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Run Statistics

Overview

The RUN_STATISTICS process generates comprehensive gene annotation statistics for Ensembl species homepages, computing counts and metrics for genes, transcripts, proteins, and other genomic features.

Process Details

  • Label: fetch_file
  • Tag: Uses genome assembly accession (meta.gca)
  • Store Directory: ${params.cacheDir}/${meta.gca}/core_statistics/statistics
  • Publish Directory: ${params.outdir}/${meta.gca}
  • Max Forks: 20 (limits parallel execution)

Inputs

Name Type Description
meta val Metadata map containing genome assembly and database connection details

Required Metadata Fields

  • gca: Genome assembly accession
  • dbname: Database name
  • production_name: Species production name

Outputs

Channel Type Description
statistics_output tuple Metadata and generated SQL files from core_statistics/ directory
versions_file path versions.yml file tracking Perl version

Parameters

Required

  • params.cacheDir: Cache directory for stored process outputs
  • params.outdir: Output directory for results
  • params.enscode: Path to Ensembl code repository
  • params.host: Database host
  • params.port: Database port

Optional

  • params.files_latency: Delay after script execution (default handled by afterScript)

Script Details

The process: 1. Executes generate_species_homepage_stats.pl Perl script 2. Connects to the specified Ensembl core database 3. Computes comprehensive annotation statistics including: - Gene counts (by biotype) - Transcript counts - Protein-coding gene metrics - Alternative splicing statistics - Non-coding RNA counts - Other genomic feature counts 4. Generates SQL files for inserting statistics into the database 5. Outputs results to core_statistics/ subdirectory 6. Captures Perl version information

Dependencies

  • Perl 5
  • generate_species_homepage_stats.pl script (from ensembl-genes/src/perl/ensembl/genes/)
  • Ensembl Perl API
  • Database read access

Generated Statistics

The SQL files typically include statistics for:

Gene Metrics

  • Total gene count
  • Protein-coding genes
  • Pseudogenes
  • Non-coding RNA genes (by type: lncRNA, miRNA, snRNA, etc.)

Transcript Metrics

  • Total transcript count
  • Protein-coding transcripts
  • Alternative splicing frequency

Protein Metrics

  • Protein-coding sequences
  • Average protein length
  • Protein domains

Other Features

  • Alternative sequences
  • Gene predictions
  • Imported annotations

Notes

  • SQL generation is cached with storeDir; clear this cache if the source core database changes
  • Results are published to a genome-specific subdirectory
  • Maximum of 20 concurrent processes to prevent database overload
  • The process includes a configurable sleep delay after completion to handle file system latency
  • Generated SQL files are designed for the Ensembl core database schema
  • Statistics are used to populate species homepage displays in Ensembl browser
  • Can be executed against production or staging databases