Usage and ExamplesLink

Table of Contents

• Usage and Examples
• Before use
• taxonkit
• list
• lineage
• reformat
• reformat2
• name2taxid
• filter
• lca
• taxid-changelog
• profile2cami
• cami-filter
• create-taxdump
• genautocomplete

Before useLink

1. Download and uncompresstaxdump.tar.gz: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
2. Copynames.dmp,nodes.dmp,delnodes.dmp andmerged.dmp to data directory:$HOME/.taxonkit,e.g.,/home/shenwei/.taxonkit ,
3. Optionally copy to some other directories, and later you can refer to using flag--data-dir,or environment variableTAXONKIT_DB.

All-in-one command:

wget -c ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz tar -zxvf taxdump.tar.gzmkdir -p $HOME/.taxonkitcp names.dmp nodes.dmp delnodes.dmp merged.dmp $HOME/.taxonkit

Update dataset: Simply re-download the taxdump files, uncompress and override old ones.

taxonkitLink

TaxonKit - A Practical and Efficient NCBI Taxonomy ToolkitVersion: 0.20.0Author: Wei Shen <shenwei356@gmail.com>Source code: https://github.com/shenwei356/taxonkitDocuments  : https://bioinf.shenwei.me/taxonkitCitation   : https://www.sciencedirect.com/science/article/pii/S1673852721000837Dataset:    Please download and uncompress "taxdump.tar.gz":    http://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz    and copy "names.dmp", "nodes.dmp", "delnodes.dmp" and "merged.dmp" to data directory:    "/home/shenwei/.taxonkit"    or some other directory, and later you can refer to using flag --data-dir,    or environment variable TAXONKIT_DB.    When environment variable TAXONKIT_DB is set, explicitly setting --data-dir will    overide the value of TAXONKIT_DB.Usage:  taxonkit [command] Available Commands:  cami-filter     Remove taxa of given TaxIds and their descendants in CAMI metagenomic profile  create-taxdump  Create NCBI-style taxdump files for custom taxonomy, e.g., GTDB and ICTV  filter          Filter TaxIds by taxonomic rank range  genautocomplete generate shell autocompletion script (bash|zsh|fish|powershell)  lca             Compute lowest common ancestor (LCA) for TaxIds  lineage         Query taxonomic lineage of given TaxIds  list            List taxonomic subtrees of given TaxIds  name2taxid      Convert taxon names to TaxIds  profile2cami    Convert metagenomic profile table to CAMI format  reformat        Reformat lineage in canonical ranks  reformat2       Reformat lineage in chosen ranks, allowing more ranks than 'reformat'  taxid-changelog Create TaxId changelog from dump archives  version         print version information and check for updateFlags:      --data-dir string   directory containing nodes.dmp and names.dmp (default "/home/shenwei/.taxonkit")  -h, --help              help for taxonkit      --line-buffered     use line buffering on output, i.e., immediately writing to stdin/file for                          every line of output  -o, --out-file string   out file ("-" for stdout, suffix .gz for gzipped out) (default "-")  -j, --threads int       number of CPUs. 4 is enough (default 4)      --verbose           print verbose information

listLink

Usage

List taxonomic subtrees of given TaxIdsAttention:  1. When multiple taxids are given, the output may contain duplicated records     if some taxids are descendants of others.Examples:    $ taxonkit list --ids 9606 -n -r --indent "    "    9606 [species] Homo sapiens        63221 [subspecies] Homo sapiens neanderthalensis        741158 [subspecies] Homo sapiens subsp. 'Denisova'    $ taxonkit list --ids 9606 --indent ""    9606    63221    741158    # from stdin    echo 9606 | taxonkit list    # from file    taxonkit list <(echo 9606)Usage:  taxonkit list [flags]Flags:  -h, --help            help for list  -i, --ids string      TaxId(s), multiple values should be separated by comma  -I, --indent string   indent (default "  ")  -J, --json            output in JSON format. you can save the result in file with suffix ".json" and                        open with modern text editor  -n, --show-name       output scientific name  -r, --show-rank       output rank

Examples

1. Default usage.

   $taxonkitlist--ids9605,2399349605960663221741158142517026659522665953239934239935349741512293512294113182212626911263034167944426089151131336...

2. Removing indent. The list could be used to extract sequences from BLAST database withblastdbcmd (seetutorial)

   $taxonkitlist--ids9605,239934--indent""96059606632217411581425170266595226659532399342399353497415122935122941131822126269112630341679444...

   Performance: Time and memory usage for whole taxon tree:

   $#emptyingthebufferscache$su-c"free && sync && echo 3 > /proc/sys/vm/drop_caches && free"$memusg-ttaxonkitlist--ids1--indent""--verbose>t0.txt21:05:01.782[INFO]parsingmergedfile:/home/shenwei/.taxonkit/names.dmp21:05:01.782[INFO]parsingnamesfile:/home/shenwei/.taxonkit/names.dmp21:05:01.782[INFO]parsingdelnodesfile:/home/shenwei/.taxonkit/names.dmp21:05:01.816[INFO]61023mergednodesparsed21:05:01.889[INFO]437929delnodesparsed21:05:03.178[INFO]2303979namesparsedelapsedtime:3.290speakrss:742.77MB

3. Adding names

   $taxonkitlist--show-rank--show-name--indent"    "--ids9605,2399349605[genus]Homo9606[species]Homosapiens63221[subspecies]Homosapiensneanderthalensis741158[subspecies]Homosapienssubsp.'Denisova'1425170[species]Homoheidelbergensis2665952[norank]environmentalsamples2665953[species]Homosapiensenvironmentalsample239934[genus]Akkermansia239935[species]Akkermansiamuciniphila349741[strain]AkkermansiamuciniphilaATCCBAA-835512293[norank]environmentalsamples512294[species]unculturedAkkermansiasp.1131822[species]unculturedAkkermansiasp.SMG251262691[species]Akkermansiasp.CAG:3441263034[species]AkkermansiamuciniphilaCAG:1541679444[species]Akkermansiaglycaniphila2608915[norank]unclassifiedAkkermansia1131336[species]Akkermansiasp.KLE16051574264[species]Akkermansiasp.KLE1797...

   Performance: Time and memory usage for whole taxonomy tree:

   $# emptying the buffers cache$su-c"free && sync && echo 3 > /proc/sys/vm/drop_caches && free"$memusg-ttaxonkitlist--show-rank--show-name--ids1>t1.txtelapsedtime:5.341speakrss:1.04GB

4. Output in JSON format, you can easily collapse and uncollapse taxonomy tree in modern text editor.

   $taxonkitlist--show-rank--show-name--indent"    "--ids9605,239934--json{"9605 [genus] Homo":{"9606 [species] Homo sapiens":{"63221 [subspecies] Homo sapiens neanderthalensis":{},"741158 [subspecies] Homo sapiens subsp. 'Denisova'":{}},"1425170 [species] Homo heidelbergensis":{}},"239934 [genus] Akkermansia":{"239935 [species] Akkermansia muciniphila":{"349741 [no rank] Akkermansia muciniphila ATCC BAA-835":{}},"512293 [no rank] environmental samples":{"512294 [species] uncultured Akkermansia sp.":{},"1131822 [species] uncultured Akkermansia sp. SMG25":{},"1262691 [species] Akkermansia sp. CAG:344":{},"1263034 [species] Akkermansia muciniphila CAG:154":{}},"1679444 [species] Akkermansia glycaniphila":{},"2608915 [no rank] unclassified Akkermansia":{"1131336 [species] Akkermansia sp. KLE1605":{},"1574264 [species] Akkermansia sp. KLE1797":{},"1574265 [species] Akkermansia sp. KLE1798":{},"1638783 [species] Akkermansia sp. UNK.MGS-1":{},"1755639 [species] Akkermansia sp. MC_55":{}}}}

