Problems understanding summary results

[itiago]

Hi
I cannot understand the results that I have in summary files. The phylogenetic classification doesn't seems to have any hierarchy, the phylogenetic groups seem scattered. Is there a way, a output that I can use with percentage of each phylogenetic group determined? Or at least a way that the phylogenetic groups are listed from order phylum class family genus species.
Please see bellow the out put of taxa_90pct_HPD that I've got.
Thank you for any help
best

#Taxon_ID Taxon_Rank Taxon_Name Probability_Mass
2323 no rank UNCLASSIFIED BACTERIA 67.7550808846286
186801 class CLOSTRIDIA 48.1818926615539
28890 phylum EURYARCHAEOTA 43.8176742723694
180252 genus MARDIVIRUS 42.239998171038
2 superkingdom BACTERIA 38.6765763967502
74152 phylum ELUSIMICROBIA 36.923412759582
2157 superkingdom ARCHAEA 29.8294179324969
28221 class DELTAPROTEOBACTERIA 23.512760549098
10294 genus SIMPLEXVIRUS 20.224253266672
10319 genus VARICELLOVIRUS 17.8272728992329
976 phylum BACTEROIDETES 17.3965667145503
200795 phylum CHLOROFLEXI 16.5205306714165
2759 superkingdom EUKARYOTA 15.8109796175687
1224 phylum PROTEOBACTERIA 14.9408172660658
80840 order BURKHOLDERIALES 14.6763287712078
104388 species ANATID HERPESVIRUS 1 14.2991791629061
203682 phylum PLANCTOMYCETES 14.1617497761839
221216 phylum PARCUBACTERIA 14.1429672734848
1046984 no rank UNCLASSIFIED PARCUBACTERIA 14.1429672734848
1046989 species PARCUBACTERIA BACTERIUM SCGC AAA011 J21 14.1429672734848
67820 no rank MICROGENOMATES 14.1348618842177
1046980 no rank UNCLASSIFIED MICROGENOMATES 14.1348618842177
80864 family COMAMONADACEAE 13.5543004201798
481315 species LEPORID HERPESVIRUS 4 10.719149311938
119065 no rank UNCLASSIFIED BURKHOLDERIALES 10.0476656257464
539000 family CLOSTRIDIALES FAMILY XVII. INCERTAE SEDIS 9.9027432647522
118964 order DEINOCOCCALES 9.35162699120047
186802 order CLOSTRIDIALES 9.09298136527913
1047003 no rank CANDIDATUS MICROGENOMATUS AURICOLA SCGC AAA011 E14 8.468109215189
1073573 species SAR324 CLUSTER BACTERIUM JCVI SC AAA005 8.33911229617494
995019 family SUTTERELLACEAE 8.2543571913185
35246 species CERCOPITHECINE HERPESVIRUS 9 8.00920190079276
1047061 species MARINIMICROBIA BACTERIUM JGI 0000059 L03 7.94884437638614
301297 class DEHALOCOCCOIDIA 7.5724624985584
180255 genus ILTOVIRUS 7.28077566279544
10386 species GALLID HERPESVIRUS 1 7.28077566279544
117743 class FLAVOBACTERIIA 7.25986974790918
189775 class THERMOMICROBIA 7.1792062248773
213468 family SYNTROPHACEAE 7.03972811623339
1047055 species MARINIMICROBIA BACTERIUM JGI 0000039 D08 6.9827342507313
699262 species MICROGENOMATES BACTERIUM SCGC AAA011 L6 6.8592697503376
255727 suborder CORIOBACTERINEAE 6.82408690691444
84999 order CORIOBACTERIALES 6.82408690691444
84107 family CORIOBACTERIACEAE 6.82408690691444
84998 subclass CORIOBACTERIDAE 6.82408690691444
68335 genus COPROTHERMOBACTER 6.78007108867223
28216 class BETAPROTEOBACTERIA 6.67683809664979
427925 genus DETHIOBACTER 6.20600555070151
555088 no rank DETHIOBACTER ALKALIPHILUS AHT 1 6.20600555070151
427926 species DETHIOBACTER ALKALIPHILUS 6.20600555070151
10240 family POXVIRIDAE 5.85215325763436
10338 no rank HUMAN HERPESVIRUS 3 STRAIN DUMAS 5.74938294322898
