SciFlow lab notebook · Shared read-only

Functional Annotation — E. coli K-12 (SciFlow)

Take a set of bacterial protein sequences and come back with orthology assignments, domain architectures, GO terms, and KEGG module completeness — all in one pass.

Overview Methods & provenance Results Raw artifacts

Run date

2026-04-29 → 2026-06-10

Stages

5 5 completed

Pipeline

eggnog-mapper → interproscan → kegg_module_completeness → annotation_merge → annotation_…

Software

2 container images eggnog-mapper, interproscan

Outputs

25 files 98.7 MB

Overview

Take a set of bacterial protein sequences and come back with orthology assignments, domain architectures, GO terms, and KEGG module completeness — all in one pass. Drop in the E. coli K-12 proteome (or your own), and the pipeline tells you what each protein probably is, where its domains came from, which pathways are intact, and which functional categories are over-represented in any subset you care about. Built for microbial genomicists who just finished an assembly, comparative genomics groups annotating new isolates, and anyone who needs a defensible functional summary without stitching five tools together by hand.

Homology, orthology, and function are three different things, and the pipeline labels them that way. eggNOG-mapper provides ortholog-based GO and KEGG transfer at controlled evolutionary distance. InterProScan adds domain- and signature-level evidence — Pfam, TIGRFAM, SUPERFAMILY — so you see the actual structural building blocks, not just a top BLAST hit. KEGG module reconstruction reports completeness per pathway with the missing steps named explicitly. The output is a single browsable report with each annotation traceable to the tool and the threshold that produced it.

Methods & per-stage provenance

5 stages, 5 completed. Each stage below lists the parameters it ran with, the software the run recorded, and the files it produced.

Not recorded by this run
  • no figures rendered (no PNG/SVG outputs and no Plotly HTML figure could be extracted)
01 eggNOG-mapper eggnog-mapper 1013.2 h completed
input fasta: ecoli_k12_proteins.fastadb type: diamondtax scope: Bacteriago evidence: non-electronic

Verbatim command / script not recorded in this run's stage record.

Container image: nanozoo/eggnog-mapper:2.1.13--c16a7d2 Image digest: sha256:d571284d255197178c467152025cd0584469eba683ee0ddcd9dffb25290efcf7
  • eggnog.emapper.annotationsANNOTATIONS · 3.6 MB
  • eggnog.emapper.hitsHITS · 915 KB
  • eggnog.emapper.seed_orthologsSEED_ORTHOLOGS · 292 KB
  • eggnog.loglog · 4 KB
  • eggnog_mapper_report.htmlreport · 42 KB
  • input_data_summary.htmlreport · 24 KB
  • summary.jsondata · 942 B
02 InterProScan interproscan 963.4 h completed
seqtype: piprlookup: yesinput fasta: ecoli_k12_proteins.fastaapplications: Pfaminclude goterms: yesinclude pathways: yes

Verbatim command / script not recorded in this run's stage record.

Container image: interpro/interproscan:5.66-98.0 Image digest: not recorded in this stage's run metadata
  • _input.cleaned.fastaFASTA · 1.7 MB
  • domain_architecture.tsvTSV · 305 KB
  • interproscan.gff3GFF3 · 11.9 MB
  • interproscan.jsondata · 58.1 MB
  • interproscan.loglog · 724 B
  • interproscan.tsvTSV · 8.1 MB
  • interproscan_report.htmlreport · 118 KB
  • summary.jsondata · 2 KB
03 KEGG module completeness kegg_module_completeness 8 s completed
noop:

Verbatim command / script not recorded in this run's stage record.

Container image: not recorded in this stage's run metadata Image digest: not recorded in this stage's run metadata
  • kegg_modules.csvtable · 11 KB
  • kegg_modules.htmlreport · 25 KB
  • summary.jsondata · 814 B
04 Annotation merge (evidence-tiered) annotation_merge 20 min completed

Verbatim command / script not recorded in this run's stage record.

Container image: not recorded in this stage's run metadata Image digest: not recorded in this stage's run metadata
  • annotation_merge_report.htmlreport · 2 KB
  • go_terms_evidenced.tsvTSV · 5.2 MB
  • merged_annotations.tsvTSV · 8.4 MB
  • summary.jsondata · 739 B
06 Annotation Report (consolidated HTML) annotation_report 20 min completed

Verbatim command / script not recorded in this run's stage record.

Container image: not recorded in this stage's run metadata Image digest: not recorded in this stage's run metadata
  • annotation_report.htmlreport · 15 KB
  • report_data.jsondata · 4 KB
  • summary.jsondata · 301 B

Results

No static figure could be embedded in this notebook — this run recorded no PNG/SVG output, and no interactive plot could be exported to a static image. Any figures this run produced are listed among the raw artifacts below and remain viewable in the project itself.

Raw artifacts

25 output files produced across all stages (98.7 MB total). This report is self-contained; structures and trajectories are listed below for reference.