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milaboratory
Failure to assembleContigs
Hi, I have used Mixcr multiple times, but never met the problem before. Now, I am sticking to this. I am running it in a private HPC with 256G memory, it would be very appreciated if I could get some help here. Thanks!
Script was:
mixcr assembleContigs \ --report .//03.AssembleContigs/RNA_REP_22062102_S6_assembleContig_report.txt \ .//02.Assemble/RNA_REP_22062102_S6_clones.clna .//03.AssembleContigs/RNA_REP_22062102_S6_full_clones.clns -f \ >> .//RNA_REP_22062102_S6.log
Error message is:
picocli.CommandLine$ExecutionException: Error while running command (com.milaboratory.mixcr.cli.CommandAssembleContigs@1950e8a6): java.lang.RuntimeException: While processing clone #108 at picocli.CommandLine.executeUserObject(CommandLine.java:1778) 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:84) at com.milaboratory.mixcr.cli.Main$1.handle(Main.java:73) at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:1968) at com.milaboratory.mixcr.cli.Main.handleParseResult(Main.java:95) at com.milaboratory.mixcr.cli.Main.main(Main.java:67) Caused by: java.lang.RuntimeException: While processing clone #108 at com.milaboratory.mixcr.cli.CommandAssembleContigs.lambda$run1$13(CommandAssembleContigs.java:231) at cc.redberry.pipe.CUtils$Indexed.process(CUtils.java:67) at cc.redberry.pipe.CUtils.lambda$orderedParallelProcessor$1(CUtils.java:96) at cc.redberry.pipe.blocks.ParallelProcessor$Worker.run(ParallelProcessor.java:305) at java.lang.Thread.run(Thread.java:750) Suppressed: java.lang.IllegalStateException: random access primitivI blocks or primitivI reader not closed at com.milaboratory.primitivio.blocks.PrimitivIHybrid.checkNullState(PrimitivIHybrid.java:174) at com.milaboratory.primitivio.blocks.PrimitivIHybrid.close(PrimitivIHybrid.java:285) at com.milaboratory.mixcr.basictypes.ClnAReader.close(ClnAReader.java:364) at com.milaboratory.mixcr.cli.CommandAssembleContigs.run1(CommandAssembleContigs.java:242) at com.milaboratory.cli.ACommandWithSmartOverwrite.run0(ACommandWithSmartOverwrite.java:118) at com.milaboratory.cli.ACommand.run(ACommand.java:100) 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:84) at com.milaboratory.mixcr.cli.Main$1.handle(Main.java:73) at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:1968) at com.milaboratory.mixcr.cli.Main.handleParseResult(Main.java:95) at com.milaboratory.mixcr.cli.Main.main(Main.java:67) Caused by: java.lang.IndexOutOfBoundsException at com.milaboratory.core.alignment.BandedMatrix.defined(BandedMatrix.java:134) at com.milaboratory.core.alignment.BandedMatrix.get(BandedMatrix.java:121) at com.milaboratory.core.alignment.BandedAffineAligner.semiGlobalRight0(BandedAffineAligner.java:377) at com.milaboratory.mixcr.assembler.fullseq.FullSeqAssembler.alignAffineSeq1FromLeft(FullSeqAssembler.java:1067) at com.milaboratory.mixcr.assembler.fullseq.FullSeqAssembler.alignSeq1FromLeft(FullSeqAssembler.java:1002) at com.milaboratory.mixcr.assembler.fullseq.FullSeqAssembler.buildClone(FullSeqAssembler.java:866) at com.milaboratory.mixcr.assembler.fullseq.FullSeqAssembler.lambda$callVariants$1(FullSeqAssembler.java:290) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1384) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:546) at java.util.stream.AbstractPipeline.evaluateToArrayNode(AbstractPipeline.java:260) at java.util.stream.ReferencePipeline.toArray(ReferencePipeline.java:505) at com.milaboratory.mixcr.assembler.fullseq.FullSeqAssembler.callVariants(FullSeqAssembler.java:291) at com.milaboratory.mixcr.cli.CommandAssembleContigs.lambda$run1$13(CommandAssembleContigs.java:229) ... 4 more
Hi! Which version of MiXCR you have?
Hi, I was using Mixcr-4.0.0 then met this error. And today I changed back to Mixcr-3.0.13, it works well. The .clna file is around 5.0G, If you want it, I can find a way to transfer it.
Thank you so much for the reply!