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Variant Discovery in High-Throughput Sequencing Data

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Funcotator Appears to have completed but with RunTimeException

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4 comments

  • Avatar
    Robert Bremel

    Tried to re-run the file

     

    Same problem, error in different place this time....

     

     

    04:56:57.259 ERROR GencodeFuncotationFactory - Problem creating a GencodeFuncotation on transcript ENST00000545537.1 for variant: chr11:130780268-130780269(TC* -> T): Variant overlaps transcript but is not completely contained within it. Funcotator cannot currently handle this case. Transcript: ENST00000545537.1 Variant: [VC Unknown @ chr11:130780268-130780269 Q. of type=INDEL alleles=[TC*, T] attr={AS_FilterStatus=weak_evidence, AS_SB_TABLE=[29, 129|1, 10], DP=241, ECNT=4, GERMQ=93, MBQ=[30, 30], MFRL=[200, 215], MMQ=[60, 60], MPOS=21, POPAF=7.30, RPA=[2, 1], RU=C, STR=true, STRQ=93, TLOD=7.83} GT=GT:AD:AF:DP:F1R2:F2R1:SB 0/1:85,6:0.069:91:33,2:44,1:14,71,1,5 0/1:73,5:0.072:78:34,3:36,2:15,58,0,5 filters=clustered_events,weak_evidence


    [June 5, 2020 5:17:24 AM UTC] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 1,674.77 minutes.

    Runtime.totalMemory()=4817158144


    java.lang.RuntimeException: java.util.concurrent.ExecutionException: com.google.cloud.storage.StorageException: www.googleapis.com
    at com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher.read(SeekableByteChannelPrefetcher.java:401)
    at htsjdk.samtools.seekablestream.SeekablePathStream.read(SeekablePathStream.java:86)
    at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
    at java.io.BufferedInputStream.read1(BufferedInputStream.java:286)
    at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
    at htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:133)
    at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:571)
    at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:560)
    at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:510)
    at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
    at htsjdk.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:380)
    at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:427)
    at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:46)
    at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:170)
    at htsjdk.tribble.TabixFeatureReader$FeatureIterator.<init>(TabixFeatureReader.java:159)
    at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:133)
    at org.broadinstitute.hellbender.engine.FeatureDataSource.refillQueryCache(FeatureDataSource.java:567)
    at org.broadinstitute.hellbender.engine.FeatureDataSource.queryAndPrefetch(FeatureDataSource.java:536)
    at org.broadinstitute.hellbender.engine.FeatureManager.getFeatures(FeatureManager.java:353)
    at org.broadinstitute.hellbender.engine.FeatureContext.getValues(FeatureContext.java:173)
    at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.queryFeaturesFromFeatureContext(DataSourceFuncotationFactory.java:304)
    at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.getFeaturesFromFeatureContext(DataSourceFuncotationFactory.java:219)
    at org.broadinstitute.hellbender.tools.funcotator.DataSourceFuncotationFactory.createFuncotations(DataSourceFuncotationFactory.java:197)
    at org.broadinstitute.hellbender.tools.funcotator.FuncotatorEngine.createFuncotationMapForVariant(FuncotatorEngine.java:173)
    at org.broadinstitute.hellbender.tools.funcotator.Funcotator.enqueueAndHandleVariant(Funcotator.java:903)
    at org.broadinstitute.hellbender.tools.funcotator.Funcotator.apply(Funcotator.java:857)
    at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
    at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    at java.util.Iterator.forEachRemaining(Iterator.java:116)
    at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
    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.VariantWalker.traverse(VariantWalker.java:102)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
    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:163)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
    at org.broadinstitute.hellbender.Main.main(Main.java:292)

    Caused by: java.util.concurrent.ExecutionException: com.google.cloud.storage.StorageException: www.googleapis.com

    at java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.util.concurrent.FutureTask.get(FutureTask.java:192)
    at com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher$WorkUnit.getBuf(SeekableByteChannelPrefetcher.java:230)
    at com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher.fetch(SeekableByteChannelPrefetcher.java:347)
    at com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher.read(SeekableByteChannelPrefetcher.java:392)
    ... 46 more

