--two-pass-mode "Basic" pipeline crash after 1st pass finished successfully

Hi guys,

I’m having problem completing my rna_fq2bam run.

My commands:

docker run --rm --gpus all --volume -volume INPUT_DIR:/workdir --volume OUTPUT_DIR:/outputdir
–workdir /workdir
nvcr.io/nvidia/clara/clara-parabricks:4.2.1-1
pbrun rna_fq2bam
–sjdb-overhang 125
–in-fq /workdir/1540_LIB18162_LDI15612_CGATGT_L002_R1.fastq /workdir/1540_LIB18162_LDI15612_CGATGT_L002_R2.fastq
–genome-lib-dir /outputdir/STARgenomeIndex/GCA_013676235.1_index/
–output-dir /outputdir/GCA_013676235.1_assembly
–ref /outputdir/GCA_013676235.1/GCA_013676235.1_HZAU_G240_1.0_genomic.fna
–out-bam /outputdir/GCA_013676235.1_assembly/1540_LIB18162_LDI15612_CGATGT_L002.bam
–two-pass-mode “Basic”
–logfile /outputdir/GCA_013676235.1_assembly/1540_LIB18162_LDI15612_CGATGT_L002.log

Here the log from the crash:
[PB Info 2024-Mar-08 16:18:27] Stage 0 clearAllQueue done
[PB Info 2024-Mar-08 16:18:27] all workers joined
[PB Info 2024-Mar-08 16:18:27] reader done
[PB Info 2024-Mar-08 16:18:27] … finished mapping
[PB Info 2024-Mar-08 16:18:28] All processing done, time 23.345
[PB Info 2024-Mar-08 16:18:32] gpu free memory: 18903728128, total 25756565504
cudaSuccess
[PB Info 2024-Mar-08 16:18:32] gpu free memory: 9940500480, total 25756565504
cudaSuccess
[PB Info 2024-Mar-08 16:18:33] setGpuConstMem: gpu const memory usage 193 bytes
[PB Info 2024-Mar-08 16:18:33] cudaSuccess
[PB Info 2024-Mar-08 16:18:35] … finished successfully
[PB Error 2024-Mar-08 16:18:35][-unknown-:0] Received signal: 11
For technical support visit Clara Parabricks v4.2.0 - NVIDIA Docs, exiting.
For technical support visit Clara Parabricks v4.2.0 - NVIDIA Docs
Exiting…
Please visit NVIDIA Clara - NVIDIA Docs for detailed documentation

Could not run rna_fq2bam
Exiting pbrun …

Hi everyone,

I’ve repeated the run with an older docker image (clara-parabricks:4.1.2-1). This worked fine!
So potentially a bug in the latest image.