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6i.ASTRAL_PRO_species_tree.log
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6i.ASTRAL_PRO_species_tree.log
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================== ASTRAL-Pro =====================
This is ASTRAL-Pro (A-Pro) version 1.1.6
Using native AVX batch computing.
Gene trees are treated as unrooted
There are 48 threads used to run.
ti: 3
tx: 3
pw: 4
The number of input tree read is 1047
14848 trees read from 6f.ASTRAL_PRO_input_gene_trees.tre
9400 extra trees.
All output trees will be *arbitrarily* rooted at S0376
======== Running the main analysis
Number of taxa: 403 (403 species)
Taxa: [S0376, S0427, S0672, S0733sl, SRR8528391, S0904, S1541sl, S0893, S1276, S0298, S0671, S0593, S0946, S0306, S0895, S0285, S0741, S1424, S0949, S0728sl, SRR8528342, S1116, S0947sl, SRR8528359, S0689, S1407, S0742, S0412sl, S0762-2, S0558, S0383, S0275, S1052sl, S0903, S0300, S0294, S0764, S0721sl, S0055, S1375, S1241, S0751, S1381, S1211, S1114-2, S0655sl, S0791, S0436, S0450, S0403sl, S1428, S1182, S0654, S0156, S0691, S0642, S0555, S1354, S0384, S0381, S1422, S0292, S1419, S1449, S1366, S0745, S1376, S0766, S1214sl, SRR8528336, S0744sl, S1336, S0416, SRR11470320, S1498, S1083, S1462, S0765, S0419, S0760, S0196sl, S1177, 8009952, S0770, S0902, S1113, S1121, S0834, S0279, S0836, S0281, S0795, S0720, S0901, SRR8528384, S0717, S0722, S0746, SRR8528399, S1074, S1077, SRR8528382, SRR8528373, S1378, SRR8528381, S0560, SRR8528338, S0329, S1561, S1328sl, SRR8528347, S0421, S1251, S1250sl, S0289, S0624, S0478, S1475, S0963, S1451, S1246, S0428sl, S1365, S1232sl, S1368, S1235sl, S0316sl, S1460, S0809, S1318-2, SRR8528350, S0612, S1204, S0641, SRR8528357, S0718, S0670, S0268, S0763, S0400, S1227, S1369, S0301, S0293, S0282, S1371, SRR8528376, S0405, S1278, S1279, S1370, S0643, S0756, SRR8528343, S_670, S0690, S0435, S1400, S0509, S0941, S0547, S0591, S0732, S0739, S1176, S1229-2, S1260, S0616, S1110, S1210, S0888, S1315, S0952, S1519, S0740, S1120, S1262, S1111, S1374, S0283, S1342, S0420sl, S1341, SRR8528394, S0753, S0277, S1043sl, S0989, S1038, S1045, S1488, SRR8528385, S1119, S1102, SRR8528364, S1093sl, SRR8528356, SRR8528397, S1089, S1095, SRR8528400, S0906, SRR8528379, S0735, S1261, S1148, S1180, S1223, S1184, S1100, S0890, S1389, S1386, S0284, PAFTOL_019361, S0688, S0957, S0562, S0956, S0964, S0758, S0552sl, S0960, S1189, S0613sl, S0959, S1129sl, S1128, S0677, S1103, S0771, SRR8528372, S0385, S0380, S1221sl, S1339, S0743, S0315, S0664, S0305, S0726, S1021, S1331, S1442, S0326-2, S1509, S0851, S0731sl, S1314, S0669, S0954, S0464, S1168, S1506, S1458, S0772, S1258-2, S1053sl, S0521, S0286, S1050, S1106sl, S1098, S1072, S0346, S1319, S1097, S0754, S1039, S1096, S1464, S0727, SRR8528341, SRR8528389, SRR8528386, S1201sl, S0335, S0280, SRR8528380, SRR8528365, S0297, S0373, S0371, S1270, S0768, S0892, S0577, S1213, S1069, S1107-2, S1579, SRR8528358, S0757, S1539, S0312, S1238sl, S0748, S0620, S1249, S1269, S1266sl, S1409, S0288, S0322, S0724sl, S0430, S0303, S0355, S0308, S0647-2, S1417, SRR8528388, S1117, S1118, S1459, SRR8528361, S1332, SRR8528398, S0345, S1044, S1040, S0512sl, S0896, S1387, PAFTOL_023515, PAFTOL_023519, S1405, S0899, SRR8528354, S0827, S1234, S0656sl, S0657, S0645sl, S0278, S0320, S0407sl, S1474, S0299, S1230, S1239, S0951, S0424, S0417, S1188, SRR8528339, S0894, S1245, S0673, SRR8528370, S0761sl, S0617, S1011sl, S1421, S0752, S0377, S0897, S0662, S1401, S0667, S0747sl, S0323, S0660sl, S1220, S1208sl, S0583, S1408, S0590, S0317, S1181-2, PAFTOL_023511, PAFTOL_019459, PAFTOL_023513, S1481sl, S0331, S0629-2, S0738sl, S0327, S0564sl, S1398, PAFTOL_023477, S1388, S0734sl, S1187sl, 8000070, SRR11470309, S1412, PAFTOL_008053, S1321, PAFTOL_005410, S0759, 8008999, S1384, PAFTOL_023503, S1049sl, ERR4210213, SRR6441723, PAFTOL_014331, MYZV, CRNC, PAFTOL_005411, HYZL, ERR2789774]
Taxon occupancy: {ERR4210213=953, S0904=4394, S0906=6025, S0660sl=3675, S0728sl=4688, PAFTOL_019361=4524, HYZL=1410, S0901=5518, S0902=4440, S0903=5415, PAFTOL_023503=605, SRR8528336=5035, SRR8528338=4944, SRR8528339=4779, S0809=5360, PAFTOL_019459=2218, SRR8528343=4166, SRR8528341=4354, SRR8528342=4481, SRR8528347=4775, S1318-2=5360, S0947sl=5832, SRR8528354=4801, SRR8528356=4624, SRR8528357=5289, SRR8528350=4269, S1083=5995, SRR8528400=5076, S1089=6070, S1072=6109, S1074=6479, S0420sl=4805, S1049sl=20, S1077=5981, S0564sl=2509, S1187sl=3665, S0629-2=1039, SRR11470309=1875, S0552sl=6233, S1095=6564, S1096=6568, SRR11470320=4808, S1481sl=1522, S1250sl=5794, S1097=4976, S1098=5707, S1229-2=5633, S0509=5654, S0753=3700, S0754=6120, S0756=5264, S0757=6210, S0758=4435, S0759=699, 8008999=843, S0751=5796, S0752=5277, S0739=5571, S0742=5242, S0743=4709, S0745=6345, S0624=5457, S0746=6336, S1043sl=5328, S0989=3753, S0748=5215, S0740=5509, S0741=5404, S0620=2746, S0761sl=2360, S0654=5150, S0896=4880, S0897=3776, S0899=5330, S0657=5365, S0416=6214, S1506=3798, S0417=5719, S0419=5605, S0890=4393, S0770=5950, S0771=5762, S0892=5621, S0893=3588, S0772=4864, S0894=5315, S0895=5279, S0764=5492, S0643=5005, S0765=5044, S0766=5935, S0888=5558, S0405=5137, S0768=4489, S0760=6131, S0641=5248, S0642=5710, S0763=5208, S0400=5075, S0521=6021, S0827=5140, S0949=5466, S0655sl=5991, S0951=3226, S0952=4771, S0954=5072, S0834=4656, S0956=5299, S0836=5208, S0957=5486, S1221sl=4982, S0941=4612, S0946=4996, S1232sl=5853, PAFTOL_005410=910, PAFTOL_005411=356, MYZV=1412, S0412sl=5251, S0732=5612, S1266sl=4839, S0612=5261, S0735=5815, S1011sl=3148, S0616=5012, S0617=4273, S0851=4970, S0717=5790, S0959=5975, S0718=5387, S0720=5927, S0963=4833, S0722=6834, S0964=5346, S0726=4401, S0727=5684, S0960=6107, S0590=3350, S0326-2=963, S0478=5174, S1204=5158, 8000070=680, S1449=6275, S0591=4506, S1106sl=5794, S0593=5136, S1561=4904, S1442=4705, S1321=1523, S0355=3467, S1129sl=6338, S1258-2=5215, S1238sl=5633, S0645sl=5951, S1314=4987, S0346=6536, S1315=5502, S0403sl=5647, S1319=5361, S1114-2=4414, S0583=4812, S0464=5080, S0345=3520, S0656sl=5267, S1227=5279, S0762-2=5523, S1460=5126, S0371=3955, S1462=6280, S1341=5357, S0373=5466, S1220=3925, S1342=4464, S1100=5666, S1464=6247, S0376=5017, S1102=5640, S1223=5548, S0512sl=3367, S1103=6087, S0377=4954, S1214sl=6263, PAFTOL_014331=1192, S1336=6003, S1458=3552, S1579=5740, S1459=5101, S1339=4531, S1451=5515, S1210=5034, S1331=4855, CRNC=1196, S1211=5450, S1332=5343, S0731sl=5063, S