Biowulf High Performance Computing at the NIH
TaxonKit on Biowulf

A Cross-platform and Efficient NCBI Taxonomy Toolkit



Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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 ~]$

Batch job
Most jobs should be run as batch jobs.

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

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