CNNscoreVariant terminated with an error exit status (2) about nextneopi

[rashidma]

I checked on Intel website.
The E5-2620 v4 was launched in 2016 and supports AVX instruction set as mentioned below:
Instruction Set Extensions Intel® AVX2

Thanks

[riederd]

Hi,

it seems that the CPU you are using does not have the AVX instruction set required by GATK CNNScoreVariants. Which type of CPU is this?

What is the output of:
cat /proc/cpuinfo | grep "model name"
and
cat /proc/cpuinfo | grep avx

[rashidma]

Hello,
yes i think so. Information are below:

cat /proc/cpuinfo | grep "model name"
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz

cat /proc/cpuinfo | grep avx

No output.
I need to run this pipeline asap. So, is this pipeline available as conda package or environment??
Thanks

[riederd]

Unfortunately your type of CPU is not supported by GATK CNNScoreVariants since lacks the AVX instruction set.
The Intel(R) Xeon(R) CPU X5650 is about 13 years old, maybe you have access to a newer system with a more up-to-date CPU.

[rashidma]

Thank you for this information.
What about the below CPU?
model name : Intel(R) Xeon(R) CPU E5-2620 v4 @ 2.10GHz

I have access to a HPC with 16 such CPUs .

Best regards

[riederd]

This model should work!