Hi everyone, I’m trying to use rna_fq2bam from parabricks with the following command
singularity exec --cleanenv --nv -B $workdir:$workdir -B $outputdir:$outputdir --pwd $workdir \
clara-parabricks_4.1.0-1.sif \
pbrun rna_fq2bam \
--in-fq $workdir/SRR10256964_1.fastq $workdir/SRR10256964_2.fastq \
--genome-lib-dir $workdir/OUT1 \
--output-dir $outputdir/ \
--ref $workdir/Genome/GCA_025026875.1_ASM2502687v1_genomic.fna \
--out-bam $outputdir/OUTPUT.bam \
--num-gpus 4
Issue
The Mapping phase completes successfully, but the Sorting Phase II fails with a generic error: Received signal: 11
Log
[PB Info 2025-Jan-04 15:33:15] Stage 2 gpu thread done
[PB Info 2025-Jan-04 15:33:15] Stage 2 cpu threads done
[PB Info 2025-Jan-04 15:33:15] Stage 0 gpu thread done
[PB Info 2025-Jan-04 15:33:15] Stage 0 cpu threads done
[PB Info 2025-Jan-04 15:33:15] Stage 1 gpu thread done
[PB Info 2025-Jan-04 15:33:15] Stage 1 cpu threads done
[PB Info 2025-Jan-04 15:33:15] Stage 3 gpu thread done
[PB Info 2025-Jan-04 15:33:15] Stage 3 cpu threads done
[PB Info 2025-Jan-04 15:33:15] Stage 2 clearAllQueue done
[PB Info 2025-Jan-04 15:33:16] Stage 0 clearAllQueue done
[PB Info 2025-Jan-04 15:33:16] Stage 1 clearAllQueue done
[PB Info 2025-Jan-04 15:33:16] Stage 3 clearAllQueue done
[PB Info 2025-Jan-04 15:33:16] all workers joined
[PB Info 2025-Jan-04 15:33:16] reader done
[PB Info 2025-Jan-04 15:33:16] ..... finished mapping
[PB Info 2025-Jan-04 15:33:16] All processing done, time 1625.363
[PB Info 2025-Jan-04 15:33:23] ..... finished successfully
[PB Info 2025-Jan-04 15:33:23] All done, total running time is 1634.592
[PB Info 2025-Jan-04 15:33:23] Memory free
[PB Info 2025-Jan-04 15:33:23] ------------------------------------------------------------------------------
[PB Info 2025-Jan-04 15:33:23] || Program: star ||
[PB Info 2025-Jan-04 15:33:23] || Version: 4.1.0-1 ||
[PB Info 2025-Jan-04 15:33:23] || Start Time: Sat Jan 4 15:06:08 2025 ||
[PB Info 2025-Jan-04 15:33:23] || End Time: Sat Jan 4 15:33:23 2025 ||
[PB Info 2025-Jan-04 15:33:23] || Total Time: 27 minutes 15 seconds ||
[PB Info 2025-Jan-04 15:33:23] ------------------------------------------------------------------------------
[PB Info 2025-Jan-04 15:33:24] ------------------------------------------------------------------------------
[PB Info 2025-Jan-04 15:33:24] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2025-Jan-04 15:33:24] || Version 4.1.0-1 ||
[PB Info 2025-Jan-04 15:33:24] || Sorting Phase-II ||
[PB Info 2025-Jan-04 15:33:24] ------------------------------------------------------------------------------
[PB Info 2025-Jan-04 15:33:24] progressMeter - Percentage
[PB Info 2025-Jan-04 15:33:24] 0.0 0.00 GB
[PB Error 2025-Jan-04 15:33:24][-unknown-:0] Received signal: 11
For technical support visit https://docs.nvidia.com/clara/parabricks/4.1.0/Help.html, exiting.
For technical support visit https://docs.nvidia.com/clara/parabricks/4.1.0/Help.html
Exiting...
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
Could not run rna_fq2bam
Exiting pbrun ...
Does anyone know how to resolve this error? Thank you!