QuickStart 2: three HCC1143 libraries

Open this guide with playable videos

Analyze three public Illumina libraries in one project. Download all six paired-end FASTQs, choose browser or terminal setup, then inspect the cohort results. Install OncoTracer first; QuickStart 1 is the smaller example. Reads total approximately 1.16 GB, plus tools, references, BAMs and results.

Sample	Public run
HCC1143_DMSO	SRR7085656
HCC1143_BEZ235	SRR7085655
HCC1143_TRAMETINIB	SRR7085657

All three are tumor libraries. DMSO is a treatment control, not a normal genome.

1. Interactive launch

Under Choose how many samples run together, review the detected CPU and RAM, then choose a total budget and concurrent sample count before saving. See multiple samples and continuation.

Watch the video, then download and verify the example reads. After installation, open setup:

oncotracer --interactive --backend conda

Or use Nextflow from the source checkout:

nextflow run main.nf --interactive --backend conda

Use the full path to main.nf from another directory. For Docker, use --backend docker. Choose 1. New analysis, then your inputs and settings; Run analysis starts the work. To reuse a saved project, choose 2. Continue an existing analysis and follow the continuation video. The videos show synthetic inventories and checks, without starting analysis.

HCC1143

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Example data: download and verify

Replace /path/to/my/analyses_dir/ with your writable analysis directory in every block. $PWD means its absolute path.

cd /path/to/my/analyses_dir/
mkdir -p oncotracer-quickstart2/input

curl --fail --location --continue-at - \
  --output oncotracer-quickstart2/input/HCC1143_DMSO_R1.fastq.gz \
  https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR708/006/SRR7085656/SRR7085656_1.fastq.gz
curl --fail --location --continue-at - \
  --output oncotracer-quickstart2/input/HCC1143_DMSO_R2.fastq.gz \
  https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR708/006/SRR7085656/SRR7085656_2.fastq.gz
curl --fail --location --continue-at - \
  --output oncotracer-quickstart2/input/HCC1143_BEZ235_R1.fastq.gz \
  https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR708/005/SRR7085655/SRR7085655_1.fastq.gz
curl --fail --location --continue-at - \
  --output oncotracer-quickstart2/input/HCC1143_BEZ235_R2.fastq.gz \
  https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR708/005/SRR7085655/SRR7085655_2.fastq.gz
curl --fail --location --continue-at - \
  --output oncotracer-quickstart2/input/HCC1143_TRAMETINIB_R1.fastq.gz \
  https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR708/007/SRR7085657/SRR7085657_1.fastq.gz
curl --fail --location --continue-at - \
  --output oncotracer-quickstart2/input/HCC1143_TRAMETINIB_R2.fastq.gz \
  https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR708/007/SRR7085657/SRR7085657_2.fastq.gz

md5sum -c <<'MD5'
419b241a073ecdbb0df5a9bec918c58b  oncotracer-quickstart2/input/HCC1143_DMSO_R1.fastq.gz
6398bf13a33c25e33693682bdeb00253  oncotracer-quickstart2/input/HCC1143_DMSO_R2.fastq.gz
3870b3fc2c693679cac9cce50cff2371  oncotracer-quickstart2/input/HCC1143_BEZ235_R1.fastq.gz
d21feb72ead870fb44c3e62d887e4974  oncotracer-quickstart2/input/HCC1143_BEZ235_R2.fastq.gz
688ee1571e591795b060963aacf942d3  oncotracer-quickstart2/input/HCC1143_TRAMETINIB_R1.fastq.gz
f5975d77f63e9b139a24fb011580fd4d  oncotracer-quickstart2/input/HCC1143_TRAMETINIB_R2.fastq.gz
MD5

Continue only when all six lines say OK. The versioned manifest records each exact size and MD5 checksum. Repeat an interrupted curl command to resume.

2. Terminal questions for headless servers

Use this option over SSH without a browser. Choose one setup route per project. The videos show real terminal questions using tiny synthetic FASTQs; no analysis runs. Use the verified public downloads above for your analysis.

HCC1143

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Answer the questions

This supplies the project, platform and input folder; the wizard asks for the remaining settings. Press Enter to accept a displayed default.

cd /path/to/my/analyses_dir/
oncotracer setup --terminal --backend conda \
  --project "$PWD/oncotracer-quickstart2/analysis" \
  --mode illumina --input-folder "$PWD/oncotracer-quickstart2/input"

For an installed Docker backend, use --backend docker.

Select all, keep the three sample names, and assign every sample cancer, including DMSO. Confirm each sample has its own R1/R2 pair. Choose cna, a CPU budget such as 4, and 100 kb bins for QDNAseq. Answer no to interpretation reports and small variants. CNA-only terminal setup does not ask Fresh/FFPE; preservation is asked when enabling variants.

For hg38 reference, choose download for about 8.0 GiB of indexes at run time. To reuse QuickStart 1's reference, answer reuse and give oncotracer-quickstart1/illumina/reference. Setup does not download indexes. See genome indexes.

At Final action, enter save. Review the checked configuration and all three sample names. When ready, launch the printed oncotracer run command. Each library is analyzed separately; GISTIC is disabled in this example.

3. Review the results

Click Open results in the browser, or open oncotracer-quickstart2/analysis/results/index.html. Check 06_workflow_summary/workflow_summary.txt for completion, then inspect the sample plots and 03_cna_codification/cna_events.tsv. See output files.

Stop or resume

For a terminal run, press Ctrl+C; use tmux to keep a remote run alive after disconnecting. For a browser run, use Stop analysis, wait for it to stop, and choose No in Delete incomplete run?. Closing its browser or setup terminal does not stop that analysis.

Follow Run, stop and resume with the saved project path. Valid completed steps are reused. Concurrent runs need separate projects and a share of the server's CPU and memory.

For unattended execution, use the complete terminal commands.