Describe the bug
After running Astral, I found there is a tip named "ROOT" on the tree. I checked the log file, in which "ROOT" also appeared.
To Reproduce
java -jar "/home/morales/Apps/ASTRAL/astral.5.7.7.jar" -i decomposed.tre -o species.tre
Log file
Send us the log file (standard error of ASTRAL)
================== ASTRAL =====================
This is ASTRAL version 5.7.7
Gene trees are treated as unrooted
433 trees read from decomposed.tre
index0
All output trees will be arbitrarily rooted at ERR5034371
gradient0: 47807
Number of Clusters after addition by distance: 47807
calculating extra bipartitions to be added at level 1 ...
Adding to X using resolutions of greedy consensus ...
Limit for sigma of degrees:5200
polytomy size limit : 17
discarded polytomies: [3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 7, 7, 7, 8, 10, 12, 14, 15, 17]
Threshold 0.0:
Threshold 0.01:
polytomy of size 5; rounds with additions with at least 5 support: 2; clusters: 47839
Threshold 0.02:
polytomy of size 6; rounds with additions with at least 5 support: 1; clusters: 47881
Threshold 0.05:
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47881
polytomy of size 7; rounds with additions with at least 5 support: 1; clusters: 47895
Threshold 0.1:
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47895
polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 47895
polytomy of size 8; rounds with additions with at least 5 support: 0; clusters: 47899
Threshold 0.2:
polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 47899
polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 47899
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47899
polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 47899
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47899
polytomy of size 7; rounds with additions with at least 5 support: 0; clusters: 47899
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47899
polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 47905
polytomy of size 10; rounds with additions with at least 5 support: 1; clusters: 47945
Threshold 0.3333333333333333:
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47945
polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 47945
polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 47945
polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 47945
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47945
polytomy of size 12; rounds with additions with at least 5 support: 0; clusters: 47947
polytomy of size 7; rounds with additions with at least 5 support: 0; clusters: 47947
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47947
polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47947
polytomy of size 15; rounds with additions with at least 5 support: 0; clusters: 47947
polytomy of size 14; rounds with additions with at least 5 support: 0; clusters: 47947
polytomy of size 17; rounds with additions with at least 5 support: 0; clusters: 47969
max k is :4
Number of Clusters after addition by greedy: 47969
gradient0 in heuristiic: 47969
partitions formed in 9.764 secs
Dynamic Programming starting after 9.764 secs
Using tree-based weight calculation.
Using polytree-based weight calculation.
Polytree max score: 11253442074
Polytree building time: 0.137 seconds.
Number of quartet trees in the gene trees: 11253442074
Size of largest cluster: 206
Greedy score: 8723044854
estimationFactor: 1.2900818764951865
Sub-optimal score: 8766920803
Calculated 100000 weights; time (seconds): 136
Total Number of elements weighted: 123494
Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.8112629473690398
Optimization score: 9129500585
Optimal tree inferred in 171.462 secs.
(ERR5033951,(ERR5033952,(ERR5033977,(ERR5034065,((ERR5033975,ERR5033972),(ERR5033954,((ERR5033964,(ERR5033960,(ERR5033950,ERR5033962))),((ERR5034972,(ERR5033963,(ERR5033958,(ERR5034827,(ERR5033966,(ERR5033968,ERR5033970)))))),((((ERR5033971,ERR5033967),(ERR5033961,ERR5033969)),(ERR5033978,(ERR5033976,(ERR5034826,(ERR5033959,((ERR5033973,ERR5033953),(ERR5034828,(ERR5033956,ERR5033974)))))))),(ERR5033965,(ERR5033957,((ERR5034829,ERR5033955),((ERR5033945,(ERR5033949,((ERR5033946,(ERR5033941,ERR5033947)),(ERR5033944,((ERR5033942,ERR5033943),(ERR5034831,(ERR5033940,ERR5033948))))))),(((ERR5033895,(ERR5033893,ERR5033894)),((((ERR5034825,ERR5034953),(ERR5034360,(ERR5034859,ERR5034952))),((ERR5034969,(ERR5033905,ERR5033902)),((ERR5033904,ERR5101682),(ERR5033903,ERR5034393)))),(((ERR5034362,(ERR5034363,ERR5034113)),((ERR5033987,(ERR5033986,ERR5034830)),((ERR5084257,ERR5034681),(ERR5034110,ERR5034115)))),(