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diff test-data/files/clsReps.aln.log @ 0:9a3a2e04f47a draft default tip
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| author | dave |
|---|---|
| date | Mon, 10 Jun 2019 16:04:10 -0400 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/files/clsReps.aln.log Mon Jun 10 16:04:10 2019 -0400 @@ -0,0 +1,354 @@ +IQ-TREE multicore version 1.6.10 for Linux 64-bit built Mar 21 2019 +Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, +Heiko Schmidt, Dominik Schrempf, Michael Woodhams. + +Host: gaius (AVX2, FMA3, 15 GB RAM) +Command: iqtree -s clsReps.aln -m GTR+R4 -nt 1 +Seed: 50990 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Tue May 28 13:09:57 2019 +Kernel: AVX+FMA - 1 threads (8 CPU cores detected) + +HINT: Use -nt option to specify number of threads because your CPU has 8 cores! +HINT: -nt AUTO will automatically determine the best number of threads to use. + +Reading alignment file clsReps.aln ... Fasta format detected +Alignment most likely contains DNA/RNA sequences +Alignment has 84 sequences with 305 columns, 301 distinct patterns +238 parsimony-informative, 52 singleton sites, 15 constant sites +WARNING: Some sequence names are changed as follows: +K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1_1_0 -> K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 +K03455|HIVHXB2CG_5977_6467_2_0_0_2_0_0_1/1_2_1 -> K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 +K03455|HIVHXB2CG_6040_6545_1_0_0_0_0_0_2/1_3_2 -> K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 +K03455|HIVHXB2CG_3580_4035_1_0_0_0_0_0_3/1_1_3 -> K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 +K03455|HIVHXB2CG_5251_5720_0_0_0_1_0_0_4/1_2_4 -> K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 +K03455|HIVHXB2CG_5574_6092_2_0_0_1_0_0_5/1_1_5 -> K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 +K03455|HIVHXB2CG_7273_7731_1_0_0_5_0_0_6/1_1_6 -> K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 +K03455|HIVHXB2CG_5438_5909_1_0_0_4_0_0_7/1_1_7 -> K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 +K03455|HIVHXB2CG_4165_4569_2_0_0_3_0_0_8/1_2_8 -> K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 +K03455|HIVHXB2CG_2832_3397_3_0_0_2_0_0_9/1_1_9 -> K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 +K03455|HIVHXB2CG_1312_1798_2_0_0_1_0_0_a/1_2_10 -> K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 +K03455|HIVHXB2CG_6501_7035_0_0_0_0_0_0_b/1_2_11 -> K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 +K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1_1_12 -> K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 +K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1_1_13 -> K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 +K03455|HIVHXB2CG_368_934_2_0_0_3_0_0_f/1_1_14 -> K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 +K03455|HIVHXB2CG_8446_8894_4_0_0_3_0_0_10/1_1_15 -> K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 +K03455|HIVHXB2CG_6869_7379_1_0_0_3_0_1_11/1_2_16 -> K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 +K03455|HIVHXB2CG_5034_5548_1_0_0_4_0_0_13/1_1_17 -> K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 +K03455|HIVHXB2CG_418_930_3_0_0_1_0_0_14/1_1_18 -> K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 +K03455|HIVHXB2CG_8325_8818_2_0_0_2_0_0_15/1_1_19 -> K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 +K03455|HIVHXB2CG_673_1207_2_0_0_2_0_0_16/1_2_20 -> K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 +K03455|HIVHXB2CG_7932_8405_1_0_0_1_0_0_17/1_1_21 -> K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 +K03455|HIVHXB2CG_2894_3537_2_0_0_0_0_0_18/1_1_22 -> K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 +K03455|HIVHXB2CG_5989_6545_2_0_0_1_0_0_19/1_1_23 -> K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 +K03455|HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b/1_1_24 -> K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 +K03455|HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d/1_1_25 -> K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 +K03455|HIVHXB2CG_7_537_2_0_0_1_0_0_1e/1_1_26 -> K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 +K03455|HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f/1_1_27 -> K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 +K03455|HIVHXB2CG_5516_5958_3_0_0_2_0_0_20/1_1_28 -> K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 +K03455|HIVHXB2CG_8434_8946_0_0_0_1_0_0_21/1_2_29 -> K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 +K03455|HIVHXB2CG_2808_3255_0_0_0_1_0_0_22/1_1_30 -> K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 +K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1_1_31 -> K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 +K03455|HIVHXB2CG_3875_4298_2_0_0_1_0_0_24/1_1_32 -> K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 +K03455|HIVHXB2CG_8231_8877_0_0_0_3_0_0_25/1_1_33 -> K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 +K03455|HIVHXB2CG_7126_7621_1_1_1_3_1_0_26/1_1_34 -> K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 +K03455|HIVHXB2CG_3672_4151_0_0_0_1_0_0_27/1_1_35 -> K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 +K03455|HIVHXB2CG_4642_5125_0_0_0_3_0_0_28/1_1_36 -> K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 +K03455|HIVHXB2CG_8349_8802_1_0_0_0_0_0_29/1_1_37 -> K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 +K03455|HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a/1_2_38 -> K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 +K03455|HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b/1_2_39 -> K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 +K03455|HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d/1_2_40 -> K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 +K03455|HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e/1_1_41 -> K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 +K03455|HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f/1_1_42 -> K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 +K03455|HIVHXB2CG_3823_4361_1_0_0_0_0_0_30/1_1_43 -> K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 +K03455|HIVHXB2CG_4420_4903_1_0_0_1_0_0_31/1_1_44 -> K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 +K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1_1_45 -> K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 +K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1_1_46 -> K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 +K03455|HIVHXB2CG_217_724_2_1_0_2_0_0_36/1_1_47 -> K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 +K03455|HIVHXB2CG_8069_8641_1_0_0_0_0_0_38/1_1_48 -> K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 +K03455|HIVHXB2CG_1786_2269_1_0_0_1_0_0_39/1_1_49 -> K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 +K03455|HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a/1_1_50 -> K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 +K03455|HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b/1_2_51 -> K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 +K03455|HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c/1_1_52 -> K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 +K03455|HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d/1_1_53 -> K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 +K03455|HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e/1_1_54 -> K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 +K03455|HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f/1_1_55 -> K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 +K03455|HIVHXB2CG_8342_8779_1_0_0_2_0_0_40/1_1_56 -> K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 +K03455|HIVHXB2CG_6619_7094_0_0_0_2_0_0_41/1_1_57 -> K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 +K03455|HIVHXB2CG_5150_5584_1_0_0_2_0_0_42/1_1_58 -> K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 +K03455|HIVHXB2CG_5329_5821_2_0_0_2_0_0_43/1_1_59 -> K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 +K03455|HIVHXB2CG_4457_4958_4_0_0_0_0_0_44/1_1_60 -> K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 +K03455|HIVHXB2CG_906_1404_1_0_0_3_0_0_45/1_1_61 -> K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 +K03455|HIVHXB2CG_2685_3250_0_0_0_0_0_0_46/1_1_62 -> K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 +K03455|HIVHXB2CG_6045_6577_2_0_0_1_0_0_47/1_1_63 -> K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 +K03455|HIVHXB2CG_1707_2205_1_0_0_3_0_0_48/1_2_64 -> K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 +K03455|HIVHXB2CG_4939_5430_1_0_0_0_0_0_49/1_1_65 -> K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 +K03455|HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a/1_1_66 -> K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 +K03455|HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e/1_1_67 -> K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 +K03455|HIVHXB2CG_2700_3243_0_0_0_3_1_0_51/1_1_68 -> K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 +K03455|HIVHXB2CG_3027_3517_0_0_0_6_0_0_53/1_2_69 -> K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 +K03455|HIVHXB2CG_313_880_0_0_0_2_0_0_54/1_1_70 -> K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 +K03455|HIVHXB2CG_1938_2460_2_0_0_0_0_0_55/1_1_71 -> K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 +K03455|HIVHXB2CG_1235_1682_3_0_0_0_0_0_56/1_1_72 -> K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 +K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1_1_73 -> K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 +K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1_1_74 -> K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 +K03455|HIVHXB2CG_3596_4110_1_0_0_2_0_0_59/1_1_75 -> K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 +K03455|HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a/1_1_76 -> K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 +K03455|HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b/1_1_77 -> K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 +K03455|HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d/1_1_78 -> K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 +K03455|HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e/1_1_79 -> K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 +K03455|HIVHXB2CG_121_652_1_0_0_0_0_0_5f/1_1_80 -> K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 +K03455|HIVHXB2CG_5585_6024_1_0_0_0_0_0_60/1_1_81 -> K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 +K03455|HIVHXB2CG_7976_8475_3_0_0_1_0_0_61/1_1_82 -> K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 +K03455|HIVHXB2CG_6322_6838_1_0_0_0_1_0_63/1_1_83 -> K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 + + Gap/Ambiguity Composition p-value + 1 K03455_HIVHXB2CG_1286_1769_0_0_0_4_0_0_0_1_1_0 77.05% passed 19.90% + 2 K03455_HIVHXB2CG_5977_6467_2_0_0_2_0_0_1_1_2_1 77.05% failed 4.53% + 3 K03455_HIVHXB2CG_6040_6545_1_0_0_0_0_0_2_1_3_2 77.05% failed 1.21% + 4 K03455_HIVHXB2CG_3580_4035_1_0_0_0_0_0_3_1_1_3 77.05% passed 25.36% + 5 K03455_HIVHXB2CG_5251_5720_0_0_0_1_0_0_4_1_2_4 77.05% passed 55.86% + 6 K03455_HIVHXB2CG_5574_6092_2_0_0_1_0_0_5_1_1_5 77.05% passed 35.72% + 7 K03455_HIVHXB2CG_7273_7731_1_0_0_5_0_0_6_1_1_6 77.05% failed 0.71% + 8 K03455_HIVHXB2CG_5438_5909_1_0_0_4_0_0_7_1_1_7 77.05% passed 85.58% + 9 K03455_HIVHXB2CG_4165_4569_2_0_0_3_0_0_8_1_2_8 77.05% passed 7.28% + 10 K03455_HIVHXB2CG_2832_3397_3_0_0_2_0_0_9_1_1_9 77.05% passed 23.71% + 11 K03455_HIVHXB2CG_1312_1798_2_0_0_1_0_0_a_1_2_10 77.05% failed 4.76% + 12 K03455_HIVHXB2CG_6501_7035_0_0_0_0_0_0_b_1_2_11 77.05% passed 36.06% + 13 K03455_HIVHXB2CG_2252_2786_0_0_0_0_0_0_c_1_1_12 77.05% failed 0.72% + 14 K03455_HIVHXB2CG_7972_8486_1_0_0_0_0_0_e_1_1_13 77.05% failed 0.74% + 15 K03455_HIVHXB2CG_368_934_2_0_0_3_0_0_f_1_1_14 77.05% failed 0.54% + 16 K03455_HIVHXB2CG_8446_8894_4_0_0_3_0_0_10_1_1_15 77.05% failed 1.66% + 17 K03455_HIVHXB2CG_6869_7379_1_0_0_3_0_1_11_1_2_16 77.05% passed 88.47% + 18 K03455_HIVHXB2CG_5034_5548_1_0_0_4_0_0_13_1_1_17 77.05% failed 0.11% + 19 K03455_HIVHXB2CG_418_930_3_0_0_1_0_0_14_1_1_18 77.05% passed 36.61% + 20 K03455_HIVHXB2CG_8325_8818_2_0_0_2_0_0_15_1_1_19 77.05% passed 81.18% + 21 K03455_HIVHXB2CG_673_1207_2_0_0_2_0_0_16_1_2_20 77.05% failed 0.00% + 22 K03455_HIVHXB2CG_7932_8405_1_0_0_1_0_0_17_1_1_21 77.05% passed 14.75% + 23 K03455_HIVHXB2CG_2894_3537_2_0_0_0_0_0_18_1_1_22 77.05% passed 65.23% + 24 K03455_HIVHXB2CG_5989_6545_2_0_0_1_0_0_19_1_1_23 77.05% passed 15.67% + 25 K03455_HIVHXB2CG_4803_5329_1_0_0_2_0_0_1b_1_1_24 77.05% failed 0.02% + 26 K03455_HIVHXB2CG_1672_2143_3_0_0_2_0_0_1d_1_1_25 77.05% passed 56.52% + 27 K03455_HIVHXB2CG_7_537_2_0_0_1_0_0_1e_1_1_26 77.05% passed 26.05% + 28 K03455_HIVHXB2CG_3447_3973_0_0_0_1_0_0_1f_1_1_27 77.05% failed 1.57% + 29 K03455_HIVHXB2CG_5516_5958_3_0_0_2_0_0_20_1_1_28 77.05% passed 10.98% + 30 K03455_HIVHXB2CG_8434_8946_0_0_0_1_0_0_21_1_2_29 77.05% passed 27.02% + 31 K03455_HIVHXB2CG_2808_3255_0_0_0_1_0_0_22_1_1_30 77.05% passed 13.08% + 32 K03455_HIVHXB2CG_5108_5621_3_0_0_2_0_0_23_1_1_31 77.05% failed 0.03% + 33 K03455_HIVHXB2CG_3875_4298_2_0_0_1_0_0_24_1_1_32 77.05% passed 12.47% + 34 K03455_HIVHXB2CG_8231_8877_0_0_0_3_0_0_25_1_1_33 77.05% passed 7.89% + 35 K03455_HIVHXB2CG_7126_7621_1_1_1_3_1_0_26_1_1_34 77.05% passed 25.36% + 36 K03455_HIVHXB2CG_3672_4151_0_0_0_1_0_0_27_1_1_35 77.05% failed 0.48% + 37 K03455_HIVHXB2CG_4642_5125_0_0_0_3_0_0_28_1_1_36 77.05% passed 7.92% + 38 K03455_HIVHXB2CG_8349_8802_1_0_0_0_0_0_29_1_1_37 77.05% passed 41.51% + 39 K03455_HIVHXB2CG_1667_2209_4_0_0_2_0_0_2a_1_2_38 77.05% failed 0.24% + 40 K03455_HIVHXB2CG_4476_4938_5_0_0_3_0_0_2b_1_2_39 77.05% passed 41.06% + 41 K03455_HIVHXB2CG_6810_7300_0_0_0_0_0_0_2d_1_2_40 77.05% passed 62.06% + 42 K03455_HIVHXB2CG_4957_5462_2_0_0_1_0_0_2e_1_1_41 77.05% failed 0.00% + 43 K03455_HIVHXB2CG_2020_2541_3_0_0_6_0_0_2f_1_1_42 77.05% passed 94.90% + 44 K03455_HIVHXB2CG_3823_4361_1_0_0_0_0_0_30_1_1_43 77.05% passed 21.68% + 45 