    Caused by: com.google.cloud.storage.StorageException: www.googleapis.com

    at com.google.cloud.storage.spi.v1.HttpStorageRpc.translate(HttpStorageRpc.java:229)
    at com.google.cloud.storage.spi.v1.HttpStorageRpc.read(HttpStorageRpc.java:704)
    at com.google.cloud.storage.BlobReadChannel$1.call(BlobReadChannel.java:127)
    at com.google.cloud.storage.BlobReadChannel$1.call(BlobReadChannel.java:124)
    at shaded.cloud_nio.com.google.api.gax.retrying.DirectRetryingExecutor.submit(DirectRetryingExecutor.java:105)
    at shaded.cloud_nio.com.google.cloud.RetryHelper.run(RetryHelper.java:76)
    at shaded.cloud_nio.com.google.cloud.RetryHelper.runWithRetries(RetryHelper.java:50)
    at com.google.cloud.storage.BlobReadChannel.read(BlobReadChannel.java:123)
    at com.google.cloud.storage.contrib.nio.CloudStorageReadChannel.read(CloudStorageReadChannel.java:158)
    at com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher$WorkUnit.call(SeekableByteChannelPrefetcher.java:225)
    at com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher$WorkUnit.call(SeekableByteChannelPrefetcher.java:193)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

    Caused by: java.net.UnknownHostException: www.googleapis.com

    at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:184)
    at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
    at java.net.Socket.connect(Socket.java:589)
    at sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:666)
    at sun.net.NetworkClient.doConnect(NetworkClient.java:175)
    at sun.net.www.http.HttpClient.openServer(HttpClient.java:463)
    at sun.net.www.http.HttpClient.openServer(HttpClient.java:558)
    at sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:264)
    at sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:367)
    at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:191)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1156)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1050)
    at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177)
    at sun.net.www.protocol.https.HttpsURLConnectionImpl.connect(HttpsURLConnectionImpl.java:162)
    at shaded.cloud_nio.com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:143)
    at shaded.cloud_nio.com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:79)
    at shaded.cloud_nio.com.google.api.client.http.HttpRequest.execute(HttpRequest.java:995)
    at shaded.cloud_nio.com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:549)
    at shaded.cloud_nio.com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:482)
    at shaded.cloud_nio.com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeMedia(AbstractGoogleClientRequest.java:510)
    at shaded.cloud_nio.com.google.api.services.storage.Storage$Objects$Get.executeMedia(Storage.java:6981)
    at com.google.cloud.storage.spi.v1.HttpStorageRpc.read(HttpStorageRpc.java:699)


    ... 13 more
    Using GATK jar /gatk/gatk-package-4.1.7.0-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-4.1.7.0-local.jar Funcotator -R mydata/refs/Homo_sapiens_assembly19.fasta -V mydata/P62820/analysis/P62820_mutect2_filtered.vcf -O mydata/P62820/analysis/P62820_mutect2_funcotator.maf --output-file-format MAF --data-sources-path mydata/dataSourcesFolder/funcotator_dataSources.v1.6.20190124s/ --verbosity ERROR --ref-version hg19

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  • Avatar
    Robert Bremel

    #5094 suggests processes that run a long time could be an issue?  I am running from a rural area with DSL with only a 5mB/sec download speed.  Might that be an issue causing it to take so long?

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  • Avatar
    Bhanu Gandham

    Hi Robert Bremel

     

    This is not a Funcotator issue. It’s a google cloud issue. You might be right about the connection being slow, but I am not sure.

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  • Avatar
    Robert Bremel

    Thanks Bhanu,

     

    I suspected it was google, but couldn't decipher the output.

     

    I split the input vcf into chromosome subfiles that get done quicker and I got it through the lot.

     

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