Test-drive the GATK tools and Best Practices pipelines on Terra
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CNNScoreVariants Hanging in 18.104.22.168 and 22.214.171.124
I had no issues running CNNScoreVariants when using GATK 126.96.36.199 but as soon as I tried to run the exact same command in 188.8.131.52 or 184.108.40.206 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 220.127.116.11. 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