10335 species HUMAN HERPESVIRUS 3 5.74938294322898
1117 phylum CYANOBACTERIA 5.67965709984567
2037 order ACTINOMYCETALES 5.67836848598464
117942 family DESULFURELLACEAE 5.5551246031969
213113 order DESULFURELLALES 5.5551246031969
68336 superphylum BACTEROIDETES/CHLOROBI GROUP 5.44635723868172
77133 species UNCULTURED BACTERIUM 5.273749733226
189384 genus CANDIDATUS TREMBLAYA 4.8009030658576
1239 phylum FIRMICUTES 4.52940696115807
62680 phylum MARINIMICROBIA 4.4903785383545
186814 family THERMOANAEROBACTERACEAE 4.48966024436195
1046981 no rank UNCLASSIFIED CANDIDATE DIVISION NKB19 4.4676703441163
142187 no rank CANDIDATE DIVISION NKB19 4.4676703441163
1046982 species HYDROGENEDENTES BACTERIUM JGI 0000039 J10 4.4676703441163
28067 genus RUBRIVIVAX 4.3801689605918
160619 species KRYPTOPERIDINIUM FOLIACEUM 4.3215639104224
160618 genus KRYPTOPERIDINIUM 4.3215639104224
28262 species THERMODESULFOVIBRIO YELLOWSTONII 4.23788520910848
28261 genus THERMODESULFOVIBRIO 4.23788520910848
289376 no rank THERMODESULFOVIBRIO YELLOWSTONII DSM 11347 4.23788520910848
224471 no rank BURKHOLDERIALES GENERA INCERTAE SEDIS 4.0959782666846
179 genus LEPTOSPIRILLUM 4.071959150315
400756 species DURINSKIA BALTICA 4.01277392951055
400754 genus DURINSKIA 4.01277392951055
1269028 no rank ACANTHAMOEBA POLYPHAGA MOUMOUVIRUS 3.72460182397907
112 order PLANCTOMYCETALES 3.56787827617837
126 family PLANCTOMYCETACEAE 3.56787827617837
94695 order METHANOSARCINALES 3.48363248555097
2258 order THERMOCOCCALES 3.33756684761244
2259 family THERMOCOCCACEAE 3.33756684761244
183968 class THERMOCOCCI 3.33756684761244
1385 order BACILLALES 3.25644370474083
212035 species ACANTHAMOEBA POLYPHAGA MIMIVIRUS 3.25394398860425
315393 genus MIMIVIRUS 3.25394398860425
265317 phylum PORIBACTERIA 3.19198513074598
700750 species CANDIDATUS PORIBACTERIA SP. WGA A3 3.19198513074598
10239 superkingdom VIRUSES 3.1289035093059
68295 order THERMOANAEROBACTERALES 3.1158362749958
35237 no rank DSDNA VIRUSES NO RNA STAGE 3.0905622273651
420506 species PSEUDOMONAS SP. TAP 9 3.084096749673
131567 no rank CELLULAR ORGANISMS 3.06928714788578
1247379 no rank MOUMOUVIRUS GOULETTE 3.02345894914011
1236 class GAMMAPROTEOBACTERIA 2.993300262158
795665 species HYDROGENOPHAGA SP. PBC 2.9760634553058
47420 genus HYDROGENOPHAGA 2.9760634553058
29547 class EPSILONPROTEOBACTERIA 2.94077337959297
412449 species LEPTOSPIRILLUM FERRODIAZOTROPHUM 2.8852383909734
49546 family FLAVOBACTERIACEAE 2.857035792411
40117 phylum NITROSPIRAE 2.73045211348307
189778 order NITROSPIRALES 2.73045211348307
189779 family NITROSPIRACEAE 2.73045211348307
203693 class NITROSPIRA 2.73045211348307
651137 phylum THAUMARCHAEOTA 2.720357514511
2191 order METHANOMICROBIALES 2.71472202727902
2158 order METHANOBACTERIALES 2.6832911993001
183925 class METHANOBACTERIA 2.6832911993001
57723 phylum ACIDOBACTERIA 2.6033722627672
28211 class ALPHAPROTEOBACTERIA 2.56217814319635
200643 class BACTEROIDIA 2.55949863836525
171549 order BACTEROIDALES 2.55949863836525
69541 order DESULFUROMONADALES 2.53151307004127
543371 family THERMOANAEROBACTERALES FAMILY III. INCERTAE SEDIS 2.52594094975175
29 order MYXOCOCCALES 2.49250615331
985780 no rank UNCLASSIFIED MIMIVIRIDAE 2.43786244480941
67818 phylum ATRIBACTERIA 2.37674806154577
