How to format the taxonomy file to retrain classifier

[yingeddi2008]

Hi rdp staff,

I am trying to retrain RDP classifier using NCBI 16s database, however, when I looked into the example taxonomy file and the fasta file, I am a bit confused how should I even generate that file.

0*Root*-1*0*rootrank
1*Bacteria*0*1*domain
2*"Actinobacteria"*1*2*phylum
3*Actinobacteria*2*3*class
4*Acidimicrobidae*3*4*subclass
5*Acidimicrobiales*4*5*order
6*"Acidimicrobineae"*5*6*suborder
7*Acidimicrobiaceae*6*7*family
8*Acidimicrobium*7*8*genus
9*Ferrimicrobium*7*8*genus
10*Ferrithrix*7*8*genus
11*Ilumatobacter*7*8*genus
12*Iamiaceae*6*7*family
3102*Aquihabitans*12*8*genus
13*Iamia*12*8*genus

Could you please explain how each line is constructed? Allow me to take a line as an example,

6*"Acidimicrobineae"*5*6*suborder

I could guess that the first number is the taxonomy id for Acidimicrobineae, which is 6, and its parent taxonomy is 5, Acidimicrobiales. I assume that the suborder at the end of the line indicates that Acidimicrobineae is at the taxonomy rank of suborder, right? Then what is the 6 before suborder mean? when I look at 12*Iamiaceae*6*7*family, I can say Iamiaceae is a family level taxonomy, which has the parent of 6 (Acidimicrobineae) and 7 (Acidimicrobiaceae)? I am not sure I am getting what's the rule of constructing the taxonomy file here. Could you please explain how this is done?

Thanks in advance,

Eddi

[rdpstaffmsu]

Hi, Eddi, I have example files and the following instructions on the procedure for preparing training files for RDP Classifier: Prepare for training RDP Classifier Files needed and format specifications and requirements: 1. Compile a sequence file (eg. rawSeq.fasta) Format: FASTA with a unique identifier for each sequence. Each sequence carries a unique identifier, a string of characters that does include any whitespace characters. 2. Compile a taxonomy file (eg. rawTaxonomy.txt) Format: tab-delimited text file (.txt) Header: First column: sequence identifier; the following columns contain taxonomic rank names one in a column in the order from root (highest) to leaf rank (lowest), such as Domain/Kingdom, Phylum, Class, Order, Family, Genus, etc.) for each taxon level you want to represent. Data rows: one row per training sequence with following info: Column 1: sequence classifier (this should be identical to that in the sequence file Column 2-N: taxon names corresponding to the rank names in the header. Fill in a '-' character for any rank column not applicable to the lineage of this sequence. Warning: make sure that the taxon names are unique between different lineages. The following ‘convergent’ evolution is not allowed: SeqID rootRank Domain Phylum Class Order Family Genus SeqID-0001 root Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium SeqID-0002 root Bacteria Firmicutes Clostridia Clostridiales Eubacteriaceae Clostridium 3. Run command: lineage2taxTrain.py rawTaxonomy.txt > ready4train_taxonomy.txt 4. Run command: addFullLineage.py ready4train_taxonomy.txt rawSeq.fasta > ready4train_seqs.fasta 5. Use the taxonomy file (eg. ready4train_taxonomy.txt) and sequence file (e.g. ready4train_seqs.fasta) to train RDP Classifier. Let me if you have questions. Benli Chai RDP Staff

…

On Wed, Nov 30, 2016 at 1:41 PM, yingeddi2008 ***@***.***> wrote: Hi rdp staff, I am trying to retrain RDP classifier using NCBI 16s database, however, when I looked into the example taxonomy file and the fasta file, I am a bit confused how should I even generate that file. 0*Root*-1*0*rootrank 1*Bacteria*0*1*domain 2*"Actinobacteria"*1*2*phylum 3*Actinobacteria*2*3*class 4*Acidimicrobidae*3*4*subclass 5*Acidimicrobiales*4*5*order 6*"Acidimicrobineae"*5*6*suborder 7*Acidimicrobiaceae*6*7*family 8*Acidimicrobium*7*8*genus 9*Ferrimicrobium*7*8*genus 10*Ferrithrix*7*8*genus 11*Ilumatobacter*7*8*genus 12*Iamiaceae*6*7*family 3102*Aquihabitans*12*8*genus 13*Iamia*12*8*genus Could you please explain how each line is constructed? Allow me to take a line as an example, 6*"Acidimicrobineae"*5*6*suborder I could guess that the first number is the taxonomy id for *Acidimicrobineae*, which is 6, and its parent taxonomy is 5, Acidimicrobiales. I assume that the *suborder* at the end of the line indicates that *Acidimicrobineae* is at the taxonomy rank of suborder, right? Then what is the 6 before *suborder* mean? when I look at 12*Iamiaceae*6*7*family, I can say Iamiaceae is a family level taxonomy, which has the parent of 6 (Acidimicrobineae) and 7 (Acidimicrobiaceae)? Thanks in advance, Eddi — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#18>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKlEVjUhOLEdgD6SbnykTyuu1Y5m8eSaks5rDcN2gaJpZM4LAiX-> .

-- RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842 Seq_ID Kingdom Phylum Class Order Family Genus Species SH213958.07FU_AF444533_refs Fungi Basidiomycota Microbotryomycetes Sporidiobolales Sporidiobolales_Incertae_sedis Rhodotorula Rhodotorula_diffluens SH213959.07FU_KJ706646_reps Fungi Basidiomycota Microbotryomycetes Sporidiobolales Sporidiobolales_Incertae_sedis Rhodotorula Rhodotorula_sp_1 SH191122.07FU_JN206370_reps Fungi Zygomycota Incertae_sedis Mucorales Mucorales_Incertae_sedis Syzygites Syzygites_megalocarpus SH177358.07FU_Z81447_reps Fungi Ascomycota Leotiomycetes Helotiales Sclerotiniaceae Valdensinia Valdensinia_heterodoxa SH177366.07FU_Z80894_reps Fungi Ascomycota Leotiomycetes Helotiales Rutstroemiaceae Rutstroemia Rutstroemia_bolaris SH177367.07FU_AY546074_reps Fungi Ascomycota Leotiomycetes Rhytismatales Rhytismataceae Lophodermium Lophodermium_conigenum SH177368.07FU_AB693917_reps Fungi Ascomycota Leotiomycetes Helotiales Sclerotiniaceae Monilinia Monilinia_sp_1 SH177370.07FU_AB026166_reps Fungi Ascomycota Leotiomycetes Helotiales Sclerotiniaceae Ciborinia Ciborinia_allii SH177371.07FU_Z73794_reps Fungi Ascomycota Leotiomycetes Helotiales Sclerotiniaceae Monilinia Monilinia_urnula SH177372.07FU_AY645900_reps Fungi Ascomycota Leotiomycetes Helotiales Hemiphacidiaceae Sarcotrochila Sarcotrochila_macrospora SH213382.07FU_JN979417_refs Fungi Ascomycota Sordariomycetes Xylariales Xylariaceae Hypoxylon Hypoxylon_fendleri SH213386.07FU_KM052716_refs Fungi Ascomycota Sordariomycetes Xylariales Xylariaceae Hypoxylon Hypoxylon_sp_1 SH194557.07FU_DQ008233_reps Fungi Ascomycota Leotiomycetes Helotiales Dermateaceae Mollisia Mollisia_sp_1 SH189856.07FU_JQ409283_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_1 SH189859.07FU_JX434665_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_2 SH189860.07FU_HE687084_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_3 SH189861.07FU_GQ985429_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_4 SH189862.07FU_AY969513_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_5 SH189857.07FU_JN102365_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae Peziza Peziza_sp_1 SH189858.07FU_EU554730_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_6 SH189863.07FU_KJ591045_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_7 SH174118.07FU_JQ081850_reps Fungi Ascomycota Sordariomycetes Sordariales Sordariales_unidentified Sordariales_unidentified Sordariales_unidentified_sp_1 SH189872.07FU_EU014071_reps Fungi Basidiomycota Pucciniomycetes Pucciniales Uropyxidaceae Tranzschelia Tranzschelia_discolor SH206047.07FU_AY559338_reps Fungi Ascomycota Dothideomycetes Capnodiales Capnodiales_unidentified Capnodiales_unidentified Capnodiales_unidentified_sp_1 SH206048.07FU_KF309965_reps Fungi Ascomycota Dothideomycetes Capnodiales Capnodiales_Incertae_sedis Monticola Monticola_elongata SH206049.07FU_AY843042_reps Fungi Ascomycota Dothideomycetes Dothideomycetes_unidentified Dothideomycetes_unidentified Dothideomycetes_unidentified Dothideomycetes_unidentified_sp_1 SH206053.07FU_JN942642_reps Fungi Ascomycota Saccharomycetes Saccharomycetales Saccharomycetales_Incertae_sedis Candida Candida_glabrata SH194562.07FU_AB498974_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Neoerysiphe Neoerysiphe_nevoi SH206057.07FU_JN709043_reps Fungi Ascomycota Dothideomycetes Capnodiales Teratosphaeriaceae Teratosphaeria Teratosphaeria_sp_1 SH206058.07FU_GU721292_reps Fungi - - - - - Fungi_unidentified_sp_1 SH194564.07FU_GU356546_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Neoerysiphe Neoerysiphe_kerribeeensis SH194565.07FU_AB329681_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Neoerysiphe Neoerysiphe_galii SH194563.07FU_AB498962_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Neoerysiphe Neoerysiphe_hiratae SH194567.07FU_AB329684_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Striatoidium Striatoidium_baccharidis SH174173.07FU_FJ362291_reps Fungi Basidiomycota Agaricomycetes Boletales Boletaceae Boletus Boletus_bicolor SH174125.07FU_FN555109_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae - Magnaporthaceae_unidentified_sp_1 SH174126.07FU_FJ541434_reps Fungi Ascomycota - - - - Ascomycota_unidentified_sp_1 SH174127.07FU_JF414846_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Gaeumannomyces Gaeumannomyces_incrustans SH174128.07FU_KJ855489_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Gaeumannomyces Gaeumannomyces_sp_1 SH174133.07FU_DQ528792_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Nakataea Nakataea_oryzae SH174134.07FU_FJ430720_reps Fungi Ascomycota Sordariomycetes - - - Sordariomycetes_unidentified_sp_1 SH174135.07FU_KJ855505_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae - Magnaporthaceae_unidentified_sp_2 SH174147.07FU_AB274433_reps Fungi Ascomycota Sordariomycetes Magnaporthales Pyriculariaceae Proxipyricularia Proxipyricularia_zingiberis SH174148.07FU_AB512785_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Pyricularia Pyricularia_sp_1 SH174137.07FU_AJ132542_reps Fungi Ascomycota Eurotiomycetes Chaetothyriales Herpotrichiellaceae Phialophora Phialophora_sp_1 SH174138.07FU_KJ855487_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae - Magnaporthaceae_unidentified_sp_3 SH174140.07FU_AB818016_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Pyricularia Pyricularia_sp_2 SH174141.07FU_EU636699_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Harpophora Harpophora_oryzae SH174142.07FU_JX134600_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Magnaporthiopsis Magnaporthiopsis_poae SH174143.07FU_KJ855497_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae - Magnaporthaceae_unidentified_sp_4 SH174145.07FU_EU144817_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae - Magnaporthaceae_unidentified_sp_5 SH174146.07FU_KC354577_reps Fungi Ascomycota Sordariomycetes - - - Sordariomycetes_unidentified_sp_2 SH199540.07FU_KC414241_reps Fungi Basidiomycota Agaricomycetes Gloeophyllales Gloeophyllaceae Veluticeps Veluticeps_ambigua SH199543.07FU_UDB016415_refs Fungi Basidiomycota Agaricomycetes Polyporales Fomitopsidaceae Postia Postia_undosa SH177464.07FU_GU055939_reps Fungi Ascomycota Eurotiomycetes Chaetothyriales - - Chaetothyriales_unidentified_sp_1 SH206064.07FU_HQ022506_reps Fungi Ascomycota Sordariomycetes Hypocreales Bionectriaceae Clonostachys Clonostachys_sp_1 SH206065.07FU_AY425633_reps Fungi Ascomycota Lecanoromycetes Lecanorales Psoraceae Psora Psora_decipiens SH206066.07FU_KF823600_reps Fungi Ascomycota Sordariomycetes - - - Sordariomycetes_unidentified_sp_3 SH199552.07FU_KF274644_refs Fungi Basidiomycota Agaricomycetes Polyporales Fomitopsidaceae Fomitella Fomitella_supina SH174175.07FU_JF449882_reps Fungi Ascomycota Leotiomycetes Helotiales - - Helotiales_unidentified_sp_1 SH206068.07FU_GU054276_reps Fungi Ascomycota - - - - Ascomycota_unidentified_sp_2 SH174177.07FU_JX192683_reps Fungi Ascomycota Sordariomycetes Hypocreales Cordycipitaceae - Cordycipitaceae_unidentified_sp_1 SH199558.07FU_HE963782_reps Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Brevicellicium Brevicellicium_olivascens SH199559.07FU_HE963789_reps Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Brevicellicium Brevicellicium_olivascens SH206069.07FU_JN811088_reps Fungi - - - - - Fungi_unidentified_sp_2 SH174183.07FU_GQ927301_reps Fungi Ascomycota Lecanoromycetes Peltigerales Pannariaceae Psoroma Psoroma_fruticulosum SH174184.07FU_GQ927299_reps Fungi Ascomycota Lecanoromycetes Peltigerales Pannariaceae Psoroma Psoroma_buchananii SH174185.07FU_GQ927305_reps Fungi Ascomycota Lecanoromycetes Peltigerales Pannariaceae Psoroma Psoroma_hypnorum_var._paleaceum SH223384.07FU_JN206297_reps Fungi Zygomycota Incertae_sedis Mucorales Phycomycetaceae Spinellus Spinellus_fusiger SH206073.07FU_JX310406_reps Fungi Basidiomycota Agaricomycetes Gomphales Gomphaceae Ramaria Ramaria_rubribrunnescens SH174196.07FU_UDB015353_refs Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_subnudipes SH174240.07FU_EF434113_reps Fungi Basidiomycota Agaricomycetes Auriculariales - - Auriculariales_unidentified_sp_1 SH174205.07FU_AM882801_refs Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_leptocystis SH206074.07FU_EU669323_reps Fungi Basidiomycota Agaricomycetes Gomphales Gomphaceae Ramaria Ramaria_maculatipes SH174194.07FU_UDB004943_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae - Inocybaceae_unidentified_sp_1 SH174195.07FU_HE687059_reps Fungi Basidiomycota Agaricomycetes Agaricales - - Agaricales_unidentified_sp_1 SH174198.07FU_HF565068_reps Fungi Basidiomycota Agaricomycetes Agaricales - - Agaricales_unidentified_sp_2 SH174199.07FU_KJ432291_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_lanatopurpurea SH174200.07FU_JQ975963_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae - Inocybaceae_unidentified_sp_2 SH174202.07FU_JF908177_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_sp_1 SH174203.07FU_JF908158_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_leptocystis SH174204.07FU_FR852254_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_sp_2 SH174242.07FU_KF359560_reps Fungi Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusidium Fusidium_sp_1 SH174229.07FU_UDB015045_reps Fungi Ascomycota Lecanoromycetes Ostropales Odontotremataceae Geltingia Geltingia_associata SH199562.07FU_JF300723_refs Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Trechispora