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 02-Jul-2021 04:48:09 as follows: raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52569/2_msa/P52569_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52569/3_mltree/P52569 --seed 2 --threads 5 --tree rand{20} pars{20} Analysis options: run mode: ML tree search start tree(s): random (20) random seed: 2 tip-inner: OFF pattern compression: ON per-rate scalers: OFF site repeats: ON fast spr radius: AUTO spr subtree cutoff: 1.000000 branch lengths: proportional (ML estimate, algorithm: NR-FAST) SIMD kernels: AVX2 parallelization: coarse-grained (auto), PTHREADS (5 threads), thread pinning: OFF [00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52569/2_msa/P52569_trimmed_msa.fasta [00:00:00] Loaded alignment with 1001 taxa and 358 sites WARNING: Sequences tr_B4QL07_B4QL07_DROSI_7240 and tr_B4HI70_B4HI70_DROSE_7238 are exactly identical! WARNING: Sequences tr_B4QPB9_B4QPB9_DROSI_7240 and tr_B4HLB6_B4HLB6_DROSE_7238 are exactly identical! WARNING: Sequences tr_G1QZL3_G1QZL3_NOMLE_61853 and tr_A0A2I2Y2E8_A0A2I2Y2E8_GORGO_9595 are exactly identical! WARNING: Sequences tr_G1QZL3_G1QZL3_NOMLE_61853 and tr_H2QNQ7_H2QNQ7_PANTR_9598 are exactly identical! WARNING: Sequences tr_G1QZL3_G1QZL3_NOMLE_61853 and tr_A0A2R9CKX3_A0A2R9CKX3_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2I2ZDG4_A0A2I2ZDG4_GORGO_9595 and tr_H2NJI7_H2NJI7_PONAB_9601 are exactly identical! WARNING: Sequences tr_A0A2I2ZDG4_A0A2I2ZDG4_GORGO_9595 and tr_H2Q7D2_H2Q7D2_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I2ZDG4_A0A2I2ZDG4_GORGO_9595 and sp_P30825_CTR1_HUMAN_9606 are exactly identical! WARNING: Sequences tr_A0A2I2ZDG4_A0A2I2ZDG4_GORGO_9595 and tr_A0A2R9BE45_A0A2R9BE45_PANPA_9597 are exactly identical! WARNING: Sequences tr_G3QFM4_G3QFM4_GORGO_9595 and tr_A0A2J8UBJ1_A0A2J8UBJ1_PONAB_9601 are exactly identical! WARNING: Sequences tr_G3REU7_G3REU7_GORGO_9595 and tr_A0A2I3TMF3_A0A2I3TMF3_PANTR_9598 are exactly identical! WARNING: Sequences tr_G3REU7_G3REU7_GORGO_9595 and tr_A0A0D9RW17_A0A0D9RW17_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G3REU7_G3REU7_GORGO_9595 and tr_A0A2R8ZGD0_A0A2R8ZGD0_PANPA_9597 are exactly identical! WARNING: Sequences tr_Q2LYJ7_Q2LYJ7_DROPS_46245 and tr_B4HBV1_B4HBV1_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q2LZ14_Q2LZ14_DROPS_46245 and tr_B4GZR9_B4GZR9_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q2M0P8_Q2M0P8_DROPS_46245 and tr_B4GRB6_B4GRB6_DROPE_7234 are exactly identical! WARNING: Sequences tr_Q2M1B3_Q2M1B3_DROPS_46245 and tr_B4GUC9_B4GUC9_DROPE_7234 are exactly identical! WARNING: Sequences tr_E2RI01_E2RI01_CANLF_9615 and tr_M3WP76_M3WP76_FELCA_9685 are exactly identical! WARNING: Sequences tr_A0A2I3RID3_A0A2I3RID3_PANTR_9598 and tr_A0A2J8IQ82_A0A2J8IQ82_PANTR_9598 are exactly identical! WARNING: Sequences tr_A0A2I3RID3_A0A2I3RID3_PANTR_9598 and tr_A0A2R9A9F8_A0A2R9A9F8_PANPA_9597 are exactly identical! WARNING: Sequences tr_A0A2J8L3H9_A0A2J8L3H9_PANTR_9598 and tr_A0A2R8ZBV3_A0A2R8ZBV3_PANPA_9597 are exactly identical! WARNING: Sequences tr_M4ANH2_M4ANH2_XIPMA_8083 and tr_A0A087XZA4_A0A087XZA4_POEFO_48698 are exactly identical! WARNING: Sequences tr_A0A158NS32_A0A158NS32_ATTCE_12957 and tr_A0A195BCE8_A0A195BCE8_9HYME_520822 are exactly identical! WARNING: Sequences tr_A0A158P296_A0A158P296_ATTCE_12957 and tr_A0A151I0Y9_A0A151I0Y9_9HYME_520822 are exactly identical! WARNING: Sequences tr_H0X3I1_H0X3I1_OTOGA_30611 and tr_A0A1U7TNY6_A0A1U7TNY6_TARSY_1868482 are exactly identical! WARNING: Sequences tr_F6RYL9_F6RYL9_MACMU_9544 and tr_G7NZF1_G7NZF1_MACFA_9541 are exactly identical! WARNING: Sequences tr_F6RYL9_F6RYL9_MACMU_9544 and tr_A0A096N7Z7_A0A096N7Z7_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F6RYL9_F6RYL9_MACMU_9544 and tr_A0A0D9RJU6_A0A0D9RJU6_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F6RYL9_F6RYL9_MACMU_9544 and tr_A0A2K5MDX3_A0A2K5MDX3_CERAT_9531 are exactly identical! WARNING: Sequences tr_F6RYL9_F6RYL9_MACMU_9544 and tr_A0A2K6E4B5_A0A2K6E4B5_MACNE_9545 are exactly identical! WARNING: Sequences tr_F6XEW1_F6XEW1_MACMU_9544 and tr_A0A2K6AQ35_A0A2K6AQ35_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F495_F7F495_MACMU_9544 and tr_G7PVY0_G7PVY0_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7F495_F7F495_MACMU_9544 and tr_A0A096MWQ0_A0A096MWQ0_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7F495_F7F495_MACMU_9544 and tr_A0A0D9RZE2_A0A0D9RZE2_CHLSB_60711 are exactly identical! WARNING: Sequences tr_F7F495_F7F495_MACMU_9544 and tr_A0A2K5L6U5_A0A2K5L6U5_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7F495_F7F495_MACMU_9544 and tr_A0A2K6E5Y3_A0A2K6E5Y3_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7F495_F7F495_MACMU_9544 and tr_A0A2K6A6K4_A0A2K6A6K4_MANLE_9568 are exactly identical! WARNING: Sequences tr_F7FKL5_F7FKL5_MACMU_9544 and tr_G7Q2Z2_G7Q2Z2_MACFA_9541 are exactly identical! WARNING: Sequences tr_F7FKL5_F7FKL5_MACMU_9544 and tr_A0A096N745_A0A096N745_PAPAN_9555 are exactly identical! WARNING: Sequences tr_F7FKL5_F7FKL5_MACMU_9544 and tr_A0A2K5N638_A0A2K5N638_CERAT_9531 are exactly identical! WARNING: Sequences tr_F7FKL5_F7FKL5_MACMU_9544 and tr_A0A2K6BS67_A0A2K6BS67_MACNE_9545 are exactly identical! WARNING: Sequences tr_F7FKL5_F7FKL5_MACMU_9544 and tr_A0A2K5YB62_A0A2K5YB62_MANLE_9568 are exactly identical! WARNING: Sequences tr_G5C136_G5C136_HETGA_10181 and tr_A0A091DQD6_A0A091DQD6_FUKDA_885580 are exactly identical! WARNING: Sequences tr_B8BN38_B8BN38_ORYSI_39946 and tr_I1R800_I1R800_ORYGL_4538 are exactly identical! WARNING: Sequences tr_B8BN38_B8BN38_ORYSI_39946 and tr_Q2QLZ1_Q2QLZ1_ORYSJ_39947 are exactly identical! WARNING: Sequences tr_H0ZK14_H0ZK14_TAEGU_59729 and tr_A0A218UIN5_A0A218UIN5_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZL09_H0ZL09_TAEGU_59729 and tr_A0A218V4K6_A0A218V4K6_9PASE_299123 are exactly identical! WARNING: Sequences tr_H0ZN67_H0ZN67_TAEGU_59729 and tr_A0A218V650_A0A218V650_9PASE_299123 are exactly identical! WARNING: Sequences tr_A0A0E0RK84_A0A0E0RK84_ORYRU_4529 and tr_A0A0E0BVF5_A0A0E0BVF5_9ORYZ_40148 are exactly identical! WARNING: Sequences tr_A8XW18_A8XW18_CAEBR_6238 and tr_A0A2G5SCI2_A0A2G5SCI2_9PELO_1611254 are exactly identical! WARNING: Sequences tr_G8F265_G8F265_MACFA_9541 and tr_A0A0D9RK44_A0A0D9RK44_CHLSB_60711 are exactly identical! WARNING: Sequences tr_G8F265_G8F265_MACFA_9541 