1047049 no rank UNCLASSIFIED ATRIBACTERIA 2.37674806154577
227387 family THERMODESULFOBIACEAE 2.20485189984919
589342 order PYRENOMONADALES 2.16901587900483
203683 class PLANCTOMYCETIA 2.1045001835608
1047007 species OMNITROPHICA BACTERIUM SCGC AAA257 O07 2.04652792031222
1047005 no rank UNCLASSIFIED OMNITROPHICA 2.04652792031222
67812 phylum OMNITROPHICA 2.04652792031222
1131291 species GALLIONELLA SP. SCGC AAA018 N21 2.04507257424681
538999 no rank CLOSTRIDIALES INCERTAE SEDIS 2.01388705743812
985782 species MOUMOUVIRUS 2.00930380869041
1150 order OSCILLATORIALES 2
72294 family CAMPYLOBACTERACEAE 2
662 genus VIBRIO 1.9999999999997
38145 species UNCULTURED GRAM POSITIVE BACTERIUM 1.999018646003
658858 no rank GIARDIA LAMBLIA P15 1.979614208809
145522 species NANNOCHLOROPSIS OCEANICA 1.970341288609
10379 genus RHADINOVIRUS 1.9416853757266
10345 species SUID HERPESVIRUS 1 1.9272726383799
641853 class ELUSIMICROBIA 1.92598437604264
423604 genus ELUSIMICROBIUM 1.92598437604264
641854 order ELUSIMICROBIALES 1.92598437604264
423605 species ELUSIMICROBIUM MINUTUM 1.92598437604264
641876 family ELUSIMICROBIACEAE 1.92598437604264
445932 no rank ELUSIMICROBIUM MINUTUM PEI191 1.92598437604264
10257 genus PARAPOXVIRUS 1.9221561426076
795748 order IGNAVIBACTERIALES 1.9155713339131
1134404 phylum IGNAVIBACTERIAE 1.9155713339131
795747 class IGNAVIBACTERIA 1.9155713339131
51290 superphylum CHLAMYDIAE/VERRUCOMICROBIA GROUP 1.8769598423322
28033 genus SULFOBACILLUS 1.8687664451935
135622 order ALTEROMONADALES 1.8615611327795
224027 family HYDROGENOTHERMACEAE 1.834863113216
637379 no rank THALASSIOSIRA OCEANICA CCMP1005 1.8132586555482
159749 species THALASSIOSIRA OCEANICA 1.8132586555482
1010676 species CANDIDATUS TREMBLAYA PHENACOLA 1.8103729462412
1266371 no rank CANDIDATUS TREMBLAYA PHENACOLA PAVE 1.8103729462412
213462 order SYNTROPHOBACTERALES 1.80928924602559
184922 no rank GIARDIA LAMBLIA ATCC 50803 1.80877747551745
183967 class THERMOPLASMATA 1.786798194799
2301 order THERMOPLASMATALES 1.786798194799
471821 no rank UNCULTURED TERMITE GROUP 1 BACTERIUM PHYLOTYPE RS D17 1.71368389281153
99260 no rank ENVIRONMENTAL SAMPLES 1.71368389281153
167965 species UNCULTURED TERMITE GROUP 1 BACTERIUM 1.71368389281153
2272 family DESULFUROCOCCACEAE 1.6840380780517
84995 subclass RUBROBACTERIDAE 1.68010734495564
91061 class BACILLI 1.63280573752817
224462 suborder NANNOCYSTINEAE 1.6272915300453
987059 no rank RUBRIVIVAX BENZOATILYTICUS JA2 = ATCC BAA 35 1.53767500001317
316997 species RUBRIVIVAX BENZOATILYTICUS 1.53767500001317
1297 phylum DEINOCOCCUS THERMUS 1.53484525470542
188787 class DEINOCOCCI 1.53484525470542
6029 phylum MICROSPORIDIA 1.52388461413431
2237 genus HALOARCULA 1.4549382304459
2787 species PORPHYRA PURPUREA 1.44652204579915
2784 genus PORPHYRA 1.44652204579915
1094566 genus PYROPIA 1.39698839390905
2788 species PYROPIA YEZOENSIS 1.39698839390905
942 family ANAPLASMATACEAE 1.39296213040913
170 family LEPTOSPIRACEAE 1.392315410263
456828 phylum CLOACIMONETES 1.38754317024111
1047070 species CLOACIMONETES BACTERIUM JGI 0000039 G13 1.38754317024111
1047068 no rank UNCLASSIFIED CLOACIMONETES 1.38754317024111
191767 genus PLESIOCYSTIS 1.36607931114235
191768 species PLESIOCYSTIS PACIFICA 1.36607931114235