Trechispora_sp_1 SH199561.07FU_AY969490_reps Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Trechispora Trechispora_sp_2 SH206078.07FU_KJ021221_reps Fungi Ascomycota Lecanoromycetes Teloschistales Teloschistaceae Eilifdahlia Eilifdahlia_dahlii SH174235.07FU_JX448358_reps Fungi Ascomycota Dothideomycetes Pleosporales - - Pleosporales_unidentified SH199563.07FU_KF718212_reps Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Trechispora Trechispora_sp_3 SH199564.07FU_HM030587_reps Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Trechispora Trechispora_sp_4 SH199565.07FU_JF519114_refs Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Trechispora Trechispora_sp_5 SH206080.07FU_KC478560_reps Fungi Basidiomycota Agaricomycetes - - - Agaricomycetes_unidentified_sp_1 SH177453.07FU_JN020964_reps Fungi Basidiomycota Agaricomycetes Agaricales Strophariaceae Agrocybe Agrocybe_erebia SH174249.07FU_AF011289_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Cystotheca Cystotheca_lanestris SH174251.07FU_AB743781_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Setoidium Setoidium_castanopsidis SH177458.07FU_AF444599_refs Fungi Basidiomycota Agaricostilbomycetes Agaricostilbales Chionosphaeraceae Chionosphaera Chionosphaera_apobasidialis SH212541.07FU_KC884399_reps Fungi - - - - - Fungi_unidentified_sp_3 SH177459.07FU_UDB015324_reps Fungi Basidiomycota Agaricomycetes Agaricales Strophariaceae Pholiota Pholiota_tuberculosa SH177460.07FU_FJ596817_reps Fungi Basidiomycota Agaricomycetes Agaricales Strophariaceae Pholiota Pholiota_sp_1 SH177463.07FU_EU139156_reps Fungi Ascomycota Eurotiomycetes Chaetothyriales Herpotrichiellaceae Capronia Capronia_sp_1 0*Root*-1*0*rootrank 1*Fungi*0*1*Kingdom 2*Basidiomycota*1*2*Phylum 3*Microbotryomycetes*2*3*Class 4*Sporidiobolales*3*4*Order 5*Sporidiobolales_Incertae_sedis*4*5*Family 6*Rhodotorula*5*6*Genus 7*Rhodotorula_diffluens*6*7*Species 8*Rhodotorula_sp_1*6*7*Species 9*Zygomycota*1*2*Phylum 10*Incertae_sedis*9*3*Class 11*Mucorales*10*4*Order 12*Mucorales_Incertae_sedis*11*5*Family 13*Syzygites*12*6*Genus 14*Syzygites_megalocarpus*13*7*Species 15*Ascomycota*1*2*Phylum 16*Leotiomycetes*15*3*Class 17*Helotiales*16*4*Order 18*Sclerotiniaceae*17*5*Family 19*Valdensinia*18*6*Genus 20*Valdensinia_heterodoxa*19*7*Species 21*Rutstroemiaceae*17*5*Family 22*Rutstroemia*21*6*Genus 23*Rutstroemia_bolaris*22*7*Species 24*Rhytismatales*16*4*Order 25*Rhytismataceae*24*5*Family 26*Lophodermium*25*6*Genus 27*Lophodermium_conigenum*26*7*Species 28*Monilinia*18*6*Genus 29*Monilinia_sp_1*28*7*Species 30*Ciborinia*18*6*Genus 31*Ciborinia_allii*30*7*Species 32*Monilinia_urnula*28*7*Species 33*Hemiphacidiaceae*17*5*Family 34*Sarcotrochila*33*6*Genus 35*Sarcotrochila_macrospora*34*7*Species 36*Sordariomycetes*15*3*Class 37*Xylariales*36*4*Order 38*Xylariaceae*37*5*Family 39*Hypoxylon*38*6*Genus 40*Hypoxylon_fendleri*39*7*Species 41*Hypoxylon_sp_1*39*7*Species 42*Dermateaceae*17*5*Family 43*Mollisia*42*6*Genus 44*Mollisia_sp_1*43*7*Species 45*Pezizomycetes*15*3*Class 46*Pezizales*45*4*Order 47*Pezizaceae*46*5*Family 48*Pezizaceae_unidentified_sp_1*47*6*Species 49*Pezizaceae_unidentified_sp_2*47*6*Species 50*Pezizaceae_unidentified_sp_3*47*6*Species 51*Pezizaceae_unidentified_sp_4*47*6*Species 52*Pezizaceae_unidentified_sp_5*47*6*Species 53*Peziza*47*6*Genus 54*Peziza_sp_1*53*7*Species 55*Pezizaceae_unidentified_sp_6*47*6*Species 56*Pezizaceae_unidentified_sp_7*47*6*Species 57*Sordariales*36*4*Order 58*Sordariales_unidentified*57*5*Family 59*Sordariales_unidentified*58*6*Genus 60*Sordariales_unidentified_sp_1*59*7*Species 61*Pucciniomycetes*2*3*Class 62*Pucciniales*61*4*Order 63*Uropyxidaceae*62*5*Family 64*Tranzschelia*63*6*Genus 65*Tranzschelia_discolor*64*7*Species 66*Dothideomycetes*15*3*Class 67*Capnodiales*66*4*Order 68*Capnodiales_unidentified*67*5*Family 69*Capnodiales_unidentified*68*6*Genus 70*Capnodiales_unidentified_sp_1*69*7*Species 71*Capnodiales_Incertae_sedis*67*5*Family 72*Monticola*71*6*Genus 73*Monticola_elongata*72*7*Species 74*Dothideomycetes_unidentified*66*4*Order 75*Dothideomycetes_unidentified*74*5*Family 76*Dothideomycetes_unidentified*75*6*Genus 77*Dothideomycetes_unidentified_sp_1*76*7*Species 78*Saccharomycetes*15*3*Class 79*Saccharomycetales*78*4*Order 80*Saccharomycetales_Incertae_sedis*79*5*Family 81*Candida*80*6*Genus 82*Candida_glabrata*81*7*Species 83*Erysiphales*16*4*Order 84*Erysiphaceae*83*5*Family 85*Neoerysiphe*84*6*Genus 86*Neoerysiphe_nevoi*85*7*Species 87*Teratosphaeriaceae*67*5*Family 88*Teratosphaeria*87*6*Genus 89*Teratosphaeria_sp_1*88*7*Species 90*Fungi_unidentified_sp_1*1*2*Species 91*Neoerysiphe_kerribeeensis*85*7*Species 92*Neoerysiphe_galii*85*7*Species 93*Neoerysiphe_hiratae*85*7*Species 94*Striatoidium*84*6*Genus 95*Striatoidium_baccharidis*94*7*Species 96*Agaricomycetes*2*3*Class 97*Boletales*96*4*Order 98*Boletaceae*97*5*Family 99*Boletus*98*6*Genus 100*Boletus_bicolor*99*7*Species 101*Magnaporthales*36*4*Order 102*Magnaporthaceae*101*5*Family 103*Magnaporthaceae_unidentified_sp_1*102*6*Species 104*Ascomycota_unidentified_sp_1*15*3*Species 105*Gaeumannomyces*102*6*Genus 106*Gaeumannomyces_incrustans*105*7*Species 107*Gaeumannomyces_sp_1*105*7*Species 108*Nakataea*102*6*Genus 109*Nakataea_oryzae*108*7*Species 110*Sordariomycetes_unidentified_sp_1*36*4*Species 111*Magnaporthaceae_unidentified_sp_2*102*6*Species 112*Pyriculariaceae*101*5*Family 113*Proxipyricularia*112*6*Genus 114*Proxipyricularia_zingiberis*113*7*Species 115*Pyricularia*102*6*Genus 116*Pyricularia_sp_1*115*7*Species 117*Eurotiomycetes*15*3*Class 118*Chaetothyriales*117*4*Order 119*Herpotrichiellaceae*118*5*Family 120*Phialophora*119*6*Genus 121*Phialophora_sp_1*120*7*Species 122*Magnaporthaceae_unidentified_sp_3*102*6*Species 123*Pyricularia_sp_2*115*7*Species 124*Harpophora*102*6*Genus 125*Harpophora_oryzae*124*7*Species 126*Magnaporthiopsis*102*6*Genus 127*Magnaporthiopsis_poae*126*7*Species 128*Magnaporthaceae_unidentified_sp_4*102*6*Species 129*Magnaporthaceae_unidentified_sp_5*102*6*Species 130*Sordariomycetes_unidentified_sp_2*36*4*Species 131*Gloeophyllales*96*4*Order 132*Gloeophyllaceae*131*5*Family 133*Veluticeps*132*6*Genus 134*Veluticeps_ambigua*133*7*Species 135*Polyporales*96*4*Order 136*Fomitopsidaceae*135*5*Family 137*Postia*136*6*Genus 138*Postia_undosa*137*7*Species 139*Chaetothyriales_unidentified_sp_1*118*5*Species 140*Hypocreales*36*4*Order 141*Bionectriaceae*140*5*Family 142*Clonostachys*141*6*Genus 143*Clonostachys_sp_1*142*7*Species 144*Lecanoromycetes*15*3*Class 145*Lecanorales*144*4*Order 146*Psoraceae*145*5*Family 147*Psora*146*6*Genus 148*Psora_decipiens*147*7*Species 149*Sordariomycetes_unidentified_sp_3*36*4*Species 150*Fomitella*136*6*Genus 151*Fomitella_supina*150*7*Species 152*Helotiales_unidentified_sp_1*17*5*Species 153*Ascomycota_unidentified_sp_2*15*3*Species 154*Cordycipitaceae*140*5*Family 155*Cordycipitaceae_unidentified_sp_1*154*6*Species 156*Trechisporales*96*4*Order 157*Hydnodontaceae*156*5*Family 158*Brevicellicium*157*6*Genus 159*Brevicellicium_olivascens*158*7*Species 160*Fungi_unidentified_sp_2*1*2*Species 161*Peltigerales*144*4*Order 162*Pannariaceae*161*5*Family 163*Psoroma*162*6*Genus 164*Psoroma_fruticulosum*163*7*Species 165*Psoroma_buchananii*163*7*Species 166*Psoroma_hypnorum_var._paleaceum*163*7*Species 167*Phycomycetaceae*11*5*Family 168*Spinellus*167*6*Genus 169*Spinellus_fusiger*168*7*Species 170*Gomphales*96*4*Order 171*Gomphaceae*170*5*Family 172*Ramaria*171*6*Genus 173*Ramaria_rubribrunnescens*172*7*Species 174*Agaricales*96*4*Order 175*Inocybaceae*174*5*Family 176*Inocybe*175*6*Genus 177*Inocybe_subnudipes*176*7*Species 178*Auriculariales*96*4*Order 179*Auriculariales_unidentified_sp_1*178*5*Species 180*Inocybe_leptocystis*176*7*Species 181*Ramaria_maculatipes*172*7*Species 182*Inocybaceae_unidentified_sp_1*175*6*Species 183*Agaricales_unidentified_sp_1*174*5*Species 184*Agaricales_unidentified_sp_2*174*5*Species 185*Inocybe_lanatopurpurea*176*7*Species 186*Inocybaceae_unidentified_sp_2*175*6*Species 187*Inocybe_sp_1*176*7*Species 188*Inocybe_sp_2*176*7*Species 189*Nectriaceae*140*5*Family 190*Fusidium*189*6*Genus 191*Fusidium_sp_1*190*7*Species 192*Ostropales*144*4*Order 193*Odontotremataceae*192*5*Family 194*Geltingia*193*6*Genus 195*Geltingia_associata*194*7*Species 196*Trechispora*157*6*Genus 197*Trechispora_sp_1*196*7*Species 198*Trechispora_sp_2*196*7*Species 199*Teloschistales*144*4*Order 200*Teloschistaceae*199*5*Family 201*Eilifdahlia*200*6*Genus 202*Eilifdahlia_dahlii*201*7*Species 203*Pleosporales*66*4*Order 204*Pleosporales_unidentified*203*5*Species 205*Trechispora_sp_3*196*7*Species 206*Trechispora_sp_4*196*7*Species 207*Trechispora_sp_5*196*7*Species 208*Agaricomycetes_unidentified_sp_1*96*4*Species 209*Strophariaceae*174*5*Family 210*Agrocybe*209*6*Genus 211*Agrocybe_erebia*210*7*Species 212*Cystotheca*84*6*Genus 213*Cystotheca_lanestris*212*7*Species 214*Setoidium*84*6*Genus 215*Setoidium_castanopsidis*214*7*Species 216*Agaricostilbomycetes*2*3*Class 217*Agaricostilbales*216*4*Order 218*Chionosphaeraceae*217*5*Family 219*Chionosphaera*218*6*Genus 220*Chionosphaera_apobasidialis*219*7*Species 221*Fungi_unidentified_sp_3*1*2*Species 222*Pholiota*209*6*Genus 223*Pholiota_tuberculosa*222*7*Species 224*Pholiota_sp_1*222*7*Species 225*Capronia*119*6*Genus 226*Capronia_sp_1*225*7*Species