1213=6220, S1541sl=5375, S0613sl=6091, S0555=5769, S0196sl=5336, S0435=6304, S0677=5668, S0436=5966, S0315=5092, S0558=5605, S1405=5491, S0317=5013, S1407=5446, S1408=4755, S1052sl=4816, S1409=4452, S0791=4518, S0670=5122, S0671=5521, S0672=5153, S0430=4541, S0673=5403, S0795=5690, S1400=6061, S0312=6230, S1401=5079, S1093sl=6478, S0316sl=2729, S1509=4705, S0303=4312, S0424=4482, S0667=4278, S0547=4861, S0305=4019, S0427=5360, S0306=2908, S0428sl=3740, S0669=5298, S0308=5233, S1519=5089, S0734sl=2011, S0662=4833, S0300=5074, S0421=5823, S0301=5277, S0664=5006, S1424=5725, S0335=5343, S0577=4915, PAFTOL_023477=1175, S1428=5935, S1053sl=4591, S1201sl=5957, S0690=4778, S0691=6256, S0450=6242, S0331=3111, S1421=4170, S0721sl=5197, S1422=6201, S0744sl=3593, 8009952=1557, S0688=5562, S0689=5064, S0327=5227, S1235sl=5050, S1417=2121, S0329=5729, S1539=6119, S1419=6172, S0560=5038, S0562=6114, S0320=5136, S0322=4525, S0733sl=5006, S0323=4945, S1412=1339, S1040=5725, S1208sl=3878, S1107-2=2504, S0724sl=5081, S1044=5683, S1045=6729, S0747sl=5308, S1168=5043, S_670=5328, S0647-2=5460, PAFTOL_008053=1216, S1270=4593, S1039=5529, S0407sl=4674, S1276=5370, S1398=1847, S1278=5165, S1279=5100, S1038=5768, S1180=5578, S1182=5566, S1184=5303, S1188=5619, S1189=6179, S1069=6447, S1050=5577, ERR2789774=1177, S1176=5134, S1177=5737, S1328sl=5596, SRR8528358=4862, SRR8528359=4303, S1369=5380, S1128=5997, S1249=4613, SRR8528365=4627, S1241=6443, S1120=5006, S1121=5273, S0275=5202, S1365=5113, SRR8528361=4304, S0156=4537, S1366=5883, S0277=5592, S1245=6011, S1246=5392, S1488=694, S0278=5034, S1181-2=4864, S0279=5882, S1368=5554, SRR8528364=5045, S0380=5230, S0381=5515, S1116=5402, S1117=5148, S1118=4530, S1239=5967, SRR8528370=4816, S1119=5533, S0738sl=3049, SRR8528376=4369, S0383=4607, S1230=5989, S0384=5359, S1110=4628, S1111=5796, SRR8528379=5062, S0385=5052, S1474=5022, S1354=6186, S1475=4862, SRR8528372=5035, S1113=4765, SRR8528373=4839, S1234=5948, S0268=5144, S1381=5476, S0292=6239, S1260=5490, S0293=4941, S1261=5036, PAFTOL_023511=1499, SRR8528380=4610, SRR8528381=4600, SRR8528382=5973, S0294=5186, S1262=4954, PAFTOL_023519=2638, S1021=5199, SRR8528388=4798, S1384=1361, SRR8528389=4344, S0055=5420, S1386=3106, S0297=3997, S0298=5610, S1387=3060, PAFTOL_023515=2712, SRR8528384=4982, S0299=5716, S1388=2005, SRR8528385=4996, S1389=2236, PAFTOL_023513=2628, S1148=5805, SRR8528386=3169, S1269=4698, S0280=5479, S0281=5645, S1370=5400, S0282=5250, S1371=5157, SRR8528391=4257, SRR6441723=1214, S1251=5617, S0283=5838, SRR8528398=4258, SRR8528399=5044, S0284=4436, S0285=4487, S1374=6008, S1375=5591, S0286=4947, S1376=6159, SRR8528394=5047, S1498=5920, S0288=3744, S1378=5570, S0289=5898, SRR8528397=5020}
Using polytree-based weight calculation.
Number of gene trees: 14848
14848 trees have missing taxa
Calculating distance matrix (for completion of X) ....with 4 distance matrices in parallel
Species tree distances calculated ...
Will attempt to complete bipartitions from X before adding using a distance matrix.
Building set of clusters (X) from gene trees
------------------------------
Number of Clusters after addition by distance: 291809
Adding to X using resolutions of greedy consensus ...
