Attention:
The frontline support team will be unavailable to answer questions until May27th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

CNNScoreVariants Hanging in 4.0.5.2 and 4.0.6.0

I had no issues running CNNScoreVariants when using GATK 4.0.5.1 but as soon as I tried to run the exact same command in 4.0.5.2 or 4.0.6.0 it would get to the part where it says: "INFO CNNScoreVariants - Done initializing engine" and then it appears to just hang with no CPU activity. I even tried to let it go for about 10 minutes with nothing happening.

Below is the command using and it works just fine when I downgrade to 4.0.5.1. I also tried the 1D model and the same issue occurs.

gatk CNNScoreVariants -V test_data.vcf -I test_data.bam -R hg19.fa -O annotated_data.vcf -tensor-type read_tensor

If it matters the Java version is 1.8.0_121

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @franec, I'll ask the developer of the CNN tools, @samwell, to take a look at what's going on here.

Sign In or Register to comment.