Here are the instructions to download the trial package when you have been granted access.
Thanks. I have finally installed parabrick. But while trying it on one sample, I am getting an error “cudaMemGetInfo returned 30” . The command and error are shown below:
date; pbrun somatic --ref /hg19/ucsc.hg19.fasta --in-tumor-fq /test/SRR3163205_1.fastq.gz /test/SRR3163205_2.fastq.gz --out-vcf /test/SRR3163205.vcf.gz --out-tumor-bam /test/SRR3163205_tumor.bam; date
Wed Jan 6 18:49:59 IST 2021
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation
[Parabricks Options Mesg]: Automatically generating ID prefix
[Parabricks Options Mesg]: Read group created for
/home/akansha/vivekruhela/parabricks_free_trial_vv3.2.0_2021-02-28/test/SRR3163205_1.fastq.gz and
/home/akansha/vivekruhela/parabricks_free_trial_vv3.2.0_2021-02-28/test/SRR3163205_2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:SRR3163205.1.1\tLB:lib1\tPL:bar\tSM:tumor\tPU:SRR3163205.1.1
[Parabricks Options Mesg]: Checking argument compatibility
[Parabricks Options Mesg]: Read group created for
/home/akansha/vivekruhela/parabricks_free_trial_vv3.2.0_2021-02-28/test/SRR3163205_1.fastq.gz and
/home/akansha/vivekruhela/parabricks_free_trial_vv3.2.0_2021-02-28/test/SRR3163205_2.fastq.gz
[Parabricks Options Mesg]: @RG\tID:SRR3163205.1.1\tLB:lib1\tPL:bar\tSM:tumor\tPU:SRR3163205.1.1
|| Parabricks accelerated Genomics Pipeline ||
|| Version v3.2.0 ||
|| GPU-BWA mem, Sorting Phase-I ||
|| Contact: Parabricks-Support@nvidia.com ||
cudaMemGetInfo returned 30
→ unknown error
Please contact Parabricks-Support@nvidia.com for any questions
Exiting…
Could not run fq2bam as part of tumor sample processing for somatic pipeline
Exiting pbrun …
Wed Jan 6 18:50:01 IST 2021
Kindly suggest. Thanks.
Hello, I have followed this stuff, but no files downloaded to my computer
Hi Vivekr1,
can you please give me more information about :
- The GPUs you are using (the output of
nvidia-smifor example) - Docker or singularity version
Can you also make sure not to run the software within the directory where you installed it.
Regards,
Myrieme
Hi nur.1233
We are sorry you are facing this error. We are aware of the download issue using the UI.
We are working on a fix and I will let you know when it is back to normal.
If you want to download it before, you can use the CLI as explained in the second part of the document.
Best,
Myrieme
Vivekr1,
We are sorry but it seems that the GPUs you are using don’t meet the minimum requirement for Clara Parabricks Pipelines software :
https://docs.nvidia.com/clara/parabricks/v3.2/text/getting_started.html#prerequisites
Does that means, for 2 GPU server there should be 100 GB CPU RAM and 24 threads. It has nothing to do with 2 units of 11 GB GPUs. Please correct me if wrong.
But my server has 126 GB RAM and 40 threads. Although 3 jobs are running and 40 GB of RAM and 30 threads are engaged.
I was referring to
Any GPU that supports CUDA architecture 60, 61, 70, 75 and has 12GB GPU RAM or more. It has been tested on NVIDIA P100, NVIDIA V100, and NVIDIA T4 GPUs.
If I replace 11 GB GPU with 12 GB GPU, will that work?? I hope the rest of the requirements are fulfilled except GPUs. So, I need confirmation so that I can initiate the process for GPU replacement.
Hello everyone,
Could anyone please tell me if it is possible to execute Parabricks on Google Colab Pro, as they also provide high end GPUs?
If possible, could I have some instructions on how to go ahead with it?
Thanks a lot
Hi, I filled the submit multiple times, but I didn’t received any e-mail for the activation of the trail or for the installation. Can you give some hint if I had only to wait for the e-mail or if there’s somethig I can do?
EDIT: I recived the e-mail, so I was able to download the tar.gz file.