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CNNScoreVariants 2D Not Working

I am trying to run the pre-trained CNNScoreVariants 2D model using the GATK docker image on my local machine. I was able to successfully run the 1D model, but the 2D keeps failing. It appears the tools attempts to run, but does not produce any results. I have posted the edited log below (system does not allow me to post links). Any help would be greatly appreciated.

```
(gatk) [email protected]:/gatk# gatk CNNScoreVariants -I my_data/NA12878_IDT_CNV_GATK4.1.Recalibrated.bam -V my_data/NA12878_IDT_CNV_GATK4.1.HC.vcf.gz -R my_data/human_g1k_v37_decoy.fasta -O CNNScore2D_Variant_GATK4.1_NA12878.vcf -inference-batch-size 2 -transfer-batch-size 2 -tensor-type read_tensor

Using GATK jar /gatk/gatk-package-4.1.0.0-local.jar

Running:

java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.1.0.0-local.jar CNNScoreVariants -I my_data/NA12878_IDT_CNV_GATK4.1.Recalibrated.bam -V my_data/NA12878_IDT_CNV_GATK4.1.HC.vcf.gz -R my_data/human_g1k_v37_decoy.fasta -O CNNScore2D_Variant_GATK4.1_NA12878.vcf -inference-batch-size 2 -transfer-batch-size 2 -tensor-type read_tensor

18:33:32.413 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so

Apr 17, 2019 6:33:33 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

WARNING: Failed to detect whether we are running on Google Compute Engine.

java.net.ConnectException: Connection refused (Connection refused)

at java.net.PlainSocketImpl.socketConnect(Native Method)

at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)

at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)

at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)

at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)

at java.net.Socket.connect(Socket.java:589)

at sun.net.NetworkClient.doConnect(NetworkClient.java:175)


at shaded.cloud_nio.com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:104)

at shaded.cloud_nio.com.google.api.client.http.HttpRequest.execute(HttpRequest.java:981)

at shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials.runningOnComputeEngine(ComputeEngineCredentials.java:210)

at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.tryGetComputeCredentials(DefaultCredentialsProvider.java:290)

at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentialsUnsynchronized(DefaultCredentialsProvider.java:207)

at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentials(DefaultCredentialsProvider.java:124)

at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:127)

at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:100)

at com.google.cloud.ServiceOptions.defaultCredentials(ServiceOptions.java:304)

at com.google.cloud.ServiceOptions.<init>(ServiceOptions.java:278)

at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:83)

at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:31)

at com.google.cloud.storage.StorageOptions$Builder.build(StorageOptions.java:78)

at org.broadinstitute.hellbender.utils.gcs.BucketUtils.setGlobalNIODefaultOptions(BucketUtils.java:353)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)

at org.broadinstitute.hellbender.Main.main(Main.java:291)




Apr 17, 2019 6:33:33 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine

WARNING: Failed to detect whether we are running on Google Compute Engine.

java.net.ConnectException: Connection refused (Connection refused)

at java.net.PlainSocketImpl.socketConnect(Native Method)

at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)

at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)

at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)

at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)

at java.net.Socket.connect(Socket.java:589)

at sun.net.NetworkClient.doConnect(NetworkClient.java:175)


at shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials.runningOnComputeEngine(ComputeEngineCredentials.java:210)

at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.tryGetComputeCredentials(DefaultCredentialsProvider.java:290)

at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentialsUnsynchronized(DefaultCredentialsProvider.java:207)

at shaded.cloud_nio.com.google.auth.oauth2.DefaultCredentialsProvider.getDefaultCredentials(DefaultCredentialsProvider.java:124)

at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:127)

at shaded.cloud_nio.com.google.auth.oauth2.GoogleCredentials.getApplicationDefault(GoogleCredentials.java:100)

at com.google.cloud.ServiceOptions.defaultCredentials(ServiceOptions.java:304)

at com.google.cloud.ServiceOptions.<init>(ServiceOptions.java:278)

at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:83)

at com.google.cloud.storage.StorageOptions.<init>(StorageOptions.java:31)

at com.google.cloud.storage.StorageOptions$Builder.build(StorageOptions.java:78)

at org.broadinstitute.hellbender.utils.gcs.BucketUtils.setGlobalNIODefaultOptions(BucketUtils.java:353)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)

at org.broadinstitute.hellbender.Main.main(Main.java:291)




18:33:33.170 INFO CNNScoreVariants - ------------------------------------------------------------

18:33:33.171 INFO CNNScoreVariants - The Genome Analysis Toolkit (GATK) v4.1.0.0

18:33:33.171 INFO CNNScoreVariants - For support and documentation go to

