U0_PAPAN_9555 and tr_A0A2K5MX97_A0A2K5MX97_CERAT_9531 are exactly identical! WARNING: Sequences tr_A9L8U0_A9L8U0_PAPAN_9555 and tr_A0A2K6CQE3_A0A2K6CQE3_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A1K0GV58_A0A1K0GV58_ERIEU_9365 and sp_P01949_HBA_ERIEU_9365 are exactly identical! WARNING: Sequences tr_A0A1U7TAR4_A0A1U7TAR4_TARSY_1868482 and sp_P13558_HBD_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A1U7TD49_A0A1U7TD49_TARSY_1868482 and sp_P13557_HBB_TARSY_1868482 are exactly identical! WARNING: Sequences tr_A0A1U7Q945_A0A1U7Q945_MESAU_10036 and sp_P29626_HBBY_MESAU_10036 are exactly identical! WARNING: Sequences tr_A0A226MB68_A0A226MB68_CALSU_9009 and tr_A0A226P3X1_A0A226P3X1_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2D0S6B3_A0A2D0S6B3_ICTPU_7998 and tr_W5U988_W5U988_ICTPU_7998 are exactly identical! WARNING: Sequences tr_A0A2K5KYI6_A0A2K5KYI6_CERAT_9531 and tr_A0A2K5YN23_A0A2K5YN23_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A2K6BQS5_A0A2K6BQS5_MACNE_9545 and sp_P02097_HBG_MACNE_9545 are exactly identical! WARNING: Sequences tr_A0A2K6DGR3_A0A2K6DGR3_MACNE_9545 and tr_A0A2K5XF24_A0A2K5XF24_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A1K0FUE0_A0A1K0FUE0_TURTR_9739 and tr_A0A2Y9PT12_A0A2Y9PT12_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U3W4T6_A0A2U3W4T6_ODORO_9708 and sp_P10778_HBA_ODORO_9708 are exactly identical! WARNING: Sequences tr_A0A384DLF1_A0A384DLF1_URSMA_29073 and sp_P68011_HBB_URSMA_29073 are exactly identical! WARNING: Duplicate sequences found: 51 NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/3_mltree/P69892.raxml.reduced.phy Alignment comprises 1 partitions and 139 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 139 / 139 Gaps: 3.56 % Invariant sites: 0.00 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/3_mltree/P69892.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 901 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 139 / 11120 [00:00:00] Data distribution: max. searches per worker: 7 Starting ML tree search with 20 distinct starting trees [00:00:00 -197824.197092] Initial branch length optimization [00:00:04 -168027.237361] Model parameter optimization (eps = 10.000000) [00:00:34 -167158.566875] AUTODETECT spr round 1 (radius: 5) [00:02:30 -116673.989279] AUTODETECT spr round 2 (radius: 10) [00:04:35 -88916.755948] AUTODETECT spr round 3 (radius: 15) [00:06:53 -76565.830978] AUTODETECT spr round 4 (radius: 20) [00:09:43 -67427.638629] AUTODETECT spr round 5 (radius: 25) [00:13:13 -64041.946649] SPR radius for FAST iterations: 25 (autodetect) [00:13:13 -64041.946649] Model parameter optimization (eps = 3.000000) [00:13:29 -64009.740163] FAST spr round 1 (radius: 25) [00:15:46 -55123.401854] FAST spr round 2 (radius: 25) [00:17:38 -54840.535401] FAST spr round 3 (radius: 25) [00:19:22 -54774.147992] FAST spr round 4 (radius: 25) [00:20:52 -54764.334267] FAST spr round 5 (radius: 25) [00:22:21 -54759.410205] FAST spr round 6 (radius: 25) [00:23:50 -54751.588039] FAST spr round 7 (radius: 25) [00:25:18 -54746.067887] FAST spr round 8 (radius: 25) [00:26:45 -54745.434344] FAST spr round 9 (radius: 25) [00:28:11 -54745.434343] Model parameter optimization (eps = 1.000000) [00:28:25 -54735.108399] SLOW spr round 1 (radius: 5) [00:30:24 -54718.722189] SLOW spr round 2 (radius: 5) [00:32:20 -54716.510642] SLOW spr round 3 (radius: 5) [00:34:11 -54716.510236] SLOW spr round 4 (radius: 10) [00:36:03 -54714.271078] SLOW spr round 5 (radius: 5) [00:38:21 -54714.270907] SLOW spr round 6 (radius: 10) [00:40:25 -54713.712117] SLOW spr round 7 (radius: 5) [00:42:41 -54712.129229] SLOW spr round 8 (radius: 5) [00:44:42 -54712.128982] SLOW spr round 9 (radius: 10) [00:46:38 -54711.878540] SLOW spr round 10 (radius: 5) [00:48:55 -54711.878521] SLOW spr round 11 (radius: 10) [00:50:58 -54711.878519] SLOW spr round 12 (radius: 15) [00:53:46 -54711.878518] SLOW spr round 13 (radius: 20) [00:57:43 -54701.397707] SLOW spr round 14 (radius: 5) [01:00:17 -54695.596912] SLOW spr round 15 (radius: 5) [01:02:25 -54695.596909] SLOW spr round 16 (radius: 10) [01:04:24 -54695.596908] SLOW spr round 17 (radius: 15) [01:07:16 -54695.596907] SLOW spr round 18 (radius: 20) [01:11:08 -54695.596906] SLOW spr round 19 (radius: 25) [01:14:53] [worker #2] ML tree search #3, logLikelihood: -54715.167503 [01:16:00 -54695.596904] Model parameter optimization (eps = 0.100000) [01:16:07] [worker #0] ML tree search #1, logLikelihood: -54695.488135 [01:16:07 -199189.948256] Initial branch length optimization [01:16:10 -168722.330918] Model parameter optimization (eps = 10.000000) [01:16:37 -167768.148369] AUTODETECT spr round 1 (radius: 5) [01:18:33 -116549.442111] AUTODETECT spr round 2 (radius: 10) [01:20:40 -88135.469764] AUTODETECT spr round 3 (radius: 15) [01:23:12 -70982.581583] AUTODETECT spr round 4 (radius: 20) [01:26:04 -65290.866120] AUTODETECT spr round 5 (radius: 25) [01:29:41 -64435.113715] SPR radius for FAST iterations: 25 (autodetect) [01:29:41 -64435.113715] Model parameter optimization (eps = 3.000000) [01:30:02 -64402.254320] FAST spr round 1 (radius: 25) [01:32:24 -55322.364113] FAST spr round 2 (radius: 25) [01:34:14 -54778.410032] FAST spr round 3 (radius: 25) [01:35:52 -54756.172118] FAST spr round 4 (radius: 25) [01:37:09] [worker #1] ML tree search #2, logLikelihood: -54728.632582 [01:37:20 -54756.171684] Model parameter optimization (eps = 1.000000) [01:37:33 -54732.772960] SLOW spr round 1 (radius: 5) [01:39:36 -54716.567417] SLOW spr round 2 (radius: 5) [01:41:34 -54715.333836] SLOW spr round 3 (radius: 5) [01:43:27 -54714.902390] SLOW spr round 4 (radius: 5) [01:45:19 -54714.901918] SLOW spr round 5 (radius: 10) [01:47:11 -54714.250302] SLOW spr round 6 (radius: 5) [01:49:28 -54711.822200] SLOW spr round 7 (radius: 5) [01:51:30 -54711.821727] SLOW spr round 8 (radius: 10) [01:53:25 -54711.821277] SLOW spr round 9 (radius: 15) [01:56:18 -54710.784428] SLOW spr round 10 (radius: 5) [01:58:41 -54703.015608] SLOW spr round 11 (radius: 5) [02:00:45 -54703.015252] SLOW spr round 12 (radius: 10) [02:02:41 -54701.295215] SLOW spr round 13 (radius: 5) [02:04:55 -54701.294910] SLOW spr round 14 (radius: 10) [02:06:58 -54701.294763] SLOW spr round 