Error while running command align java.lang.RuntimeException: Different number of reads in single-readers.

[pursellta]

I am trying to run the non-enriched 10x analysis pipeline on SRA fastqs. I have suceessfully run this pipeline with this custom reference on other files, but I get the following error I have never seen before. Information and the stacktrace: Version: 4.7.0; built=Wed Aug 07 12:19:48 PDT 2024; rev=976ba14139; lib=repseqio.v5.1 OS: Linux Java: 11.0.13 Abs path: /home/tpursell
Cmd args: align --report /home/tpursell/bats/Arjam_Flu_10x/mixcr.Tony.ML.bcr.20241024/align.report.txt --json-report /home/tpursell/bats/Arjam_Flu_10x/mixcr.Tony.ML.bcr.20241024/align.report.json --threads 20 --preset 10x-sc-5gex --save-output-file-names /home/tpursell/bats/Arjam_Flu_10x/mixcr.Tony.ML.bcr.20241024/align.list.tsv --split-by-sample --species ajam --library Arjam-IG-V1.json.gz --assemble-contigs-by VDJRegion /home/tpursell/bats/Arjam_Flu_10x/TonyFilesSampleSheet.tsv /home/tpursell/bats/Arjam_Flu_10x/mixcr.Tony.ML.bcr.20241024/alignments.vdjca

Error: picocli.CommandLine$ExecutionException: Error while running command align java.lang.RuntimeException: Different number of reads in single-readers. at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$lambda-17(SourceFile:420) at picocli.CommandLine.execute(CommandLine.java:2088) at com.milaboratory.mixcr.cli.Main.execute(SourceFile:105) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd$PlanBuilder.executeSteps(SourceFile:543) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd.run0(SourceFile:444) at com.milaboratory.mixcr.cli.MiXCRCommand.run(SourceFile:37) at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at com.milaboratory.mixcr.cli.Main.registerLogger$lambda-32(SourceFile:539) at picocli.CommandLine.execute(CommandLine.java:2078) at com.milaboratory.mixcr.cli.Main.execute(SourceFile:105) at com.milaboratory.mixcr.cli.Main.main(SourceFile:101) Caused by: java.lang.RuntimeException: Different number of reads in single-readers. at com.milaboratory.o.aS.a(SourceFile:62) at com.milaboratory.o.ba.take(SourceFile:1028) at com.milaboratory.o.c.a(SourceFile:89) at com.milaboratory.o.c.take(SourceFile:69) at cc.redberry.pipe.util.SimpleProcessorWrapper.take(SimpleProcessorWrapper.java:40) at com.milaboratory.o.FG.take(SourceFile) at cc.redberry.pipe.util.Chunk.readChunk(Chunk.java:78) at cc.redberry.pipe.CUtils$2.take(CUtils.java:169) at cc.redberry.pipe.CUtils$2.take(CUtils.java:161) at cc.redberry.pipe.blocks.O2ITransmitter.run(O2ITransmitter.java:63) at java.base/java.lang.Thread.run(Thread.java:829) Suppressed: java.lang.RuntimeException: java.lang.IllegalStateException: Footer not set at com.milaboratory.o.e$b.close(SourceFile:54) at com.milaboratory.o.g.close(SourceFile:75) at kotlin.jdk7.AutoCloseableKt.closeFinally(AutoCloseable.kt:64) at com.milaboratory.mixcr.cli.CommandAlign$Cmd.run1(SourceFile:1635) at com.milaboratory.mixcr.cli.MiXCRCommandWithOutputs.run0(SourceFile:69) at com.milaboratory.mixcr.cli.MiXCRCommand.run(SourceFile:37) at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at com.milaboratory.mixcr.cli.Main.registerLogger$lambda-32(SourceFile:539) at picocli.CommandLine.execute(CommandLine.java:2078) at com.milaboratory.mixcr.cli.Main.execute(SourceFile:105) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd$PlanBuilder.executeSteps(SourceFile:543) at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd.run0(SourceFile:444) at com.milaboratory.mixcr.cli.MiXCRCommand.run(SourceFile:37) at picocli.CommandLine.executeUserObject(CommandLine.java:1939) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) at com.milaboratory.mixcr.cli.Main.registerLogger$lambda-32(SourceFile:539) at picocli.CommandLine.execute(CommandLine.java:2078) at com.milaboratory.mixcr.cli.Main.execute(SourceFile:105) at com.milaboratory.mixcr.cli.Main.main(SourceFile:101) Caused by: java.lang.IllegalStateException: Footer not set at com.milaboratory.o.ka.close(SourceFile:167) at com.milaboratory.o.e$b.close(SourceFile:46) ... 29 more Suppressed: java.lang.IllegalStateException: Footer not set ... 31 more Suppressed: java.lang.IllegalStateException: Footer not set ... 31 more

[mizraelson]

Hi, I see you closed the issue, did you solve it?

[pursellta]

Hey Mark! Yeah, I assume it is a problem with my fastqs (i.e. they got corrupted or didn’t download fully) based on another thread. I am redownloading them and will try again. -Taylor

From: mizraelson @.> Date: Thursday, October 24, 2024 at 4:33 PM To: milaboratory/mixcr @.> Cc: Taylor Pursell @.>, State change @.> Subject: Re: [milaboratory/mixcr] Error while running command align java.lang.RuntimeException: Different number of reads in single-readers. (Issue #1834)

Hi, I see you closed the issue, did you solve it?

— Reply to this email directly, view it on GitHubhttps://github.com/milaboratory/mixcr/issues/1834#issuecomment-2436515633, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUICXEIOCASG4AR2BIZUAGLZ5F7TRAVCNFSM6AAAAABQSDFPUCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZWGUYTKNRTGM. You are receiving this because you modified the open/close state.Message ID: @.***>

[mizraelson]

Understood! Please let me know if re-downloading helps!

Sincerely, Mark