[yingeddi2008]

Hi Benli,

Thanks for your prompt response. I am now looking for the two scripts you mentioned in the reply, lineage2taxTrain.py and addFullLineage.py. Could you please show me where they are included? Are they in the RDP zipped folder?

Thanks,

Eddi

[chaibenl]

Sorry I thought I attached them. Here they are. Benli

…

On Thu, Dec 1, 2016 at 11:21 AM, yingeddi2008 ***@***.***> wrote: Hi Benli, Thanks for your prompt response. I am now looking for the two scripts you mentioned in the reply, *lineage2taxTrain.py* and *addFullLineage.py*. Could you please show me where they are included? Are they in the RDP zipped folder? Thanks, Eddi — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQAQFRbu8HL78spLI0sWyY_Yqkxa0OKcks5rDvP4gaJpZM4LAiX-> .

[yingeddi2008]

I still don't see them...

[rdpstaffmsu]

Would you send your email address other than the one from github? Benli

…

On Thu, Dec 1, 2016 at 1:03 PM, yingeddi2008 ***@***.***> wrote: I still don't see them... — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKlEVj8LmrDs0FE7U8C6YLzbE-N3a8JTks5rDwv8gaJpZM4LAiX-> .

-- RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

[yingeddi2008]

You can send the scripts to hlin2@luc.edu. Thanks.

[yingeddi2008]

Hi Benli,

Haven't heard from you for the scripts for a while. I'd be really appreciated if you could follow up on this issue.

Thanks a lot!

Eddi

[chaibenl]

Hi, Eddi, I sent them to you account hlin2@luc.edu 4 days ago. Here I attach them to the email again. Benli

On Mon, Dec 5, 2016 at 11:20 AM, yingeddi2008 ***@***.***> wrote: Hi Benli, Haven't heard from you for the scripts for a while. I'd really appreciated if you could follow up on this issue. Thanks a lot! Eddi — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQAQFe4Xc6PzpSwNK5mRdfUI6k7NR0y0ks5rFDnDgaJpZM4LAiX-> .

