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via broadinstitute.org by Unknown author, 1 year ago
java.io.FileNotFoundException: /rd/tmp/org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub8005277156701491219.tmp (Too many open files)	at java.io.FileInputStream.open(Native Method)	at java.io.FileInputStream.(FileInputStream.java:120)	at org.broad.tribble.util.ParsingUtils.openInputStream(ParsingUtils.java:56)	at org.broad.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:96)	at org.broad.tribble.TribbleIndexedFeatureReader.(TribbleIndexedFeatureReader.java:58)	at org.broad.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:69)	at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:182)	at org.broadinstitute.sting.gatk.io.storage.VariantContextWriterStorage.mergeInto(VariantContextWriterStorage.java:52)	at org.broadinstitute.sting.gatk.executive.OutputMergeTask.merge(OutputMergeTask.java:48)	at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.mergeExistingOutput(HierarchicalMicroScheduler.java:263)	at org.broadinstitute.sting.gatk.executive.HierarchicalMicroScheduler.execute(HierarchicalMicroScheduler.java:105)	at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:269)	at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)	at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)