and tr_A0A2K6BNK9_A0A2K6BNK9_MACNE_9545 are exactly identical! WARNING: Sequences tr_M4EFZ4_M4EFZ4_BRARP_51351 and tr_A0A078IV90_A0A078IV90_BRANA_3708 are exactly identical! WARNING: Sequences tr_A0A3B6KCN8_A0A3B6KCN8_WHEAT_4565 and tr_A0A3B6MIU6_A0A3B6MIU6_WHEAT_4565 are exactly identical! WARNING: Sequences tr_A0A096NA16_A0A096NA16_PAPAN_9555 and tr_A0A2K5KUJ9_A0A2K5KUJ9_CERAT_9531 are exactly identical! WARNING: Sequences tr_A0A096NA16_A0A096NA16_PAPAN_9555 and tr_A0A2K5ZFJ5_A0A2K5ZFJ5_MANLE_9568 are exactly identical! WARNING: Sequences tr_A0A151MSI4_A0A151MSI4_ALLMI_8496 and tr_A0A1U7RQL8_A0A1U7RQL8_ALLSI_38654 are exactly identical! WARNING: Sequences tr_A0A087QM88_A0A087QM88_APTFO_9233 and tr_A0A0A0AER8_A0A0A0AER8_CHAVO_50402 are exactly identical! WARNING: Sequences tr_A0A2I0LKF7_A0A2I0LKF7_COLLI_8932 and tr_A0A1V4J2A8_A0A1V4J2A8_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A2I0M4S7_A0A2I0M4S7_COLLI_8932 and tr_A0A1V4L024_A0A1V4L024_PATFA_372326 are exactly identical! WARNING: Sequences tr_A0A1S3HC24_A0A1S3HC24_LINUN_7574 and tr_A0A1S3JF49_A0A1S3JF49_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3HQV2_A0A1S3HQV2_LINUN_7574 and tr_A0A1S3JQF6_A0A1S3JQF6_LINUN_7574 are exactly identical! WARNING: Sequences tr_A0A1S3PI45_A0A1S3PI45_SALSA_8030 and tr_A0A060WF39_A0A060WF39_ONCMY_8022 are exactly identical! WARNING: Sequences tr_A0A226MG83_A0A226MG83_CALSU_9009 and tr_A0A226PHX6_A0A226PHX6_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MIC2_A0A226MIC2_CALSU_9009 and tr_A0A226PN37_A0A226PN37_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A226MP64_A0A226MP64_CALSU_9009 and tr_A0A226PR83_A0A226PR83_COLVI_9014 are exactly identical! WARNING: Sequences tr_A0A2U4A8B8_A0A2U4A8B8_TURTR_9739 and tr_A0A2Y9MY25_A0A2Y9MY25_DELLE_9749 are exactly identical! WARNING: Sequences tr_A0A2U4A8B8_A0A2U4A8B8_TURTR_9739 and tr_A0A2Y9TEE3_A0A2Y9TEE3_PHYCD_9755 are exactly identical! WARNING: Sequences tr_A0A2U3WDR2_A0A2U3WDR2_ODORO_9708 and tr_A0A384C7P6_A0A384C7P6_URSMA_29073 are exactly identical! WARNING: Sequences tr_A0A2U3WKZ7_A0A2U3WKZ7_ODORO_9708 and tr_A0A2Y9J9M1_A0A2Y9J9M1_ENHLU_391180 are exactly identical! WARNING: Duplicate sequences found: 70 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/P52569/3_mltree/P52569.raxml.reduced.phy Alignment comprises 1 partitions and 358 patterns Partition 0: noname Model: LG4X+R4 Alignment sites / patterns: 358 / 358 Gaps: 1.01 % Invariant sites: 0.28 % NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52569/3_mltree/P52569.raxml.rba Parallelization scheme autoconfig: 5 worker(s) x 1 thread(s) Parallel reduction/worker buffer size: 1 KB / 0 KB [00:00:00] Generating 20 random starting tree(s) with 1001 taxa [00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 358 / 28640 [00:00:00] Data distribution: max. searches per worker: 4 Starting ML tree search with 20 distinct starting trees [00:00:00 -485503.473969] Initial branch length optimization [00:00:08 -403704.139404] Model parameter optimization (eps = 10.000000) [00:01:19 -401423.553812] AUTODETECT spr round 1 (radius: 5) [00:05:46 -280622.858871] AUTODETECT spr round 2 (radius: 10) [00:10:46 -197312.113253] AUTODETECT