K03455_HIVHXB2CG_4420_4903_1_0_0_1_0_0_31_1_1_44 77.05% passed 22.88% + 46 K03455_HIVHXB2CG_1739_2301_2_0_0_2_0_0_33_1_1_45 77.05% passed 32.28% + 47 K03455_HIVHXB2CG_756_1235_2_0_0_1_0_0_34_1_1_46 77.05% passed 14.89% + 48 K03455_HIVHXB2CG_217_724_2_1_0_2_0_0_36_1_1_47 77.05% failed 3.69% + 49 K03455_HIVHXB2CG_8069_8641_1_0_0_0_0_0_38_1_1_48 77.05% passed 19.81% + 50 K03455_HIVHXB2CG_1786_2269_1_0_0_1_0_0_39_1_1_49 77.05% passed 8.95% + 51 K03455_HIVHXB2CG_6065_6509_1_0_0_1_0_0_3a_1_1_50 77.05% passed 15.20% + 52 K03455_HIVHXB2CG_9061_9383_1_0_0_4_0_0_3b_1_2_51 77.05% passed 16.44% + 53 K03455_HIVHXB2CG_9142_9638_2_0_0_2_0_0_3c_1_1_52 77.05% passed 72.71% + 54 K03455_HIVHXB2CG_4276_4897_1_0_0_1_0_0_3d_1_1_53 77.05% passed 46.60% + 55 K03455_HIVHXB2CG_3569_4048_0_0_0_4_0_0_3e_1_1_54 77.05% failed 2.49% + 56 K03455_HIVHXB2CG_5990_6505_1_0_0_0_0_0_3f_1_1_55 77.05% passed 25.92% + 57 K03455_HIVHXB2CG_8342_8779_1_0_0_2_0_0_40_1_1_56 77.05% passed 36.75% + 58 K03455_HIVHXB2CG_6619_7094_0_0_0_2_0_0_41_1_1_57 77.05% passed 12.72% + 59 K03455_HIVHXB2CG_5150_5584_1_0_0_2_0_0_42_1_1_58 77.05% passed 33.57% + 60 K03455_HIVHXB2CG_5329_5821_2_0_0_2_0_0_43_1_1_59 77.05% passed 89.40% + 61 K03455_HIVHXB2CG_4457_4958_4_0_0_0_0_0_44_1_1_60 77.05% passed 20.77% + 62 K03455_HIVHXB2CG_906_1404_1_0_0_3_0_0_45_1_1_61 77.05% passed 20.83% + 63 K03455_HIVHXB2CG_2685_3250_0_0_0_0_0_0_46_1_1_62 77.05% failed 0.48% + 64 K03455_HIVHXB2CG_6045_6577_2_0_0_1_0_0_47_1_1_63 77.05% passed 16.69% + 65 K03455_HIVHXB2CG_1707_2205_1_0_0_3_0_0_48_1_2_64 77.05% passed 24.64% + 66 K03455_HIVHXB2CG_4939_5430_1_0_0_0_0_0_49_1_1_65 77.05% failed 1.23% + 67 K03455_HIVHXB2CG_3199_3700_2_0_0_1_0_0_4a_1_1_66 77.05% failed 0.65% + 68 K03455_HIVHXB2CG_9174_9651_1_0_0_0_0_0_4e_1_1_67 77.05% passed 68.90% + 69 K03455_HIVHXB2CG_2700_3243_0_0_0_3_1_0_51_1_1_68 77.05% passed 51.19% + 70 K03455_HIVHXB2CG_3027_3517_0_0_0_6_0_0_53_1_2_69 77.05% failed 0.60% + 71 K03455_HIVHXB2CG_313_880_0_0_0_2_0_0_54_1_1_70 77.05% failed 0.10% + 72 K03455_HIVHXB2CG_1938_2460_2_0_0_0_0_0_55_1_1_71 77.05% passed 5.03% + 73 K03455_HIVHXB2CG_1235_1682_3_0_0_0_0_0_56_1_1_72 77.05% passed 33.28% + 74 K03455_HIVHXB2CG_1835_2322_3_0_0_1_0_0_57_1_1_73 77.05% passed 50.17% + 75 K03455_HIVHXB2CG_2276_2810_0_0_0_0_0_0_58_1_1_74 77.05% failed 0.26% + 76 K03455_HIVHXB2CG_3596_4110_1_0_0_2_0_0_59_1_1_75 77.05% passed 6.77% + 77 K03455_HIVHXB2CG_7233_7687_1_0_0_1_0_0_5a_1_1_76 77.05% failed 2.37% + 78 K03455_HIVHXB2CG_5794_6187_2_0_0_0_0_0_5b_1_1_77 77.05% passed 10.04% + 79 K03455_HIVHXB2CG_2928_3444_5_0_0_1_0_0_5d_1_1_78 77.05% failed 3.16% + 80 K03455_HIVHXB2CG_7609_8146_1_0_0_1_0_0_5e_1_1_79 77.05% passed 32.98% + 81 K03455_HIVHXB2CG_121_652_1_0_0_0_0_0_5f_1_1_80 77.05% passed 51.70% + 82 K03455_HIVHXB2CG_5585_6024_1_0_0_0_0_0_60_1_1_81 77.05% passed 14.88% + 83 K03455_HIVHXB2CG_7976_8475_3_0_0_1_0_0_61_1_1_82 77.05% passed 82.25% + 84 K03455_HIVHXB2CG_6322_6838_1_0_0_0_1_0_63_1_1_83 77.05% passed 68.89% +WARNING: 84 sequences contain more than 50% gaps/ambiguity +**** TOTAL 77.05% 26 sequences failed composition chi2 test (p-value<5%; df=3) + +Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.017 seconds + +NOTE: 3 MB RAM (0 GB) is required! +Estimate model parameters (epsilon = 0.100) +1. Initial log-likelihood: -7393.152 +2. Current log-likelihood: -6850.590 +3. Current log-likelihood: -6814.795 +4. Current log-likelihood: -6812.204 +5. Current log-likelihood: -6811.732 +6. Current log-likelihood: -6811.618 +Optimal log-likelihood: -6811.491 +Rate parameters: A-C: 1.16582 A-G: 3.17373 A-T: 0.69428 C-G: 1.33012 C-T: 3.22998 G-T: 1.00000 +Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287 +Site proportion and rates: (0.080,0.274) (0.303,0.606) (0.379,0.714) (0.238,2.200) +Parameters optimization took 6 rounds (0.508 sec) +Computing ML distances based on estimated model parameters... 