ERR4180211,(ERR5060317,(ERR5084279,(ERR5034060,(ERR5034677,(ERR5034680,(ERR4180132,(ERR5034678,(ERR5034858,ERR5033399)))))))))))),((ERR5034815,(ERR5033999,(ERR5033996,(ERR5034000,(((ERR5034860,(ERR5034959,ERR5033993)),(ERR5034861,(ERR5033406,(ERR5034066,ERR5034961)))),(((ERR5034371,ERR5034064),(ERR5034380,(ERR5034875,((ERR5034963,ERR5034375),(ERR5034679,ERR5034962))))),(ERR5101684,((ERR5034063,(ERR5033995,ERR5033994)),((ERR5034396,(ERR5084301,(ERR5101681,ERR5034960))),((ERR5034964,ERR5034376),((ERR5034379,ERR5034378),(ERR5034370,(ERR5034372,(ERR5034377,ERR5034373)))))))))))))),(((ERR5033998,ERR5033997),(ERR5034114,(ERR5033900,(ERR5033899,ERR5033901)))),(ERR5101669,(ROOT,(((ERR5033898,(ERR5033896,(ERR5034817,(ERR5033897,ERR5034816)))),(MMIR_1928,((ERR5034956,ERR5034955),(ERR5034954,(ERR5034361,ERR5034109))))),((ERR5033988,(ERR5033991,ERR5033990)),(((ERR5033982,(ERR5033981,((ERR5033980,ERR5033979),(ERR5033983,(ERR5033985,ERR5033984))))),(ERR5034061,((ERR5034971,(ERR5033930,ERR5034394)),((ERR5033939,(ERR5033937,ERR5034395)),(((ERR5033932,ERR5033934),(ERR5033927,ERR5034970)),((ERR5033926,(ERR5033935,ERR5033933)),((ERR5033929,ERR5033931),(ERR5033936,ERR5033928)))))))),(ERR5033992,(ERR5033913,((ERR5033919,ERR5033918),(((ERR5034873,(ERR5034111,ERR5033925)),((ERR5034374,ERR5084315),(ERR5034366,((ERR5033910,(ERR5034364,ERR5034682)),((ERR5034368,(ERR4180091,ERR5033914)),(ERR5034369,((ERR5034958,ERR5034957),(ERR5034876,(ERR5034365,ERR5034062))))))))),(ERR5033922,(ERR5033909,((ERR5034822,(ERR5033924,(ERR5034821,((ERR5034824,ERR5034810),(ERR5034818,ERR5033921))))),(((ERR5101683,ERR5033923),(ERR5034820,(ERR5034823,ERR5033911))),((ERR5033989,(ERR5033920,ERR5033917)),((ERR5033908,ERR5033915),(ERR5033907,ERR5033906))))))))))))))))))))))))))))))));
Final quartet score is: 9129500585
Final normalized quartet score is: 0.8112629473690398
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 2:
{ERR5034959, ERR5033993}
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:
{ERR5034959, ERR5034860, ERR5033993}
Extended species tree:
(ERR5034371,(ERR5034064,((ERR5034380,(ERR5034875,((ERR5034963,ERR5034375)1:0.7948902903957221,(ERR5034679,ERR5034962)0.51:0.06368480152147532)0.99:0.14164354573132523)1:0.5121498324249502)0.8:0.06296561118824413,((ERR5101684,((ERR5034063,(ERR5033995,ERR5033994)0.82:0.13082603336638077)0.66:0.046891141375994205,((ERR5034396,(ERR5084301,(ERR5101681,ERR5034960)1:0.6888661632124554)0.53:0.13369839911047182)0.96:0.1282197981686057,((ERR5034964,ERR5034376)1:0.1413874265390755,((ERR5034379,ERR5034378)1:0.2555501609270514,(ERR5034370,(ERR5034372,(ERR5034377,ERR5034373)1:0.6637225810626474)0.77:0.07468312283064686)0.54:0.03267721168995944)1:0.1754310451514702)0.28:0.0)0.99:0.11786899610815199)0.42:0.03373835403078581)0.83:0.11222929324757101,(((ERR5034860,(ERR5034959,ERR5033993)0.87:0.6931471805599453)0.11:0.0,(ERR5034861,(ERR5033406,(ERR5034066,ERR5034961)0.5:0.023358403397272708)0.93:0.10237982343321782)0.94:0.10077267740416301)1:0.23156667722782898,(ERR5034000,(ERR5033996,(ERR5033999,(ERR5034815,((((ERR5033998,ERR5033997)1:0.9027898714798148,(ERR5034114,(ERR5033900,(ERR5033899,ERR5033901)1:0.8087127622073482)0.99:0.17230384806492233)1:0.7585643152180725)1:0.5701578312736789,(ERR5101669,(ROOT,(((ERR5033898,(ERR5033896,(ERR5034817,(ERR5033897,ERR5034816)1:1.0769954207936867)1:1.5265588317953422)1:0.1705157895449287)1:0.9287468939401693,(MMIR_1928,((ERR5034956,ERR5034955)1:0.6422518915580342,(ERR5034954,(ERR5034361,ERR5034109)0.95:0.12847854813284468)1:0.5478027188851016)1:1.760836469014693)1:1.9016398039855498)0.95:0.0926957161342512,((ERR5033988,(ERR5033991,ERR5033990)1:0.769621191011156)1:1.6219710376292227,(((ERR5033982,(ERR5033981,((ERR5033980,ERR5033979)0.8:0.08582764795356905,(ERR5033983,(ERR5033985,ERR5033984)0.71:0.08305946058354437)0.55:0.06599464771164294)1:0.7123872656194854)1:1.271488296387741)1:2.293269843331113,(ERR5034061,((ERR5034971,(ERR5033930,ERR5034394)1:2.307280275617791)1:0.47871768499592277,((ERR5033939,(ERR5033937,ERR5034395)1:1.2748533764251633)1:0.6758921536719052,(((ERR5033932,ERR5033934)1:1.3404535034389586,(ERR5033927,ERR5034970)1:1.7498932892192822)0.85:0.0727181256668271,((ERR5033926,(ERR5033935,ERR5033933)1:0.5117186382663811)1:0.34335674823753276,((ERR5033929,ERR5033931)0.27:0.12180985096153035,(ERR5033936,ERR5033928)1:0.317635869829924)1:1.0059827108037012)1:0.4288766395075893)0.94:0.09248477888127572)1:0.32535768703748763)0.55:0.03063456068475865)1:1.4906710984603124)1:0.19444768964082157,(ERR5033992,(ERR5033913,((ERR5033919,ERR5033918)1:0.43417820600227264,(((ERR5034873,(ERR5034111,ERR5033925