Seq_ID Kingdom Phylum Class Order Family Genus Species SH213958.07FU_AF444533_refs Fungi Basidiomycota Microbotryomycetes Sporidiobolales Sporidiobolales_Incertae_sedis Rhodotorula Rhodotorula_diffluens SH213959.07FU_KJ706646_reps Fungi Basidiomycota Microbotryomycetes Sporidiobolales Sporidiobolales_Incertae_sedis Rhodotorula Rhodotorula_sp_1 SH191122.07FU_JN206370_reps Fungi Zygomycota Incertae_sedis Mucorales Mucorales_Incertae_sedis Syzygites Syzygites_megalocarpus SH177358.07FU_Z81447_reps Fungi Ascomycota Leotiomycetes Helotiales Sclerotiniaceae Valdensinia Valdensinia_heterodoxa SH177366.07FU_Z80894_reps Fungi Ascomycota Leotiomycetes Helotiales Rutstroemiaceae Rutstroemia Rutstroemia_bolaris SH177367.07FU_AY546074_reps Fungi Ascomycota Leotiomycetes Rhytismatales Rhytismataceae Lophodermium Lophodermium_conigenum SH177368.07FU_AB693917_reps Fungi Ascomycota Leotiomycetes Helotiales Sclerotiniaceae Monilinia Monilinia_sp_1 SH177370.07FU_AB026166_reps Fungi Ascomycota Leotiomycetes Helotiales Sclerotiniaceae Ciborinia Ciborinia_allii SH177371.07FU_Z73794_reps Fungi Ascomycota Leotiomycetes Helotiales Sclerotiniaceae Monilinia Monilinia_urnula SH177372.07FU_AY645900_reps Fungi Ascomycota Leotiomycetes Helotiales Hemiphacidiaceae Sarcotrochila Sarcotrochila_macrospora SH213382.07FU_JN979417_refs Fungi Ascomycota Sordariomycetes Xylariales Xylariaceae Hypoxylon Hypoxylon_fendleri SH213386.07FU_KM052716_refs Fungi Ascomycota Sordariomycetes Xylariales Xylariaceae Hypoxylon Hypoxylon_sp_1 SH194557.07FU_DQ008233_reps Fungi Ascomycota Leotiomycetes Helotiales Dermateaceae Mollisia Mollisia_sp_1 SH189856.07FU_JQ409283_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_1 SH189859.07FU_JX434665_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_2 SH189860.07FU_HE687084_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_3 SH189861.07FU_GQ985429_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_4 SH189862.07FU_AY969513_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_5 SH189857.07FU_JN102365_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae Peziza Peziza_sp_1 SH189858.07FU_EU554730_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_6 SH189863.07FU_KJ591045_reps Fungi Ascomycota Pezizomycetes Pezizales Pezizaceae - Pezizaceae_unidentified_sp_7 SH174118.07FU_JQ081850_reps Fungi Ascomycota Sordariomycetes Sordariales Sordariales_unidentified Sordariales_unidentified Sordariales_unidentified_sp_1 SH189872.07FU_EU014071_reps Fungi Basidiomycota Pucciniomycetes Pucciniales Uropyxidaceae Tranzschelia Tranzschelia_discolor SH206047.07FU_AY559338_reps Fungi Ascomycota Dothideomycetes Capnodiales Capnodiales_unidentified Capnodiales_unidentified Capnodiales_unidentified_sp_1 SH206048.07FU_KF309965_reps Fungi Ascomycota Dothideomycetes Capnodiales Capnodiales_Incertae_sedis Monticola Monticola_elongata SH206049.07FU_AY843042_reps Fungi Ascomycota Dothideomycetes Dothideomycetes_unidentified Dothideomycetes_unidentified Dothideomycetes_unidentified Dothideomycetes_unidentified_sp_1 SH206053.07FU_JN942642_reps Fungi Ascomycota Saccharomycetes Saccharomycetales Saccharomycetales_Incertae_sedis Candida Candida_glabrata SH194562.07FU_AB498974_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Neoerysiphe Neoerysiphe_nevoi SH206057.07FU_JN709043_reps Fungi Ascomycota Dothideomycetes Capnodiales Teratosphaeriaceae Teratosphaeria Teratosphaeria_sp_1 SH206058.07FU_GU721292_reps Fungi - - - - - Fungi_unidentified_sp_1 SH194564.07FU_GU356546_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Neoerysiphe Neoerysiphe_kerribeeensis SH194565.07FU_AB329681_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Neoerysiphe Neoerysiphe_galii SH194563.07FU_AB498962_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Neoerysiphe Neoerysiphe_hiratae SH194567.07FU_AB329684_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Striatoidium Striatoidium_baccharidis SH174173.07FU_FJ362291_reps Fungi Basidiomycota Agaricomycetes Boletales Boletaceae Boletus Boletus_bicolor SH174125.07FU_FN555109_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae - Magnaporthaceae_unidentified_sp_1 SH174126.07FU_FJ541434_reps Fungi Ascomycota - - - - Ascomycota_unidentified_sp_1 SH174127.07FU_JF414846_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Gaeumannomyces Gaeumannomyces_incrustans SH174128.07FU_KJ855489_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Gaeumannomyces Gaeumannomyces_sp_1 SH174133.07FU_DQ528792_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Nakataea Nakataea_oryzae SH174134.07FU_FJ430720_reps Fungi Ascomycota Sordariomycetes - - - Sordariomycetes_unidentified_sp_1 SH174135.07FU_KJ855505_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae - Magnaporthaceae_unidentified_sp_2 SH174147.07FU_AB274433_reps Fungi Ascomycota Sordariomycetes Magnaporthales Pyriculariaceae Proxipyricularia Proxipyricularia_zingiberis SH174148.07FU_AB512785_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Pyricularia Pyricularia_sp_1 SH174137.07FU_AJ132542_reps Fungi Ascomycota Eurotiomycetes Chaetothyriales Herpotrichiellaceae Phialophora Phialophora_sp_1 SH174138.07FU_KJ855487_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae - Magnaporthaceae_unidentified_sp_3 SH174140.07FU_AB818016_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Pyricularia Pyricularia_sp_2 SH174141.07FU_EU636699_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Harpophora Harpophora_oryzae SH174142.07FU_JX134600_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae Magnaporthiopsis Magnaporthiopsis_poae SH174143.07FU_KJ855497_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae - Magnaporthaceae_unidentified_sp_4 SH174145.07FU_EU144817_reps Fungi Ascomycota Sordariomycetes Magnaporthales Magnaporthaceae - Magnaporthaceae_unidentified_sp_5 SH174146.07FU_KC354577_reps Fungi Ascomycota Sordariomycetes - - - Sordariomycetes_unidentified_sp_2 SH199540.07FU_KC414241_reps Fungi Basidiomycota Agaricomycetes Gloeophyllales Gloeophyllaceae Veluticeps Veluticeps_ambigua SH199543.07FU_UDB016415_refs Fungi Basidiomycota Agaricomycetes Polyporales Fomitopsidaceae Postia Postia_undosa SH177464.07FU_GU055939_reps Fungi Ascomycota Eurotiomycetes Chaetothyriales - - Chaetothyriales_unidentified_sp_1 