spr round 3 (radius: 15) [00:16:54 -163185.157891] AUTODETECT spr round 4 (radius: 20) [00:25:21 -152560.516434] AUTODETECT spr round 5 (radius: 25) [00:32:25 -145809.107704] SPR radius for FAST iterations: 25 (autodetect) [00:32:25 -145809.107704] Model parameter optimization (eps = 3.000000) [00:33:09 -145529.025538] FAST spr round 1 (radius: 25) [00:37:47 -123036.938175] FAST spr round 2 (radius: 25) [00:41:02 -122146.321380] FAST spr round 3 (radius: 25) [00:44:03 -122061.139764] FAST spr round 4 (radius: 25) [00:46:44 -122053.767381] FAST spr round 5 (radius: 25) [00:49:18 -122046.567784] FAST spr round 6 (radius: 25) [00:51:47 -122046.567666] Model parameter optimization (eps = 1.000000) [00:52:08 -122044.589711] SLOW spr round 1 (radius: 5) [00:55:53 -121999.959247] SLOW spr round 2 (radius: 5) [00:59:27 -121990.834662] SLOW spr round 3 (radius: 5) [01:02:51 -121990.834478] SLOW spr round 4 (radius: 10) [01:06:19 -121989.431628] SLOW spr round 5 (radius: 5) [01:10:46 -121989.431592] SLOW spr round 6 (radius: 10) [01:14:38 -121989.431591] SLOW spr round 7 (radius: 15) [01:19:35 -121989.431591] SLOW spr round 8 (radius: 20) [01:29:53 -121989.431591] SLOW spr round 9 (radius: 25) [01:40:06 -121989.431591] Model parameter optimization (eps = 0.100000) [01:40:20] [worker #0] ML tree search #1, logLikelihood: -121989.324885 [01:40:20 -485683.778689] Initial branch length optimization [01:40:27 -403812.692616] Model parameter optimization (eps = 10.000000) [01:41:42 -401504.891856] AUTODETECT spr round 1 (radius: 5) [01:46:10 -272922.992411] AUTODETECT spr round 2 (radius: 10) [01:50:10] [worker #4] ML tree search #5, logLikelihood: -121975.924727 [01:51:09 -200067.966366] AUTODETECT spr round 3 (radius: 15) [01:56:47 -178572.876943] AUTODETECT spr round 4 (radius: 20) [02:02:36 -173176.528211] AUTODETECT spr round 5 (radius: 25) [02:05:27] [worker #3] ML tree search #4, logLikelihood: -122027.878321 [02:09:28] [worker #1] ML tree search #2, logLikelihood: -121987.951135 [02:09:59] [worker #2] ML tree search #3, logLikelihood: -121992.416594 [02:10:45 -154636.755119] SPR radius for FAST iterations: 25 (autodetect) [02:10:45 -154636.755119] Model parameter optimization (eps = 3.000000) [02:11:24 -154361.083477] FAST spr round 1 (radius: 25) [02:16:03 -123171.689864] FAST spr round 2 (radius: 25) [02:19:22 -122117.687567] FAST spr round 3 (radius: 25) [02:22:19 -122044.249073] FAST spr round 4 (radius: 25) [02:24:56 -122038.431240] FAST spr round 5 (radius: 25) [02:27:25 -122038.431237] Model parameter optimization (eps = 1.000000) [02:27:50 -122033.239846] SLOW spr round 1 (radius: 5) [02:31:44 -122003.346617] SLOW spr round 2 (radius: 5) [02:35:24 -121999.779061] SLOW spr round 3 (radius: 5) [02:38:54 -121999.648396] SLOW spr round 4 (radius: 5) [02:42:21 -121999.648365] SLOW spr round 5 (radius: 10) [02:45:54 -121995.589679] SLOW spr round 6 (radius: 5) [02:50:29 -121995.378266] SLOW spr round 7 (radius: 5) [02:54:25 -121995.142808] SLOW spr round 8 (radius: 5) [02:58:01 -121995.142738] SLOW spr round 9 (radius: 10) [03:01:30 -121995.142738] SLOW spr round 10 (radius: 15) [03:06:47 -121995.142738] SLOW spr round 11 (radius: 