gistfile1.txt

17:13:34.819 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/xchip/scarter/dmccabe/software/gatk-protected_e54dac3/build/libs/gatk-protected-package-e54dac3-SNAPSHOT-local.jar!/com/intel/gkl/native/libgkl_compression.so
[April 12, 2017 5:13:34 PM EDT] org.broadinstitute.hellbender.tools.exome.convertbed.ConvertBedToTargetFile  --input test2.bed --output test2.target  --help false --version false --showHidden false --verbosity INFO --QUIET false --use_jdk_deflater false --use_jdk_inflater false
[April 12, 2017 5:13:34 PM EDT] Executing as dmccabe@ccpm.broadinstitute.org on Linux 2.6.32-642.13.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Version: Version:e54dac3-SNAPSHOT
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.BUFFER_SIZE : 131072
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.COMPRESSION_LEVEL : 5
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.CREATE_INDEX : false
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.CREATE_MD5 : false
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.CUSTOM_READER_FACTORY :
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.EBI_REFERENCE_SERVICE_URL_MASK : http://www.ebi.ac.uk/ena/cram/md5/%s
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.NON_ZERO_BUFFER_SIZE : 131072
17:13:34.858 INFO  ConvertBedToTargetFile - Defaults.REFERENCE_FASTA : null
17:13:34.859 INFO  ConvertBedToTargetFile - Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
17:13:34.859 INFO  ConvertBedToTargetFile - Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:13:34.859 INFO  ConvertBedToTargetFile - Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : false
17:13:34.859 INFO  ConvertBedToTargetFile - Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:13:34.859 INFO  ConvertBedToTargetFile - Defaults.USE_CRAM_REF_DOWNLOAD : false
17:13:34.859 INFO  ConvertBedToTargetFile - Deflater IntelDeflater
17:13:34.859 INFO  ConvertBedToTargetFile - Inflater IntelInflater
17:13:34.859 INFO  ConvertBedToTargetFile - Initializing engine
17:13:34.859 INFO  ConvertBedToTargetFile - Done initializing engine
17:13:35.397 INFO  ConvertBedToTargetFile - Shutting down engine
[April 12, 2017 5:13:35 PM EDT] org.broadinstitute.hellbender.tools.exome.convertbed.ConvertBedToTargetFile done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=760741888
org.broadinstitute.hellbender.exceptions.GATKException: Multiple codecs found able to decode file file:///xchip/scarter/dmccabe/data/targets/test2.bed. This indicates a misconfiguration on the part of the codec authors. Matching codecs are: htsjdk.tribble.bed.BEDCodec org.broadinstitute.hellbender.utils.codecs.TargetCodec
	at org.broadinstitute.hellbender.engine.FeatureManager.getCodecForFile(FeatureManager.java:445)
	at org.broadinstitute.hellbender.engine.FeatureManager.getCodecForFile(FeatureManager.java:369)
	at org.broadinstitute.hellbender.tools.exome.convertbed.ConvertBedToTargetFile.doWork(ConvertBedToTargetFile.java:54)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:116)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:121)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:142)
	at org.broadinstitute.hellbender.Main.main(Main.java:218)