SH206064.07FU_HQ022506_reps Fungi Ascomycota Sordariomycetes Hypocreales Bionectriaceae Clonostachys Clonostachys_sp_1 SH206065.07FU_AY425633_reps Fungi Ascomycota Lecanoromycetes Lecanorales Psoraceae Psora Psora_decipiens SH206066.07FU_KF823600_reps Fungi Ascomycota Sordariomycetes - - - Sordariomycetes_unidentified_sp_3 SH199552.07FU_KF274644_refs Fungi Basidiomycota Agaricomycetes Polyporales Fomitopsidaceae Fomitella Fomitella_supina SH174175.07FU_JF449882_reps Fungi Ascomycota Leotiomycetes Helotiales - - Helotiales_unidentified_sp_1 SH206068.07FU_GU054276_reps Fungi Ascomycota - - - - Ascomycota_unidentified_sp_2 SH174177.07FU_JX192683_reps Fungi Ascomycota Sordariomycetes Hypocreales Cordycipitaceae - Cordycipitaceae_unidentified_sp_1 SH199558.07FU_HE963782_reps Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Brevicellicium Brevicellicium_olivascens SH199559.07FU_HE963789_reps Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Brevicellicium Brevicellicium_olivascens SH206069.07FU_JN811088_reps Fungi - - - - - Fungi_unidentified_sp_2 SH174183.07FU_GQ927301_reps Fungi Ascomycota Lecanoromycetes Peltigerales Pannariaceae Psoroma Psoroma_fruticulosum SH174184.07FU_GQ927299_reps Fungi Ascomycota Lecanoromycetes Peltigerales Pannariaceae Psoroma Psoroma_buchananii SH174185.07FU_GQ927305_reps Fungi Ascomycota Lecanoromycetes Peltigerales Pannariaceae Psoroma Psoroma_hypnorum_var._paleaceum SH223384.07FU_JN206297_reps Fungi Zygomycota Incertae_sedis Mucorales Phycomycetaceae Spinellus Spinellus_fusiger SH206073.07FU_JX310406_reps Fungi Basidiomycota Agaricomycetes Gomphales Gomphaceae Ramaria Ramaria_rubribrunnescens SH174196.07FU_UDB015353_refs Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_subnudipes SH174240.07FU_EF434113_reps Fungi Basidiomycota Agaricomycetes Auriculariales - - Auriculariales_unidentified_sp_1 SH174205.07FU_AM882801_refs Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_leptocystis SH206074.07FU_EU669323_reps Fungi Basidiomycota Agaricomycetes Gomphales Gomphaceae Ramaria Ramaria_maculatipes SH174194.07FU_UDB004943_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae - Inocybaceae_unidentified_sp_1 SH174195.07FU_HE687059_reps Fungi Basidiomycota Agaricomycetes Agaricales - - Agaricales_unidentified_sp_1 SH174198.07FU_HF565068_reps Fungi Basidiomycota Agaricomycetes Agaricales - - Agaricales_unidentified_sp_2 SH174199.07FU_KJ432291_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_lanatopurpurea SH174200.07FU_JQ975963_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae - Inocybaceae_unidentified_sp_2 SH174202.07FU_JF908177_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_sp_1 SH174203.07FU_JF908158_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_leptocystis SH174204.07FU_FR852254_reps Fungi Basidiomycota Agaricomycetes Agaricales Inocybaceae Inocybe Inocybe_sp_2 SH174242.07FU_KF359560_reps Fungi Ascomycota Sordariomycetes Hypocreales Nectriaceae Fusidium Fusidium_sp_1 SH174229.07FU_UDB015045_reps Fungi Ascomycota Lecanoromycetes Ostropales Odontotremataceae Geltingia Geltingia_associata SH199562.07FU_JF300723_refs Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Trechispora Trechispora_sp_1 SH199561.07FU_AY969490_reps Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Trechispora Trechispora_sp_2 SH206078.07FU_KJ021221_reps Fungi Ascomycota Lecanoromycetes Teloschistales Teloschistaceae Eilifdahlia Eilifdahlia_dahlii SH174235.07FU_JX448358_reps Fungi Ascomycota Dothideomycetes Pleosporales - - Pleosporales_unidentified SH199563.07FU_KF718212_reps Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Trechispora Trechispora_sp_3 SH199564.07FU_HM030587_reps Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Trechispora Trechispora_sp_4 SH199565.07FU_JF519114_refs Fungi Basidiomycota Agaricomycetes Trechisporales Hydnodontaceae Trechispora Trechispora_sp_5 SH206080.07FU_KC478560_reps Fungi Basidiomycota Agaricomycetes - - - Agaricomycetes_unidentified_sp_1 SH177453.07FU_JN020964_reps Fungi Basidiomycota Agaricomycetes Agaricales Strophariaceae Agrocybe Agrocybe_erebia SH174249.07FU_AF011289_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Cystotheca Cystotheca_lanestris SH174251.07FU_AB743781_refs Fungi Ascomycota Leotiomycetes Erysiphales Erysiphaceae Setoidium Setoidium_castanopsidis SH177458.07FU_AF444599_refs Fungi Basidiomycota Agaricostilbomycetes Agaricostilbales Chionosphaeraceae Chionosphaera Chionosphaera_apobasidialis SH212541.07FU_KC884399_reps Fungi - - - - - Fungi_unidentified_sp_3 SH177459.07FU_UDB015324_reps Fungi Basidiomycota Agaricomycetes Agaricales Strophariaceae Pholiota Pholiota_tuberculosa SH177460.07FU_FJ596817_reps Fungi Basidiomycota Agaricomycetes Agaricales Strophariaceae Pholiota Pholiota_sp_1 SH177463.07FU_EU139156_reps Fungi Ascomycota Eurotiomycetes Chaetothyriales Herpotrichiellaceae Capronia Capronia_sp_1 0*Root*-1*0*rootrank 1*Fungi*0*1*Kingdom 2*Basidiomycota*1*2*Phylum 3*Microbotryomycetes*2*3*Class 4*Sporidiobolales*3*4*Order 5*Sporidiobolales_Incertae_sedis*4*5*Family 6*Rhodotorula*5*6*Genus 7*Rhodotorula_diffluens*6*7*Species 8*Rhodotorula_sp_1*6*7*Species 9*Zygomycota*1*2*Phylum 10*Incertae_sedis*9*3*Class 11*Mucorales*10*4*Order 12*Mucorales_Incertae_sedis*11*5*Family 13*Syzygites*12*6*Genus 14*Syzygites_megalocarpus*13*7*Species 15*Ascomycota*1*2*Phylum 16*Leotiomycetes*15*3*Class 17*Helotiales*16*4*Order 18*Sclerotiniaceae*17*5*Family 19*Valdensinia*18*6*Genus 20*Valdensinia_heterodoxa*19*7*Species 21*Rutstroemiaceae*17*5*Family 22*Rutstroemia*21*6*Genus 23*Rutstroemia_bolaris*22*7*Species 24*Rhytismatales*16*4*Order 25*Rhytismataceae*24*5*Family 26*Lophodermium*25*6*Genus 27*Lophodermium_conigenum*26*7*Species 28*Monilinia*18*6*Genus 29*Monilinia_sp_1*28*7*Species 30*Ciborinia*18*6*Genus 31*Ciborinia_allii*30*7*Species 32*Monilinia_urnula*28*7*Species 33*Hemiphacidiaceae*17*5*Family 34*Sarcotrochila*33*6*Genus 35*Sarcotrochila_macrospora*34*7*Species 36*Sordariomycetes*15*3*Class 37*Xylariales*36*4*Order 38*Xylariaceae*37*5*Family 39*Hypoxylon*38*6*Genus 40*Hypoxylon_fendleri*39*7*Species 41*Hypoxylon_sp_1*39*7*Species 42*Dermateaceae*17*5*Family 43*Mollisia*42*6*Genus 44*Mollisia_sp_1*43*7*Species 45*Pezizomycetes*15*3*Class 46*Pezizales*45*4*Order 47*Pezizaceae*46*5*Family 