20) [03:14:23 -121991.557241] SLOW spr round 12 (radius: 5) [03:19:13 -121991.557234] SLOW spr round 13 (radius: 10) [03:23:22 -121991.557234] SLOW spr round 14 (radius: 15) [03:28:15 -121991.557234] SLOW spr round 15 (radius: 20) [03:36:06 -121991.557234] SLOW spr round 16 (radius: 25) [03:46:37 -121991.557234] Model parameter optimization (eps = 0.100000) [03:46:54] [worker #0] ML tree search #6, logLikelihood: -121991.425283 [03:46:55 -481483.593662] Initial branch length optimization [03:47:04 -401550.468349] Model parameter optimization (eps = 10.000000) [03:48:23 -399285.567515] AUTODETECT spr round 1 (radius: 5) [03:54:08 -274882.178419] AUTODETECT spr round 2 (radius: 10) [03:55:19] [worker #3] ML tree search #9, logLikelihood: -121991.245985 [03:58:58 -202284.717643] AUTODETECT spr round 3 (radius: 15) [04:01:17] [worker #1] ML tree search #7, logLikelihood: -121997.159491 [04:05:15 -172919.635269] AUTODETECT spr round 4 (radius: 20) [04:09:22] [worker #2] ML tree search #8, logLikelihood: -121988.499309 [04:11:50 -156398.208056] AUTODETECT spr round 5 (radius: 25) [04:13:04] [worker #4] ML tree search #10, logLikelihood: -122004.952650 [04:19:39 -150123.402248] SPR radius for FAST iterations: 25 (autodetect) [04:19:39 -150123.402248] Model parameter optimization (eps = 3.000000) [04:20:23 -149837.484031] FAST spr round 1 (radius: 25) [04:25:19 -122885.346759] FAST spr round 2 (radius: 25) [04:28:33 -122100.070336] FAST spr round 3 (radius: 25) [04:31:29 -122051.971670] FAST spr round 4 (radius: 25) [04:34:01 -122048.153184] FAST spr round 5 (radius: 25) [04:36:28 -122042.738024] FAST spr round 6 (radius: 25) [04:38:50 -122042.738008] Model parameter optimization (eps = 1.000000) [04:39:07 -122041.183951] SLOW spr round 1 (radius: 5) [04:42:47 -122005.843182] SLOW spr round 2 (radius: 5) [04:46:23 -122002.424572] SLOW spr round 3 (radius: 5) [04:49:49 -122000.942015] SLOW spr round 4 (radius: 5) [04:53:12 -122000.941984] SLOW spr round 5 (radius: 10) [04:56:40 -121993.080091] SLOW spr round 6 (radius: 5) [05:01:10 -121990.257970] SLOW spr round 7 (radius: 5) [05:05:00 -121990.257965] SLOW spr round 8 (radius: 10) [05:08:30 -121990.257965] SLOW spr round 9 (radius: 15) [05:13:43 -121990.257965] SLOW spr round 10 (radius: 20) [05:22:05 -121986.649952] SLOW spr round 11 (radius: 5) [05:26:53 -121986.649944] SLOW spr round 12 (radius: 10) [05:30:55 -121986.649944] SLOW spr round 13 (radius: 15) [05:35:55 -121986.649944] SLOW spr round 14 (radius: 20) [05:44:27 -121986.649944] SLOW spr round 15 (radius: 25) [05:55:28 -121986.649944] Model parameter optimization (eps = 0.100000) [05:55:36] [worker #0] ML tree search #11, logLikelihood: -121986.615416 [05:55:36 -485832.700418] Initial branch length optimization [05:55:44 -403145.965401] Model parameter optimization (eps = 10.000000) [05:56:47 -400850.333868] AUTODETECT spr round 1 (radius: 5) [06:01:11 -269826.591115] AUTODETECT spr round 2 (radius: 10) [06:06:05 -210411.456431] AUTODETECT spr round 3 (radius: 15) [06:12:28 -169296.524822] AUTODETECT spr round 4 (radius: 20) [06:13:21] [worker #1] ML tree search #12, logLikelihood: -121997.908377 [06:13:51] [worker #4] ML tree search #15, logLikelihood: -121998.502406 [06:17:00] [worker #2] ML tree search #13, logLikelihood: -121961.019196 [06:18:32 -149069.524987] AUTODETECT spr round 5 (radius: 25) [06:24:31 -147356.467614] SPR radius for FAST iterations: 25 (autodetect) [06:24:31 -147356.467614] Model parameter optimization (eps = 3.000000) [06:25:14 -147053.740869] FAST spr round 1 (radius: 25) [06:30:03 -122917.596636] FAST spr round 2 (radius: 25) [06:33:27 -122124.751299] FAST spr round 3 (radius: 25) [06:34:39] [worker #3] ML tree search #14, logLikelihood: -122003.319823 [06:36:29 -122036.799142] FAST spr round 4 (radius: 25) [06:39:02 -122033.259855] FAST spr round 5 (radius: 25) [06:41:26 -122033.259838] Model parameter optimization (eps = 1.000000) [06:41:41 -122031.683578] SLOW spr round 1 (radius: 5) [06:45:27 -122013.869088] SLOW spr round 2 (radius: 5) [06:49:03 -122012.151967] SLOW spr round 3 (radius: 5) [06:52:36 -122009.967710] SLOW spr round 4 (radius: 5) [06:56:00 -122006.786521] SLOW spr round 5 (radius: 5) [06:59:22 -122006.786425] SLOW spr round 6 (radius: 10) [07:02:45 -122005.472374] SLOW spr round 7 (radius: 5) [07:07:13 -122004.618413] SLOW spr round 8 (radius: 5) [07:11:03 -122004.616079] SLOW spr round 9 (radius: 10) [07:14:37 -122004.374143] SLOW spr round 10 (radius: 5) [07:19:04 -122003.877610] SLOW spr round 11 (radius: 5) [07:22:51 -122003.877604] SLOW spr round 12 (radius: 10) [07:26:22 -122003.877604] SLOW spr round 13 (radius: 15) [07:31:50 -122000.271859] SLOW spr round 14 (radius: 5) [07:36:31 -122000.271852] SLOW spr round 15 (radius: 10) [07:40:32 -122000.271852] SLOW spr round 16 (radius: 15) [07:45:44 -122000.271852] SLOW spr round 17 (radius: 20) [07:54:22 -122000.271852] SLOW spr round 18 (radius: 25) [07:59:59] [worker #1] ML tree search #17, logLikelihood: -121999.643247 [08:05:16 -122000.271852] Model parameter optimization (eps = 0.100000) [08:05:30] [worker #0] ML tree search #16, logLikelihood: -122000.050407 [08:17:23] [worker #2] ML tree search #18, logLikelihood: -122005.748815 [08:18:23] [worker #3] ML tree search #19, logLikelihood: -122002.129514 [08:20:02] [worker #4] ML tree search #20, logLikelihood: -121995.861369 Optimized model parameters: Partition 0: noname Rate heterogeneity: FREE (4 cats, mean), weights&rates: (0.350192,0.596548) (0.383169,0.692630) (0.216556,1.724388) (0.050084,3.040381) 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: -121961.019196 AIC score: 247932.038392 / AICc score: 8291992.038392 / BIC score: 255712.507030 Free parameters (model + branch lengths): 2005 WARNING: Number of free parameters (K=2005) is larger than alignment size (n=358). 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/P52569/3_mltree/P52569.raxml.bestTree All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52569/3_mltree/P52569.raxml.mlTrees Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52569/3_mltree/P52569.raxml.bestModel Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/P52569/3_mltree/P52569.raxml.log Analysis started: 02-Jul-2021 04:48:09 / finished: 02-Jul-2021 13:08:12 Elapsed time: 30002.910 seconds Consumed energy: 2776.006 Wh (= 14 km in an electric car, or 69 km with an e-scooter!)