AttributeError: 'NoneType' object has no attribute 'get_child_at'
lychen83 opened this issue · comments
Hello Emmanuel,
I am using profileNJ to fix gene tree.
My gene tree is as following:
(red_Nyctaginaceae_Anulocaulis_annulatus@27853:1.00000050003e-06,((red_Nyctaginaceae_Boerhavia_ciliata@13258:0.0750229228896,red_Nyctaginaceae_Boerhavia_ciliata@47639:0.393322292936)81:0.0503980792703,((red_Nyctaginaceae_Commicarpus_scandens@37240:0.0853400496541,(red_Nyctaginaceae_Commicarpus_scandens@37241:0.0693061575783,red_Nyctaginaceae_Commicarpus_scandens@37242:1.00000050003e-06)52:0.00188295368716)99:0.118423458122,(red_Nyctaginaceae_Anulocaulis_annulatus@27850:1.00000050003e-06,((((((red_Sarcobataceae_Sarcobatus_vermiculatus@10866:0.122532346073,red_Phytolaccaceae_Rivina_humilis@6133:0.0771373097868)77:0.0457652835781,red_Phytolaccaceae_Phytolacca_americana@19681:0.0957523478508)24:0.0232077280165,((((red_Gisekiaceae_Gisekia_pharnaceoides@65620:0.0162456785951,(red_Gisekiaceae_Gisekia_pharnaceoides@65621:0.00681970420165,red_Gisekiaceae_Gisekia_pharnaceoides@65622:1.00000050003e-06)93:0.0137781609124)95:0.132874653756,(red_Aizoaceae_Mesembryanthemum_crystallinum@8529:0.223075138192,(blue_Kewaceae_Kewa_bowkeriana@31410:0.228851579754,red_Aizoaceae_Delosperma_echinatum@7254:0.141714511709)29:0.0396085895611)17:0.0154021255408)20:0.0367093001471,((((red_Anacampserotaceae_Anacampseros_filamentosa@14002:0.0826118742079,red_Anacampserotaceae_Anacampseros_filamentosa@14001:0.003197010308)100:0.109493084342,(red_Talinaceae_Talinum_fruticosum@66847:0.0676274464062,red_Talinaceae_Talinum_fruticosum@66849:0.0139847411967)74:0.0511618653015)70:0.091045419994,((red_Didieraceae_Decarya_madagascariensis@23199:0.0852317909327,((red_Amaranthaceae_Alternanthera_philoxeroides@17136:0.454697936118,red_Basellaceae_Basella_alba@23542:0.0199662285352)23:0.046662612322,red_Anacampserotaceae_Anacampseros_filamentosa@49652:0.595301597061)4:0.0337060396382)4:0.0429593180478,((red_Anacampserotaceae_Anacampseros_filamentosa@14000:0.0841031764793,blue_Portulacaceae_Portulaca_oleracea_SRA@46368:0.109269449235)26:0.0268324229235,(red_Cactaceae_Opuntia_arenaria@39809:0.0315454355484,red_Cactaceae_Opuntia_arenaria@39810:0.00343597093487)100:0.09104635865)39:0.0515253411516)2:0.037503228393)5:0.0635440257922,(unknown_Microteaceae_Microtea_debilis@17540:0.145860437869,red_Montiaceae_Claytonia_nevadensis@56211:0.187699045965)20:0.0705402302503)4:0.0742239111562)0:0.0184869798936,(((blue_Molluginaceae_Glinus_lotoides_var_virens@36790:0.146012741869,(((blue_Molluginaceae_Glinus_lotoides_var_virens@14738:0.00983571271816,blue_Molluginaceae_Glinus_lotoides_var_virens@14739:0.0269370027329)99:0.195303617112,blue_Molluginaceae_Mollugo_verticillata@40080:0.150193781851)26:0.0320365128929,blue_Molluginaceae_Mollugo_pentaphylla@44374:0.218825470856)24:0.0361546632693)19:0.022154212428,(((blue_Macarthuriaceae_Macarthuria_australis@11352:0.00512290112574,blue_Macarthuriaceae_Macarthuria_australis@11351:0.0125256548542)96:0.142732271888,(((unknow_Achatocarpaceae_Achatocarpus_gracilis@77644:0.0105323245142,unknow_Achatocarpaceae_Phaulothamnus_spinescens@17223:0.0137385511835)99:0.174326161,((blue_Limeaceae_Limeum_aethiopicum@23901:0.00347291975739,(blue_Limeaceae_Limeum_aethiopicum@23900:0.020879247556,blue_Limeaceae_Limeum_aethiopicum@23899:0.0204887166203)69:0.