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Caused by: java.lang.ClassCastException: class com.milaboratory.core.io.sequence.SingleReadImpl cannot be cast to class com.milaboratory.core.io.sequence.PairedRead (com.milaboratory.core.io.sequence.SingleReadImpl and com.milaboratory.core.io.sequence.PairedRead are in unnamed module of loader 'app')
at com.milaboratory.mixcr.vdjaligners.VDJCAlignerWithMerge.process0(VDJCAlignerWithMerge.java:27)
at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:75)
at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:31)
at com.milaboratory.mixcr.cli.CommandAlign$run0$1$1$1$alignedChunks$1.invoke(CommandAlign.kt:797)
at com.milaboratory.mixcr.cli.CommandAlign$run0$1$1$1$alignedChunks$1.invoke(CommandAlign.kt:622)
at com.milaboratory.primitivio.PritmitivIExtesionsKt.mapInParallel$lambda-6(PritmitivIExtesions.kt:102)
at cc.redberry.pipe.blocks.ParallelProcessor$Worker.run(ParallelProcessor.java:305)
at java.base/java.lang.Thread.run(Unknown Source)
Suppressed: java.lang.IllegalStateException: Footer not written
at com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter.close(VDJCAlignmentsWriter.java:187)
at kotlin.jdk7.AutoCloseableKt.closeFinally(AutoCloseable.kt:64)
at com.milaboratory.mixcr.cli.CommandAlign.run0(CommandAlign.kt:550)
at com.milaboratory.cli.ACommand.run(ACommand.java:112)
at com.milaboratory.mixcr.cli.CommandAnalyze.run0(CommandAnalyze.kt:518)
at com.milaboratory.cli.ACommand.run(ACommand.java:112)
at picocli.CommandLine.executeUserObject(CommandLine.java:1769)
at picocli.CommandLine.access$900(CommandLine.java:145)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2141)
at com.milaboratory.mixcr.cli.Main$1.handle(Main.java:83)
at com.milaboratory.mixcr.cli.Main$1.handle(Main.java:72)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:1968)
at com.milaboratory.mixcr.cli.Main.handleParseResult(Main.java:94)
at com.milaboratory.mixcr.cli.Main.main(Main.java:66)
The text was updated successfully, but these errors were encountered:
Caused by: java.lang.ClassCastException: class com.milaboratory.core.io.sequence.SingleReadImpl cannot be cast to class com.milaboratory.core.io.sequence.PairedRead (com.milaboratory.core.io.sequence.SingleReadImpl and com.milaboratory.core.io.sequence.PairedRead are in unnamed module of loader 'app')
at com.milaboratory.mixcr.vdjaligners.VDJCAlignerWithMerge.process0(VDJCAlignerWithMerge.java:27)
at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:75)
at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:31)
at com.milaboratory.mixcr.cli.CommandAlign$run0$1$1$1$alignedChunks$1.invoke(CommandAlign.kt:797)
at com.milaboratory.mixcr.cli.CommandAlign$run0$1$1$1$alignedChunks$1.invoke(CommandAlign.kt:622)
at com.milaboratory.primitivio.PritmitivIExtesionsKt.mapInParallel$lambda-6(PritmitivIExtesions.kt:102)
at cc.redberry.pipe.blocks.ParallelProcessor$Worker.run(ParallelProcessor.java:305)
at java.base/java.lang.Thread.run(Unknown Source)
Suppressed: java.lang.IllegalStateException: Footer not written
at com.milaboratory.mixcr.basictypes.VDJCAlignmentsWriter.close(VDJCAlignmentsWriter.java:187)
at kotlin.jdk7.AutoCloseableKt.closeFinally(AutoCloseable.kt:64)
at com.milaboratory.mixcr.cli.CommandAlign.run0(CommandAlign.kt:550)
at com.milaboratory.cli.ACommand.run(ACommand.java:112)
at com.milaboratory.mixcr.cli.CommandAnalyze.run0(CommandAnalyze.kt:518)
at com.milaboratory.cli.ACommand.run(ACommand.java:112)
at picocli.CommandLine.executeUserObject(CommandLine.java:1769)
at picocli.CommandLine.access$900(CommandLine.java:145)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2141)
at com.milaboratory.mixcr.cli.Main$1.handle(Main.java:83)
at com.milaboratory.mixcr.cli.Main$1.handle(Main.java:72)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:1968)
at com.milaboratory.mixcr.cli.Main.handleParseResult(Main.java:94)
at com.milaboratory.mixcr.cli.Main.main(Main.java:66)
The text was updated successfully, but these errors were encountered: