SourceTracker2

Overview

SourceTracker2: Contamination is a critical issue in high-throughput metagenomic studies, yet progress toward a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments. We applied SourceTracker to microbial surveys from neonatal intensive care units (NICUs), offices and molecular biology laboratories, and provide a database of known contaminants for future testing.

Using

Use the module name sourcetracker2 to discover versions available and to load the application.

Beartooth

Compared to earlier versions on Teton, the gibbs command is NOT required:

sourcetracker2 -i otu_table.biom -m map.txt -o example1/

Teton

On Teton, the gibbs command has to be used:

[]$ sourcetracker2 --help
Usage: sourcetracker2 [OPTIONS] COMMAND [ARGS]...
Options:
  --version  Show the version and exit.
  --help     Show this message and exit.
Commands:
  gibbs  Gibb's sampler for Bayesian estimation of microbial sample sources.

[]$ sourcetracker2 gibbs --help
Usage: sourcetracker2 gibbs [OPTIONS]
  Gibb's sampler for Bayesian estimation of microbial sample sources.
  For details, see the project README file.
Options:
  -i, --table_fp FILE             Path to input BIOM table.  [required]
...

# Example
[]$ sourcetracker2 gibbs -i otu_table.biom -m map.txt -o example1/

Error: No --per_sink_feature_assignments option

Following the examples on the website: Running the following on Teton:

sourcetracker2 gibbs -i otu_table.biom -m map.txt -o example7/ --jobs 5 --per_sink_feature_assignments

fails with error message:

Error: no such option: --per_sink_feature_assignments

Multicore

The sourcetracker2command can be ran with multiple threads, see the sourcetracker2 --help for more details on the --jobs option.

Example: Beartooth:

#SBATCH --cpus-per-task=16

The example that uses:

sourcetracker2 -i otu_table.biom -m map.txt -o example6/ --jobs 16