0.032 sec +WARNING: Some pairwise ML distances are too long (saturated) +Computing BIONJ tree... +0.003 seconds +Log-likelihood of BIONJ tree: -6859.680 +-------------------------------------------------------------------- +| INITIALIZING CANDIDATE TREE SET | +-------------------------------------------------------------------- +Generating 98 parsimony trees... 1.076 second +Computing log-likelihood of 98 initial trees ... 1.196 seconds +Current best score: -6803.399 + +Do NNI search on 20 best initial trees +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 1: -6746.667 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 4: -6743.453 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 8: -6739.399 +Iteration 10 / LogL: -6755.382 / Time: 0h:0m:8s +Iteration 20 / LogL: -6783.485 / Time: 0h:0m:12s +Finish initializing candidate tree set (20) +Current best tree score: -6739.399 / CPU time: 11.455 +Number of iterations: 20 +-------------------------------------------------------------------- +| OPTIMIZING CANDIDATE TREE SET | +-------------------------------------------------------------------- +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 24: -6738.697 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 25: -6730.006 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 27: -6728.392 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 29: -6725.172 +Iteration 30 / LogL: -6728.632 / Time: 0h:0m:15s (0h:0m:53s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 31: -6723.283 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 37: -6720.321 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 39: -6717.689 +Iteration 40 / LogL: -6719.783 / Time: 0h:0m:19s (0h:0m:48s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 41: -6717.333 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 44: -6715.754 +Iteration 50 / LogL: -6716.133 / Time: 0h:0m:21s (0h:0m:42s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 56: -6714.598 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 59: -6714.257 +Iteration 60 / LogL: -6715.774 / Time: 0h:0m:25s (0h:0m:42s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 66: -6713.872 +Iteration 70 / LogL: -6714.239 / Time: 0h:0m:28s (0h:0m:39s left) +Iteration 80 / LogL: -6714.049 / Time: 0h:0m:30s (0h:0m:33s left) +Iteration 90 / LogL: -6716.076 / Time: 0h:0m:33s (0h:0m:28s left) +Iteration 100 / LogL: -6715.577 / Time: 0h:0m:36s (0h:0m:24s left) +BETTER TREE FOUND at iteration 105: -6713.864 +Iteration 110 / LogL: -6715.309 / Time: 0h:0m:39s (0h:0m:34s left) +Iteration 120 / LogL: -6713.877 / Time: 0h:0m:42s (0h:0m:30s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 123: -6712.300 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 126: -6710.985 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 127: -6710.445 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 130: -6709.739 +Iteration 130 / LogL: -6709.739 / Time: 0h:0m:45s (0h:0m:35s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 136: -6709.364 +Iteration 140 / LogL: -6710.807 / Time: 0h:0m:48s (0h:0m:33s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 142: -6709.294 