Running CNN Score Variants

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Priyadarshini Thirunavukkarasu

• October 16, 2021 14:36

Hello

I am running GATK/4.2.2.0-foss-2018b-Java-1.8. When I try to run the CNNScoreVariants, I get the below error:

python exited with 1
Command Line: python -c import gatktool

Stdout: 
Stderr: Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'gatktool'

Command:

ml GATK/4.2.2.0-foss-2018b-Java-1.8

gatk CNNScoreVariants \
-I /scicore/home/cichon/GROUP/memory_optimization/variants/1.bamout.bam \
-V /scicore/home/cichon/GROUP/memory_optimization/variants/1.vcf.gz \
-R /scicore/home/cichon/GROUP/memory_optimization/data/reference/gch38.fa \
-O /scicore/home/cichon/GROUP/memory_optimization/variants/filtered/1_scored.vcf \
--tensor-type read_tensor \
--transfer-batch-size 8 \
--inference-batch-size 8

Should I install python module for gatktools?.

 

Thanks

0

• 

  Pamela Bretscher

  • October 18, 2021 13:03

  Hi Priyadarshini Thirunavukkarasu,

  Some GATK tools require specific python dependencies to run which is most likely causing your error. It is recommended that you either use the GATK docker image which contains everything needed to run the GATK tools or that you install a Conda environment. Please see this document on how to install a Conda environment and let me know if you are able to follow the steps and run CNNScoreVariants without error. 

  Kind regards,

  Pamela

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