Processing of public metagenomic data that has been analysed with SingleM.

Most code here is not intended for public usage as many paths etc are specific to CMR / QUT / Woodcroft group, but nonetheless may be useful for others.

Post-processing a singlem renew run of SRA data

First modify paths at the top of the Snakemake

Then setup:

pixi install --all

and run

pixi run snakemake --cores 1

Make sure the correct taxonomic level is chosen for applying predictions in the Snakemake file. See {base_output_directory}/logs/host_or_not_prediction.log for the results of the cross validation.

Host-vs-not metagenome prediction

Example code for host-vs-not prediction is contained within the Snakefile. In

Publishing a release to Zenodo

push_to_zenodo.smk creates a new draft (unpublished) Zenodo version of the sandpiper record from the data in /work/microbiome/db/sandpiper/<data_version>. It bases the new version on the published parent record (PARENT_RECORD_ID near the top of the file), uploads the gtdb / per-acc-summary / parsed-metadata / kingfisher-metadata files (renamed to sandpiper<version>.*), removes the files inherited from the previous version, and sets the version metadata.

Run it with the API token in the environment:

ZENODO_TOKEN="$(cat ~/.zenodo_draft_release_api_token)" \
  pixi run snakemake -s push_to_zenodo.smk --config version=2.0.1 -j 1

• version sets the Zenodo version and the uploaded filenames.
• data_version (optional) is the source data dir under /work/microbiome/db/sandpiper/ to read from; defaults to version. Use it to build a release from a different data dir, e.g. version=2.0.1 data_version=2.0.0.
• Logs and the resulting draft URL are written under zenodo_drafts/<version>/ (kept local because /work is often mounted read-only).

The draft is not published — review it in the Zenodo web UI and publish manually. Two things still need handling by hand before publishing:

• The GlobDB file (sandpiper<x>.globdb.csv.gz) is uploaded separately.
• Grants under the legacy DOE funder (0114b2m14::, the DE-SC... grants) are rejected by the current Zenodo API and are dropped automatically; re-add them in the web UI if they are needed.