Illumina · terminal setup

DEMO: synthetic FASTQs; real setup wizard; explicit save; no analysis.
Video presentation replays captured output at a readable pace.

$ oncotracer setup --terminal --backend conda \
  --project "$PWD/oncotracer-quickstart1/illumina" \
  --mode illumina \
  --input-folder "$PWD/oncotracer-quickstart1/input/illumina"
OncoTracer setup: select FASTQs, assign sample types, choose settings, then save or run.

Detected 2 FASTQ files in 1 samples under /tmp/oncotracer-terminal-recording-20261018/illumina/oncotracer-quickstart1/input/illumina:
  1. ERR12341627: 2 FASTQs, paired-end
       ERR12341627_1.fastq.gz
       ERR12341627_2.fastq.gz
Samples to include (numbers, ranges, or all) [1]: all

Assign sample types explicitly. Controls are analyzed independently; they are not pooled or subtracted.

Selected: ERR12341627 (2 FASTQs)
Sample name [ERR12341627]: 
Type for ERR12341627 (cancer/normal/control/other): cancer
Analysis (--analysis; cna=copy-number) (cna) [cna]: cna

Available CPU workers: 128
RAM total: 995.5 GiB
RAM available: 971.4 GiB
GPU devices reported: 1
  GPU 0: NVIDIA RTX A5000; 24.0 GiB VRAM (22.1 GiB free)
NVIDIA driver inventory only; CUDA access and model compatibility are not tested. GPU processing core counts are not reported.
Suggested CPU threads: 4. CNA analysis uses CPU.
CPU threads (--threads) [4]: 4
CNA bin size (kb) (1/5/10/15/30/50/100/500/1000) [100]: 100
Add CNA interpretation reports? (yes/no) [no]: no
Add small-variant calling? (yes/no) [no]: no
hg38 reference (download/reuse/build) [download]: download

Configuration saved: /tmp/oncotracer-terminal-recording-20261018/illumina/oncotracer-quickstart1/illumina/config/run.yml
Inputs stay in their existing folders. Results will be written to: /tmp/oncotracer-terminal-recording-20261018/illumina/oncotracer-quickstart1/illumina/results

Review analysis
  ERR12341627: cancer (study); 2 FASTQs
Platform: illumina; analysis: cna; threads: 4; tools: conda
CNA method: qdnaseq; bin size: 100 kb
CNA interpretation reports: disabled
Reference: download prebuilt indexes when needed
Reference folder: /tmp/oncotracer-terminal-recording-20261018/illumina/oncotracer-quickstart1/illumina/reference
Sample types: /tmp/oncotracer-terminal-recording-20261018/illumina/oncotracer-quickstart1/illumina/config/sample_metadata.csv
Analysis may download reference files and prepare missing tools when it starts.
Configuration OK
  Hardware: 971.4 GiB RAM available; 128 CPU workers
  Capacity details: oncotracer system --config /tmp/oncotracer-terminal-recording-20261018/illumina/oncotracer-quickstart1/illumina/config/run.yml
  Samples: ERR12341627
  Results: /tmp/oncotracer-terminal-recording-20261018/illumina/oncotracer-quickstart1/illumina/results
  CPU threads: 4
  Analysis: reference-validation -> illumina-alignment -> qdnaseq -> bam-refinement -> cna-codification -> cna-plots -> workflow-summary
No analysis or downloads were started. Check the installed tools with oncotracer doctor before running.
Final action (run/save) [save]: save
Saved without starting analysis. Run later with:
oncotracer run --backend conda --config /tmp/oncotracer-terminal-recording-20261018/illumina/oncotracer-quickstart1/illumina/config/run.yml