On junction-rich RNA-seq samples, pbrun rna_fq2bam aborts during GPU-STAR alignment with:
[src/stitchWindowAligns_gpu.cu:6488] cudaSafeCall() failed: an illegal memory access was encountered, exiting.
(process exits rc=255, no BAM produced).
We traced this to the number of collapsed splice junctions reaching ~1,000,000. Critically, raising --max-collapsed-junctions does NOT help — it crashes at the identical read offset whether the limit is the default 1,000,000 or 2,000,000. The flag only governs STAR’s per-chunk, host-side graceful check (ReadAlignChunk.cpp:570); there appears to be a separate, fixed-size GPU-side buffer in stitchWindowAligns_gpu.cu that overflows at ~1M collapsed junctions regardless of the flag.
| Parabricks image | nvcr.io/nvidia/clara/clara-parabricks:4.7.0-1 |
|---|---|
| Bundled STAR | 2.7.2a (genome index built with STAR 2.7.2a, --sjdbOverhang 250) |
| GPU | NVIDIA H100 PCIe (80 GB) |
| NVIDIA driver | 580.159.03 |
| Host | AMD EPYC 9124 (Genoa), 188 GB RAM |
| OS / kernel | Ubuntu 24.04.4 LTS, kernel 6.8.0-124-generic |
| Container runtime | Docker 29.6.0 |