Error when run germline pipeline with NA12878

Healthcare & Life Sciences Parabricks
1

Hi,

We use eight Tesla P100 to run germline pipeline with NA12878 data, But getting the following error:

|| Parabricks accelerated Genomics Pipeline ||
|| Version v2.5.0 ||
|| GPU-BWA mem, Sorting, Marking Duplicates, BQSR ||
|| Contact: Parabricks-Support@nvidia.com ||

[M::bwa_idx_load_from_disk] read 0 ALT contigs

GPU-BWA mem
ProgressMeter Reads Base Pairs Aligned
[09:55:00] 5061412 750000000
[09:55:22] 10122400 1510000000
[09:55:44] 15182642 2280000000
[09:56:07] 20242532 3030000000
[09:56:30] 25301622 3810000000
[09:56:53] 30361222 4570000000
[09:57:15] 35421664 5320000000
[09:57:37] 40481834 6090000000
[09:58:00] 45541066 6830000000
[09:58:24] 50599860 7600000000
[09:58:46] 55658706 8350000000
[09:59:09] 60719092 9090000000
cudaSafeCall() failed at ParaBricks/src/mem_chain_kernel.cu:3920 : an illegal memory access was encountered
GPU: 3, cudaSafeCall() failed at ParaBricks/src/mem_chain_kernel.cu:3889 : an illegal memory access was encountered
GPU: 0, cudaSafeCall() failed at ParaBricks/src/mem_chain2aln_kernel.cu:5145 : an illegal memory access was encountered
GPU: 1, cudaSafeCall() failed at ParaBricks/src/mem_chain2aln_kernel.cu:5145 : an illegal memory access was encountered

Any suggestions or advice will be appreciated

2

Thanks for your interest in Parabricks. Would you kindly try running with a new version of Parabricks - version 3.1 for example?

3

But we only found v2.5.0 and v2.3.2 on the NGC, could you kindly provide the link or website to get version 3.1? Thanks

4

Thanks for clarifying. While we update our NGC repository with the latest Parabricks code version; please use this link to run Parabricks:

wget -O parabricks.tar.gz " https://s3.amazonaws.com/parabricks.licenses/v310_OCT_END/parabricks.tar.gz?AWSAccessKeyId=AKIAJGDUNN2G2ZAH3Q3A&Expires=1602532746&Signature=yVstD6Ga%2FQVZawj05bmeWFFGXDY%3D "

5

We are still working on running the parabricks on our server, but it looks like the trial license has expired. Is it possible the extend the trail license to the end of year?