   Snapshot of taxonomy (taxid 1) in kate:

lineageLink

Usage

Query taxonomic lineage of given TaxIdsInput:  - List of TaxIds, one TaxId per line.  - Or tab-delimited format, please specify TaxId field     with flag -i/--taxid-field (default 1).  - Supporting (gzipped) file or STDIN.Output:  1. Input line data.  2. (Optional) Status code (-c/--show-status-code), values:     - "-1" for queries not found in whole database.     - "0" for deleted TaxIds, provided by "delnodes.dmp".     - New TaxIds for merged TaxIds, provided by "merged.dmp".     - Taxids for these found in "nodes.dmp".  3. Lineage, delimiter can be changed with flag -d/--delimiter.  4. (Optional) TaxIds taxons in the lineage (-t/--show-lineage-taxids)  5. (Optional) Name (-n/--show-name)  6. (Optional) Rank (-r/--show-rank)Filter out invalid and deleted taxids, and replace merged taxids with new ones:    # input is one-column-taxid    $ taxonkit lineage -c taxids.txt \        | awk '$2>0' \        | cut -f 2-    # taxids are in 3rd field in a 4-columns tab-delimited file,    # for $5, where 5 = 4 + 1.    $ cat input.txt \        | taxonkit lineage -c -i 3 \        | csvtk filter2 -H -t -f '$5>0' \        | csvtk -H -t cut -f -3Usage:  taxonkit lineage [flags]Flags:  -d, --delimiter string      field delimiter in lineage (default ";")  -h, --help                  help for lineage  -L, --no-lineage            do not show lineage, when user just want names or/and ranks  -R, --show-lineage-ranks    appending ranks of all levels  -t, --show-lineage-taxids   appending lineage consisting of taxids  -n, --show-name             appending scientific name  -r, --show-rank             appending rank of taxids  -c, --show-status-code      show status code before lineage  -i, --taxid-field int       field index of taxid. input data should be tab-separated (default 1)

Examples

1. Full lineage:

   #notethat123124124isafaketaxid,3wasdeleted,92489,1458427weremerged$cattaxids.txt960699133766193497412399353141011193213270371231241243924891458427$taxonkitlineagetaxids.txt|teelineage.txt19:22:13.077[WARN]taxid92489wasmergedinto79633419:22:13.077[WARN]taxid1458427wasmergedinto145842519:22:13.077[WARN]taxid123124124notfound19:22:13.077[WARN]taxid3wasdeleted9606cellularorganisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homosapiens9913cellularorganisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Laurasiatheria;Artiodactyla;Ruminantia;Pecora;Bovidae;Bovinae;Bos;Bostaurus376619cellularorganisms;Bacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;Francisellatularensis;Francisellatularensissubsp.holarctica;Francisellatularensissubsp.holarcticaLVS349741cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila;AkkermansiamuciniphilaATCCBAA-835239935cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila314101cellularorganisms;Bacteria;environmentalsamples;unculturedmurinelargebowelbacteriumBAC54B11932Viruses;Riboviria;Pararnavirae;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;unclassifiedRetroviridae;IntracisternalA-particles;MouseIntracisternalA-particle1327037Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;unclassifiedSiphoviridae;CroceibacterphageP2559Y123124124392489cellularorganisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwiniaoleae1458427cellularorganisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonasraicheisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonasraichei#wrappedtablewithcsvtkpretty(>v0.26.0)$taxonkitlineagetaxids.txt|csvtkpretty-Ht-x';'-W70-Sbold┏━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓┃9606┃cellularorganisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;┃┃┃Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;┃┃┃Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;┃┃┃Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;┃┃┃Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;┃┃┃Homo;Homosapiens┃┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫┃9913┃cellularorganisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;┃┃┃Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;┃┃┃Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;┃┃┃Mammalia;Theria;Eutheria;Boreoeutheria;Laurasiatheria;Artiodactyla;┃┃┃Ruminantia;Pecora;Bovidae;Bovinae;Bos;Bostaurus┃┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫┃376619┃cellularorganisms;Bacteria;Proteobacteria;Gammaproteobacteria;┃┃┃Thiotrichales;Francisellaceae;Francisella;Francisellatularensis;┃┃┃Francisellatularensissubsp.holarctica;┃┃┃Francisellatularensissubsp.holarcticaLVS┃┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫┃349741┃cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;┃┃┃Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;┃┃┃Akkermansiamuciniphila;AkkermansiamuciniphilaATCCBAA-835┃┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫┃239935┃cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;┃┃┃Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;┃┃┃Akkermansiamuciniphila┃┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫┃314101┃cellularorganisms;Bacteria;environmentalsamples;┃┃┃unculturedmurinelargebowelbacteriumBAC54B┃┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫┃11932┃Viruses;Riboviria;Pararnavirae;Artverviricota;Revtraviricetes;┃┃┃Ortervirales;Retroviridae;unclassifiedRetroviridae;┃┃┃IntracisternalA-particles;MouseIntracisternalA-particle┃┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫┃1327037┃Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;┃┃┃Caudovirales;Siphoviridae;unclassifiedSiphoviridae;┃┃┃CroceibacterphageP2559Y┃┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫┃92489┃cellularorganisms;Bacteria;Proteobacteria;Gammaproteobacteria;┃┃┃Enterobacterales;Erwiniaceae;Erwinia;Erwiniaoleae┃┣━━━━━━━━━╋━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┫┃1458427┃cellularorganisms;Bacteria;Proteobacteria;Betaproteobacteria;┃┃┃Burkholderiales;Comamonadaceae;Serpentinomonas;┃┃┃Serpentinomonasraichei┃┗━━━━━━━━━┻━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛

2. Speed.

   $timeecho9606|taxonkitlineage9606cellularorganisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homosapiensreal0m1.190suser0m2.365ssys0m0.170s# all TaxIds$timetaxonkitlist--ids1--indent""|taxonkitlineage>treal0m4.249suser0m16.418ssys0m1.221s

3. Checking deleted or merged taxids

   $taxonkitlineage--show-status-codetaxids.txt|teelineage.withcode.txt# valid$catlineage.withcode.txt|awk'$2 > 0'|cut-f1,296069606991399133766193766193497413497412399352399353141013141011193211932132703713270379248979633414584271458425# merged$catlineage.withcode.txt|awk'$2 > 0 && $2 != $1'|cut-f1,29248979633414584271458425# deleted$catlineage.withcode.txt|awk'$2 == 0'|cut-f13# invalid$catlineage.withcode.txt|awk'$2 < 0'|cut-f1123124124

4. Filter out invalid and deleted taxids, and replace merged taxids with new ones, you may installcsvtk.

   #inputisone-column-taxid$taxonkitlineage-ctaxids.txt\|awk'$2>0'\|cut-f2-#taxidsarein3rdfieldina4-columnstab-delimitedfile,#for$5,where5=4+1.$catinput.txt\|taxonkitlineage-c-i3\|csvtkfilter2-H-t-f'$5>0'\|csvtk-H-tcut-f-3

