0:12:00 runtime
franzoso2025 Parabricks SRR11012403 runtime
- Tested configuration
- NVIDIA Parabricks Germline v4.0.1-1 on a GCP VM with 48 vCPUs, 58 GB memory and 1 T4 GPU (Franzoso et al. 2025)
- Protocol
- WES FASTQ-to-VCF runtime and cost on GCP, Sentieon versus Parabricks (Franzoso et al. 2025 Table S2)
- Dataset
- Five WES samples (Twist Core Exome, Illumina NextSeq 500, 2x75 bp) from an HLH-like syndrome study
- Procedure
- model-execution-20261009-protocol-franzoso2025-wes-gcp
- Evaluation
- Parabricks on GCP, WES samples (Franzoso et al. 2025)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source: Single run per cell
- Evidence
- Independent external evaluation · source checkedRapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial; Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Table S2 (CTS-18-e70416-s002.xlsx), C4; ID 'SRR11012403'; Software 'Parabricks'; column 'Runtime (h/m/s)'
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Five samples
- Adaptation
- Not reported
- Scoring implementation
- GCP monitoring start and end times; GCP cost
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0:12:00 Individual claims | Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial Table S2 (CTS-18-e70416-s002.xlsx), C4; ID 'SRR11012403'; Software 'Parabricks'; column 'Runtime (h/m/s)' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Clinical and Translational Science 18(11):e70416, published 2025-11-18; PMC12627752 full-text XML | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09T20:46:48Z independent paper Audit detailsExtracted by deterministic parse of the pinned XLSX cell XML (extract/extract_model_execution.py with extract/rawxlsx.py), with the title, headers, sample identifiers (checked against Table S1) and software labels asserted. Runtime cells use built-in number format 21 (h:mm:ss); printed_value is that rendering of the stored day fraction and numeric_value is the same duration in seconds. Cost printed_value is the shortest round-trip decimal of the stored double. Independent review 2026-10-09: printed value, numeric value, metric, qualifier, unit, direction, locator and configuration and protocol identity match the source. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 0:12:00 Individual claims | Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) Table S2 (CTS-18-e70416-s002.xlsx), C4; ID 'SRR11012403'; Software 'Parabricks'; column 'Runtime (h/m/s)' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: CTS-18-e70416-s002.xlsx (Table S2) inside the Europe PMC supplementary files bundle for PMC12627752 | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09T20:46:48Z independent paper Audit detailsExtracted by deterministic parse of the pinned XLSX cell XML (extract/extract_model_execution.py with extract/rawxlsx.py), with the title, headers, sample identifiers (checked against Table S1) and software labels asserted. Runtime cells use built-in number format 21 (h:mm:ss); printed_value is that rendering of the stored day fraction and numeric_value is the same duration in seconds. Cost printed_value is the shortest round-trip decimal of the stored double. Independent review 2026-10-09: printed value, numeric value, metric, qualifier, unit, direction, locator and configuration and protocol identity match the source. Field: Source artifact SHA-256: Hash scope: SHA-256 of CTS-18-e70416-s002.xlsx. Table S1 (CTS-18-e70416-s001.xlsx) from the same bundle has SHA-256 b221919e435217c607ff426d80fc5718c7f4d3e0fbaa6261cf13e8c5b7ae0f4e and is used only to assert sample identifiers. The bundle is assembled per request, so only member hashes are pinned. Archive member: CTS-18-e70416-s002.xlsx Extraction artifact SHA-256: |
Sources and history
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
2 source records and release history
- Rapid NGS Analysis on Google Cloud Platform: Performance Benchmark and User Tutorial · Original source · Clinical and Translational Science 18(11):e70416, published 2025-11-18; PMC12627752 full-text XML
- Franzoso et al. 2025, Table S2 (runtime and costs per sample) and Table S1 (sample identifiers) · Original source · CTS-18-e70416-s002.xlsx (Table S2) inside the Europe PMC supplementary files bundle for PMC12627752
Technical metadata and extraction receipts
Stable ID: model-execution-20261009-result-franzoso2025-parabricks-germline-4-0-1-1-gcp-t4-srr11012403-runtime
- metric
- runtime
- metric direction
- lower
- unit
- second
- metric qualifier
- FASTQ to VCF; sample SRR11012403
- printed value
- 0:12:00
- numeric value
- 720
- raw xml value
- 8.3333333333333332E-3
- workbook number format
- built-in 21 (h:mm:ss)
- printed value basis
- Rendering of the stored day fraction in the cell's h:mm:ss number format; numeric_value is seconds
- source locator
- Table S2 (CTS-18-e70416-s002.xlsx), C4; ID 'SRR11012403'; Software 'Parabricks'; column 'Runtime (h/m/s)'
- missing metadata
- uncertainty: reason: unreported; note: Single run per cell
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the Europe PMC supplementaryFiles zip and matched the SHA-256 of CTS-18-e70416-s002.xlsx (and s001.xlsx for sample identifiers). Read the cell XML with a separate stdlib parser written for this review (the extractor's scripts were not imported or run) and checked the number format (built-in 21, h:mm:ss) in xl/styles.xml. Checked raw cell value, printed value (h:mm:ss rendering of the day fraction, or shortest round-trip decimal of the cost), numeric value, metric, qualifier, unit, direction, locator, and the linked evaluation's configuration and protocol.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; reviewed at: 2026-10-09T20:46:48Z; artifact sha256: 0b32a6146536f820e547ed5ac458ae789477358dbfdf339a634a9b78e6c60bd7; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12627752/supplementaryFiles; note: Extracted by deterministic parse of the pinned XLSX cell XML (extract/extract_model_execution.py with extract/rawxlsx.py), with the title, headers, sample identifiers (checked against Table S1) and software labels asserted. Runtime cells use built-in number format 21 (h:mm:ss); printed_value is that rendering of the stored day fraction and numeric_value is the same duration in seconds. Cost printed_value is the shortest round-trip decimal of the stored double. Independent review 2026-10-09: printed value, numeric value, metric, qualifier, unit, direction, locator and configuration and protocol identity match the source.