)1:0.6732267629703049)0.98:0.1284390463581106,((ERR5034374,ERR5084315)1:0.835169248904636,(ERR5034366,((ERR5033910,(ERR5034364,ERR5034682)1:2.005357924432424)0.99:0.14447818352848824,((ERR5034368,(ERR4180091,ERR5033914)1:0.5773679887410463)1:0.34209714441804445,(ERR5034369,((ERR5034958,ERR5034957)0.99:0.13582450365737755,(ERR5034876,(ERR5034365,ERR5034062)0.64:0.04845363887144815)1:0.20845190063224117)0.98:0.13098491153668668)1:0.15056751301156773)1:0.24033925803109293)1:0.5412414340403672)1:0.5480703240164244)0.98:0.10606579121448294)1:0.6051092568724784,(ERR5033922,(ERR5033909,((ERR5034822,(ERR5033924,(ERR5034821,((ERR5034824,ERR5034810)0.99:0.16619234377801392,(ERR5034818,ERR5033921)0.99:0.1364188004754894)0.68:0.0672830337711759)0.69:0.05580414273348501)1:0.6722141320911796)0.46:0.019210386614708367,(((ERR5101683,ERR5033923)1:0.8067513849516001,(ERR5034820,(ERR5034823,ERR5033911)1:1.1610824173481227)0.61:0.040964025345670625)1:1.2161123013022443,((ERR5033989,(ERR5033920,ERR5033917)1:1.0642189352090636)1:0.44766437541943593,((ERR5033908,ERR5033915)1:1.2029197362884445,(ERR5033907,ERR5033906)1:0.45537971010145745)1:0.9115413671169774)1:0.1826252323751366)0.67:0.06085166065018862)0.99:0.13493476517987094)0.99:0.1334699907154588)1:0.23049870400685796)0.81:0.0609793835350329)0.71:0.04850956408101899)1:2.451327482482113)0.39:0.009884471674850237)1:0.39695688243672667)1:1.2704259079354336)1:0.19662680476882188)0.96:0.17528072085096688)0.99:0.19405779164580128)1:0.1574299784431539,(((ERR5033895,(ERR5033893,ERR5033894)1:0.6911507340496619)1:1.2625190462328182,((((ERR5034825,ERR5034953)1:1.2152962431623424,(ERR5034360,(ERR5034859,ERR5034952)0.97:0.11741083671971228)1:1.014569813824271)1:0.7666587966199675,((ERR5034969,(ERR5033905,ERR5033902)1:0.49386365029755575)1:1.4613723902391282,((ERR5033904,ERR5101682)1:0.38087884275554135,(ERR5033903,ERR5034393)1:0.9131272372999477)1:0.8764662822689399)1:0.3426891230544121)1:0.3288727676949412,(((ERR5034362,(ERR5034363,ERR5034113)1:0.6056464186255108)1:3.85628040060211,((ERR5033987,(ERR5033986,ERR5034830)1:1.3437523981724557)1:0.5849166660291106,((ERR5084257,ERR5034681)1:2.204259275232968,(ERR5034110,ERR5034115)0.82:0.08393900451355184)1:0.21118050744131528)1:2.5330902771923474)0.59:0.06780146787187422,(ERR4180211,(ERR5060317,(ERR5084279,(ERR5034060,(ERR5034677,(ERR5034680,(ERR4180132,(ERR5034678,(ERR5034858,ERR5033399)0.81:0.10951715481376666)0.45:0.02558617271920903)0.98:0.22870542498989563)0.83:0.07392401591091445)1:1.326534173824037)0.27:0.0)1:0.5758181584491667)1:1.019047682343446)1:3.7753890913621353)1:2.368517952986583)1:0.5557744571282061)0.57:0.049266719463048544,((ERR5033945,(ERR5033949,((ERR5033946,(ERR5033941,ERR5033947)1:0.5651596103423371)1:0.8913407691211406,(ERR5033944,((ERR5033942,ERR5033943)1:0.6573728001534197,(ERR5034831,(ERR5033940,ERR5033948)1:0.3531273606753341)1:0.41908395848968305)0.96:0.1799318009100168)1:0.2985622635830515)0.96:0.14937618115020054)0.99:0.16872439456546173)1:0.499245543005497,((ERR5034829,ERR5033955)1:0.8980936320147064,(ERR5033957,(ERR5033965,((((ERR5033971,ERR5033967)1:0.2990890247628594,(ERR5033961,ERR5033969)0.99:0.11563709702879872)1:0.4520056810036198,(ERR5033978,(ERR5033976,(ERR5034826,(ERR5033959,((ERR5033973,ERR5033953)1:0.7451081981027968,(ERR5034828,(ERR5033956,ERR5033974)1:1.3378926337855588)0.53:0.03961994330937237)0.99:0.12295213849880597)0.52:0.038505131919001685)1:0.20958928761244366)1:0.19527223680470226)0.34:0.0)0.39:0.017105007266451498,((ERR5034972,(ERR5033963,(ERR5033958,(ERR5034827,(ERR5033966,(ERR5033968,ERR5033970)1:0.2888233546884957)1:0.22071202275136062)1:0.23279060794974268)0.43:0.014741271899822599)0.59:0.06350533242529029)1:0.78438763636323,((ERR5033964,(ERR5033960,(ERR5033950,ERR5033962)1:0.37984289290771633)0.93:0.09382610098759366)1:0.18174788888283774,(ERR5033954,((ERR5033975,ERR5033972)1:0.6104209622995638,(ERR5034065,(ERR5033977,(ERR5033952,ERR5033951)1:1.473343055518063)1:0.26633451570490246)1:0.5555197525377128)0.99:0.11591424203556779)1:0.25624618670389626)0.97:0.10002617773097026)1:0.1772175923614498)0.98:0.10244901574010357)1:0.3035917225527433)0.99:0.12465724114655377)1:1.511454764717533)1:0.7706708044115681)1:0.15274891627449835)1:0.24412525408371152)1:0.30984647322663045)1:0.9642625891149215)1:0.21392849275485312)1:0.587263906845592)1:0.4600007674060357)0.48:0.020004661706054475)1:0.3605424401248607));
Weight calculation took 152.461756225 secs
ASTRAL finished in 172.97 secs
** Version
astral.5.7.7
Additional context
I haven't encountered this issue when I was running astral analyses for other data sets.