5. Only show name and rank.

   $taxonkitlineage-r-n-Ltaxids.txt\|csvtkpretty-H-t9606Homosapiensspecies9913Bostaurusspecies376619Francisellatularensissubsp.holarcticaLVSstrain349741AkkermansiamuciniphilaATCCBAA-835strain239935Akkermansiamuciniphilaspecies314101unculturedmurinelargebowelbacteriumBAC54Bspecies11932MouseIntracisternalA-particlespecies1327037CroceibacterphageP2559Yspecies123124124392489Erwiniaoleaespecies1458427Serpentinomonasraicheispecies

6. Show lineage consisting of taxids:

   $taxonkitlineage-ttaxids.txt9606cellularorganisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homosapiens131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;40674;32525;9347;1437010;314146;9443;376913;314293;9526;314295;9604;207598;9605;96069913cellularorganisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Laurasiatheria;Artiodactyla;Ruminantia;Pecora;Bovidae;Bovinae;Bos;Bostaurus131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;40674;32525;9347;1437010;314145;91561;9845;35500;9895;27592;9903;9913376619cellularorganisms;Bacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;Francisellatularensis;Francisellatularensissubsp.holarctica;Francisellatularensissubsp.holarcticaLVS131567;2;1224;1236;72273;34064;262;263;119857;376619349741cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila;AkkermansiamuciniphilaATCCBAA-835131567;2;1783257;74201;203494;48461;1647988;239934;239935;349741239935cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila131567;2;1783257;74201;203494;48461;1647988;239934;239935314101cellularorganisms;Bacteria;environmentalsamples;unculturedmurinelargebowelbacteriumBAC54B131567;2;48479;31410111932Viruses;Riboviria;Pararnavirae;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;unclassifiedRetroviridae;IntracisternalA-particles;MouseIntracisternalA-particle10239;2559587;2732397;2732409;2732514;2169561;11632;35276;11749;119321327037Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;unclassifiedSiphoviridae;CroceibacterphageP2559Y10239;2731341;2731360;2731618;2731619;28883;10699;196894;1327037123124124392489cellularorganisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwiniaoleae131567;2;1224;1236;91347;1903409;551;7963341458427cellularorganisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonasraichei131567;2;1224;28216;80840;80864;2490452;1458425

   or read taxids from STDIN:

   $cattaxids.txt|taxonkitlineage

7. And ranks of all nodes:

   $echo2697049\|taxonkitlineage-t-R\|csvtktranspose-Ht2697049Viruses;Riboviria;Orthornavirae;Pisuviricota;Pisoniviricetes;Nidovirales;Cornidovirineae;Coronaviridae;Orthocoronavirinae;Betacoronavirus;Sarbecovirus;Severeacuterespiratorysyndrome-relatedcoronavirus;Severeacuterespiratorysyndromecoronavirus210239;2559587;2732396;2732408;2732506;76804;2499399;11118;2501931;694002;2509511;694009;2697049superkingdom;clade;kingdom;phylum;class;order;suborder;family;subfamily;genus;subgenus;species;norank

   Another way to show lineage detail of a TaxId

   $echo2697049\|taxonkitlineage-t\|csvtkcut-Ht-f3\|csvtkunfold-Ht-f1-s";"\|taxonkitlineage-r-n-L\|csvtkcut-Ht-f1,3,2\|csvtkpretty-H-t10239superkingdomViruses2559587cladeRiboviria2732396kingdomOrthornavirae2732408phylumPisuviricota2732506classPisoniviricetes76804orderNidovirales2499399suborderCornidovirineae11118familyCoronaviridae2501931subfamilyOrthocoronavirinae694002genusBetacoronavirus2509511subgenusSarbecovirus694009speciesSevereacuterespiratorysyndrome-relatedcoronavirus2697049norankSevereacuterespiratorysyndromecoronavirus2

reformatLink

Usage

Reformat lineage in canonical ranksWarning:  - 'taxonkit reformat2' is recommended since Match 2025 when NCBI made    big changes to ranks.    See more: https://ncbiinsights.ncbi.nlm.nih.gov/2025/02/27/new-ranks-ncbi-taxonomy/Input:  - List of TaxIds or lineages, one record per line.    The lineage can be a complete lineage or only one taxonomy name.  - Or tab-delimited format.    Plese specify the lineage field with flag -i/--lineage-field (default 2).    Or specify the TaxId field with flag -I/--taxid-field (default 0),    which overrides -i/--lineage-field.  - Supporting (gzipped) file or STDIN.Output:  1. Input line data.  2. Reformated lineage.  3. (Optional) TaxIds taxons in the lineage (-t/--show-lineage-taxids)Ambiguous names:  - Some TaxIds have the same complete lineage, empty result is returned     by default. You can use the flag -a/--output-ambiguous-result to    return one possible resultOutput format can be formated by flag --format, available placeholders:    {C}: cellular root    {a}: acellular root    {r}: realm    {d}: domain    {k}: superkingdom    {K}: kingdom    {p}: phylum    {c}: class    {o}: order    {f}: family    {g}: genus    {s}: species    {t}: subspecies/strain    {S}: subspecies    {T}: strainWhen these're no nodes of rank "subspecies" nor "strain",you can switch on -S/--pseudo-strain to use the node with lowest rankas subspecies/strain name, if which rank is lower than "species". This flag affects {t}, {S}, {T}.Output format can contains some escape charactors like "\t".Usage:  taxonkit reformat [flags] Flags:  -P, --add-prefix                     add prefixes for all ranks, single prefix for a rank is defined                                       by flag --prefix-X  -d, --delimiter string               field delimiter in input lineage (default ";")  -F, --fill-miss-rank                 fill missing rank with lineage information of the next higher rank  -f, --format string                  output format, placeholders of rank are needed (default                                       "{k};{p};{c};{o};{f};{g};{s}")  -h, --help                           help for reformat  -i, --lineage-field int              field index of lineage. data should be tab-separated (default 2)  -r, --miss-rank-repl string          replacement string for missing rank  -p, --miss-rank-repl-prefix string   prefix for estimated taxon names (default "unclassified ")  -s, --miss-rank-repl-suffix string   suffix for estimated taxon names. "rank" for rank name, "" for no                                       suffix (default "rank")  -R, --miss-taxid-repl string         replacement string for missing taxid  -a, --output-ambiguous-result        output one of the ambigous result      --prefix-C string                prefix for cellular root, used along with flag -P/--add-prefix                                       (default "d__")      --prefix-K string                prefix for kingdom, used along with flag -P/--add-prefix (default                                       "K__")      --prefix-S string                prefix for subspecies, used along with flag -P/--add-prefix                                       (default "S__")      --prefix-T string                prefix for strain, used along with flag -P/--add-prefix (default                                       "T__")      --prefix-a string                prefix for acellular root, used along with flag -P/--add-prefix                                       (default "d__")      --prefix-c string                prefix for class, used along with flag -P/--add-prefix (default "c__")      --prefix-d string                prefix for domain, used along with flag -P/--add-prefix (default                                       "d__")      --prefix-f string                prefix for family, used along with flag -P/--add-prefix (default                                       "f__")      --prefix-g string                prefix for genus, used along with flag -P/--add-prefix (default "g__")      --prefix-k string                prefix for superkingdom, used along with flag -P/--add-prefix                                       (default "k__")      --prefix-o string                prefix for order, used along with flag -P/--add-prefix (default "o__")      --prefix-p string                prefix for phylum, used along with flag -P/--add-prefix (default                                       "p__")      --prefix-r string                prefix for realm, used along with flag -P/--add-prefix (default "r__")      --prefix-s string                prefix for species, used along with flag -P/--add-prefix (default                                       "s__")      --prefix-t string                prefix for subspecies/strain, used along with flag                                       -P/--add-prefix (default "t__")  -S, --pseudo-strain                  use the node with lowest rank as strain name, only if which rank                                       is lower than "species" and not "subpecies" nor "strain". It                                       affects {t}, {S}, {T}. This flag needs flag -F  -t, --show-lineage-taxids            show corresponding taxids of reformated lineage  -I, --taxid-field int                field index of taxid. input data should be tab-separated. it                                       overrides -i/--lineage-field  -T, --trim                           do not fill or add prefix for missing rank lower than current rank