15 (radius: 15) [02:09:45 -54701.294683] SLOW spr round 16 (radius: 20) [02:13:33 -54701.294632] SLOW spr round 17 (radius: 25) [02:18:23 -54701.294597] Model parameter optimization (eps = 0.100000) [02:18:31] [worker #0] ML tree search #4, logLikelihood: -54701.243421 [02:18:31 -197854.507790] Initial branch length optimization [02:18:34 -167666.390713] Model parameter optimization (eps = 10.000000) [02:18:59 -166726.879242] AUTODETECT spr round 1 (radius: 5) [02:20:53 -117345.021841] AUTODETECT spr round 2 (radius: 10) [02:22:58 -91382.756726] AUTODETECT spr round 3 (radius: 15) [02:25:25 -79900.870660] AUTODETECT spr round 4 (radius: 20) [02:28:18 -74128.516781] AUTODETECT spr round 5 (radius: 25) [02:31:11 -71273.745512] SPR radius for FAST iterations: 25 (autodetect) [02:31:11 -71273.745512] Model parameter optimization (eps = 3.000000) [02:31:29 -71244.683533] FAST spr round 1 (radius: 25) [02:33:50 -60873.887816] FAST spr round 2 (radius: 25) [02:35:38 -57561.903120] FAST spr round 3 (radius: 25) [02:37:16 -55210.744521] FAST spr round 4 (radius: 25) [02:38:49 -54841.832934] FAST spr round 5 (radius: 25) [02:40:24 -54798.566848] FAST spr round 6 (radius: 25) [02:41:50 -54795.384399] FAST spr round 7 (radius: 25) [02:43:15 -54795.383978] Model parameter optimization (eps = 1.000000) [02:43:31 -54788.257741] SLOW spr round 1 (radius: 5) [02:44:57] [worker #1] ML tree search #5, logLikelihood: -54675.400584 [02:45:32 -54756.971182] SLOW spr round 2 (radius: 5) [02:47:28 -54746.489342] SLOW spr round 3 (radius: 5) [02:49:23 -54743.868777] SLOW spr round 4 (radius: 5) [02:51:14 -54743.868146] SLOW spr round 5 (radius: 10) [02:52:38] [worker #2] ML tree search #6, logLikelihood: -54713.021136 [02:53:06 -54742.379578] SLOW spr round 6 (radius: 5) [02:55:22 -54742.378944] SLOW spr round 7 (radius: 10) [02:57:27 -54742.378484] SLOW spr round 8 (radius: 15) [03:00:15 -54742.378328] SLOW spr round 9 (radius: 20) [03:04:31 -54722.964967] SLOW spr round 10 (radius: 5) [03:06:55 -54722.964171] SLOW spr round 11 (radius: 10) [03:09:08 -54722.964001] SLOW spr round 12 (radius: 15) [03:11:54 -54722.963845] SLOW spr round 13 (radius: 20) [03:16:10 -54722.963689] SLOW spr round 14 (radius: 25) [03:21:26 -54722.963533] Model parameter optimization (eps = 0.100000) [03:21:43] [worker #0] ML tree search #7, logLikelihood: -54719.726210 [03:21:43 -199797.644737] Initial branch length optimization [03:21:47 -168495.636882] Model parameter optimization (eps = 10.000000) [03:22:22 -167582.664034] AUTODETECT spr round 1 (radius: 5) [03:24:20 -117007.340283] AUTODETECT spr round 2 (radius: 10) [03:26:22 -89168.148527] AUTODETECT spr round 3 (radius: 15) [03:28:40 -73860.854176] AUTODETECT spr round 4 (radius: 20) [03:31:29 -66706.803239] AUTODETECT spr round 5 (radius: 25) [03:34:08 -65157.543156] SPR radius for FAST iterations: 25 (autodetect) [03:34:08 -65157.543156] Model parameter optimization (eps = 3.000000) [03:34:30 -65117.937417] FAST spr round 1 (radius: 25) [03:36:50 -55643.250022] FAST spr round 2 (radius: 25) [03:38:43 -54801.594435] FAST spr round 3 (radius: 25) [03:40:20 -54757.614117] FAST spr round 4 (radius: 25) [03:41:50 -54755.621827] FAST spr round 5 (radius: 25) [03:43:16 -54755.621447] Model parameter optimization (eps = 1.000000) [03:43:29 -54750.926426] SLOW spr round 1 (radius: 5) [03:45:35 -54731.122367] SLOW spr round 2 (radius: 5) [03:47:33 -54727.555651] SLOW spr round 3 (radius: 5) [03:47:57] [worker #1] ML tree search #8, logLikelihood: -54657.772464 [03:49:25 -54726.996567] SLOW spr round 4 (radius: 5) [03:51:15 -54726.996085] SLOW spr round 5 (radius: 10) [03:53:09 -54723.372119] SLOW spr round 6 (radius: 5) [03:55:28 -54722.044636] SLOW spr round 7 (radius: 5) [03:57:32 -54717.624605] SLOW spr round 8 (radius: 5) [03:59:27 -54717.624110] SLOW spr round 9 (radius: 10) [04:01:19 -54717.623774] SLOW spr round 10 (radius: 15) [04:04:13 -54716.238511] SLOW spr round 11 (radius: 5) [04:06:35 -54716.238352] SLOW spr round 12 (radius: 10) [04:08:44 -54716.238194] SLOW spr round 13 (radius: 15) [04:11:29 -54716.238035] SLOW spr round 14 (radius: 20) [04:15:36 -54715.602345] SLOW spr round 15 (radius: 5) [04:18:03 -54715.602186] SLOW spr round 16 (radius: 10) [04:20:18 -54715.602027] SLOW spr round 17 (radius: 15) [04:23:03 -54715.601869] SLOW spr round 18 (radius: 20) [04:27:08 -54715.601711] SLOW spr round 19 (radius: 25) [04:32:11 -54715.601557] Model parameter optimization (eps = 0.100000) [04:32:17] [worker #0] ML tree search #10, logLikelihood: -54715.561379 [04:32:17 -198442.301308] Initial branch length optimization [04:32:20 -167731.858045] Model parameter optimization (eps = 10.000000) [04:32:48 -166840.111807] AUTODETECT spr round 1 (radius: 5) [04:34:45 -117242.604918] AUTODETECT spr round 2 (radius: 10) [04:36:50 -88259.676536] AUTODETECT spr round 3 (radius: 15) [04:39:06 -72131.552973] AUTODETECT spr round 4 (radius: 20) [04:41:47 -67352.758631] AUTODETECT spr round 5 (radius: 25) [04:44:45 -65377.054074] SPR radius for FAST iterations: 25 (autodetect) [04:44:45 -65377.054074] Model parameter optimization (eps = 3.000000) [04:45:02 -65358.086949] FAST spr round 1 (radius: 25) [04:46:04] [worker #2] ML tree search #9, logLikelihood: -54680.470924 [04:47:23 -57282.875821] FAST spr round 2 (radius: 25) [04:49:16 -56758.109662] FAST spr round 3 (radius: 25) [04:50:56 -55635.150424] FAST spr round 4 (radius: 25) [04:52:36 -55246.466861] FAST spr round 5 (radius: 25) [04:54:07 -55223.505134] FAST spr round 6 (radius: 25) [04:55:36 -55218.167803] FAST spr round 7 (radius: 25) [04:55:56] [worker #1] ML tree search #11, logLikelihood: -54710.595818 [04:57:03 -55218.167634] Model parameter optimization (eps = 1.000000) [04:57:21 -55193.274284] SLOW spr round 1 (radius: 5) [04:59:25 -55162.082503] SLOW spr round 2 (radius: 5) [05:01:25 -55158.527009] SLOW spr round 3 (radius: 5) [05:03:17 -55158.526639] SLOW spr round 4 (radius: 10) [05:05:10 -55157.157803] SLOW spr round 5 (radius: 5) [05:07:27 -55157.157484] SLOW spr round 6 (radius: 10) [05:09:33 -55157.157169] SLOW spr round 7 (radius: 15) [05:12:20 -55154.865304] SLOW spr round 8 (radius: 5) [05:14:48 -55152.999365] SLOW spr round 9 (radius: 5) [05:16:56 -55152.998692] SLOW spr round 10 (radius: 10) [05:18:55 -55151.819026] SLOW spr round 11 (radius: 5) [05:21:13 -55151.818683] SLOW spr round 12 (radius: 10) [05:23:19 -55151.818518] SLOW spr round 13 (radius: 15) [05:26:05 -55151.818353] SLOW spr round 14 (radius: 20) [05:30:11 -55148.981543] SLOW spr round 15 (radius: 5) [05:32:39 -55147.182529] SLOW spr round 16 (radius: 5) [05:34:50 -55147.182363] SLOW spr round 17 (radius: 10) [05:36:50 -55147.182198] SLOW spr round 18 (radius: 15) [05:39:38 -55147.182033] SLOW spr round 19 (radius: 20) [05:43:41 -55147.181868] SLOW spr round 20 (radius: 25) [05:48:55 -55147.181703] Model parameter optimization (eps = 0.100000) [05:49:03] [worker #0] ML tree search #13, logLikelihood: -55147.137524 [05:49:03 -198859.233361] Initial branch length optimization [05:49:07 -168606.130370] Model parameter optimization (eps = 10.000000) [05:49:33 -167679.460602] AUTODETECT spr round 1 (radius: 5) [05:51:29 -115858.661442] AUTODETECT spr round 2 (radius: 10) [05:53:39 -87331.829184] AUTODETECT spr round 3 (radius: 15) [05:55:57 -75644.366926] AUTODETECT spr round 4 (radius: 20) [05:58:39 -69187.124686] AUTODETECT spr round 5 (radius: 25) [06:01:35 -65940.090224] SPR radius for FAST iterations: 25 (autodetect) [06:01:35 -65940.090224] Model parameter optimization (eps = 3.000000) [06:02:02 -65879.814498] FAST spr round 1 (radius: 25) [06:04:22 -55311.848553] FAST spr round 2 (radius: 25) [06:06:16 -54811.293218] FAST spr round 3 (radius: 25) [06:07:55 -54757.789019] FAST spr round 4 (radius: 25) [06:09:28 -54746.456125] FAST spr round 5 (radius: 25) [06:10:55 -54746.455782] Model parameter optimization (eps = 1.000000) [06:11:06 -54744.103346] SLOW spr round 1 (radius: 5) [06:13:09 -54711.674782] SLOW spr round 2 (radius: 5) [06:15:07 -54705.979135] SLOW spr round 3 (radius: 5) [06:16:49] [worker #1] ML tree search #14, logLikelihood: -54685.984203 [06:16:59 -54705.978711] SLOW spr round 4 (radius: 10) [06:18:51 -54704.575579] SLOW spr round 5 (radius: 5) [06:21:08 -54704.575412] SLOW spr round 6 (radius: 10) [06:23:11 -54704.296436] SLOW spr round 7 (radius: 5) [06:25:26 -54704.296251] SLOW spr round 8 (radius: 10) [06:26:58] [worker #2] ML tree search #12, logLikelihood: -54697.280391 [06:27:28 -54704.296085] SLOW spr round 9 (radius: 15) [06:30:13 -54703.388143] SLOW spr round 10 (radius: 5) [06:32:37 -54702.460215] SLOW spr round 11 (radius: 5) [06:34:43 -54702.460041] SLOW spr round 12 (radius: 10) [06:36:40 -54702.459964] SLOW spr round 13 (radius: 15) [06:39:27 -54702.459962] SLOW spr round 14 (radius: 20) [06:43:08 -54702.459961] SLOW spr round 15 (radius: 25) [06:47:44 -54702.459961] Model parameter optimization (eps = 0.100000) [06:47:52] [worker #0] ML tree search #16, logLikelihood: -54702.331089 [06:47:52 -197546.317998] Initial branch length optimization [06:47:55 -167369.486988] Model parameter optimization (eps = 10.000000) [06:48:25 -166488.704142] AUTODETECT spr round 1 (radius: 5) [06:50:22 -114890.042972] AUTODETECT spr round 2 (radius: 10) [06:52:25 -88418.342244] AUTODETECT spr round 3 (radius: 15) [06:54:46 -73387.665484] AUTODETECT spr round 4 (radius: 20) [06:57:27 -67866.229525] AUTODETECT spr round 5 (radius: 25) [07:00:33 -66126.622633] SPR radius for FAST iterations: 25 (autodetect) [07:00:33 -66126.622633] Model parameter optimization (eps = 3.000000) [07:00:56 -66048.205653] FAST spr round 1 (radius: 25) [07:03:20 -55415.900950] FAST spr round 2 (radius: 25) [07:05:16 -54755.760176] FAST spr round 3 (radius: 25) [07:06:56 -54722.041232] FAST spr round 4 (radius: 25) [07:08:26 -54714.889781] FAST spr round 5 (radius: 25) [07:09:52 -54714.387541] FAST spr round 6 (radius: 25) [07:11:19 -54711.973227] FAST spr round 7 (radius: 25) [07:12:44 -54710.232078] FAST spr round 8 (radius: 25) [07:14:09 -54710.231797] Model parameter optimization (eps = 1.000000) [07:14:27 -54706.659354] SLOW spr round 1 (radius: 5) [07:16:28 -54689.933005] SLOW spr round 2 (radius: 5) [07:18:08] [worker #2] ML tree search #15, logLikelihood: -54691.035557 [07:18:25 -54686.800158] SLOW spr round 3 (radius: 5) [07:20:15 -54686.799627] SLOW spr round 4 (radius: 10) [07:22:07 -54683.933416] SLOW spr round 5 (radius: 5) [07:24:24 -54682.003818] SLOW spr round 6 (radius: 5) [07:26:26 -54682.003351] SLOW spr round 7 (radius: 10) [07:28:21 -54682.002888] SLOW spr round 8 (radius: 15) [07:31:15 -54682.002428] SLOW spr round 9 (radius: 20) [07:35:09 -54676.146478] SLOW spr round 10 (radius: 5) [07:37:35 -54676.145917] SLOW spr round 11 (radius: 10) [07:39:50 -54676.145465] SLOW spr round 12 (radius: 15) [07:42:34 -54676.145016] SLOW spr round 13 (radius: 20) [07:46:24 -54676.144570] SLOW spr round 14 (radius: 25) [07:51:05 -54676.144126] Model parameter optimization (eps = 0.100000) [07:51:15] [worker #0] ML tree search #19, logLikelihood: -54675.748698 [08:04:24] [worker #1] ML tree search #17, logLikelihood: -54695.080804 [08:29:17] [worker #2] ML tree search #18, logLikelihood: -54694.812755 [09:31:15] [worker #1] ML tree search #20, logLikelihood: -54690.922283 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.213680,0.716024) (0.225286,0.581452) (0.387536,0.946002) (0.173499,2.013835) 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: -54657.772464 AIC score: 112925.544929 / AICc score: 6632585.544929 / BIC score: 118222.270378 Free parameters (model + branch lengths): 1805 WARNING: Number of free parameters (K=1805) is larger than alignment size (n=139). This might lead to overfitting and compromise tree inference results! WARNING: Best ML tree contains 105 near-zero branches! Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/3_mltree/P69892.raxml.bestTreeCollapsed Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/3_mltree/P69892.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/3_mltree/P69892.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/3_mltree/P69892.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/020621_run/phylogeny-snakemake/results/P69892/3_mltree/P69892.raxml.log Analysis started: 04-Jun-2021 03:53:15 / finished: 04-Jun-2021 13:24:31 Elapsed time: 34276.025 seconds Consumed energy: 2589.449 Wh (= 13 km in an electric car, or 65 km with an e-scooter!)