Describe the bug After running Astral, I found there is a tip named "ROOT" on the tree. I checked the log file, in which "ROOT" also appeared.
To Reproduce java -jar "/home/morales/Apps/ASTRAL/astral.5.7.7.jar" -i decomposed.tre -o species.tre
Log file Send us the log file (standard error of ASTRAL)
================== ASTRAL =====================
This is ASTRAL version 5.7.7 Gene trees are treated as unrooted 433 trees read from decomposed.tre index0 All output trees will be arbitrarily rooted at ERR5034371
======== Running the main analysis Number of taxa: 206 (206 species) Taxa: [ERR5034371, ERR5034365, ERR5034368, ERR5034958, ERR5034957, ERR5034369, ERR4180091, ERR5033914, ERR5034876, ERR5034062, ERR5033910, ERR5034364, ERR5034682, ERR5034366, ERR5034821, ERR5033924, ERR5034823, ERR5033911, ERR5034820, ERR5101683, ERR5033923, ERR5033920, ERR5033917, ERR5033989, ERR5033908, ERR5033915, ERR5033907, ERR5033906, ERR5033909, ERR5034873, ERR5034111, ERR5033925, ERR5033922, ERR5034818, ERR5033921, ERR5034374, ERR5084315, ERR5034822, ERR5033919, ERR5034824, ERR5034810, ERR5033913, ERR5033991, ERR5033990, ERR5033988, ERR5033982, ERR5033980, ERR5033985, ERR5033983, ERR5033979, ERR5033984, ERR5033981, ERR5033992, ERR5033939, ERR5033937, ERR5034395, ERR5033930, ERR5034394, ERR5034061, ERR5033935, ERR5033933, ERR5033927, ERR5034970, ERR5033932, ERR5033926, ERR5033929, ERR5033936, ERR5033928, ERR5033931, ERR5034971, ERR5033896, ERR5034817, ERR5033897, ERR5033898, ERR5034816, ERR5034361, ERR5034954, ERR5034109, ERR5034956, ERR5034955, MMIR_1928, ERR5034815, ERR5101684, ERR5034114, ERR5033899, ERR5033900, ERR5033901, ERR5033999, ERR5033944, ERR5033895, ERR5033893, ERR5033894, ERR5033949, ERR5033904, ERR5101682, ERR5034396, ERR5033903, ERR5034393, ERR5033905, ERR5034969, ERR5033902, ERR5084301, ERR5033998, ERR5033942, ERR5033943, ERR5033940, ERR5033948, ERR5034831, ERR5033941, ERR5033947, ERR5033945, ERR5033946, ERR5034064, ERR5034377, ERR5034875, ERR5033406, ERR5034679, ERR5034963, ERR5034372, ERR5034379, ERR5034959, ERR5034063, ERR5034964, ERR5034861, ERR5033995, ERR5034380, ERR5101681, ERR5034378, ERR5034066, ERR5034376, ERR5034961, ERR5034859, ERR5034952, ERR5034360, ERR5034825, ERR5034953, ERR5033952, ERR5033975, ERR5034972, ERR5033956, ERR5033974, ERR5033964, ERR5034829, ERR5033961, ERR5033973, ERR5033959, ERR5033977, ERR5034065, ERR5033958, ERR5033963, ERR5033951, ERR5033950, ERR5034827, ERR5033966, ERR5033968, ERR5033970, ERR5033972, ERR5033976, ERR5033957, ERR5033955, ERR5033960, ERR5034826, ERR5033969, ERR5033971, ERR5033953, ERR5033967, ERR5033965, ERR5034828, ERR5033954, ERR5033978, ERR5034375, ERR5034060, ERR5060317, ERR4180211, ERR5034858, ERR4180132, ERR5034680, ERR5033399, ERR5034677, ERR5034678, ERR5084279, ERR5034363, ERR5034362, ERR5033997, ERR5033986, ERR5034830, ERR5034110, ERR5033987, ERR5084257, ERR5034681, ERR5033934, ERR5034962, ERR5034373, ERR5034960, ROOT, ERR5034370, ERR5033996, ERR5034000, ERR5033994, ERR5033962, ERR5034115, ERR5034113, ERR5033918, ERR5101669, ERR5034860, ERR5033993] Taxon occupancy: {ERR5034860=14, ERR5033894=257, ERR5033893=314, ERR5034861=257, ERR5033896=313, ERR5033895=333, ERR5033898=299, ERR5033897=325, ERR5033899=260, ERR5101669=157, MMIR_1928=195, ERR5034060=169, ERR5034062=245, ERR5034061=252, ERR5034064=269, ERR5034063=297, ERR5034066=281, ERR5034065=261, ERR5034873=247, ERR5034875=217, ERR5034876=274, ERR5033991=282, ERR5033990=272, ERR5034961=288, ERR5033993=25, ERR5033992=300, ERR5034960=300, ERR5034963=307, ERR5033995=212, ERR5034962=329, ERR5033994=89, ERR5033997=199, ERR5034964=340, ERR5033996=298, ERR5033999=292, ERR5033998=281, ERR5034969=323, ERR5034970=323, ERR5034972=313, ERR5034971=281, ERR5033406=310, ERR5034859=280, ERR5034858=109, ERR4180132=77, ERR5034677=275, ERR5034679=322, ERR5034678=243, ERR5033900=294, ERR5033902=286, ERR5033901=297, ERR5033904=206, ERR5033903=304, ERR5033906=295, ERR5033905=300, ROOT=324, ERR5084301=71, ERR5084315=291