Examples:

1. For version > 0.8.0,reformat accept input of TaxIds via flag-I/--taxid-field.

   $echo239935|taxonkitreformat-I1239935Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila$echo349741|taxonkitreformat-I1-f"{k}|{p}|{c}|{o}|{f}|{g}|{s}|{t}"-F-t349741Bacteria|Verrucomicrobia|Verrucomicrobiae|Verrucomicrobiales|Akkermansiaceae|Akkermansia|Akkermansiamuciniphila|AkkermansiamuciniphilaATCCBAA-8352|74201|203494|48461|1647988|239934|239935|349741

2. Example lineage (produced by:taxonkit lineage taxids.txt | awk '$2!=""' > lineage.txt).

   $catlineage.txt9606cellularorganisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homosapiens9913cellularorganisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Laurasiatheria;Artiodactyla;Ruminantia;Pecora;Bovidae;Bovinae;Bos;Bostaurus376619cellularorganisms;Bacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;Francisellatularensis;Francisellatularensissubsp.holarctica;Francisellatularensissubsp.holarcticaLVS349741cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila;AkkermansiamuciniphilaATCCBAA-835239935cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila314101cellularorganisms;Bacteria;environmentalsamples;unculturedmurinelargebowelbacteriumBAC54B11932Viruses;Riboviria;Pararnavirae;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;unclassifiedRetroviridae;IntracisternalA-particles;MouseIntracisternalA-particle1327037Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;unclassifiedSiphoviridae;CroceibacterphageP2559Y92489cellularorganisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwiniaoleae1458427cellularorganisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonasraichei

3. Default output format ("{k};{p};{c};{o};{f};{g};{s}").

   #reformatedlineagesareappendedtotheinputdata$taxonkitreformatlineage.txt...239935cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;AkkermansiamuciniphilaBacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila...$$taxonkitreformatlineage.txt|teelineage.txt.reformat$cut-f1,3lineage.txt.reformat9606Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;Homosapiens9913Eukaryota;Chordata;Mammalia;Artiodactyla;Bovidae;Bos;Bostaurus376619Bacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;Francisellatularensis349741Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila239935Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila314101Bacteria;;;;;;unculturedmurinelargebowelbacteriumBAC54B11932Viruses;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;IntracisternalA-particles;MouseIntracisternalA-particle1327037Viruses;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;;CroceibacterphageP2559Y92489Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwiniaoleae1458427Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonasraichei#aligned$catlineage.txt\|taxonkitreformat\|csvtk-H-tcut-f1,3\|csvtk-H-tsep-f2-s';'-R\|csvtkadd-header-t-ntaxid,kindom,phylum,class,order,family,genus,species\|csvtkpretty-ttaxidkindomphylumclassorderfamilygenusspecies------------------------------------------------------------------------------------------------------------------------------------------------------------9606EukaryotaChordataMammaliaPrimatesHominidaeHomoHomosapiens9913EukaryotaChordataMammaliaArtiodactylaBovidaeBosBostaurus376619BacteriaProteobacteriaGammaproteobacteriaThiotrichalesFrancisellaceaeFrancisellaFrancisellatularensis349741BacteriaVerrucomicrobiaVerrucomicrobiaeVerrucomicrobialesAkkermansiaceaeAkkermansiaAkkermansiamuciniphila239935BacteriaVerrucomicrobiaVerrucomicrobiaeVerrucomicrobialesAkkermansiaceaeAkkermansiaAkkermansiamuciniphila314101BacteriaunculturedmurinelargebowelbacteriumBAC54B11932VirusesArtverviricotaRevtraviricetesOrterviralesRetroviridaeIntracisternalA-particlesMouseIntracisternalA-particle1327037VirusesUroviricotaCaudoviricetesCaudoviralesSiphoviridaeCroceibacterphageP2559Y92489BacteriaProteobacteriaGammaproteobacteriaEnterobacteralesErwiniaceaeErwiniaErwiniaoleae1458427BacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeSerpentinomonasSerpentinomonasraichei

4. Andsubspecies/strain ({t}),subspecies ({S}), andstrain ({T}) are also available.

   #defaultoperation$echo-ne"239935\n83333\n1408252\n2697049\n2605619\n"\|taxonkitlineage-n-r\|taxonkitreformat-f'{t};{S};{T}'\|csvtk-H-tcut-f1,4,3,5\|csvtk-H-tsep-f4-s';'-R\|csvtk-H-tadd-header-n"taxid,rank,name,subspecies/strain,subspecies,strain"\|csvtkpretty-ttaxidranknamesubspecies/strainsubspeciesstrain-------------------------------------------------------------------------------------------------------------------------------239935speciesAkkermansiamuciniphila83333strainEscherichiacoliK-12EscherichiacoliK-12EscherichiacoliK-121408252subspeciesEscherichiacoliR178EscherichiacoliR178EscherichiacoliR1782697049norankSevereacuterespiratorysyndromecoronavirus22605619norankEscherichiacoliO16:H48#fillmissingranks#seeexamplebelowfor-F/--fill-miss-rank#$echo-ne"239935\n83333\n1408252\n2697049\n2605619\n"\|taxonkitlineage-n-r\|taxonkitreformat-f'{t};{S};{T}'--fill-miss-rank\|csvtk-H-tcut-f1,4,3,5\|csvtk-H-tsep-f4-s';'-R\|csvtk-H-tadd-header-n"taxid,rank,name,subspecies/strain,subspecies,strain"\|csvtkpretty-ttaxidranknamesubspecies/strainsubspeciesstrain----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------239935speciesAkkermansiamuciniphilaunclassifiedAkkermansiamuciniphilasubspecies/strainunclassifiedAkkermansiamuciniphilasubspeciesunclassifiedAkkermansiamuciniphilastrain83333strainEscherichiacoliK-12EscherichiacoliK-12unclassifiedEscherichiacolisubspeciesEscherichiacoliK-121408252subspeciesEscherichiacoliR178EscherichiacoliR178EscherichiacoliR178unclassifiedEscherichiacoliR178strain2697049norankSevereacuterespiratorysyndromecoronavirus2unclassifiedSevereacuterespiratorysyndrome-relatedcoronavirussubspecies/strainunclassifiedSevereacuterespiratorysyndrome-relatedcoronavirussubspeciesunclassifiedSevereacuterespiratorysyndrome-relatedcoronavirusstrain2605619norankEscherichiacoliO16:H48unclassifiedEscherichiacolisubspecies/strainunclassifiedEscherichiacolisubspeciesunclassifiedEscherichiacolistrain

5. When these's no nodes of rank "subspecies" nor "strain", you can switch-S/--pseudo-strain to use the node with lowest rank as subspecies/strain name, if which rank is lower than "species". Recommend using v0.14.1 or later versions.

