I am using gatk 4.1.0.0 Command: ./gatk FastaAlternateReferenceMaker -R Vervet_UCP1.fasta -O VBOA1003.fasta -V VBOA1003.vcf.gz Log: OUTPUT: Using GATK jar /Users/christiangagnon/Desktop/gatk-4.1.0.0/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 /Users/christiangagnon/Desktop/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar FastaAlternateReferenceMaker -R Vervet_UCP1.fasta -O VBOA1003.fasta -V VBOA1003.vcf.gz 00:31:30.878 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Users/christiangagnon/Desktop/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.dylib Feb 22, 2019 12:31:31 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine WARNING: Failed to detect whether we are running on Google Compute Engine. java.net.ConnectException: Host is down (connect failed) 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 sun.net.www.http.HttpClient.openServer(HttpClient.java:463) at sun.net.www.http.HttpClient.openServer(HttpClient.java:558) at sun.net.www.http.HttpClient.(HttpClient.java:242) at sun.net.www.http.HttpClient.New(HttpClient.java:339) at sun.net.www.http.HttpClient.New(HttpClient.java:357) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1220) 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.http.HttpURLConnection.connect(HttpURLConnection.java:984) 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.(ServiceOptions.java:278) at com.google.cloud.storage.StorageOptions.(StorageOptions.java:83) at com.google.cloud.storage.StorageOptions.(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) Feb 22, 2019 12:31:31 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine WARNING: Failed to detect whether we are running on Google Compute Engine. java.net.ConnectException: Host is down (connect failed) 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 sun.net.www.http.HttpClient.openServer(HttpClient.java:463) at sun.net.www.http.HttpClient.openServer(HttpClient.java:558) at sun.net.www.http.HttpClient.(HttpClient.java:242) at sun.net.www.http.HttpClient.New(HttpClient.java:339) at sun.net.www.http.HttpClient.New(HttpClient.java:357) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1220) 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.http.HttpURLConnection.connect(HttpURLConnection.java:984) 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.(ServiceOptions.java:278) at com.google.cloud.storage.StorageOptions.(StorageOptions.java:83) at com.google.cloud.storage.StorageOptions.(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) Feb 22, 2019 12:31:31 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine WARNING: Failed to detect whether we are running on Google Compute Engine. java.net.ConnectException: Host is down (connect failed) 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 sun.net.www.http.HttpClient.openServer(HttpClient.java:463) at sun.net.www.http.HttpClient.openServer(HttpClient.java:558) at sun.net.www.http.HttpClient.(HttpClient.java:242) at sun.net.www.http.HttpClient.New(HttpClient.java:339) at sun.net.www.http.HttpClient.New(HttpClient.java:357) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1220) 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.http.HttpURLConnection.connect(HttpURLConnection.java:984) 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.(ServiceOptions.java:278) at com.google.cloud.storage.StorageOptions.(StorageOptions.java:83) at com.google.cloud.storage.StorageOptions.(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) 00:31:31.091 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------ 00:31:31.092 INFO FastaAlternateReferenceMaker - The Genome Analysis Toolkit (GATK) v4.1.0.0 00:31:31.092 INFO FastaAlternateReferenceMaker - For support and documentation go to https://software.broadinstitute.org/gatk/ 00:31:31.092 INFO FastaAlternateReferenceMaker - Executing as christiangagnon@Christians-Air.fios-router.home on Mac OS X v10.14 x86_64 00:31:31.092 INFO FastaAlternateReferenceMaker - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_201-b09 00:31:31.092 INFO FastaAlternateReferenceMaker - Start Date/Time: February 22, 2019 12:31:30 AM EST 00:31:31.092 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------ 00:31:31.092 INFO FastaAlternateReferenceMaker - ------------------------------------------------------------ 00:31:31.093 INFO FastaAlternateReferenceMaker - HTSJDK Version: 2.18.2 00:31:31.093 INFO FastaAlternateReferenceMaker - Picard Version: 2.18.25 00:31:31.093 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.COMPRESSION_LEVEL : 2 00:31:31.093 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 00:31:31.093 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 00:31:31.093 INFO FastaAlternateReferenceMaker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 00:31:31.093 INFO FastaAlternateReferenceMaker - Deflater: IntelDeflater 00:31:31.094 INFO FastaAlternateReferenceMaker - Inflater: IntelInflater 00:31:31.094 INFO FastaAlternateReferenceMaker - GCS max retries/reopens: 20 00:31:31.094 INFO FastaAlternateReferenceMaker - Requester pays: disabled 00:31:31.094 INFO FastaAlternateReferenceMaker - Initializing engine 00:31:31.516 INFO FeatureManager - Using codec VCFCodec to read file file:///Users/christiangagnon/Desktop/gatk-4.1.0.0/VBOA1003.vcf.gz 00:31:31.532 INFO FastaAlternateReferenceMaker - Shutting down engine [February 22, 2019 12:31:31 AM EST] org.broadinstitute.hellbender.tools.walkers.fasta.FastaAlternateReferenceMaker done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=386400256 htsjdk.tribble.TribbleException: Contig CAE1 does not have a length field. at htsjdk.variant.vcf.VCFContigHeaderLine.getSAMSequenceRecord(VCFContigHeaderLine.java:80) at htsjdk.variant.vcf.VCFHeader.getSequenceDictionary(VCFHeader.java:206) at org.broadinstitute.hellbender.engine.FeatureDataSource.getSequenceDictionary(FeatureDataSource.java:390) at org.broadinstitute.hellbender.engine.FeatureManager.lambda$getAllSequenceDictionaries$6(FeatureManager.java:314) 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:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499) at org.broadinstitute.hellbender.engine.FeatureManager.getAllSequenceDictionaries(FeatureManager.java:316) at org.broadinstitute.hellbender.engine.GATKTool.validateSequenceDictionaries(GATKTool.java:668) at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:643) at org.broadinstitute.hellbender.engine.ReferenceWalker.onStartup(ReferenceWalker.java:36) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:136) 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)