391625 no rank PLESIOCYSTIS PACIFICA SIR 1 1.36607931114235
224463 family NANNOCYSTACEAE 1.36607931114235
1760 class ACTINOBACTERIA 1.35673083698003
201174 phylum ACTINOBACTERIA 1.35673083698003
872 genus DESULFOVIBRIO 1.336824002792
10242 genus ORTHOPOXVIRUS 1.3215620149395
247490 species PLANCTOMYCETE KSU 1 1.3021940557083
69476 no rank UNCLASSIFIED PLANCTOMYCETACEAE 1.3021940557083
330214 species CANDIDATUS NITROSPIRA DEFLUVII 1.27389721904703
1234 genus NITROSPIRA 1.27389721904703
755731 species CLOSTRIDIUM SP. BNL1100 1.2601456810057
2222 genus METHANOSAETA 1.24147524584447
143067 family METHANOSAETACEAE 1.24147524584447
10353 species SAIMIRIINE HERPESVIRUS 1 1.21878041873767
354090 species UR2 SARCOMA VIRUS 1.214774232221
11884 species Y73 SARCOMA VIRUS 1.214774232221
598745 no rank GIARDIA INTESTINALIS ATCC 50581 1.2132565524329
67799 class THERMODESULFOBACTERIA 1.21092396017029
188710 order THERMODESULFOBACTERIALES 1.21092396017029
200940 phylum THERMODESULFOBACTERIA 1.21092396017029
188711 family THERMODESULFOBACTERIACEAE 1.21092396017029
1118 order CHROOCOCCALES 1.1658239059307
40544 genus SUTTERELLA 1.1616687908745
119060 family BURKHOLDERIACEAE 1.1114885419057
70448 species OSTREOCOCCUS TAURI 1.106822045131
28889 phylum CRENARCHAEOTA 1.0995984079726
2806 class FLORIDEOPHYCEAE 1.09653928955472
913317 species ATRIBACTERIA BACTERIUM SCGC AAA252 M02 1.09285041937267
1265734 species RHODOPIRELLULA MAIORICA 1.05493140367965
1265738 no rank RHODOPIRELLULA MAIORICA SM1 1.05493140367965
33807 no rank UNCLASSIFIED ALPHAPROTEOBACTERIA MISCELLANEOUS 1.049145183805
589343 family GEMINIGERACEAE 1.04871424088512
55529 species GUILLARDIA THETA 1.04871424088512
55528 genus GUILLARDIA 1.04871424088512
1051663 class NANOHALOARCHAEA 1.0406524871422
32069 order AQUIFICALES 1.02453410725023
200783 phylum AQUIFICAE 1.02453410725023
187857 class AQUIFICAE 1.02453410725023
1047051 species ATRIBACTERIA BACTERIUM SCGC AAA255 G05 1.0137548519169
913331 species SAR324 CLUSTER BACTERIUM SCGC AAA240 J09 1.000010255579
186823 family ALICYCLOBACILLACEAE 1.0000000000004
89374 family SAPROSPIRACEAE 1
766 order RICKETTSIALES 1
1485 genus CLOSTRIDIUM 1
1169103 species MOCKFORDIA XANTHOCAECILIAE 1
332054 species TRICHOPLUSIA NI SINGLE NUCLEOPOLYHEDROVIRUS 1
662758 genus CANDIDATUS PARVARCHAEUM 1
379 genus RHIZOBIUM 1
1279 genus STAPHYLOCOCCUS 1
5794 phylum APICOMPLEXA 1
913329 species SAR324 CLUSTER BACTERIUM SCGC AAA001 C10 0.999989744421
379546 genus ACIDULIPROFUNDUM 0.9997194925934
909929 order SELENOMONADALES 0.988311817725275
909932 class NEGATIVICUTES 0.988311817725275
1048260 no rank LEPTOSPIRILLUM FERRIPHILUM ML 04 0.984775747824265
178606 species LEPTOSPIRILLUM FERRIPHILUM 0.984775747824265
189385 species CANDIDATUS TREMBLAYA PRINCEPS 0.98455926915
891398 no rank CANDIDATUS TREMBLAYA PRINCEPS PCIT 0.98455926915
580370 class ZETAPROTEOBACTERIA 0.965937643663
89373 family CYTOPHAGACEAE 0.965303468128
1293498 class NITROSPINIA 0.94616966965988
407032 family NITROSPINACEAE 0.94616966965988
35800 genus NITROSPINA 0.94616966965988
1293499 order NITROSPINALES 0.94616966965988
1293497 phylum NITROSPINAE 0.94616966965988
939844 species MARINIMICROBIA BACTERIUM SCGC AAA003 L8 0.945562869442