   $echo-ne"239935\n83333\n1408252\n2697049\n2605619\n"\|taxonkitlineage-n-r\|taxonkitreformat-f'{t};{S};{T}'--pseudo-strain\|csvtk-H-tcut-f1,4,3,5\|csvtk-H-tsep-f4-s';'-R\|csvtk-H-tadd-header-n"taxid,rank,name,subspecies/strain,subspecies,strain"\|csvtkpretty-ttaxidranknamesubspecies/strainsubspeciesstrain-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------239935speciesAkkermansiamuciniphila83333strainEscherichiacoliK-12EscherichiacoliK-12EscherichiacoliK-121408252subspeciesEscherichiacoliR178EscherichiacoliR178EscherichiacoliR1782697049norankSevereacuterespiratorysyndromecoronavirus2Severeacuterespiratorysyndromecoronavirus2Severeacuterespiratorysyndromecoronavirus2Severeacuterespiratorysyndromecoronavirus22605619norankEscherichiacoliO16:H48EscherichiacoliO16:H48EscherichiacoliO16:H48EscherichiacoliO16:H48

6. Add prefix (-P/--add-prefix).

   $catlineage.txt\|taxonkitreformat-P\|csvtk-H-tcut-f1,39606k__Eukaryota;p__Chordata;c__Mammalia;o__Primates;f__Hominidae;g__Homo;s__Homosapiens9913k__Eukaryota;p__Chordata;c__Mammalia;o__Artiodactyla;f__Bovidae;g__Bos;s__Bostaurus376619k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Francisellaceae;g__Francisella;s__Francisellatularensis349741k__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;s__Akkermansiamuciniphila239935k__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;s__Akkermansiamuciniphila314101k__Bacteria;p__;c__;o__;f__;g__;s__unculturedmurinelargebowelbacteriumBAC54B11932k__Viruses;p__Artverviricota;c__Revtraviricetes;o__Ortervirales;f__Retroviridae;g__IntracisternalA-particles;s__MouseIntracisternalA-particle1327037k__Viruses;p__Uroviricota;c__Caudoviricetes;o__Caudovirales;f__Siphoviridae;g__;s__CroceibacterphageP2559Y92489k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Erwiniaceae;g__Erwinia;s__Erwiniaoleae1458427k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Comamonadaceae;g__Serpentinomonas;s__Serpentinomonasraichei

7. Show corresponding taxids of reformated lineage (flag-t/--show-lineage-taxids)

   $catlineage.txt\|taxonkitreformat-t\|csvtk-H-tcut-f1,4\|csvtk-H-tsep-f2-s';'-R\|csvtkadd-header-t-ntaxid,kindom,phylum,class,order,family,genus,species\|csvtkpretty-ttaxidkindomphylumclassorderfamilygenusspecies-------------------------------------------------------960627597711406749443960496059606991327597711406749156198959903991337661921224123672273340642622633497412742012034944846116479882399342399352399352742012034944846116479882399342399353141012314101119321023927324092732514216956111632117491193213270371023927316182731619288831069913270379248921224123691347190340955179633414584272122428216808408086424904521458425# both node name and taxidsecho562\|taxonkitreformat-I1-t\|csvtk-H-tsep-f2-s';'-R\|csvtk-H-tsep-f2-s';'-R\|csvtkadd-header-t-n"taxid,kingdom,phylum,class,order,family,genus,species,kingdom_taxid,phylum_taxid,class_taxid,order_taxid,family_taxid,genus_taxid,species_taxid"\|csvtkpretty-ttaxidkingdomphylumclassorderfamilygenusspecieskingdom_taxidphylum_taxidclass_taxidorder_taxidfamily_taxidgenus_taxidspecies_taxid----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------562BacteriaPseudomonadotaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichiaEscherichiacoli21224123691347543561562

8. Use custom symbols for unclassfied ranks (-r/--miss-rank-repl)

   $taxonkitreformatlineage.txt-r"__"|cut-f3Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;HomosapiensEukaryota;Chordata;Mammalia;Artiodactyla;Bovidae;Bos;BostaurusBacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;FrancisellatularensisBacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;AkkermansiamuciniphilaBacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;AkkermansiamuciniphilaBacteria;__;__;__;__;__;unculturedmurinelargebowelbacteriumBAC54BViruses;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;IntracisternalA-particles;MouseIntracisternalA-particleViruses;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;__;CroceibacterphageP2559YBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;ErwiniaoleaeBacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonasraichei$taxonkitreformatlineage.txt-rUnassigned|cut-f3Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;HomosapiensEukaryota;Chordata;Mammalia;Artiodactyla;Bovidae;Bos;BostaurusBacteria;Proteobacteria;Gammaproteobacteria;Thiotrichales;Francisellaceae;Francisella;FrancisellatularensisBacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;AkkermansiamuciniphilaBacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;AkkermansiamuciniphilaBacteria;Unassigned;Unassigned;Unassigned;Unassigned;Unassigned;unculturedmurinelargebowelbacteriumBAC54BViruses;Artverviricota;Revtraviricetes;Ortervirales;Retroviridae;IntracisternalA-particles;MouseIntracisternalA-particleViruses;Uroviricota;Caudoviricetes;Caudovirales;Siphoviridae;Unassigned;CroceibacterphageP2559YBacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;ErwiniaoleaeBacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonasraichei

9. Estimate and fill missing rank with original lineage information (-F, --fill-miss-rank, very useful for formatting input data forLEfSe). You can change the prefix "unclassified" using flag-p/--miss-rank-repl-prefix.

   $catlineage.txt\|taxonkitreformat-F\|csvtk-H-tcut-f1,3\|csvtk-H-tsep-f2-s';'-R\|csvtkadd-header-t-ntaxid,kindom,phylum,class,order,family,genus,species\|csvtkpretty-ttaxidkindomphylumclassorderfamilygenusspecies------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------9606EukaryotaChordataMammaliaPrimatesHominidaeHomoHomosapiens9913EukaryotaChordataMammaliaArtiodactylaBovidaeBosBostaurus376619BacteriaProteobacteriaGammaproteobacteriaThiotrichalesFrancisellaceaeFrancisellaFrancisellatularensis349741BacteriaVerrucomicrobiaVerrucomicrobiaeVerrucomicrobialesAkkermansiaceaeAkkermansiaAkkermansiamuciniphila239935BacteriaVerrucomicrobiaVerrucomicrobiaeVerrucomicrobialesAkkermansiaceaeAkkermansiaAkkermansiamuciniphila314101BacteriaunclassifiedBacteriaphylumunclassifiedBacteriaclassunclassifiedBacteriaorderunclassifiedBacteriafamilyunclassifiedBacteriagenusunculturedmurinelargebowelbacteriumBAC54B11932VirusesArtverviricotaRevtraviricetesOrterviralesRetroviridaeIntracisternalA-particlesMouseIntracisternalA-particle1327037VirusesUroviricotaCaudoviricetesCaudoviralesSiphoviridaeunclassifiedSiphoviridaegenusCroceibacterphageP2559Y92489BacteriaProteobacteriaGammaproteobacteriaEnterobacteralesErwiniaceaeErwiniaErwiniaoleae1458427BacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeSerpentinomonasSerpentinomonasraichei

   Do not add prefix or suffix for estimated nodes:

   $echo314101|taxonkitreformat-I1314101Bacteria;;;;;;unculturedmurinelargebowelbacteriumBAC54B$echo314101|taxonkitreformat-I1-F-p""-s""314101Bacteria;Bacteria;Bacteria;Bacteria;Bacteria;Bacteria;unculturedmurinelargebowelbacteriumBAC54B

10. Only some ranks.

    $catlineage.txt\|taxonkitreformat-F-f"{s};{p}"\|csvtk-H-tcut-f1,3\|csvtk-H-tsep-f2-s';'-R\|csvtkadd-header-t-ntaxid,species,phylum\|csvtkpretty-ttaxidspeciesphylum----------------------------------------------------------------------------------9606HomosapiensChordata9913BostaurusChordata376619FrancisellatularensisProteobacteria349741AkkermansiamuciniphilaVerrucomicrobia239935AkkermansiamuciniphilaVerrucomicrobia314101unculturedmurinelargebowelbacteriumBAC54BunclassifiedBacteriaphylum11932MouseIntracisternalA-particleArtverviricota1327037CroceibacterphageP2559YUroviricota92489ErwiniaoleaeProteobacteria1458427SerpentinomonasraicheiProteobacteria

11. For some taxids which rank is higher than the lowest rank in-f/--format, use-T/--trim to avoid fill missing rank lower than current rank.

    $echo-ne"2\n239934\n239935\n"\|taxonkitlineage\|taxonkitreformat-F\|sed-r"s/;+$//"\|csvtk-H-tcut-f1,32Bacteria;unclassifiedBacteriaphylum;unclassifiedBacteriaclass;unclassifiedBacteriaorder;unclassifiedBacteriafamily;unclassifiedBacteriagenus;unclassifiedBacteriaspecies239934Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;unclassifiedAkkermansiaspecies239935Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila$echo-ne"2\n239934\n239935\n"\|taxonkitlineage\|taxonkitreformat-F-T\|sed-r"s/;+$//"\|csvtk-H-tcut-f1,32Bacteria239934Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia239935Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila

12. Support tab in format string

    $echo9606\|taxonkitlineage\|taxonkitreformat-f"{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}\t{S}"\|csvtkcut-t-f-29606EukaryotaChordataMammaliaPrimatesHominidaeHomoHomosapiens

13. List seven-level lineage for all TaxIds.

    #replaceemptytaxonwith"Unassigned"$taxonkitlist--ids1\|taxonkitlineage\|taxonkitreformat-rUnassigned|gzip-c>all.lineage.tsv.gz#tab-delimitedseven-levels$taxonkitlist--ids1\|taxonkitlineage\|taxonkitreformat-rUnassigned-f"{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}"\|csvtkcut-H-t-f-2\|head-n5\|csvtkpretty-H-t#8-level$taxonkitlist--ids1\|taxonkitlineage\|taxonkitreformat-rUnassigned-f"{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}\t{t}"\|csvtkcut-H-t-f-2\|head-n5\|csvtkpretty-H-t#Fillandtrim$memusg-t-s'taxonkitlist--ids1\|taxonkitlineage\|taxonkitreformat-F-T\|sed-r"s/;+$//"\|gzip-c>all.lineage.tsv.gz'elapsedtime:19.930speakrss:6.25GB

14. From taxid to 7-ranks lineage:

    $cattaxids.txt|taxonkitlineage|taxonkitreformat# for taxonkit v0.8.0 or later versions$cattaxids.txt|taxonkitreformat-I1

15. Some TaxIds have the same complete lineage, empty result is returned by default. You can use the flag-a/--output-ambiguous-result to return one possible result.see #42

    $echo-ne"2507530\n2516889\n"|taxonkitlineage--data-dir.|taxonkitreformat--data-dir.-t19:18:29.770[WARN]wecan't distinguish the TaxIds (2507530, 2516889) for lineage: cellular organisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Basidiomycota;Agaricomycotina;Agaricomycetes;Agaricomycetes incertae sedis;Russulales;Russulaceae;Russula;unclassified Russula;Russula sp. 8 KA-2019. But you can use -a/--output-ambiguous-result to return one possible result19:18:29.770 [WARN] we can'tdistinguishtheTaxIds(2507530,2516889)forlineage:cellularorganisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Basidiomycota;Agaricomycotina;Agaricomycetes;Agaricomycetesincertaesedis;Russulales;Russulaceae;Russula;unclassifiedRussula;Russulasp.8KA-2019.Butyoucanuse-a/--output-ambiguous-resulttoreturnonepossibleresult2507530cellularorganisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Basidiomycota;Agaricomycotina;Agaricomycetes;Agaricomycetesincertaesedis;Russulales;Russulaceae;Russula;unclassifiedRussula;Russulasp.8KA-20192516889cellularorganisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Basidiomycota;Agaricomycotina;Agaricomycetes;Agaricomycetesincertaesedis;Russulales;Russulaceae;Russula;unclassifiedRussula;Russulasp.8KA-2019$echo-ne"2507530\n2516889\n"|taxonkitlineage--data-dir.|taxonkitreformat--data-dir.-t-a2507530cellularorganisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Basidiomycota;Agaricomycotina;Agaricomycetes;Agaricomycetesincertaesedis;Russulales;Russulaceae;Russula;unclassifiedRussula;Russulasp.8KA-2019Eukaryota;Basidiomycota;Agaricomycetes;Russulales;Russulaceae;Russula;Russulasp.8KA-20192759;5204;155619;452342;5401;5402;25075302516889cellularorganisms;Eukaryota;Opisthokonta;Fungi;Dikarya;Basidiomycota;Agaricomycotina;Agaricomycetes;Agaricomycetesincertaesedis;Russulales;Russulaceae;Russula;unclassifiedRussula;Russulasp.8KA-2019Eukaryota;Basidiomycota;Agaricomycetes;Russulales;Russulaceae;Russula;Russulasp.8KA-20192759;5204;155619;452342;5401;5402;2507530

reformat2Link

Usage

Reformat lineage in chosen ranks, allowing more ranks than 'reformat'Input:  - List of TaxIds, one record per line.  - Or tab-delimited format.    Please specify the TaxId field with flag -I/--taxid-field (default 1)  - Supporting (gzipped) file or STDIN.Output:  1. Input line data.  2. Reformated lineage.  3. (Optional) TaxIds taxons in the lineage (-t/--show-lineage-taxids)Output format:  1. It can contain some escape characters like "\t".  2. You can use "|" to set multiple ranks, and the first valid one will be outputted.     This is useful for a rank with different rank names, especially since NCBI     made big changes to some ranks in March 2025:        - "Domain" replaces "superkingdom" for Archaea, Bacteria, and Eukaryota        - "Acellular root" replaces "superkingdom" for Viruses        - Six viral groups are designated with the new rank "realm", the equivalent of "domain"     So, we can use "{domain|acellular root|superkingdom}" to handle all these cases     and keep compatible with old taxonomy data.       $ echo -ne "Eukaryota\nBacteria\nViruses\n" \           | taxonkit name2taxid -s -r \           | taxonkit reformat2 -I 2 -f "{domain|acellular root|superkingdom}" \           | csvtk add-header -Ht -n name,taxid,rank,kingdom/domain \           | csvtk pretty -t       name        taxid   rank             kingdom/domain       ---------   -----   --------------   --------------       Eukaryota   2759    domain           Eukaryota       Bacteria    2       domain           Bacteria       Viruses     10239   acellular root   Viruses     Another example is for subspecies nodes, the rank might be "subpecies", "strain", or "no rank".     For example,       $ echo -ne "562\n83333\n2697049\n" \          | taxonkit lineage -L -r \          | taxonkit reformat2 -f "{species};{strain|subspecies|no rank}"       562     species Escherichia coli;       83333   strain  Escherichia coli;Escherichia coli K-12       2697049 no rank Severe acute respiratory syndrome-related coronavirus;Severe acute respiratory syndrome coronavirus 2Differences from 'taxonkit reformat':  - [input] only accept TaxIDs  - [format] accept more rank place holders, not just the seven canonical ones.  - [format] use the full name of ranks, such as "{species}", rather than "{s}"  - [format] support multiple ranks in one place holder, such as "{subspecies|strain}"  - do not automatically add prefixes, but you can simply set them in the formatUsage:  taxonkit reformat2 [flags] Flags:  -f, --format string            output format, placeholders of rank are needed (default                                 "{domain|acellular                                 root|superkingdom};{phylum};{class};{order};{family};{genus};{species}")  -h, --help                     help for reformat2  -r, --miss-rank-repl string    replacement string for missing rank  -R, --miss-taxid-repl string   replacement string for missing taxid  -B, --no-ranks strings         rank names of no-rank. A lineage might have many "no rank" ranks, we                                 only keep the last one below known ranks (default [no rank,clade])  -t, --show-lineage-taxids      show corresponding taxids of reformated lineage  -I, --taxid-field int          field index of taxid. input data should be tab-separated. it overrides                                 -i/--lineage-field (default 1)  -T, --trim                     do not replace missing ranks lower than the rank of the current node