48*Pezizaceae_unidentified_sp_1*47*6*Species 49*Pezizaceae_unidentified_sp_2*47*6*Species 50*Pezizaceae_unidentified_sp_3*47*6*Species 51*Pezizaceae_unidentified_sp_4*47*6*Species 52*Pezizaceae_unidentified_sp_5*47*6*Species 53*Peziza*47*6*Genus 54*Peziza_sp_1*53*7*Species 55*Pezizaceae_unidentified_sp_6*47*6*Species 56*Pezizaceae_unidentified_sp_7*47*6*Species 57*Sordariales*36*4*Order 58*Sordariales_unidentified*57*5*Family 59*Sordariales_unidentified*58*6*Genus 60*Sordariales_unidentified_sp_1*59*7*Species 61*Pucciniomycetes*2*3*Class 62*Pucciniales*61*4*Order 63*Uropyxidaceae*62*5*Family 64*Tranzschelia*63*6*Genus 65*Tranzschelia_discolor*64*7*Species 66*Dothideomycetes*15*3*Class 67*Capnodiales*66*4*Order 68*Capnodiales_unidentified*67*5*Family 69*Capnodiales_unidentified*68*6*Genus 70*Capnodiales_unidentified_sp_1*69*7*Species 71*Capnodiales_Incertae_sedis*67*5*Family 72*Monticola*71*6*Genus 73*Monticola_elongata*72*7*Species 74*Dothideomycetes_unidentified*66*4*Order 75*Dothideomycetes_unidentified*74*5*Family 76*Dothideomycetes_unidentified*75*6*Genus 77*Dothideomycetes_unidentified_sp_1*76*7*Species 78*Saccharomycetes*15*3*Class 79*Saccharomycetales*78*4*Order 80*Saccharomycetales_Incertae_sedis*79*5*Family 81*Candida*80*6*Genus 82*Candida_glabrata*81*7*Species 83*Erysiphales*16*4*Order 84*Erysiphaceae*83*5*Family 85*Neoerysiphe*84*6*Genus 86*Neoerysiphe_nevoi*85*7*Species 87*Teratosphaeriaceae*67*5*Family 88*Teratosphaeria*87*6*Genus 89*Teratosphaeria_sp_1*88*7*Species 90*Fungi_unidentified_sp_1*1*2*Species 91*Neoerysiphe_kerribeeensis*85*7*Species 92*Neoerysiphe_galii*85*7*Species 93*Neoerysiphe_hiratae*85*7*Species 94*Striatoidium*84*6*Genus 95*Striatoidium_baccharidis*94*7*Species 96*Agaricomycetes*2*3*Class 97*Boletales*96*4*Order 98*Boletaceae*97*5*Family 99*Boletus*98*6*Genus 100*Boletus_bicolor*99*7*Species 101*Magnaporthales*36*4*Order 102*Magnaporthaceae*101*5*Family 103*Magnaporthaceae_unidentified_sp_1*102*6*Species 104*Ascomycota_unidentified_sp_1*15*3*Species 105*Gaeumannomyces*102*6*Genus 106*Gaeumannomyces_incrustans*105*7*Species 107*Gaeumannomyces_sp_1*105*7*Species 108*Nakataea*102*6*Genus 109*Nakataea_oryzae*108*7*Species 110*Sordariomycetes_unidentified_sp_1*36*4*Species 111*Magnaporthaceae_unidentified_sp_2*102*6*Species 112*Pyriculariaceae*101*5*Family 113*Proxipyricularia*112*6*Genus 114*Proxipyricularia_zingiberis*113*7*Species 115*Pyricularia*102*6*Genus 116*Pyricularia_sp_1*115*7*Species 117*Eurotiomycetes*15*3*Class 118*Chaetothyriales*117*4*Order 119*Herpotrichiellaceae*118*5*Family 120*Phialophora*119*6*Genus 121*Phialophora_sp_1*120*7*Species 122*Magnaporthaceae_unidentified_sp_3*102*6*Species 123*Pyricularia_sp_2*115*7*Species 124*Harpophora*102*6*Genus 125*Harpophora_oryzae*124*7*Species 126*Magnaporthiopsis*102*6*Genus 127*Magnaporthiopsis_poae*126*7*Species 128*Magnaporthaceae_unidentified_sp_4*102*6*Species 129*Magnaporthaceae_unidentified_sp_5*102*6*Species 130*Sordariomycetes_unidentified_sp_2*36*4*Species 131*Gloeophyllales*96*4*Order 132*Gloeophyllaceae*131*5*Family 133*Veluticeps*132*6*Genus 134*Veluticeps_ambigua*133*7*Species 135*Polyporales*96*4*Order 136*Fomitopsidaceae*135*5*Family 137*Postia*136*6*Genus 138*Postia_undosa*137*7*Species 139*Chaetothyriales_unidentified_sp_1*118*5*Species 140*Hypocreales*36*4*Order 141*Bionectriaceae*140*5*Family 142*Clonostachys*141*6*Genus 143*Clonostachys_sp_1*142*7*Species 144*Lecanoromycetes*15*3*Class 145*Lecanorales*144*4*Order 146*Psoraceae*145*5*Family 147*Psora*146*6*Genus 148*Psora_decipiens*147*7*Species 149*Sordariomycetes_unidentified_sp_3*36*4*Species 150*Fomitella*136*6*Genus 151*Fomitella_supina*150*7*Species 152*Helotiales_unidentified_sp_1*17*5*Species 153*Ascomycota_unidentified_sp_2*15*3*Species 154*Cordycipitaceae*140*5*Family 155*Cordycipitaceae_unidentified_sp_1*154*6*Species 156*Trechisporales*96*4*Order 157*Hydnodontaceae*156*5*Family 158*Brevicellicium*157*6*Genus 159*Brevicellicium_olivascens*158*7*Species 160*Fungi_unidentified_sp_2*1*2*Species 161*Peltigerales*144*4*Order 162*Pannariaceae*161*5*Family 163*Psoroma*162*6*Genus 164*Psoroma_fruticulosum*163*7*Species 165*Psoroma_buchananii*163*7*Species 166*Psoroma_hypnorum_var._paleaceum*163*7*Species 167*Phycomycetaceae*11*5*Family 168*Spinellus*167*6*Genus 169*Spinellus_fusiger*168*7*Species 170*Gomphales*96*4*Order 171*Gomphaceae*170*5*Family 172*Ramaria*171*6*Genus 173*Ramaria_rubribrunnescens*172*7*Species 174*Agaricales*96*4*Order 175*Inocybaceae*174*5*Family 176*Inocybe*175*6*Genus 177*Inocybe_subnudipes*176*7*Species 178*Auriculariales*96*4*Order 179*Auriculariales_unidentified_sp_1*178*5*Species 180*Inocybe_leptocystis*176*7*Species 181*Ramaria_maculatipes*172*7*Species 182*Inocybaceae_unidentified_sp_1*175*6*Species 183*Agaricales_unidentified_sp_1*174*5*Species 184*Agaricales_unidentified_sp_2*174*5*Species 185*Inocybe_lanatopurpurea*176*7*Species 186*Inocybaceae_unidentified_sp_2*175*6*Species 187*Inocybe_sp_1*176*7*Species 188*Inocybe_sp_2*176*7*Species 189*Nectriaceae*140*5*Family 190*Fusidium*189*6*Genus 191*Fusidium_sp_1*190*7*Species 192*Ostropales*144*4*Order 193*Odontotremataceae*192*5*Family 194*Geltingia*193*6*Genus 195*Geltingia_associata*194*7*Species 196*Trechispora*157*6*Genus 197*Trechispora_sp_1*196*7*Species 198*Trechispora_sp_2*196*7*Species 199*Teloschistales*144*4*Order 200*Teloschistaceae*199*5*Family 201*Eilifdahlia*200*6*Genus 202*Eilifdahlia_dahlii*201*7*Species 203*Pleosporales*66*4*Order 204*Pleosporales_unidentified*203*5*Species 205*Trechispora_sp_3*196*7*Species 206*Trechispora_sp_4*196*7*Species 207*Trechispora_sp_5*196*7*Species 208*Agaricomycetes_unidentified_sp_1*96*4*Species 209*Strophariaceae*174*5*Family 210*Agrocybe*209*6*Genus 211*Agrocybe_erebia*210*7*Species 212*Cystotheca*84*6*Genus 213*Cystotheca_lanestris*212*7*Species 214*Setoidium*84*6*Genus 215*Setoidium_castanopsidis*214*7*Species 216*Agaricostilbomycetes*2*3*Class 217*Agaricostilbales*216*4*Order 218*Chionosphaeraceae*217*5*Family 219*Chionosphaera*218*6*Genus 220*Chionosphaera_apobasidialis*219*7*Species 221*Fungi_unidentified_sp_3*1*2*Species 222*Pholiota*209*6*Genus 223*Pholiota_tuberculosa*222*7*Species 224*Pholiota_sp_1*222*7*Species 225*Capronia*119*6*Genus 226*Capronia_sp_1*225*7*Species