Computing greedy consensus took 59 seconds
Limit for sigma of degrees:10125
polytomy size limit : > 24
[3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 5, 5, 6, 6, 7, 7, 8, 10, 12, 24]
discarded polytomies:
Threshold 0.0:
Threshold 0.01:
Threshold 0.02:
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 291819
Threshold 0.05:
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 291819
Threshold 0.1:
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 291819
Threshold 0.2:
polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 12; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 7; rounds with additions with at least 5 support: 1; clusters: 291819
Threshold 0.3333333333333333:
polytomy of size 6; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 7; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 6; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 10; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 291819
polytomy of size 24; rounds with additions with at least 5 support: 1; clusters: 291819
polytomy of size 8; rounds with additions with at least 5 support: 0; clusters: 291819
Number of Clusters after addition by greedy: 291819
calculating extra bipartitions from extra input trees ...
Number of Clusters after additions from extra trees: 363105
partitions formed in 332.9 secs
Dynamic Programming starting after 332.9 secs
Polytree max score: 264291152780
Polytree building time: 4.749 seconds.
Number of quartet trees in the gene trees: 264291152780
Computing hash values took 0 seconds
Size of largest cluster: 403
Size of largest cluster: 403
Calculated 100000 weights; time (seconds): 149
100032 weights calculated 131.968
Calculated 200000 weights; time (seconds): 126
200576 weights calculated 126.663
300864 weights calculated 126.7
Calculated 300000 weights; time (seconds): 126
Calculated 400000 weights; time (seconds): 128
401216 weights calculated 128.961
500096 weights calculated 142.225
Calculated 500000 weights; time (seconds): 142
Calculated 600000 weights; time (seconds): 141
600512 weights calculated 141.457
Calculated 700000 weights; time (seconds): 141
700800 weights calculated 141.194
Calculated 800000 weights; time (seconds): 132
800128 weights calculated 132.379
900032 weights calculated 123.554
Calculated 900000 weights; time (seconds): 123
1000448 weights calculated 122.648
Calculated 1000000 weights; time (seconds): 122
1101056 weights calculated 131.303
Calculated 1100000 weights; time (seconds): 131
1200512 weights calculated 148.064
Calculated 1200000 weights; time (seconds): 148
1300352 weights calculated 134.384
Calculated 1300000 weights; time (seconds): 134
1400704 weights calculated 131.85
Calculated 1400000 weights; time (seconds): 131
1500160 weights calculated 125.919
Calculated 1500000 weights; time (seconds): 125
Calculated 1600000 weights; time (seconds): 120
1600960 weights calculated 120.109
Total Number of elements: 1679317
Final optimization score: 0
1679318 1678784 1679317
Total Number of elements: 1679317
Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.7526344148363512
Final optimization score: 198914617119
Optimal tree inferred in 2570.879 secs.
Weight calculation cumulatively took 103915.021975863 secs