1293577 species CANDIDATE DIVISION SR1 BACTERIUM MGEHA 0.93495366769275
221235 no rank CANDIDATE DIVISION SR1 0.93495366769275
53433 order HALANAEROBIALES 0.9311695915812
2263 genus THERMOCOCCUS 0.930215266329778
180 species LEPTOSPIRILLUM FERROOXIDANS 0.912449441838557
1162668 no rank LEPTOSPIRILLUM FERROOXIDANS C2 3 0.912449441838557
655606 species group LEPTOSPIRILLUM SP. GROUP I 0.912449441838557
378210 genus METHYLOVERSATILIS 0.90375368264
1095747 no rank FUSOBACTERIUM NECROPHORUM SUBSP. FUNDULIFORME ATCC 51357 0.899323322414
213481 order BDELLOVIBRIONALES 0.895564693138
191412 family CHLOROBIACEAE 0.82390431245765
191411 order CHLOROBIALES 0.82390431245765
1090 phylum CHLOROBI 0.82390431245765
191410 class CHLOROBIA 0.82390431245765
79206 genus DESULFOSPOROSINUS 0.8161058434098
1332188 species CANDIDATUS SACCHARIMONAS AALBORGENSIS 0.812767914254
95818 phylum CANDIDATUS SACCHARIBACTERIA 0.812767914254
1331051 genus CANDIDATUS SACCHARIMONAS 0.812767914254
51368 no rank UNCLASSIFIED DSDNA VIRUSES 0.78695671726095
508458 phylum SYNERGISTETES 0.766508356538
1176514 no rank BURKHOLDERIA GLUMAE AU6208 0.756447093936
85003 subclass ACTINOBACTERIDAE 0.750094927835643
662756 genus CANDIDATUS MICRARCHAEUM 0.7389033472169
425595 no rank CANDIDATUS MICRARCHAEUM ACIDIPHILUM ARMAN 2 0.7389033472169
662757 species CANDIDATUS MICRARCHAEUM ACIDIPHILUM 0.7389033472169
1297582 no rank CANDIDATUS PORTIERA ALEYRODIDARUM TV 0.7384721953327
65047 genus MITSUARIA 0.7366995882105
557855 species MITSUARIA SP. H24L5A 0.7366995882105
693272 species CAFETERIA ROENBERGENSIS VIRUS BV PW1 0.71340237203445
191393 order DEFERRIBACTERALES 0.706131530240114
200930 phylum DEFERRIBACTERES 0.706131530240114
68337 class DEFERRIBACTERES 0.706131530240114
191394 family DEFERRIBACTERACEAE 0.706131530240114
1144315 species VARIOVORAX SP. CF313 0.697761069402
44249 genus PAENIBACILLUS 0.6884149870332
1239881 no rank CANDIDATUS PORTIERA ALEYRODIDARUM BT QVLC 0.686899682077
506 family ALCALIGENACEAE 0.667517561103
208447 genus OCEANITHERMUS 0.666666666666667
187137 species OCEANITHERMUS PROFUNDUS 0.666666666666667
670487 no rank OCEANITHERMUS PROFUNDUS DSM 14977 0.666666666666667
203486 class DICTYOGLOMIA 0.660056056043753
203487 order DICTYOGLOMALES 0.660056056043753
13 genus DICTYOGLOMUS 0.660056056043753
203488 family DICTYOGLOMACEAE 0.660056056043753
68297 phylum DICTYOGLOMI 0.660056056043753
28219 genus BRACHYMONAS 0.65896581460957
1121116 no rank BRACHYMONAS CHIRONOMI DSM 19884 0.65896581460957
491919 species BRACHYMONAS CHIRONOMI 0.65896581460957
44000 genus CALDICELLULOSIRUPTOR 0.6511141873124
649638 no rank TRUEPERA RADIOVICTRIX DSM 17093 0.64127567799025
332247 family TRUEPERACEAE 0.64127567799025
332248 genus TRUEPERA 0.64127567799025
332249 species TRUEPERA RADIOVICTRIX 0.64127567799025
213121 family DESULFOBULBACEAE 0.632507265463
693075 species CALDISERICUM EXILE 0.628852808829214
511051 no rank CALDISERICUM EXILE AZM16C01 0.628852808829214
67814 phylum CALDISERICA 0.628852808829214
693073 family CALDISERICACEAE 0.628852808829214
693071 class CALDISERICIA 0.628852808829214
693074 genus CALDISERICUM 0.628852808829214
693072 order CALDISERICALES 0.628852808829214
2232 family ARCHAEOGLOBACEAE 0.590864961582667