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 147: -6708.895 +Iteration 150 / LogL: -6712.081 / Time: 0h:0m:51s (0h:0m:33s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 160: -6708.749 +Iteration 160 / LogL: -6708.749 / Time: 0h:0m:54s (0h:0m:34s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 163: -6708.686 +Iteration 170 / LogL: -6710.289 / Time: 0h:0m:57s (0h:0m:31s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 173: -6708.554 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 180: -6708.518 +Iteration 180 / LogL: -6708.518 / Time: 0h:1m:0s (0h:0m:33s left) +Iteration 190 / LogL: -6709.408 / Time: 0h:1m:3s (0h:0m:30s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 193: -6705.296 +BETTER TREE FOUND at iteration 200: -6705.295 +Iteration 200 / LogL: -6705.295 / Time: 0h:1m:6s (0h:0m:33s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 202: -6705.270 +Iteration 210 / LogL: -6705.378 / Time: 0h:1m:8s (0h:0m:30s left) +Iteration 220 / LogL: -6708.516 / Time: 0h:1m:11s (0h:0m:26s left) +Iteration 230 / LogL: -6705.293 / Time: 0h:1m:14s (0h:0m:23s left) +Iteration 240 / LogL: -6707.618 / Time: 0h:1m:17s (0h:0m:20s left) +Iteration 250 / LogL: -6705.961 / Time: 0h:1m:20s (0h:0m:16s left) +Iteration 260 / LogL: -6705.327 / Time: 0h:1m:22s (0h:0m:13s left) +Iteration 270 / LogL: -6705.292 / Time: 0h:1m:25s (0h:0m:10s left) +Iteration 280 / LogL: -6707.215 / Time: 0h:1m:28s (0h:0m:6s left) +Iteration 290 / LogL: -6705.310 / Time: 0h:1m:31s (0h:0m:3s left) +BETTER TREE FOUND at iteration 293: -6705.270 +BETTER TREE FOUND at iteration 295: -6705.269 +Iteration 300 / LogL: -6705.416 / Time: 0h:1m:33s (0h:0m:29s left) +Iteration 310 / LogL: -6708.491 / Time: 0h:1m:36s (0h:0m:26s left) +Iteration 320 / LogL: -6705.394 / Time: 0h:1m:39s (0h:0m:23s left) +UPDATE BEST LOG-LIKELIHOOD: -6705.269 +Iteration 330 / LogL: -6707.929 / Time: 0h:1m:41s (0h:0m:20s left) +Iteration 340 / LogL: -6705.373 / Time: 0h:1m:44s (0h:0m:16s left) +Iteration 350 / LogL: -6706.548 / Time: 0h:1m:47s (0h:0m:13s left) +Iteration 360 / LogL: -6705.366 / Time: 0h:1m:50s (0h:0m:10s left) +Iteration 370 / LogL: -6708.694 / Time: 0h:1m:52s (0h:0m:7s left) +Iteration 380 / LogL: -6707.358 / Time: 0h:1m:55s (0h:0m:4s left) +Iteration 390 / LogL: -6705.825 / Time: 0h:1m:58s (0h:0m:1s left) +TREE SEARCH COMPLETED AFTER 396 ITERATIONS / Time: 0h:1m:59s + +-------------------------------------------------------------------- +| FINALIZING TREE SEARCH | +-------------------------------------------------------------------- +Performs final model parameters optimization +Estimate model parameters (epsilon = 0.010) +1. Initial log-likelihood: -6705.269 +Optimal log-likelihood: -6705.266 +Rate parameters: A-C: 1.13682 A-G: 3.52293 A-T: 0.74232 C-G: 0.82784 C-T: 3.38691 G-T: 1.00000 +Base frequencies: A: 0.281 C: 0.222 G: 0.210 T: 0.287 +Site proportion and rates: (0.052,0.226) (0.340,0.517) (0.301,0.517) (0.307,2.143) +Parameters optimization took 1 rounds (0.062 sec) +BEST SCORE FOUND : -6705.266 +Total tree length: 81.560 + +Total number of iterations: 396 +CPU time used for tree search: 114.612 sec (0h:1m:54s) +Wall-clock time used for tree search: 119.058 sec (0h:1m:59s) +Total CPU time used: 115.545 sec (0h:1m:55s) +Total wall-clock time used: 120.013 sec (0h:2m:0s) + +Analysis results written to: + IQ-TREE report: clsReps.aln.iqtree + Maximum-likelihood tree: clsReps.aln.treefile + Likelihood distances: clsReps.aln.mldist + Screen log file: clsReps.aln.log + +Date and Time: Tue May 28 13:11:57 2019