18:33:33.171 INFO CNNScoreVariants - Executing as [email protected] on Linux v4.9.125-linuxkit amd64

18:33:33.171 INFO CNNScoreVariants - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12

18:33:33.172 INFO CNNScoreVariants - Start Date/Time: April 17, 2019 6:33:32 PM UTC

18:33:33.172 INFO CNNScoreVariants - ------------------------------------------------------------

18:33:33.172 INFO CNNScoreVariants - ------------------------------------------------------------

18:33:33.173 INFO CNNScoreVariants - HTSJDK Version: 2.18.2

18:33:33.173 INFO CNNScoreVariants - Picard Version: 2.18.25

18:33:33.173 INFO CNNScoreVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2

18:33:33.173 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false

18:33:33.173 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true

18:33:33.174 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false

18:33:33.174 INFO CNNScoreVariants - Deflater: IntelDeflater

18:33:33.174 INFO CNNScoreVariants - Inflater: IntelInflater

18:33:33.174 INFO CNNScoreVariants - GCS max retries/reopens: 20

18:33:33.174 INFO CNNScoreVariants - Requester pays: disabled

18:33:33.174 INFO CNNScoreVariants - Initializing engine

WARNING: BAM index file /gatk/my_data/NA12878_IDT_CNV_GATK4.1.Recalibrated.bai is older than BAM /gatk/my_data/NA12878_IDT_CNV_GATK4.1.Recalibrated.bam

18:33:33.572 INFO FeatureManager - Using codec VCFCodec to read file file:///gatk/my_data/NA12878_IDT_CNV_GATK4.1.HC.vcf.gz

18:33:33.698 INFO CNNScoreVariants - Done initializing engine

18:33:33.699 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so

18:33:36.040 INFO CNNScoreVariants - Using key:CNN_2D for CNN architecture:/tmp/small_2d.1767057937227156485.json and weights:/tmp/small_2d.3995843942938171054.hd5

18:33:36.567 INFO ProgressMeter - Starting traversal

18:33:36.567 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute

18:33:36.573 INFO CNNScoreVariants - Starting first pass through the variants

18:33:43.926 INFO CNNScoreVariants - Done scoring variants with CNN.

18:33:43.945 INFO CNNScoreVariants - Shutting down engine

[April 17, 2019 6:33:44 PM UTC] org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants done. Elapsed time: 0.20 minutes.

Runtime.totalMemory()=218628096

org.broadinstitute.hellbender.exceptions.GATKException: Exception waiting for ack from Python: org.broadinstitute.hellbender.exceptions.GATKException: Expected message of length 3 but only found 0 bytes

at org.broadinstitute.hellbender.utils.runtime.StreamingProcessController.waitForAck(StreamingProcessController.java:233)

at org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor.waitForAck(StreamingPythonScriptExecutor.java:207)

at org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor.waitForPreviousBatchCompletion(StreamingPythonScriptExecutor.java:284)

at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.sendBatchIfReady(CNNScoreVariants.java:406)

at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.firstPassApply(CNNScoreVariants.java:326)

at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.lambda$traverseVariants$0(TwoPassVariantWalker.java:76)

at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)

at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)

at java.util.Iterator.forEachRemaining(Iterator.java:116)

at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)

at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)

at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)

at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)

at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)

at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)

at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)

at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.traverseVariants(TwoPassVariantWalker.java:74)

at org.broadinstitute.hellbender.engine.TwoPassVariantWalker.traverse(TwoPassVariantWalker.java:27)

at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:966)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:138)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)

at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)

at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)

at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)

at org.broadinstitute.hellbender.Main.main(Main.java:291)

Caused by: java.util.concurrent.ExecutionException: org.broadinstitute.hellbender.exceptions.GATKException: Expected message of length 3 but only found 0 bytes

at java.util.concurrent.FutureTask.report(FutureTask.java:122)

at java.util.concurrent.FutureTask.get(FutureTask.java:192)

at org.broadinstitute.hellbender.utils.runtime.StreamingProcessController.waitForAck(StreamingProcessController.java:228)


Caused by: org.broadinstitute.hellbender.exceptions.GATKException: Expected message of length 3 but only found 0 bytes

at org.broadinstitute.hellbender.utils.runtime.StreamingProcessController.getBytesFromStream(StreamingProcessController.java:261)

at org.broadinstitute.hellbender.utils.runtime.StreamingProcessController.lambda$waitForAck$0(StreamingProcessController.java:208)

at java.util.concurrent.FutureTask.run(FutureTask.java:266)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

at java.lang.Thread.run(Thread.java:748)
```

Answers

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