(S0376,(S0672,((S0427,SRR8528391),((S0734sl,((S0298,S0671),((S0904,((((((((S0283,(((((S1201sl,((SRR6441723,((SRR8528386,(S0373,(((((S0731sl,((S0326-2,(S0617,(S1401,(((S1011sl,(((S0667,(S0377,S0323)),(S0660sl,(S1421,S0752))),(S0747sl,((S0583,S1408),(S1509,S0590))))),(S0662,(S0897,(S0317,S0331)))),(S1220,S1208sl))))),(S0851,S1314))),(S0305,((S0726,S1021),(S0664,(S0743,S0315))))),((S1331,S1442),(S1339,(S0380,(S0385,S1221sl))))),((S0669,S1458),(S1506,(S0772,(S0954,(S0464,S1168)))))),(S0297,(S0768,(S0371,S1270)))))),(S1412,((S1481sl,(S0759,(S1417,((((S1117,(((S1098,(S0754,S1039)),(S1096,(S1044,(S1106sl,S1464)))),(S0647-2,(S1040,(SRR8528388,(S0346,(S1072,S0727))))))),(S1319,(S0512sl,(S1459,(S1097,S1118))))),(S1053sl,(S1258-2,(S1050,(S0521,S0286))))),(S1332,(S0345,(SRR11470309,(SRR8528361,SRR8528398)))))))),(SRR8528341,SRR8528389))))),(SRR8528365,(S0629-2,(ERR4210213,(S0335,(S0280,SRR8528380))))))),((S0744sl,(((S1376,(S1214sl,SRR8528336)),((S0766,S0738sl),(S0384,S0745))),((S0381,S1422),(S1449,(S0292,(S1419,S1366)))))),(S1336,S0416))),(S1238sl,(S0757,S0312))),(SRR8528372,(S1103,(((S0562,(S0552sl,(S0960,(S0758,(S0956,S0964))))),(S0959,(S1189,S0613sl))),(S0771,(S1128,(S1129sl,S0677))))))),(SRR8528400,(S0906,SRR8528379)))),(((S1354,((S0691,((S0642,S0555),((S0436,S0450),(S0791,(S1114-2,S0655sl))))),((S0654,S0156),(S1182,(S0403sl,S1428))))),(SRR8528373,S0284)),(S0688,S0957))),(((SRR8528381,((((S1095,(SRR8528397,S1089)),(S0753,(S1093sl,(SRR8528364,(S1119,S1102))))),((S1045,S1488),(S0277,(S0989,(S1043sl,S1038))))),(SRR8528394,SRR8528385))),(S1579,(S1378,(S0892,(S1107-2,(S0577,(S1213,S1069))))))),(SRR8528356,(S1341,(S1342,S0420sl))))),((S0329,(S0560,SRR8528338)),(SRR8528382,(S1077,(SRR8528399,(S0746,S1074)))))),((S1374,(((S0952,((S1249,(S0288,(S0430,(S1269,(S1266sl,S1409))))),((S0355,(S0322,S0724sl)),(S0303,(S0748,S0620))))),(S1519,(S1111,S0308))),(((S1262,(S0740,S1120)),((S1110,S1210),(S0888,S1315))),((S0732,S0616),((S1229-2,S1260),(S0739,S1176)))))),(SRR8528384,((((S0901,(S0281,((S0834,(S0279,S0836)),(S0902,(S1113,S1121))))),(SRR11470320,(S1498,S1083))),(8000070,(8008999,(S0795,S0720)))),(S0196sl,(8009952,((S0770,(S0419,S0760)),(S1177,(S1462,S0765))))))))),(((S1328sl,((S0478,((S0327,(S1474,((((S0424,((S0645sl,((S0299,(SRR8528347,S0421)),(S0624,(S1241,(S1251,S0278))))),(S0289,(S1230,(S1451,S0320))))),(S1365,S0951)),(S0963,(S1475,S0407sl))),(S1239,S0417)))),(S1232sl,(S0428sl,S1368)))),(S1405,((S0899,S0657),(SRR8528354,(S0656sl,(S1250sl,(SRR8528358,(S0827,S1234))))))))),((S0761sl,(SRR8528370,((S1539,S0673),(S1246,(S0894,S1245))))),(SRR8528339,(S1188,S1187sl)))),((PAFTOL_019361,(((S1398,((CRNC,(PAFTOL_023511,((S1321,PAFTOL_014331),((PAFTOL_019459,PAFTOL_023477),(MYZV,(S1384,(S1049sl,HYZL))))))),(PAFTOL_005410,(PAFTOL_008053,(PAFTOL_023503,PAFTOL_005411))))),(PAFTOL_023513,(S0564sl,(PAFTOL_023515,PAFTOL_023519)))),((S1386,S1387),(S1389,S1388)))),((S0890,(S1184,S1100)),((S0735,S1261),(S1148,(S1180,S1223))))))),(S0717,S0722)),((((((((((S0941,((S0509,(S0947sl,((S0285,(S1424,(S0895,(S0741,(S0946,S0306))))),(S0896,(S1116,(S0728sl,(ERR2789774,(S0949,SRR8528342)))))))),(S0435,S1400))),(S1371,SRR8528376)),((((S1227,S1369),(S0690,((S0400,(S0293,S0282)),((S0301,S_670),(S0268,S0763))))),((S1278,S1279),(S0405,(S1370,S0643)))),(S0756,SRR8528343))),((S0718,S0670),(S1204,S0641))),((SRR8528350,S0612),(SRR8528357,(S0721sl,(S1318-2,(S0316sl,(S1460,(S1235sl,S0809)))))))),((S1052sl,(S0383,S0275)),(S0903,(S0294,(S0300,S0764))))),(S1381,S1211)),(S0055,S1375)),((SRR8528359,S0689),((S0762-2,S0558),(S0412sl,(S1407,S0742))))),(S0751,(S0591,(S1181-2,(S1561,S0547))))))),(S0733sl,S0593)))),(S1541sl,(S0893,S1276))))));
Final quartet score is: 198914617119
Final normalized quartet score is: 0.7526344148363512
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 0:
{S1049sl, HYZL}
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 11:
{S0949, SRR8528342}
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ASTRAL-Pro finished in 2619.754 secs