I am not able to run pbrun germline on tiny sample fastq files with the following error message. Any insight is greatly appreciated. My machine info is at the very end. Not sure if it is compatibility issue or singularity issue.
-bash-4.2$ singularity run --nv \
–bind $(pwd):/data
…/clara-parabricks_4.3.0-1.sif
pbrun germline
–ref Ref/Homo_sapiens_assembly38.fasta
–in-fq Data/sample_1.fq.gz Data/sample_2.fq.gz
–knownSites Ref/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
–out-bam output.bam
–out-variants germline.vcf
–out-recal-file recal.txt
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[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for
/lrlhps/users/c085541/nfprojects/parabricks/parabricks_sample/Data/sample_1.fq.gz and
/lrlhps/users/c085541/nfprojects/parabricks/parabricks_sample/Data/sample_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Read group created for
/lrlhps/users/c085541/nfprojects/parabricks/parabricks_sample/Data/sample_1.fq.gz and
/lrlhps/users/c085541/nfprojects/parabricks/parabricks_sample/Data/sample_2.fq.gz
[Parabricks Options Mesg]: @RG\tID:HK3TJBCX2.1\tLB:lib1\tPL:bar\tSM:sample\tPU:HK3TJBCX2.1
/usr/local/parabricks/binaries/bin/bwa: symbol lookup error: /usr/local/parabricks/binaries/bin/bwa: undefined symbol: cuGraphAddKernelNode_v2
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Exiting…
Could not run fq2bam as part of germline pipeline
Exiting pbrun …
-bash-4.2$ nvidia-smi --format=csv --query-gpu=index,name,temperature.gpu
index, name, temperature.gpu
0, Tesla K80, 58
1, Tesla K80, 27