Hi,
I got the following ERROR when I ran GATK4 Mutect2 pipeline. Is it a NIO related issue? Or, Can I fix it by turning off NIO mode? Thanks!
06:33:45.601 INFO ProgressMeter - 14:25095814 1026.0 4952000 4826.6 06:36:25.799 INFO GetPileupSummaries - Shutting down engine [June 29, 2018 6:36:25 AM UTC] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 1,028.94 minutes. Runtime.totalMemory()=5855248384 java.lang.RuntimeException: java.util.concurrent.ExecutionException: com.google.cloud.storage.StorageException: www.googleapis.com at org.broadinstitute.hellbender.utils.nio.SeekableByteChannelPrefetcher.read(SeekableByteChannelPrefetcher.java:309) at htsjdk.samtools.seekablestream.SeekablePathStream.read(SeekablePathStream.java:86) 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.samtools.BAMFileReader$BAMFileIndexIterator.getNextRecord(BAMFileReader.java:977) at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:803) at htsjdk.samtools.BAMFileReader$BAMFileIndexIterator.<init>(BAMFileReader.java:963) at htsjdk.samtools.BAMFileReader.createIndexIterator(BAMFileReader.java:918) at htsjdk.samtools.BAMFileReader.query(BAMFileReader.java:575) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:528) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.loadNextIterator(SamReaderQueryingIterator.java:125) at org.broadinstitute.hellbender.utils.iterators.SamReaderQueryingIterator.<init>(SamReaderQueryingIterator.java:66) at org.broadinstitute.hellbender.engine.ReadsDataSource.prepareIteratorsForTraversal(ReadsDataSource.java:404) at org.broadinstitute.hellbender.engine.ReadsDataSource.prepareIteratorsForTraversal(ReadsDataSource.java:381) at org.broadinstitute.hellbender.engine.ReadsDataSource.query(ReadsDataSource.java:346) at org.broadinstitute.hellbender.engine.ReadsContext.iterator(ReadsContext.java:110) at org.broadinstitute.hellbender.engine.ReadsContext.iterator(ReadsContext.java:93) at java.lang.Iterable.spliterator(Iterable.java:101) at org.broadinstitute.hellbender.utils.GATKProtectedVariantContextUtils.getPileup(GATKProtectedVariantContextUtils.java:286) at org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries.apply(GetPileupSummaries.java:176) at org.broadinstitute.hellbender.engine.VariantWalkerBase.lambda$traverse$0(VariantWalkerBase.java:109) at java.util.stream.ForEachOps$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$OfRef.evaluateSequential(ForEachOps.java:174) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) at org.broadinstitute.hellbender.engine.VariantWalkerBase.traverse(VariantWalkerBase.java:107) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:994) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:135) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:180) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:199) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203) at org.broadinstitute.hellbender.Main.main(Main.java:289) Caused by: java.util.concurrent.ExecutionException: com.google.cloud.storage.StorageException: www.googleapis.com at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at org.broadinstitute.hellbender.utils.nio.SeekableByteChannelPrefetcher$WorkUnit.getBuf(SeekableByteChannelPrefetcher.java:136) at org.broadinstitute.hellbender.utils.nio.SeekableByteChannelPrefetcher.fetch(SeekableByteChannelPrefetcher.java:268) at org.broadinstitute.hellbender.utils.nio.SeekableByteChannelPrefetcher.read(SeekableByteChannelPrefetcher.java:300) ... 42 more Caused by: com.google.cloud.storage.StorageException: www.googleapis.com at com.google.cloud.storage.spi.v1.HttpStorageRpc.translate(HttpStorageRpc.java:189) at com.google.cloud.storage.spi.v1.HttpStorageRpc.read(HttpStorageRpc.java:515) at com.google.cloud.storage.BlobReadChannel$1.call(BlobReadChannel.java:127) at com.google.cloud.storage.BlobReadChannel$1.call(BlobReadChannel.java:124) at shaded.cloud_nio.com.google.api.gax.retrying.DirectRetryingExecutor.submit(DirectRetryingExecutor.java:94) at com.google.cloud.RetryHelper.runWithRetries(RetryHelper.java:54) at com.google.cloud.storage.BlobReadChannel.read(BlobReadChannel.java:124) at com.google.cloud.storage.contrib.nio.CloudStorageReadChannel.read(CloudStorageReadChannel.java:114) at org.broadinstitute.hellbender.utils.nio.SeekableByteChannelPrefetcher$WorkUnit.call(SeekableByteChannelPrefetcher.java:131) at org.broadinstitute.hellbender.utils.nio.SeekableByteChannelPrefetcher$WorkUnit.call(SeekableByteChannelPrefetcher.java:104) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$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:668) 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:1138) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1032) at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:177) at sun.net.www.protocol.https.HttpsURLConnectionImpl.connect(HttpsURLConnectionImpl.java:153) at shaded.cloud_nio.com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:93) at shaded.cloud_nio.com.google.api.client.http.HttpRequest.execute(HttpRequest.java:972) at shaded.cloud_nio.com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:419) at shaded.cloud_nio.com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:352) at shaded.cloud_nio.com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeMedia(AbstractGoogleClientRequest.java:380) at shaded.cloud_nio.com.google.api.services.storage.Storage$Objects$Get.executeMedia(Storage.java:6133) at com.google.cloud.storage.spi.v1.HttpStorageRpc.read(HttpStorageRpc.java:494) ... 12 more Using GATK jar /root/gatk.jar defined in environment variable GATK_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 -Xmx6500m -jar /root/gatk.jar GetPileupSummaries -R gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta -I gs://fc-f96be298-ca57-4799-ba17-d436195872b5/WGS_bam/10_11_EAC1.bam -L gs://fc-16adb3e5-7c0a-4805-aa5e-374b579d03e1/Homo_sapiens_assembly19.fasta.wgs_intervals.1_22X.interval_list -V gs://fc-ccdec940-7452-40c8-ad6c-fe0a94b89512/823a0e4d-1254-4223-b2c0-f6946b298934/MutectResources/f934484c-5e6c-4244-b438-8b48ed96f9dc/call-SelectCommonBiallelicSNPs/mutect2-contamination-variants.vcf.gz -O pileups.table