Hi all,
I am trying to run parabricks on GPU nodes with RTX 3090, RTX 2080Ti or Telsa P100.
And I got this error when running the following command:
singularity run
–nv
-B /storage/scratch/iee/zl19g775/Ga_Gw_pop_gen:/input
-W /storage/scratch/iee/zl19g775/Ga_Gw_pop_gen
clara-parabricks_4.1.2-1.sif
pbrun fq2bam
–ref /input/index/GaA/stickleback_v5_assembly.noY.fa
–in-fq /input/0_fastq_files/Gw_data_trimmed/A01a_F.1.fastq.gz /input/0_fastq_files/Gw_data_trimmed/A01a_F.2.fastq.gz “@RG\tID:HG002\tLB:lib\tPL:Illumina\tSM:HG002\tPU:HG002”
–out-bam /input/1_silver_set_3xB/1_default_calling/DeepVariant/
And it returned with these messages always:
please visit NVIDIA Clara - NVIDIA Docs for detailed documentation
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Read group created for /input/0_fastq_files/Gw_data_trimmed/A01a_F.1.fastq.gz and
/input/0_fastq_files/Gw_data_trimmed/A01a_F.2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:HG002\tLB:lib\tPL:Illumina\tSM:HG002\tPU:HG002
/usr/local/parabricks/binaries//bin/bwa: symbol lookup error: /usr/local/parabricks/binaries//bin/bwa: undefined symbol: cuGraphAddKernelNode_v2
For technical support visit Help - NVIDIA Docs
Exiting…
Could not run fq2bam
Exiting pbrun …
There is an NVIDIA driver (520.61.05) installed and the CUDA version is 11.8.
Is it possible for you to help me to figure out what the problem is?
Thank a lot!
Zuyao