Test dataset too small to run/test GPU accelerated cohort runs

[leahkemp]

Errors out at the filtering step, see the parabricks log:

------------------------------------------------------------------------------
||                 Parabricks accelerated Genomics Pipeline                 ||
||                              Version 3.6.1-1                             ||
||                                   vqsr                                   ||
||                  Contact: Parabricks-Support@nvidia.com                  ||
------------------------------------------------------------------------------

-------VariantRecalibrator-------
[W::bcf_hdr_check_sanity] GL should be declared as Number=G
Initializing engine...
Starting traversal...
Processed 21328 total variants.
Training with 641 variants after standard deviation thresholding.
WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.
Initializing model with 100 k-means iterations...
  Finished iteration 0.
  Finished iteration 5. 	Current change in mixture coefficients = 0.61419
  Finished iteration 10. 	Current change in mixture coefficients = 0.07312
  Finished iteration 15. 	Current change in mixture coefficients = 0.12022
  Finished iteration 20. 	Current change in mixture coefficients = 0.33595
  Finished iteration 25. 	Current change in mixture coefficients = 0.00318
  Finished iteration 30. 	Current change in mixture coefficients = 0.00481
  Finished iteration 35. 	Current change in mixture coefficients = 0.00801
  Finished iteration 40. 	Current change in mixture coefficients = 0.01013
  Finished iteration 45. 	Current change in mixture coefficients = 0.00830
  Finished iteration 50. 	Current change in mixture coefficients = 0.00544
  Finished iteration 55. 	Current change in mixture coefficients = 0.00379
  Finished iteration 60. 	Current change in mixture coefficients = 0.00281
  Finished iteration 65. 	Current change in mixture coefficients = 0.00217
Convergence after 67 iterations!
Evaluating full set of 1793 variants...
Selected worst 0 scoring variants --> variants with LOD <= -5.0000.
No data found.
For technical support, updated user guides and other Parabricks documentation can be found at https://docs.nvidia.com/clara/#parabricks
Answers to most FAQ’s can be found on the developer forum https://forums.developer.nvidia.com/c/healthcare/Parabricks/290
Customers with paid Parabricks licenses have direct access to support and can contact EnterpriseSupport@nvidia.com
Users of free evaluation licenses can contact parabricks-eval-support@nvidia.com for troubleshooting any questions.
Exiting...
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation


Could not run vqsr
Exiting pbrun ...

Note. this doesn't seem to be an issue for non-GPU accelerated cohort runs