Output¶

Results are written to <outdir>/<sample>/ for each sample:

<outdir>/
└── <sample>/
    ├── detected_mobile_elements/
    │   ├── <sample>_detected_ME.tsv
    │   ├── <sample>_detected_ME.summary
    │   ├── <sample>_detected_SP_withMEIds.tsv
    │   └── standard_genome_annotation_formats/
    │       ├── <sample>_icescreen.gff.gz
    │       ├── <sample>_icescreen.embl.gz
    │       ├── <sample>_icescreen.gb.gz
    │       ├── <sample>_source.fa.gz
    │       └── <sample>_source.gff.gz
    ├── detected_signature_proteins/
    │   └── <sample>_detected_SP.tsv
    ├── param.conf.gz
    ├── tmp_intermediate_files.tar.gz
    └── pipeline_info/
        ├── execution_report_<timestamp>.html
        ├── execution_timeline_<timestamp>.html
        ├── execution_trace_<timestamp>.txt
        └── pipeline_dag_<timestamp>.html

Detected mobile elements¶

`<sample>_detected_ME.tsv`¶

Tab-separated table of detected ICE and IME structures. Each row represents one mobile element, with columns for genomic coordinates, element type, boundary signature proteins, and associated CDS.

`<sample>_detected_ME.summary`¶

Human-readable summary of detection results: counts of detected ICEs, IMEs, and unclassified elements per replicon.

`<sample>_detected_SP_withMEIds.tsv`¶

Signature protein table annotated with the mobile element ID to which each protein was assigned.

Genome annotation formats¶

All annotation files are gzip-compressed.

File	Format	Contents
`<sample>_icescreen.gff.gz`	GFF3	ICE/IME features overlaid on the source GFF3
`<sample>_icescreen.embl.gz`	EMBL	ICE/IME features in EMBL flat-file format
`<sample>_icescreen.gb.gz`	GenBank	ICE/IME features in GenBank flat-file format
`<sample>_source.fa.gz`	FASTA	Genome nucleotide sequence
`<sample>_source.gff.gz`	GFF3	Source genome annotation (CDS features)

Detected signature proteins¶

`<sample>_detected_SP.tsv`¶

Final table of signature proteins after false positive removal and XerS re-annotation. Each row is one detected signature protein with its type, locus tag, replicon, and position.

Run archive¶

`tmp_intermediate_files.tar.gz`¶

Archive of all intermediate analysis files, organised to mirror the original ICEscreen directory structure under results/<sample>/. Includes BLASTP output per database, HMM scan output per profile, filtered results, merged SP tables, FP screening results, and re-annotation files.

`param.conf.gz`¶

Gzip-compressed parameter summary combining the ICEscreen detection log (search thresholds, counts of detected elements) with the full detection mode configuration (from the ICEscreen mode YAML file). Mirrors the param.conf output of the original Snakemake pipeline.

Pipeline info¶

Nextflow execution reports written to pipeline_info/:

File	Contents
`execution_report_<ts>.html`	Per-task resource usage and status
`execution_timeline_<ts>.html`	Gantt chart of task execution timing
`execution_trace_<ts>.txt`	Tab-separated task metadata
`pipeline_dag_<ts>.html`	Directed acyclic graph of the workflow

Output¶

Detected mobile elements¶

<sample>_detected_ME.tsv¶

<sample>_detected_ME.summary¶

<sample>_detected_SP_withMEIds.tsv¶