00440202539874)100:0.257186692901,(blue_Molluginaceae_Mollugo_nudicaulis@169477:0.0411641859481,(blue_Molluginaceae_Pharnaceum_exiguum@2865:0.111007925512,(blue_Molluginaceae_Suessenguthiella_caespitosa@36653:0.0710636432298,blue_Molluginaceae_Mollugo_cerviana@40369:0.0791069642423)44:0.0211564098103)86:0.0655998388691)51:0.0241342277802)33:0.018360023148)12:0.0257142317318,((((blue_Caryophyllaceae_Paronychia_jamesii@203596:1.00000050003e-06,blue_Caryophyllaceae_Paronychia_jamesii@59891:1.00000050003e-06)100:0.116801488685,blue_Caryophyllaceae_Paronychia_jamesii@87181:0.0367037061832)100:0.154892753682,((blue_Caryophyllaceae_Polycarpon_tetraphyllum@79315:0.00943712161928,blue_Caryophyllaceae_Polycarpon_tetraphyllum@79314:1.00000050003e-06)97:0.135688581605,(((blue_Caryophyllaceae_Arenaria_serpyllifolia@39076:0.140821562494,blue_Caryophyllaceae_Dianthus_caryophyllus@29848_1:0.235153719659)28:0.0207193309636,(blue_Caryophyllaceae_Spergularia_marina@25124:0.00857472979863,(blue_Caryophyllaceae_Spergularia_marina@25123:1.00000050003e-06,blue_Caryophyllaceae_Spergularia_marina@25125:0.032413342875)96:0.0360590845676)100:0.171391427605)16:0.00742687466695,(blue_Caryophyllaceae_Silene_latifoliasra@61371:0.608803217036,((blue_Caryophyllaceae_Cerastium_arvense@29092:0.176471004778,(blue_Caryophyllaceae_Eremogone_hookeri_ssp_desertorum@24385:1.00000050003e-06,blue_Caryophyllaceae_Eremogone_hookeri_ssp_desertorum@24384:0.028997709389)100:0.102532078937)63:0.0615824913541,(blue_Caryophyllaceae_Silene_latifoliasra@33251:0.0860763478519,blue_Caryophyllaceae_Silene_latifoliasra@33249:0.0473470645264)100:0.142510307827)28:0.0086055003488)23:0.0298212089246)57:0.0785513976465)36:0.0397157106442)46:0.0858246940584,(((((unknow_Achatocarpaceae_Achatocarpus_gracilis@15738:0.0751052162584,(unknow_Achatocarpacea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0817617987936)100:0.020620013969,red_Nyctaginaceae_Anulocaulis_annulatus@27852:1.00000050003e-06):0;
The species tree is as ：
(red_Aizoaceae_Mesembryanthemum_crystallinum:0.0450604,red_Aizoaceae_Delosperma_echinatum:0.0661721,((((((((red_Talinaceae_Talinum_fruticosum:0.04799,((blue_Portulacaceae_Portulaca_oleracea_SRA:0.086149,red_Anacampserotaceae_Anacampseros_filamentosa:0.0710509)0.227561:0.0243853,red_Cactaceae_Opuntia_arenaria:0.0592674)0.204741:0.0204919)0.192849:0.0215703,red_Didieraceae_Decarya_madagascariensis:0.0756626)0.158779:0.0255401,red_Basellaceae_Basella_alba:0.0977187)0.172439:0.0252723,red_Montiaceae_Claytonia_nevadensis:0.142093)0.489594:0.0515856,(((blue_Molluginaceae_Mollugo_verticillata:0.0762864,blue_Molluginaceae_Glinus_lotoides_var_virens:0.0952005)0.517477:0.0502438,(((blue_Molluginaceae_Suessenguthiella_caespitosa:0.0280913,blue_Molluginaceae_Pharnaceum_exiguum:0.0355129)0.899156:0.0675433,blue_Molluginaceae_Mollugo_cerviana:0.0546466)0.763359:0.0706458,blue_Molluginaceae_Mollugo_nudicaulis:0.0725936)0.241623:0.0323627)0.139654:0.0280663,blue_Molluginaceae_Mollugo_pentaphylla:0.0869379)0.349136:0.0419757)0.0882282:0.0184875,((unknown_Microteaceae_Microtea_debilis:0.115314,((((((((outgroup_Zea_mays:0.123303,outgroup_Oryza_sativa:0.103723)0.98409:0.389963,outgroup_Amborella_trichopoda:0.333062)0.54552:0.092093,outgroup_Aquilegia_coerulea:0.235061)0.46131:0.0676768,(outgroup_Vitis_vinifera:0.143998,((outgroup_Populus_trichocarpa:0.172474,outgroup