Examples

1. Default format

   $echo562|taxonkitreformat2562Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichiacoli

2. Change the format

   $echo562|taxonkitreformat2-f"g__{genus}\ts__{species}"562g__Escherichias__Escherichiacoli

3. Subspecies

   $echo511145|taxonkitlineage511145cellularorganisms;Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichiacoli;EscherichiacoliK-12;Escherichiacolistr.K-12substr.MG1655$echo511145|taxonkitreformat-I1-f"{d};{p};{c};{o};{f};{g};{s};{t}"511145Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichiacoli;EscherichiacoliK-12$echo511145|taxonkitreformat2-I1-f"{domain|acellular root|superkingdom};{phylum};{class};{order};{family};{genus};{species};{subspecies|strain|no rank}"511145Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichiacoli;EscherichiacoliK-12

4. Trim

   $echo561|taxonkitreformat2-runknown561Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;unknown$echo561|taxonkitreformat2-runknown-T561Bacteria;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;# -----------------------------------------------------------# another example where the order rank is missing$echo102403|taxonkitreformat2-I1-r"0"-f"{domain|acellular root|superkingdom};{phylum};{class};{order};{family};{genus};{species}"102403Eukaryota;Mollusca;Bivalvia;0;Poromyidae;Tropidomya;0$echo102403|taxonkitreformat2-I1-r"0"-f"{domain|acellular root|superkingdom};{phylum};{class};{order};{family};{genus};{species}"-T102403Eukaryota;Mollusca;Bivalvia;0;Poromyidae;Tropidomya;# and now, the lowest rank in the output format is order, but the tailing "0" is not trimmed.$echo102403|taxonkitreformat2-I1-r"0"-f"{domain|acellular root|superkingdom};{phylum};{class};{order}"102403Eukaryota;Mollusca;Bivalvia;0$echo102403|taxonkitreformat2-I1-r"0"-f"{domain|acellular root|superkingdom};{phylum};{class};{order}"-T102403Eukaryota;Mollusca;Bivalvia;0

name2taxidLink

Usage

Convert taxon names to TaxIdsAttention:  1. Some TaxIds share the same names, e.g, Drosophila.     These input lines are duplicated with multiple TaxIds.    $ echo Drosophila | taxonkit name2taxid | taxonkit lineage -i 2 -r -L    Drosophila      7215    genus    Drosophila      32281   subgenus    Drosophila      2081351 genusUsage:  taxonkit name2taxid [flags]Flags:  -h, --help             help for name2taxid  -i, --name-field int   field index of name. data should be tab-separated (default 1)  -s, --sci-name         only searching scientific names  -r, --show-rank        show rank

Examples

Example data

$catnames.txtHomosapiensAkkermansiamuciniphilaATCCBAA-835AkkermansiamuciniphilaMouseIntracisternalA-particleWeiShenunculturedmurinelargebowelbacteriumBAC54BCroceibacterphageP2559Y

1. Default.

   # taxonkit name2taxid names.txt$ cat names.txt | taxonkit name2taxid | csvtk pretty -H -tHomo sapiens                                      9606Akkermansia muciniphila ATCC BAA-835              349741Akkermansia muciniphila                           239935Mouse Intracisternal A-particle                   11932Wei Shen                                          uncultured murine large bowel bacterium BAC 54B   314101Croceibacter phage P2559Y                         1327037

2. Show rank.

   $catnames.txt|taxonkitname2taxid--show-rank|csvtkpretty-H-tHomosapiens9606speciesAkkermansiamuciniphilaATCCBAA-835349741strainAkkermansiamuciniphila239935speciesMouseIntracisternalA-particle11932speciesWeiShenunculturedmurinelargebowelbacteriumBAC54B314101speciesCroceibacterphageP2559Y1327037species

3. From name to lineage.

   $catnames.txt|taxonkitname2taxid|taxonkitlineage--taxid-field2Homosapiens9606cellularorganisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;HomosapiensAkkermansiamuciniphilaATCCBAA-835349741cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila;AkkermansiamuciniphilaATCCBAA-835Akkermansiamuciniphila239935cellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;AkkermansiamuciniphilaMouseIntracisternalA-particle11932Viruses;Ortervirales;Retroviridae;unclassifiedRetroviridae;IntracisternalA-particles;MouseIntracisternalA-particleWeiShenunculturedmurinelargebowelbacteriumBAC54B314101cellularorganisms;Bacteria;environmentalsamples;unculturedmurinelargebowelbacteriumBAC54BCroceibacterphageP2559Y1327037Viruses;Caudovirales;Siphoviridae;unclassifiedSiphoviridae;CroceibacterphageP2559Y

4. Convert old names to new names.

   $echoLactobacillusfermentum|taxonkitname2taxid|taxonkitlineage-i2-n|cut-f1,2,4Lactobacillusfermentum1613Limosilactobacillusfermentum

