Good afternoon!
I was launching Clara Parabricks v4.0.1 fq2bam GPU workflow on trimmed data by cutadapt (pair-ended reads) and faced the following error message:
[PB Info 2024-Jul-22 08:36:24] ------------------------------------------------------------------------------
[PB Info 2024-Jul-22 08:36:24] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Jul-22 08:36:24] || Version 4.0.0-1 ||
[PB Info 2024-Jul-22 08:36:24] || GPU-BWA mem, Sorting Phase-I ||
[PB Info 2024-Jul-22 08:36:24] ------------------------------------------------------------------------------
[PB Info 2024-Jul-22 08:36:30] GPU-BWA mem
[PB Info 2024-Jul-22 08:36:30] ProgressMeter Reads Base Pairs Aligned
[PB Info 2024-Jul-22 08:36:43] 6039906 0
[PB Warning 2024-Jul-22 08:36:43][ParaBricks/src/check_error.cu:41] cudaSafeCall() failed at ParaBricks/src/mem_chain2aln_kernel.cu/4993: an illegal memory access was encountered
[PB Warning 2024-Jul-22 08:36:43][ParaBricks/src/check_error.cu:41] cudaSafeCall() failed at ParaBricks/src/mem_chain_kernel.cu/3822: an illegal memory access was encountered
[PB Warning 2024-Jul-22 08:36:43][ParaBricks/src/check_error.cu:41] cudaSafeCall() failed at ParaBricks/src/mem_chain_kernel.cu/3822: an illegal memory access was encountered
[PB Warning 2024-Jul-22 08:36:43][ParaBricks/src/check_error.cu:41] cudaSafeCall() failed at ParaBricks/src/bwamem_GPU.cu/329: an illegal memory access was encountered
[PB Error 2024-Jul-22 08:36:43][ParaBricks/src/check_error.cu:44] No GPUs active, shutting down due to previous error., exiting.
More over, it was the same no matter which data was used: Clara Parabricks test data or personal one.
The command of trimming is the following:
cutadapt -a AGATCGGAAGAGC -g GCTCTTCCGATCT -A AGATCGGAAGAGC -G GCTCTTCCGATCT
–trim-n --quality-cutoff 20,20 --error-rate 0.1 --times 99 --minimum-length 30
–pair-filter both -o “$CUT_FQ1” -p “$CUT_FQ2” “$IN_FQ1” “$IN_FQ2” 2> “$CUT_LOG”
Could you help to resolve the issue, please?