_Glycine_max:0.253492)0.263158:0.0539216,outgroup_Arabidopsis_thalinana:0.328932)0.292166:0.0451055)0.114825:0.0309429)0.126476:0.0274854,(outgroup_Solanum_lycopersicum:0.205785,outgroup_Coffea_arabica:0.176291)0.696264:0.0778749)0.646766:0.0867224,(((blue_Tamaricaceae_Tamarix_hispida:0.123722,blue_Frankeniaceae_Frankenia_laevis:0.130271)0.792527:0.108798,((((blue_Polygonaceae_Polygonum_aviculare:0.0996086,blue_Polygonaceae_Rumex_hastatulus:0.114415)0.490317:0.043164,blue_Polygonaceae_Fagopyrum_esculentum:0.115399)0.246203:0.0315209,(blue_Polygonaceae_Persicaria_virginiana:0.065746,blue_Polygonaceae_Bistorta_bistortoides:0.0667565)0.569225:0.0429856)0.821776:0.120827,blue_Plumbagianceae_Limonium_californicum:0.230353)0.629088:0.0671343)0.211169:0.0295152,((blue_Nepenthaceae_Nepenthes_alata:0.143197,blue_Droseraceae_Dionaea_muscipula:0.210585)0.289514:0.0445673,(blue_Drosophyllaceae_Drosophyllum_lusitanicum:0.12284,blue_Ancistrocladaceae_Ancistrocladus_robertsoniorum:0.092231)0.577822:0.0480156)0.467979:0.0461271)0.166734:0.0249106)0.367376:0.0394082,unknow_Simmondsiaceae_Simmondsia_chinensis:0.146691)0.307513:0.0399512,unknown_Physenaceae_Physena_madagascariensis:0.130179)0.44781:0.0583514)0.0903978:0.0304107,(((red_Stegnospermataceae_Stegnosperma_halimifolium:0.128971,blue_Macarthuriaceae_Macarthuria_australis:0.0993202)0.128646:0.026511,blue_Limeaceae_Limeum_aethiopicum:0.107646)0.0405785:0.0221891,(((unknow_Achatocarpaceae_Phaulothamnus_spinescens:0.0109613,unknow_Achatocarpaceae_Achatocarpus_gracilis:0.0125008)0.906147:0.0845274,((((red_Chenopodiaceae_Chenopodium_quinoa:0.084165,red_Chenopodiaceae_Spinacia_oleracea:0.0576629)0.696344:0.0359273,(red_Chenopodiaceae_Suaeda_glauca:0.0880383,(red_Chenopodiaceae_Haloxylon_ammodendron:0.0228602,red_Chenopodiaceae_Halogeton_glomeratus:0.0253254)0.904701:0.0704752)0.623865:0.0342216)0.188027:0.0168836,red_Amaranthaceae_Beta_vulgaris:0.0647222)0.212696:0.0173415,(red_Amaranthaceae_Amaranthus_hypochondriacus:0.116166,red_Amaranthaceae_Alternanthera_philoxeroides:0.139112)0.446766:0.0346947)0.627079:0.0499217)0.311209:0.0232434,(((((blue_Caryophyllaceae_Silene_latifoliasra:0.076559,blue_Caryophyllaceae_Eremogone_hookeri_ssp_desertorum:0.0918624)0.247248:0.0267116,((blue_Caryophyllaceae_Arenaria_serpyllifolia:0.0866925,blue_Caryophyllaceae_Cerastium_arvense:0.103289)0.306308:0.0289678,blue_Caryophyllaceae_Dianthus_caryophyllus:0.116041)0.1227:0.0224426)0.434873:0.0324654,blue_Caryophyllaceae_Spergularia_marina:0.107852)0.548895:0.0430384,blue_Caryophyllaceae_Polycarpon_tetraphyllum:0.15344)0.41366:0.0363426,blue_Caryophyllaceae_Paronychia_jamesii:0.158148)0.607955:0.0537153)0.289675:0.0271112)0.0171957:0.0133588)0.05681:0.0157166)0.119807:0.0196167,((red_Phytolaccaceae_Phytolacca_americana:0.055412,(((red_Nyctaginaceae_Commicarpus_scandens:0.0309045,(red_Nyctaginaceae_Boerhavia_ciliata:0.0291848,red_Nyctaginaceae_Anulocaulis_annulatus:0.0191104)0.597589:0.0282621)0.923423:0.131052,red_Phytolaccaceae_Rivina_humilis:0.123754)0.213821:0.0288509,red_Sarcobataceae_Sarcobatus_vermiculatus:0.159495)0.1272:0.0240484)0.146726:0.0212431,red_Gisekiaceae_Gisekia_pharnaceoides:0.0978699)0.168582:0.0211642)0.100763:0.0189328,blue_Kewaceae_Kewa_bowkeriana:0.0993581)0.751145:0.0619381);
I have confirmed that the species names in gene tree and species tree are completely identifcal.