5. Some TaxIds share the same scientific names, e.g, Drosophila.

   $echoDrosophila\|taxonkitname2taxid\|taxonkitlineage-i2-r\|taxonkitreformat-i3\|csvtkcut-H-t-f1,2,4,5\|csvtkpretty-H-tDrosophila7215genusEukaryota;Arthropoda;Insecta;Diptera;Drosophilidae;Drosophila;Drosophila32281subgenusEukaryota;Arthropoda;Insecta;Diptera;Drosophilidae;Drosophila;Drosophila2081351genusEukaryota;Basidiomycota;Agaricomycetes;Agaricales;Psathyrellaceae;Drosophila;

filterLink

Usage

Filter TaxIds by taxonomic rank rangeAttention:  1. Flag -L/--lower-than and -H/--higher-than are exclusive, and can be     used along with -E/--equal-to which values can be different.  2. A list of pre-ordered ranks is in ~/.taxonkit/ranks.txt, you can use     your list by -r/--rank-file, the format specification is below.  3. All ranks in taxonomy database should be defined in rank file.  4. Ranks can be removed with black list via -B/--black-list.  5. TaxIDs with no rank (those starting with ! in the rank file) are kept     by default! They can be optionally discarded by -N/--discard-noranks.     One exception: -N/--discard-noranks is switched on automatically     when only -E/--equal-to is given and the value is not one of ranks     without order ("no rank", "clade").  6. [Recommended] When filtering with -L/--lower-than, you can use    -n/--save-predictable-norank to save some special ranks without order,    where rank of the closest higher node is still lower than rank cutoff.Rank file:  1. Blank lines or lines starting with "#" are ignored.  2. Ranks are in decending order and case ignored.  3. Ranks with same order should be in one line separated with comma (",", no space).  4. Ranks without order should be assigned a prefix symbol "!" for each rank.Usage:  taxonkit filter [flags] Flags:  -B, --black-list strings        black list of ranks to discard, e.g., '-B "no rank" -B "clade"  -N, --discard-noranks           discard all ranks without order, type "taxonkit filter --help" for details  -R, --discard-root              discard root taxid, defined by --root-taxid  -E, --equal-to strings          output TaxIds with rank equal to some ranks, multiple values can be                                  separated with comma "," (e.g., -E "genus,species"), or give multiple                                  times (e.g., -E genus -E species)  -h, --help                      help for filter  -H, --higher-than string        output TaxIds with rank higher than a rank, exclusive with --lower-than      --list-order                list user defined ranks in order, from "$HOME/.taxonkit/ranks.txt"      --list-ranks                list ordered ranks in taxonomy database, sorted in user defined order  -L, --lower-than string         output TaxIds with rank lower than a rank, exclusive with --higher-than  -r, --rank-file string          user-defined ordered taxonomic ranks, type "taxonkit filter --help"                                  for details      --root-taxid uint32         root taxid (default 1)  -n, --save-predictable-norank   do not discard some special ranks without order when using -L, where                                  rank of the closest higher node is still lower than rank cutoff  -i, --taxid-field int           field index of taxid. input data should be tab-separated (default 1)

Examples

1. Example data

   $echo349741|taxonkitlineage-t|cut-f3|sed's/;/\n/g'>taxids2.txt$cattaxids2.txt1315672178325774201203494484611647988239934239935349741$cattaxids2.txt|taxonkitlineage-r|csvtk-Htcut-f1,3,2|csvtkpretty-H-t131567cellularrootcellularorganisms2domaincellularorganisms;Bacteria1783257cladecellularorganisms;Bacteria;Pseudomonadati;PVCgroup74201phylumcellularorganisms;Bacteria;Pseudomonadati;PVCgroup;Verrucomicrobiota203494classcellularorganisms;Bacteria;Pseudomonadati;PVCgroup;Verrucomicrobiota;Verrucomicrobiia48461ordercellularorganisms;Bacteria;Pseudomonadati;PVCgroup;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales1647988familycellularorganisms;Bacteria;Pseudomonadati;PVCgroup;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae239934genuscellularorganisms;Bacteria;Pseudomonadati;PVCgroup;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae;Akkermansia239935speciescellularorganisms;Bacteria;Pseudomonadati;PVCgroup;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila349741straincellularorganisms;Bacteria;Pseudomonadati;PVCgroup;Verrucomicrobiota;Verrucomicrobiia;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansiamuciniphila;AkkermansiamuciniphilaATCCBAA-835

2. Equal to certain rank(s) (-E/--equal-to)

   $cattaxids2.txt\|taxonkitfilter-EPhylum-EClass-N\|taxonkitlineage-r\|csvtk-Htcut-f1,3,2\|csvtkpretty-H-t74201phylumcellularorganisms;Bacteria;PVCgroup;Verrucomicrobia203494classcellularorganisms;Bacteria;PVCgroup;Verrucomicrobia;Verrucomicrobiae

3. Lower than a rank (-L/--lower-than)

   $cattaxids2.txt\|taxonkitfilter-Lgenus-N\|taxonkitlineage-r-n-L\|csvtk-Htcut-f1,3,2\|csvtkpretty-H-t239935speciesAkkermansiamuciniphila349741strainAkkermansiamuciniphilaATCCBAA-835

4. Higher than a rank (-H/--higher-than)

   $cattaxids2.txt\|taxonkitfilter-Hphylum-N\|taxonkitlineage-r-n-L\|csvtk-Htcut-f1,3,2\|csvtkpretty-H-t131567cellularrootcellularorganisms2domainBacteria

5. TaxIDs with no rank are kept by default!!! "no rank" and "clade" have no rank and can be filter out via-N/--discard-noranks. Futher ranks can be removed with black list via-B/--black-list.

   #562istheTaxIdofEscherichiacoli$taxonkitlist--ids562\|taxonkitfilter-Lspecies\|taxonkitlineage-r-n-L\|csvtkcut-Ht-f1,3,2\|csvtkfreq-Ht-f2-nr\|csvtkpretty-H-tstrain2940norank486serotype176serogroup110isolate1subspecies1$taxonkitlist--ids562\|taxonkitfilter-Lspecies-N-Bstrain\|taxonkitlineage-r-n-L\|csvtkcut-Ht-f1,3,2\|csvtkfreq-Ht-f2-nr\|csvtkpretty-H-tserotype176serogroup110isolate1subspecies1

6. Combine of-L/-H with-E.

   $cattaxids2.txt\|taxonkitfilter-Lgenus-Egenus-N\|taxonkitlineage-r-n-L\|csvtkcut-Ht-f1,3,2\|csvtkpretty-H-t239934genusAkkermansia239935speciesAkkermansiamuciniphila349741strainAkkermansiamuciniphilaATCCBAA-835

7. Special cases of "no rank". (-n/--save-predictable-norank). When filtering with-L/--lower-than, you can use-n/--save-predictable-norank to save some special ranks without order, where rank of the closest higher node is still lower than rank cutoff.

   $echo-ne"2605619\n1327037\n"\|taxonkitlineage-t\|csvtkcut-Ht-f3\|csvtkunfold-Ht-f1-s";"\|taxonkitlineage-r-n-L\|csvtkcut-Ht-f1,3,2\|csvtkpretty-H-t131567cellularrootcellularorganisms2domainBacteria3379134kingdomPseudomonadati1224phylumPseudomonadota1236classGammaproteobacteria91347orderEnterobacterales543familyEnterobacteriaceae561genusEscherichia562speciesEscherichiacoli2605619norankEscherichiacoliO16:H4810239acellularrootViruses2731341realmDuplodnaviria2731360kingdomHeunggongvirae2731618phylumUroviricota2731619classCaudoviricetes2788787norankunclassifiedCaudoviricetes1327037speciesCroceibacterphageP2559Y# save taxids$echo-ne"2605619\n1327037\n"\|taxonkitlineage-t\|csvtkcut-Ht-f3\|csvtkunfold-Ht-f1-s";"\|teetaxids4.txt13156721224123691347543561562260561910239273134127313602731618273161928883106991968941327037

   Now, filter nodes of rank <= species.

   $cattaxids4.txt\|taxonkitfilter-Lspecies-Especies-N-n\|taxonkitlineage-r-n-L\|csvtkcut-Ht-f1,3,2\|csvtkpretty-H-t562speciesEscherichiacoli2605619norankEscherichiacoliO16:H481327037speciesCroceibacterphageP2559Y

   Note that 2605619 (no rank) is saved because its parent node 562 is <= species.