[yingeddi2008]

Thanks Benli, I received them.

[yingeddi2008]

Hi Benli,

I am trying the scripts you provided in the email to re-train RDP classifier using NCBI 16s database, but I encountered some error messages when I use the files generated by your scripts to train.

I have generated the fasta file with lineage added to the sequence ID, and you can download from https://www.dropbox.com/s/86uqecg3iflrom5/16SMicrobial.ready4train.fasta?dl=0

I also have the taxonomy file in RDP compatible format, and you can download from https://www.dropbox.com/s/rnmw2izjdsdc39f/16SMicrobial.ready4train.taxonomy?dl=0.

When I tried to train using the following command: (I am using 2.12 version)
java -Xmx1g -jar /Users/huaiyinglin/Downloads/rdp_classifier_2.12/dist/classifier.jar train -o 16S_ncbi -s 16SMicrobial.ready4train.fasta -t 16SMicrobial.ready4train.taxonomy

Error Messages like the following appears:

edu.msu.cme.rdp.classifier.train.NameRankDupException: Error: duplicate taxon name and rank in the taxonomy file.
ponticoccus genus 2
at edu.msu.cme.rdp.classifier.train.TreeFactory.creatTaxidMap(TreeFactory.java:126)
at edu.msu.cme.rdp.classifier.train.TreeFactory.(TreeFactory.java:61)
at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.(ClassifierTraineeMaker.java:63)
at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.main(ClassifierTraineeMaker.java:170)
at edu.msu.cme.rdp.classifier.cli.ClassifierMain.main(ClassifierMain.java:77)

I have looked up the genus name "ponticoccus" listed as part of the error message, I did find three entries for ponticoccus at genus level, but for three different species. Since I want to train at species level, when I made the taxonomy file, I made sure there is no duplicated taxonomy information, so each sequence should be unique taxonomy-wise on species level.

It seems to me that the RDP classifier can only be trained on genus level even after I provided Species level information. Could you please help me figure out how I can train at species level?

Thanks a lot in advance!

Eddi

[rdpstaffmsu]

I don't have your tab-delimited (raw) taxonomy file to point to you, but I see genus name "Ponticoccus" appears under two different families: 125**Propionibacteriaceae**124*4*Family 177**Rhodobacteraceae**176*4*Family Remember 'convergent' evolution is not allowed here! Benli

…

On Mon, Dec 5, 2016 at 2:50 PM, yingeddi2008 ***@***.***> wrote: Hi Benli, I am trying the scripts you provided in the email to re-train RDP classifier using NCBI 16s database, but I encountered some error messages when I use the files generated by your scripts to train. I have generated the fasta file with lineage added to the sequence ID, and you can download from https://www.dropbox.com/s/ 86uqecg3iflrom5/16SMicrobial.ready4train.fasta?dl=0 I also have the taxonomy file in RDP compatible format, and you can download from https://www.dropbox.com/s/rnmw2izjdsdc39f/16SMicrobial. ready4train.taxonomy?dl=0. When I tried to train using the following command: (I am using *2.12 version*) java -Xmx1g -jar /Users/huaiyinglin/Downloads/rdp_classifier_2.12/dist/classifier.jar train -o 16S_ncbi -s 16SMicrobial.ready4train.fasta -t 16SMicrobial.ready4train.taxonomy Error Messages like the following appears: edu.msu.cme.rdp.classifier.train.NameRankDupException: Error: duplicate taxon name and rank in the taxonomy file. ponticoccus genus 2 at edu.msu.cme.rdp.classifier.train.TreeFactory.creatTaxidMap(TreeFactory. java:126) at edu.msu.cme.rdp.classifier.train.TreeFactory.(TreeFactory.java:61) at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.( ClassifierTraineeMaker.java:63) at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker. main(ClassifierTraineeMaker.java:170) at edu.msu.cme.rdp.classifier.cli.ClassifierMain.main( ClassifierMain.java:77) I have looked up the genus name "ponticoccus" listed as part of the error message, I couldn't find there is any duplication of this genus.When I made the taxonomy file, I made sure there is no duplicated taxonomy information, so each sequence should be unique taxonomy-wise. Could you please help me figure out what the problem is here? Thanks a lot in advance! Eddi — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKlEVjq_FJzvDehp3NFcADILcKvm8wThks5rFGr8gaJpZM4LAiX-> .

-- RDP Staff Ribosomal Database Project Center for Microbial Ecology Michigan State University 567 Wilson Rd. Room 2225 A East Lansing, MI 48824 (517) 353-3842

[yingeddi2008]

Thanks Benli, I see where the problem is. I will remove any convergent evolution and try again.

[AnnyYoung]

Hi Eddi,

I met some problem about rdp_classifier-2.4.jar, I already checked the .fasta and taxonomy.txt's format like you said in "How to format the taxonomy file to retrain classifier #18" , but I get the same error information , so I want to try lineage2taxTrain.py and addFullLineage.py . Clould you give me this two script please?

the error information like this:
Exception in thread "main" java.lang.IllegalArgumentException:
Illegal taxonomy format at 3260**32597genus
at edu.msu.cme.rdp.classifier.train.TreeFactory.creatTaxidMap(TreeFactory.java:79)
at edu.msu.cme.rdp.classifier.train.TreeFactory.(TreeFactory.java:58)
at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.(ClassifierTraineeMaker.java:40)
at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.main(ClassifierTraineeMaker.java:131)

Thanks a lot!

anny

[TurbulentCupcake]

Hi RDP Staff,

Can you pass on the script used to create the taxonomy file mentioned earlier in the thread? I would greatly appreciate it.

Thanks,
Adithya

[chaibenl]

Hi, Adithya, Here they are. Benli Chai RDP Staff

…

On Thu, Jun 22, 2017 at 10:54 PM, Adithya Murali ***@***.***> wrote: Hi RDP Staff, Can you pass on the script used to create the taxonomy file mentioned earlier in the thread? I would greatly appreciate it. Thanks, Adithya — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#18 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AQAQFb3D8TfmnRz48oGqdoO_vLuPZFcsks5sGyj-gaJpZM4LAiX-> .