However, when I run the command:
profileNJ -s species_tree.tre -g gene_tree.tre --sep '@' --spos 'prefix' -r best
I got error:
Traceback (most recent call last):
File "/home/yangya/clingyun/biosofts/python2.7.6_installed/bin/profileNJ", line 4, in
import('pkg_resources').run_script('ProfileNJ==20161018', 'profileNJ')
File "/home/yangya/clingyun/biosofts/python2.7.6_installed/lib/python2.7/site-packages/pkg_resources/init.py", line 765, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/yangya/clingyun/biosofts/python2.7.6_installed/lib/python2.7/site-packages/pkg_resources/init.py", line 1545, in run_script
exec(code, namespace, namespace)
File "/panfs/roc/groups/0/yangya/clingyun/biosofts/python2.7.6_installed/lib/python2.7/site-packages/ProfileNJ-20161018-py2.7.egg/EGG-INFO/scripts/profileNJ", line 285, in
verbose=args.verbose, sol_limit=args.sol_limit, method=args.cluster, path_limit=args.path_limit)
File "/home/yangya/clingyun/biosofts/python2.7.6_installed/lib/python2.7/site-packages/ProfileNJ-20161018-py2.7.egg/profileNJ/PolytomySolver/Multipolysolver.py", line 660, in solvePolytomy
path_limit) + method), ptree, sptree, matrice, order, path_limit, cluster_method=method, verbose=verbose)
File "/home/yangya/clingyun/biosofts/python2.7.6_installed/lib/python2.7/site-packages/ProfileNJ-20161018-py2.7.egg/profileNJ/TreeLib/memorize.py", line 26, in call
output = self.function(*args, **kwargs)
File "/home/yangya/clingyun/biosofts/python2.7.6_installed/lib/python2.7/site-packages/ProfileNJ-20161018-py2.7.egg/profileNJ/PolytomySolver/Multipolysolver.py", line 140, in polySolver
:], verbose=verbose, method=cluster_method, cost=cost_table[xsize - 1, 0]))
File "/home/yangya/clingyun/biosofts/python2.7.6_installed/lib/python2.7/site-packages/ProfileNJ-20161018-py2.7.egg/profileNJ/PolytomySolver/Multipolysolver.py", line 454, in constructFromPath
[dup_tree.get_child_at(0).name, dup_tree.get_child_at(1).name])
AttributeError: 'NoneType' object has no attribute 'get_child_at'
The example data in your software package can run. Could you kindly help me resolve this prolem?
Thank you so much
Best
Lingyun
Hi Lingyun,
ProfileNJ only accepts rooted species tree as input, since its a requirement of the gene tree polytomy resolution algorithm.
But yes, the error is not informative at all, and I will fix it as soon as I have some time.
If you root your species tree, it should work. I have noticed, there are outgroups in the species tree. Try rooting the tree with the corresponding clade (or maybe just midpoint rooting).
Also please note that, as correction relies on the species tree, different rooting will produce different results. Although the method is somewhat robust to that, you should still keep that in mind.
Best
Emmanuel
Hi Emmanuel,
Thank you for help. After rooting the species tree, the analysis working.
I still have one issue. I did not see any change on the topology of my gene tree, although there is obviously some strange topology (bootstrap value is lower than 30 for them) comparing to the species tree. Is it possible to set the profileNJ more aggressive? Can I use the bootstrap rather than distance matrix?
Thank you so much.
Best regards,
Lingyun
Hello Lingyun,
You just need to define a bootstrap threshold to contract edges with low support.
(Since the threshold is not defined and you input genetree is not rooted profileNJ only test the best rooting with the lowest reconciliation score, therefore, RF = 0 compared to your original tree).
If you set the threshold to 90 for example (any subtree with parental branch below that threshold will be modified), the correct command line is:
profileNJ -s species_tree.tre -g gene_tree.tre --sep '@' --spos 'prefix' -r best --seuil 90
For more options see: profileNJ -h
As a side note, you could test several threshold (and even different dup/loss cost), then use consel to evaluate the statistical significance of corrected trees against your input, that I assume is the, maximum likelihood tree. This will allow you to somewhat explore the distribution of trees that are equivalent to the best ML tree, but are in agreement with the species phylogeny.
Best,
Emmanuel
Thanks Emmanuel,
After used the command '--seuil 90', it working!
Best
Lingyun