A Cross-platform and Efficient NCBI Taxonomy Toolkit

Subcommands

• list: list taxon tree of given taxids
• lineage: query lineage of given taxids (supporting STDIN)
• reformat: reformat lineage (supporting STDIN)
• name2taxid: query taxid by taxon scientific name (supporting STDIN)
• taxid-changelog: create taxid changelog from dump archives

References:

• Shen W, Xiong J. TaxonKit: a cross-platform and efficient NCBI taxonomy toolkit. doi:https://doi.org/10.1101/513523

• taxonkit Main Site:Main Site

• Module Name: taxonkit (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load taxonkit
[user@cn3144 ~]$ taxonkit list --show-rank --show-name --ids 9605
9605 [genus] Homo
  9606 [species] Homo sapiens
    63221 [subspecies] Homo sapiens neanderthalensis
    741158 [subspecies] Homo sapiens subsp. 'Denisova'
    2665952 [no rank] environmental samples
      2665953 [species] Homo sapiens environmental sample
  1425170 [species] Homo heidelbergensis

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. taxonkit.sh). For example:

#!/bin/bash
set -e
module load taxonkit
#This will download the whole taxon tree
taxonkit list --show-rank --show-name --ids 1 >t1.txt

Submit this job using the Slurm sbatch command.

sbatch  --mem=2g taxonkit.sh