In a previous post, we walked through several examples of using BioMetaDB - a Bio-focused command-line SQL wrapper package - to query the results of our MetaSanity pipeline runs. The contents of each project is self-contained, making it very easy for users to focus their attention on getting specific information.

Given the complexity and volume of this application, we will walk through the raw and parsed output from each of the programs that MetaSanity runs. This information is also available as a PowerPoint presentation (views best using PowerPoint Online).

MetaSanity output

out/
├── evaluation.tsv
├── functions.tsv
├── checkm_results/
├── fastani_results/
├── gtdbtk_results/
├── prodigal_results​/
├── prokka_results​/
├── interproscan_results​/
├── kegg_results​/
├── cazymerops_results​/
├── virsorter_results/
├── mag1.annotation.tsv
...

The first two .tsv files contain the parsed results of the MetaSanity pipelines. These are simple tab-delimited text files. PhyloSanity results are contained in evaluation.tsv. FuncSanity results are in a set of files. functions.tsv contains functional and metabolic information for all genomes that were studies. A file ending with the extension .annotation.tsv will be generated for each genome that was analyzed.

The remaining directories contain the raw output from each of the programs that were incorporated into the user’s annotation pipeline. The resulting file(s) are parsed for specific information to generate the workflow’s results.

PhyloSanity

CheckM

checkm_results/checkm_lineageWF_results.qa.txt is parsed for contamination and completion estimates.

FastANI

fastani_results/fastani_results.txt contains ANI information used in redundancy determination

GTDB-Tk

gtdbtk_results/GTDBTK.bac120.summary.tsv and gtdbtk_results/GTDBTK.ar122.summary.tsv optionally provide putative phylogeny.

FuncSanity

For each MAG that is analyzed, a series or files may be generated.

Prodigal gene caller

prodigal_results/
├── mag1.mrna.fna
├── mag1.protein.faa
├── mag1.txt

Prokka (optional gene caller and annotation pipeline)

prokka_results/
├── mag1/
  ├── mag1.tsv  # Original output
  ├── mag1.prk.tsv.amd  # Parsed output for BioMetaDB
  ├── mag1.prk.tsv.prokka.nucl  # RNA features
├── diamond/
  ├── mag1.prk-to-prd.tsv  # Protein annotations

The remaining files in each directory are the outputs from each Prokka run.

InterProScan

interproscan_results/
├── mag1.tsv  # Original output
├── mag1.amended.tsv  # Parsed output

InterProScan contributes the most to MetaSanity runtimes.

KoFamScan and KEGG-Decoder

kegg_results/
├── biodata_results/  # KEGG-Decoder-derived metabolic pathway estimation counts
  ├── KEGG.final.tsv
  ├── KEGG.decoder.tsv 
├── combined_results/
  ├── combined.ko  # kofamscan matches for KEGG-Decoder input
  ├── combined.protein  # gene calls for KEGG-Decoder input
  ├── combined.expander.tbl  # HMM search results (part of BioData pipeline)
  ├── combined.expander.tsv  # Raw counts from BioData pipeline
  ├── combined.html  # Heatmap of putative metabolic pathway completion estimates
├── kofamscan_results/
  ├── mag1.tsv  # KO matches per protein
  ├── mag1.detailed  # Detailed kofamscan output
  ├── mag1.amended.tbl  # Parsed output for BioMetaDB

MEROPS

cazymerops_results/
├── mag1.merops.tsv  # MEROPS matches
├── mag1.pfam.tsv  # MEROPS matches by PFam id
├── merops/
  ├── mag1.merops.protein.faa  # MEROPS protein matches
  ├── hmmconvert_data/  # HMM prep
  ├── hmmsearch_results/  # HMMSearch output

CAZy

cazymerops_results/
├── cazy/
  ├── hmmsearch_results/  # HMMSearch output
  ├── mag1.cazy_assignments.tsv  # Raw counts of CAZy HMM matches
  ├── mag1.cazy_assignments.byprot.tsv  # Protein annotations

PSORTb and SignalP

cazymerops_results/
├── psortb_results/
  ├── mag1.tbl  # Raw PSORTb output
├── signalp_results/
  ├── mag1.signalp.tbl  # Raw SignalP output

Extracellular Peptidase

cazymerops_results/
├── mag1.pfam.by_prot.tsv  # PFam annotations for peptidase results

VirSorter

virsorter_results/
├── mag1
  ├── virsorter_results/
    ├── VIRSorter_global-phage-signal.csv  # Original output
    ├── mag1.VIRSorter_adj_out.tsv  # Parsed output for BioMetaDB

The remaining files in each virsorter_results directory are the raw outputs of the VirSorter run for each MAG.