, ERR5033931=298, ERR5033930=292, ERR5033933=285, ERR5034109=204, ERR5033932=310, ERR5033935=284, ERR5033934=287, ERR5033937=252, ERR5033936=288, ERR5033939=245, ERR5033929=301, ERR5034111=276, ERR5034114=153, ERR5034113=132, ERR5033940=282, ERR5034115=169, ERR5033942=309, ERR5033941=257, ERR5033944=147, ERR5033943=303, ERR5033946=234, ERR5033945=270, ERR5033948=313, ERR5033947=251, ERR5033949=183, ERR5034110=266, ERR5033911=276, ERR5033910=262, ERR5033913=303, ERR5033915=298, ERR5033914=192, ERR5033917=248, ERR5033908=270, ERR5033907=220, ERR5033909=279, ERR5034680=259, ERR5034682=261, ERR5034681=278, ERR5033920=276, ERR5033922=287, ERR5033921=279, ERR4180091=315, ERR5033924=242, ERR5033923=240, ERR5033926=311, ERR5033925=284, ERR5033928=313, ERR5033927=282, ERR5033919=286, ERR5033918=246, ERR5033971=280, ERR5033970=273, ERR5034820=272, ERR5033973=296, ERR5033972=312, ERR5034822=266, ERR5033975=311, ERR5060317=201, ERR5034821=232, ERR5033974=298, ERR5034824=230, ERR5033977=293, ERR5034823=269, ERR5033976=278, ERR5033979=268, ERR5034826=299, ERR5034825=301, ERR5033978=313, ERR5034828=280, ERR5034827=299, ERR5034829=293, ERR5034380=329, ERR5033980=272, ERR5033982=251, ERR5033981=285, ERR5033984=229, ERR5034831=244, ERR5034952=320, ERR5033983=133, ERR5034830=298, ERR5034954=333, ERR5033986=321, ERR5033985=240, ERR5034953=340, ERR5033988=281, ERR5034956=312, ERR5034955=333, ERR5033987=288, ERR5034958=327, ERR5034957=298, ERR5033989=287, ERR5034959=310, ERR5084257=308, ERR5034394=305, ERR5034393=330, ERR5034396=230, ERR5034395=285, ERR5034365=244, ERR5034364=318, ERR5034366=329, ERR5033399=182, ERR5034369=277, ERR5033951=298, ERR5034368=280, ERR5033950=272, ERR5033953=313, ERR5033952=292, ERR5033955=325, ERR5033954=322, ERR5101684=147, ERR5033957=305, ERR5033956=308, ERR5033959=306, ERR5033958=293, ERR5101682=331, ERR5101683=277, ERR5101681=330, ERR5034361=332, ERR5034360=333, ERR5034363=333, ERR5034000=276, ERR5034362=333, ERR5034376=334, ERR5034375=315, ERR5034378=300, ERR5033960=331, ERR5034377=313, ERR5033962=297, ERR5034379=331, ERR5033961=304, ERR5033964=304, ERR5034810=204, ERR5033963=280, ERR5033966=296, ERR5033965=307, ERR5034815=295, ERR5033968=317, ERR5033967=308, ERR5034817=290, ERR5034816=301, ERR5033969=323, ERR5034818=296, ERR5084279=271, ERR5034370=293, ERR5034372=318, ERR4180211=233, ERR5034371=240, ERR5034374=337, ERR5034373=325} Number of gene trees: 433 433 trees have missing taxa Calculating quartet distance matrix (for completion of X) 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
gradient0: 47807 Number of Clusters after addition by distance: 47807 calculating extra bipartitions to be added at level 1 ... Adding to X using resolutions of greedy consensus ... Limit for sigma of degrees:5200 polytomy size limit : 17 discarded polytomies: [3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 7, 7, 7, 8, 10, 12, 14, 15, 17] Threshold 0.0: Threshold 0.01: polytomy of size 5; rounds with additions with at least 5 support: 2; clusters: 47839 Threshold 0.02: polytomy of size 6; rounds with additions with at least 5 support: 1; clusters: 47881 Threshold 0.05: polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47881 polytomy of size 7; rounds with additions with at least 5 support: 1; clusters: 47895 Threshold 0.1: polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47895 polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 47895 polytomy of size 8; rounds with additions with at least 5 support: 0; clusters: 47899 Threshold 0.2: polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 47899 polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 47899 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47899 polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 47899 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47899 polytomy of size 7; rounds with additions with at least 5 support: 0; clusters: 47899 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47899 polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 47905 polytomy of size 10; rounds with additions with at least 5 support: 1; clusters: 47945 Threshold 0.3333333333333333: polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47945 polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 47945 polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 47945 polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 47945 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47945 polytomy of size 12; rounds with additions with at least 5 support: 0; clusters: 47947 polytomy of size 7; rounds with additions with at least 5 support: 0; clusters: 47947 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47947 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 47947 polytomy of size 15; rounds with additions with at least 5 support: 0; clusters: 47947 polytomy of size 14; rounds with additions with at least 5 support: 0; clusters: 47947 polytomy of size 17; rounds with additions with at least 5 support: 0; clusters: 47969 max k is :4 Number of Clusters after addition by greedy: 47969 gradient0 in heuristiic: 47969 partitions formed in 9.764 secs Dynamic Programming starting after 9.764 secs Using tree-based weight calculation. Using polytree-based weight calculation. Polytree max score: 11253442074 Polytree building time: 0.137 seconds. Number of quartet trees in the gene trees: 11253442074 Size of largest cluster: 206 Greedy score: 8723044854 estimationFactor: 1.2900818764951865 Sub-optimal score: 8766920803 Calculated 100000 weights; time (seconds): 136 Total Number of elements weighted: 123494 Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.8112629473690398 Optimization score: 9129500585 Optimal tree inferred in 171.462 secs. (ERR5033951,(ERR5033952,(ERR5033977,(ERR5034065,((ERR5033975,ERR5033972),(ERR5033954,((ERR5033964,(ERR5033960,(ERR5033950,ERR5033962))),((ERR5034972,(ERR5033963,(ERR5033958,(ERR5034827,(ERR5033966,(ERR5033968,ERR5033970)))))),((((ERR5033971,ERR5033967),(ERR5033961,ERR5033969)),(ERR5033978,(ERR5033976,(ERR5034826,(ERR5033959,((ERR5033973,ERR5033953),(ERR5034828,(ERR5033956,ERR5033974)))))))),(ERR5033965,(ERR5033957,((ERR5034829,ERR5033955),((ERR5033945,(ERR5033949,((ERR5033946,(ERR5033941,ERR5033947)),(ERR5033944,((ERR5033942,ERR5033943),(ERR5034831,(ERR5033940,ERR5033948))))))),(((ERR5033895,(ERR5033893,ERR5033894)),((((ERR5034825,ERR5034953),(ERR5034360,(ERR5034859,ERR5034952))),((ERR5034969,(ERR5033905,ERR5033902)),((ERR5033904,ERR5101682),(ERR5033903,ERR5034393)))),(((ERR5034362,(ERR5034363,ERR5034113)),((ERR5033987,(ERR5033986,ERR5034830)),((ERR5084257,ERR5034681),(ERR5034110,ERR5034115)))),(ERR4180211,(ERR5060317,(ERR5084279,(ERR5034060,(ERR5034677,(ERR5034680,(ERR4180132,(ERR5034678,(ERR5034858,ERR5033399)))))))))))),((ERR5034815,(ERR5033999,(ERR5033996,(ERR5034000,(((ERR5034860,(ERR5034959,ERR5033993)),(ERR5034861,(ERR5033406,(ERR5034066,ERR5034961)))),(((ERR5034371,ERR5034064),(ERR5034380,(ERR5034875,((ERR5034963,ERR5034375),(ERR5034679,ERR5034962))))),(ERR5101684,((ERR5034063,(ERR5033995,ERR5033994)),((ERR5034396,(ERR5084301,(ERR5101681,ERR5034960))),((ERR5034964,ERR5034376),((ERR5034379,ERR5034378),(ERR5034370,(ERR5034372,(ERR5034377,ERR5034373)))))))))))))),(((ERR5033998,ERR5033997),(ERR5034114,(ERR5033900,(ERR5033899,ERR5033901)))),(ERR5101669,(ROOT,(((ERR5033898,(ERR5033896,(ERR5034817,(ERR5033897,ERR5034816)))),(MMIR_1928,((ERR5034956,ERR5034955),(ERR5034954,(ERR5034361,ERR5034109))))),((ERR5033988,(ERR5033991,ERR5033990)),(((ERR5033982,(ERR5033981,((ERR5033980,ERR5033979),(ERR5033983,(ERR5033985,ERR5033984))))),(ERR5034061,((ERR5034971,(ERR5033930,ERR5034394)),((ERR5033939,(ERR5033937,ERR5034395)),(((ERR5033932,ERR5033934),(ERR5033927,ERR5034970)),((ERR5033926,(ERR5033935,ERR5033933)),((ERR5033929,ERR5033931),(ERR5033936,ERR5033928)))))))),(ERR5033992,(ERR5033913,((ERR5033919,ERR5033918),(((ERR5034873,(ERR5034111,ERR5033925)),((ERR5034374,ERR5084315),(ERR5034366,((ERR5033910,(ERR5034364,ERR5034682)),((ERR5034368,(ERR4180091,ERR5033914)),(ERR5034369,((ERR5034958,ERR5034957),(ERR5034876,(ERR5034365,ERR5034062))))))))),(ERR5033922,(ERR5033909,((ERR5034822,(ERR5033924,(ERR5034821,((ERR5034824,ERR5034810),(ERR5034818,ERR5033921))))),(((ERR5101683,ERR5033923),(ERR5034820,(ERR5034823,ERR5033911))),((ERR5033989,(ERR5033920,ERR5033917)),((ERR5033908,ERR5033915),(ERR5033907,ERR5033906)))))))))))))))))))))))))))))))); Final