CBFlow
CBFlow analytics web
Rosario Biancheri Prof. Ciro Botta
Dettaglio job

20260327_121756_2189ff73

Creato: 2026-03-27 12:17:56

Avvio: 2026-03-27 12:17:56 · Fine: 2026-03-27 12:20:23

Runner backend: Wrapper completo

completed
Tempo trascorso
--:--:--
Step attualeCompletato
Progressione4/4 · 100%
File FCS2
Output17

Messaggio: Completato

Apri CSV annotazioni Modifica annotazioni

Avanzamento pipeline

Stato live degli step
1
Validazione input
done
Rilevati 2 file FCS
2
Preparazione esecuzione
done
Comando pronto
3
Analisi FlowCT
done
Wrapper terminato con successo
4
Raccolta output
done
Trovati 17 file
Job creato 2026-03-27 12:17:56
File caricati correttamente · backend: Wrapper completo
Job avviato 2026-03-27 12:17:56
Modalità real · runner: Wrapper completo
Validazione input 2026-03-27 12:17:56
Preparazione esecuzione 2026-03-27 12:17:56
Costruzione comando wrapper
Analisi FlowCT 2026-03-27 12:17:56
Wrapper run_pipeline_with_reports.py in esecuzione
Raccolta output 2026-03-27 12:20:23
Indicizzazione dei file generati
Completato 2026-03-27 12:20:23
Pipeline terminata con successo

Input

  • Metadata: inputs/sample_metadata.csv
  • FCS: 2 file
  • Nota: -

Comandi eseguiti

/opt/anaconda3/bin/python /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/scripts/run_pipeline_with_reports.py --fcs /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/inputs/BM_P02_compensated_demo.fcs /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/inputs/PB_P01_compensated_demo.fcs --sample-metadata /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/inputs/sample_metadata.csv --output /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap.h5ad --cluster-method leiden --report-output-stem /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_final_report --cluster-annotations-csv /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/results/demo_full_umap.cluster_annotations_curated.csv

Output scaricabili

I file vengono raggruppati per estensione per facilitare il download.

Apri tabella annotazioni Modifica annotazioni

Report

3 file

Dati

8 file

Immagini

6 file

Log

Aggiornamento automatico durante queued/running 
$ /opt/anaconda3/bin/python /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/scripts/run_pipeline_with_reports.py --fcs /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/inputs/BM_P02_compensated_demo.fcs /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/inputs/PB_P01_compensated_demo.fcs --sample-metadata /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/inputs/sample_metadata.csv --output /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap.h5ad --cluster-method leiden --report-output-stem /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_final_report --cluster-annotations-csv /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/results/demo_full_umap.cluster_annotations_curated.csv
/opt/anaconda3/lib/python3.13/functools.py:934: ImplicitModificationWarning: Transforming to str index.
  return dispatch(args[0].__class__)(*args, **kw)
/opt/anaconda3/lib/python3.13/functools.py:934: ImplicitModificationWarning: Transforming to str index.
  return dispatch(args[0].__class__)(*args, **kw)
[RUN] Avvio pipeline
[PIPELINE] Import FCS + costruzione AnnData
[IO] Lettura di 2 file FCS...
[IO]   1/2  BM_P02_compensated_demo.fcs  -> 22000 eventi
[IO]   2/2  PB_P01_compensated_demo.fcs  -> 18000 eventi
[PIPELINE] QC + rimozione doublets/singlets
[QC] Eventi in input: 40000
[QC] Eventi dopo filtro: 38139  (rimossi: 1861)
[PIPELINE] Clustering: leiden
[PIPELINE] Riduzione dimensionale: pca, umap
[PIPELINE] Fine pipeline. Eventi finali: 38139
[PIPELINE] Tempi:
[PIPELINE]   - import_fcs_and_build_adata: 0.25s
[PIPELINE]   - qc_and_remove_doublets: 0.16s
[PIPELINE]   - clustering_leiden: 1m 9.44s
[PIPELINE]   - dimensionality_reduction: 43.21s
[PIPELINE]   - total_pipeline: 1m 53.06s
[RUN] Pipeline completata. Output principale: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap.h5ad
[RUN] Abbondanze cluster: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap.clusters.csv
[RUN] QC summary: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap.qc_summary.csv
[RUN] Run summary JSON: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap.run_summary.json
[RUN] Mediane marker per cluster: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap.cluster_marker_medians.csv
[RUN] Plot salvato: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_plots/umap_cluster.png
[RUN] Plot salvato: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_plots/umap_sample_id.png
[RUN] Heatmap marker-per-cluster: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_plots/cluster_marker_heatmap.png
Creato: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated.h5ad
Colonne aggiunte in obs: annotazione_curata, confidence_curata, metacluster
Aggiunta anche: cluster_note
[METACLUSTER] UMAP: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated_plots/umap_metacluster.png
[METACLUSTER] By sample CSV: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated.metacluster_abundance_by_sample.csv
[METACLUSTER] By sample type CSV: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated.metacluster_abundance_by_sample_type.csv
[METACLUSTER] By sample plot: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated_plots/metacluster_abundance_by_sample.png
[METACLUSTER] By sample type plot: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated_plots/metacluster_abundance_by_sample_type.png
[REPORT] HTML: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_final_report.html
[REPORT] DOCX: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_final_report.docx
[REPORT] PDF: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_final_report.pdf
[WRAPPER] Eseguo: /opt/anaconda3/bin/python '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/scripts/run_pipeline.py' --fcs '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/inputs/BM_P02_compensated_demo.fcs' '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/inputs/PB_P01_compensated_demo.fcs' --sample-metadata '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/inputs/sample_metadata.csv' --output '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap.h5ad' --cluster-method leiden
[WRAPPER] Eseguo: /opt/anaconda3/bin/python '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/scripts/apply_cluster_annotations_fixed.py' --h5ad '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap.h5ad' --annotations '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/results/demo_full_umap.cluster_annotations_curated.csv' --output '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated.h5ad'
[WRAPPER] Eseguo: /opt/anaconda3/bin/python '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/scripts/report_metaclusters.py' --h5ad '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated.h5ad' --sample-metadata '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/inputs/sample_metadata.csv'
[WRAPPER] Eseguo: /opt/anaconda3/bin/python '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/scripts/generate_final_report.py' --abundance-by-type-csv '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated.metacluster_abundance_by_sample_type.csv' --plot-dir '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated_plots' --output-stem '/Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_final_report' --title 'Report finale BM vs PB'
[WRAPPER] Workflow completo terminato con successo.
[WRAPPER] H5AD annotato: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_output_umap_annotated.h5ad
[WRAPPER] Report finale base name: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_final_report
[WRAPPER] HTML: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_final_report.html
[WRAPPER] DOCX: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_final_report.docx
[WRAPPER] PDF: /Users/rosariobiancheri/Desktop/FLUO Progetto/flowct_py_v2_project/web_mpv/job_runs/20260327_121756_2189ff73/outputs/cbflow_final_report.pdf