Genomics short-read, HG002 GIAB, Wave 2 GPU re-queue (2026-05-08)
phalaena:run:PA-R-1-1-wave2-2026-05-08
Wave 2 GPU re-queue of paper 1.1 (GIAB HG002, 11.2 million paired Illumina HiSeq 2500 reads). End-to-end through the Parabricks GPU branch (PARABRICKS_FQ2BAM plus PARABRICKS_HAPLOTYPECALLER) with non-GPU stages on Spot, completing in 3 h 49 min wall clock. SUCCESS at 20:29:18Z on 2026-05-08. Empirically validates GATK retry idempotency (validation finding #20), the BWA-MEM1 patch (finding #1), and the CLINVAR_ANNOTATE snpsift container fix (finding #23). Numeric outputs match the pinned headlines in MANIFEST.json to the digit.
- kind
- run
- pipeline
- Genomics short-read pipeline, release p1.1
- status
- reviewed
- googlebatch:e0b4b638...
- phalaena:run:e0b4b638
View Genomics short-read, HG002 GIAB, Wave 2 GPU re-queue (2026-05-08) on the Phalaena Wiki