quartet score is: 9129500585 Final normalized quartet score is: 0.8112629473690398 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 2: {ERR5034959, ERR5033993} 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: {ERR5034959, ERR5034860, ERR5033993} Extended species tree: (ERR5034371,(ERR5034064,((ERR5034380,(ERR5034875,((ERR5034963,ERR5034375)1:0.7948902903957221,(ERR5034679,ERR5034962)0.51:0.06368480152147532)0.99:0.14164354573132523)1:0.5121498324249502)0.8:0.06296561118824413,((ERR5101684,((ERR5034063,(ERR5033995,ERR5033994)0.82:0.13082603336638077)0.66:0.046891141375994205,((ERR5034396,(ERR5084301,(ERR5101681,ERR5034960)1:0.6888661632124554)0.53:0.13369839911047182)0.96:0.1282197981686057,((ERR5034964,ERR5034376)1:0.1413874265390755,((ERR5034379,ERR5034378)1:0.2555501609270514,(ERR5034370,(ERR5034372,(ERR5034377,ERR5034373)1:0.6637225810626474)0.77:0.07468312283064686)0.54:0.03267721168995944)1:0.1754310451514702)0.28:0.0)0.99:0.11786899610815199)0.42:0.03373835403078581)0.83:0.11222929324757101,(((ERR5034860,(ERR5034959,ERR5033993)0.87:0.6931471805599453)0.11:0.0,(ERR5034861,(ERR5033406,(ERR5034066,ERR5034961)0.5:0.023358403397272708)0.93:0.10237982343321782)0.94:0.10077267740416301)1:0.23156667722782898,(ERR5034000,(ERR5033996,(ERR5033999,(ERR5034815,((((ERR5033998,ERR5033997)1:0.9027898714798148,(ERR5034114,(ERR5033900,(ERR5033899,ERR5033901)1:0.8087127622073482)0.99:0.17230384806492233)1:0.7585643152180725)1:0.5701578312736789,(ERR5101669,(ROOT,(((ERR5033898,(ERR5033896,(ERR5034817,(ERR5033897,ERR5034816)1:1.0769954207936867)1:1.5265588317953422)1:0.1705157895449287)1:0.9287468939401693,(MMIR_1928,((ERR5034956,ERR5034955)1:0.6422518915580342,(ERR5034954,(ERR5034361,ERR5034109)0.95:0.12847854813284468)1:0.5478027188851016)1:1.760836469014693)1:1.9016398039855498)0.95:0.0926957161342512,((ERR5033988,(ERR5033991,ERR5033990)1:0.769621191011156)1:1.6219710376292227,(((ERR5033982,(ERR5033981,((ERR5033980,ERR5033979)0.8:0.08582764795356905,(ERR5033983,(ERR5033985,ERR5033984)0.71:0.08305946058354437)0.55:0.06599464771164294)1:0.7123872656194854)1:1.271488296387741)1:2.293269843331113,(ERR5034061,((ERR5034971,(ERR5033930,ERR5034394)1:2.307280275617791)1:0.47871768499592277,((ERR5033939,(ERR5033937,ERR5034395)1:1.2748533764251633)1:0.6758921536719052,(((ERR5033932,ERR5033934)1:1.3404535034389586,(ERR5033927,ERR5034970)1:1.7498932892192822)0.85:0.0727181256668271,((ERR5033926,(ERR5033935,ERR5033933)1:0.5117186382663811)1:0.34335674823753276,((ERR5033929,ERR5033931)0.27:0.12180985096153035,(ERR5033936,ERR5033928)1:0.317635869829924)1:1.0059827108037012)1:0.4288766395075893)0.94:0.09248477888127572)1:0.32535768703748763)0.55:0.03063456068475865)1:1.4906710984603124)1:0.19444768964082157,(ERR5033992,(ERR5033913,((ERR5033919,ERR5033918)1:0.43417820600227264,(((ERR5034873,(ERR5034111,ERR5033925)1:0.6732267629703049)0.98:0.1284390463581106,((ERR5034374,ERR5084315)1:0.835169248904636,(ERR5034366,((ERR5033910,(ERR5034364,ERR5034682)1:2.005357924432424)0.99:0.14447818352848824,((ERR5034368,(ERR4180091,ERR5033914)1:0.5773679887410463)1:0.34209714441804445,(ERR5034369,((ERR5034958,ERR5034957)0.99:0.13582450365737755,(ERR5034876,(ERR5034365,ERR5034062)0.64:0.04845363887144815)1:0.20845190063224117)0.98:0.13098491153668668)1:0.15056751301156773)1:0.24033925803109293)1:0.5412414340403672)1:0.5480703240164244)0.98:0.10606579121448294)1:0.6051092568724784,(ERR5033922,(ERR5033909,((ERR5034822,(ERR5033924,(ERR5034821,((ERR5034824,ERR