CNNScoreVariants Error

Question

[bestone]

Hello guys, I have a problem with CNNScoreVariants code. When I use the code : gatk CNNScoreVariants \ -V input.vcf \ -R reference.fasta \ -O annotated.vcf

It has given the error :

 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: CNNScoreVariants is an EXPERIMENTAL tool and should not be used for production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


10:48:47.145 INFO  CNNScoreVariants - Initializing engine
10:48:47.621 INFO  FeatureManager - Using codec VCFCodec to read file file:///Users/uguremre/snpEff/snpEff/input.vcf
10:48:47.667 INFO  CNNScoreVariants - Done initializing engine
10:48:49.258 INFO  CNNScoreVariants - Shutting down engine
[June 5, 2023 10:48:49 AM TRT] org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=353894400
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: Traceback detected: Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'keras'
>>> 
    at org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor.getAccumulatedOutput(StreamingPythonScriptExecutor.java:214)
    at org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor.sendSynchronousCommand(StreamingPythonScriptExecutor.java:153)
    at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.onTraversalStart(CNNScoreVariants.java:264)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:992)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)

Could you pls help me with this issue?

Answer 1

[Pierre Lindenbaum]

check you have a complete environment for GATK , including the python module "keras". https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-for-GATK4

Go to the directory where you have stored the GATK4 jars and the gatk wrapper script, and make sure gatkcondaenv.yml is present. Run: conda env create -n gatk -f gatkcondaenv.yml then source activate gatk

[bestone]

Thank you for replying I updated it worked but it gives another Error A USER ERROR has occurred: Invalid argument ' -V'.

[Pierre Lindenbaum]

that is another question