5034810)0.99:0.16619234377801392,(ERR5034818,ERR5033921)0.99:0.1364188004754894)0.68:0.0672830337711759)0.69:0.05580414273348501)1:0.6722141320911796)0.46:0.019210386614708367,(((ERR5101683,ERR5033923)1:0.8067513849516001,(ERR5034820,(ERR5034823,ERR5033911)1:1.1610824173481227)0.61:0.040964025345670625)1:1.2161123013022443,((ERR5033989,(ERR5033920,ERR5033917)1:1.0642189352090636)1:0.44766437541943593,((ERR5033908,ERR5033915)1:1.2029197362884445,(ERR5033907,ERR5033906)1:0.45537971010145745)1:0.9115413671169774)1:0.1826252323751366)0.67:0.06085166065018862)0.99:0.13493476517987094)0.99:0.1334699907154588)1:0.23049870400685796)0.81:0.0609793835350329)0.71:0.04850956408101899)1:2.451327482482113)0.39:0.009884471674850237)1:0.39695688243672667)1:1.2704259079354336)1:0.19662680476882188)0.96:0.17528072085096688)0.99:0.19405779164580128)1:0.1574299784431539,(((ERR5033895,(ERR5033893,ERR5033894)1:0.6911507340496619)1:1.2625190462328182,((((ERR5034825,ERR5034953)1:1.2152962431623424,(ERR5034360,(ERR5034859,ERR5034952)0.97:0.11741083671971228)1:1.014569813824271)1:0.7666587966199675,((ERR5034969,(ERR5033905,ERR5033902)1:0.49386365029755575)1:1.4613723902391282,((ERR5033904,ERR5101682)1:0.38087884275554135,(ERR5033903,ERR5034393)1:0.9131272372999477)1:0.8764662822689399)1:0.3426891230544121)1:0.3288727676949412,(((ERR5034362,(ERR5034363,ERR5034113)1:0.6056464186255108)1:3.85628040060211,((ERR5033987,(ERR5033986,ERR5034830)1:1.3437523981724557)1:0.5849166660291106,((ERR5084257,ERR5034681)1:2.204259275232968,(ERR5034110,ERR5034115)0.82:0.08393900451355184)1:0.21118050744131528)1:2.5330902771923474)0.59:0.06780146787187422,(ERR4180211,(ERR5060317,(ERR5084279,(ERR5034060,(ERR5034677,(ERR5034680,(ERR4180132,(ERR5034678,(ERR5034858,ERR5033399)0.81:0.10951715481376666)0.45:0.02558617271920903)0.98:0.22870542498989563)0.83:0.07392401591091445)1:1.326534173824037)0.27:0.0)1:0.5758181584491667)1:1.019047682343446)1:3.7753890913621353)1:2.368517952986583)1:0.5557744571282061)0.57:0.049266719463048544,((ERR5033945,(ERR5033949,((ERR5033946,(ERR5033941,ERR5033947)1:0.5651596103423371)1:0.8913407691211406,(ERR5033944,((ERR5033942,ERR5033943)1:0.6573728001534197,(ERR5034831,(ERR5033940,ERR5033948)1:0.3531273606753341)1:0.41908395848968305)0.96:0.1799318009100168)1:0.2985622635830515)0.96:0.14937618115020054)0.99:0.16872439456546173)1:0.499245543005497,((ERR5034829,ERR5033955)1:0.8980936320147064,(ERR5033957,(ERR5033965,((((ERR5033971,ERR5033967)1:0.2990890247628594,(ERR5033961,ERR5033969)0.99:0.11563709702879872)1:0.4520056810036198,(ERR5033978,(ERR5033976,(ERR5034826,(ERR5033959,((ERR5033973,ERR5033953)1:0.7451081981027968,(ERR5034828,(ERR5033956,ERR5033974)1:1.3378926337855588)0.53:0.03961994330937237)0.99:0.12295213849880597)0.52:0.038505131919001685)1:0.20958928761244366)1:0.19527223680470226)0.34:0.0)0.39:0.017105007266451498,((ERR5034972,(ERR5033963,(ERR5033958,(ERR5034827,(ERR5033966,(ERR5033968,ERR5033970)1:0.2888233546884957)1:0.22071202275136062)1:0.23279060794974268)0.43:0.014741271899822599)0.59:0.06350533242529029)1:0.78438763636323,((ERR5033964,(ERR5033960,(ERR5033950,ERR5033962)1:0.37984289290771633)0.93:0.09382610098759366)1:0.18174788888283774,(ERR5033954,((ERR5033975,ERR5033972)1:0.6104209622995638,(ERR5034065,(ERR5033977,(ERR5033952,ERR5033951)1:1.473343055518063)1:0.26633451570490246)1:0.5555197525377128)0.99:0.11591424203556779)1:0.25624618670389626)0.97:0.10002617773097026)1:0.1772175923614498)0.98:0.10244901574010357)1:0.3035917225527433)0.99:0.12465724114655377)1:1.511454764717533)1:0.7706708044115681)1:0.15274891627449835)1:0.24412525408371152)1:0.30984647322663045)1:0.9642625891149215)1:0.21392849275485312)1:0.587263906845592)1:0.4600007674060357)0.48:0.020004661706054475)1:0.3605424401248607)); Weight calculation took 152.461756225 secs ASTRAL finished in 172.97 secs
** Version astral.5.7.7
Additional context I haven't encountered this issue when I was running astral analyses for other data sets.