exportAlignments ERROR

[Z-YWJ]

Hello, thank for fantastic software. Recently, I meet an error when I try to export reads alignment.

Data format

my fastq data is PE150 TBCR data.

This is my code:

`
name=result
mixcr_latest align -Xmx400g -p rna-seq --species hsa -f -OsaveOriginalReads=true --impute-germline-on-export $file_1.fq.gz $file_2.fq.gz ${name}.vdjca --report ${name}.align.report.txt ;
mixcr_latest assemble -Xmx500g --write-alignments -f ${name}.vdjca ${name}.clna --report ${name}.assemble.report.txt
mixcr_latest exportAlignments -Xmx400g -vGene -dGene -jGene -cGene -cFamily -f -descrsR2 -descrsR1 -cloneId -readIds -targetSequences -topChains -chains -cloneIdWithMappingType ${name}.clna ${name}.exportAlignment.report.tsv
mixcr_latest exportClones --filter-stops --filter-out-of-frames -f -topChains -targets --impute-germline-on-export ${name}.clna ${name}.clones.tsv

`
When I run 'exportAlignments' command, there is a error, like this:

ERROR info

Exporting alignments: 1.2% ETA: 02:42:14 Exporting alignments: 2.5% ETA: 02:30:03 Exporting alignments: 4.1% ETA: 02:04:19 Exporting alignments: 5.5% ETA: 02:11:04 Exporting alignments: 7.4% ETA: 01:35:37 App version: 4.6.0-195-develop; built=Wed May 15 10:10:39 EDT 2024; rev=1a90bc5691; lib=repseqio.v5.0 java.lang.AssertionError: [{false 0 119 120}, {false 1 102 120}, {true 1 68 80}] [{false 1 101 120}, {true 1 68 80}] -1 at com.milaboratory.o.jP.c(SourceFile:524) at com.milaboratory.o.EF.a(SourceFile:98) at com.milaboratory.o.EF.a(SourceFile:105) at com.milaboratory.o.jP.j(SourceFile:356) at com.milaboratory.o.un.invoke(SourceFile:1428) at com.milaboratory.o.lB.extractValue(SourceFile:57) at com.milaboratory.mixcr.export.FieldWithParameters$create$2.invoke(SourceFile:583) at com.milaboratory.mixcr.export.FieldWithParameters$create$2.invoke(SourceFile:582) at com.milaboratory.o.lK.a(SourceFile:25) at com.milaboratory.o.my.put(SourceFile:40) at cc.redberry.pipe.CUtils.drain(CUtils.java:82) at cc.redberry.pipe.util.PipeExtensionsKt.drainToAndClose(PipeExtensions.kt:155) at com.milaboratory.mixcr.cli.CommandExportAlignments$Cmd.run1(SourceFile:169) 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$lambda-32(SourceFile:538) at picocli.CommandLine.execute(CommandLine.java:2078) at com.milaboratory.mixcr.cli.Main.execute(SourceFile:105) at com.milaboratory.mixcr.cli.Main.main(SourceFile:101) Suppressed: java.lang.IllegalStateException: random access primitivI blocks or primitivI reader not closed at com.milaboratory.o.Er.a(SourceFile:174) at com.milaboratory.o.Er.close(SourceFile:287) at com.milaboratory.o.iV.close(SourceFile) at com.milaboratory.mixcr.cli.CommandExportAlignments$AlignmentsAndMetaInfo.close(SourceFile) at kotlin.jdk7.AutoCloseableKt.closeFinally(AutoCloseable.kt:64) at com.milaboratory.mixcr.cli.CommandExportAlignments$Cmd.run1(SourceFile:139) ... 13 more
Looking forward to your help!!!

[Z-YWJ]

My mixcr version is

MiXCR v4.6.0-195-develop (built Wed May 15 10:10:39 EDT 2024; rev=1a90bc5691; branch=develop; host=fv-az1024-873)

[mizraelson]

Could you please try using the latest available version and let me know if the issue persists?

[Z-YWJ]

OK, thank you, I will try

[Z-YWJ]

However, when I try same command and data with MiXCR v4.7.0 (built Wed Aug 07 15:19:48 EDT 2024; rev=976ba14139; branch=no_branch; host=fv-az1019-185)

I still meet the same error, just like

Exporting alignments: 0%
Exporting alignments: 1.2% ETA: 02:40:59
Exporting alignments: 2.4% ETA: 02:40:14
Exporting alignments: 3.8% ETA: 02:21:40
Exporting alignments: 5.2% ETA: 02:13:58
Exporting alignments: 6.8% ETA: 01:58:35
App version: 4.7.0; built=Wed Aug 07 15:19:48 EDT 2024; rev=976ba14139; lib=repseqio.v5.1
java.lang.AssertionError: [{false 0 119 120}, {false 1 102 120}, {true 1 68 80}][{false 1 101 120}, {true 1 68 80}]
-1
at com.milaboratory.o.kd.c(SourceFile:524)
at com.milaboratory.o.EV.a(SourceFile:98)
at com.milaboratory.o.EV.a(SourceFile:105)
at com.milaboratory.o.kd.j(SourceFile:356)
at com.milaboratory.o.uA.invoke(SourceFile:1428)
at com.milaboratory.o.lO.extractValue(SourceFile:57)
at com.milaboratory.mixcr.export.FieldWithParameters$create$2.invoke(SourceFile:583)
at com.milaboratory.mixcr.export.FieldWithParameters$create$2.invoke(SourceFile:582)
at com.milaboratory.o.lX.a(SourceFile:25)
at com.milaboratory.o.mL.put(SourceFile:40)
at cc.redberry.pipe.CUtils.drain(CUtils.java:82)
at cc.redberry.pipe.util.PipeExtensionsKt.drainToAndClose(PipeExtensions.kt:155)
at com.milaboratory.mixcr.cli.CommandExportAlignments$Cmd.run1(SourceFile:169)
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$lambda-32(SourceFile:539)
at picocli.CommandLine.execute(CommandLine.java:2078)
at com.milaboratory.mixcr.cli.Main.execute(SourceFile:105)
at com.milaboratory.mixcr.cli.Main.main(SourceFile:101)
Suppressed: java.lang.IllegalStateException: random access primitivI blocks or primitivI reader not closed
at com.milaboratory.o.EH.a(SourceFile:174)
at com.milaboratory.o.EH.close(SourceFile:287)
at com.milaboratory.o.je.close(SourceFile)
at com.milaboratory.mixcr.cli.CommandExportAlignments$AlignmentsAndMetaInfo.close(SourceFile)
at kotlin.jdk7.AutoCloseableKt.closeFinally(AutoCloseable.kt:64)
at com.milaboratory.mixcr.cli.CommandExportAlignments$Cmd.run1(SourceFile:139)
... 13 more

[mizraelson]

It seems that the issue is due to a bug when using the --impute-germline-on-export parameter. Could you try running the command without it? If possible, please share the .clna file with us at [email protected], and I will take a look to address this potential bug.

[Z-YWJ]

Thanks for your kindess response. When I remove the --impute-germline-on-export paramter the command run smoothly. But because my clna file is so large that I can email to you.

[mizraelson]

If possible you can share the file via Google Drive or any other convenient way.

[Z-YWJ]

Hello, due to some reason, the original .clna file (about ~70G) is deleted, but I reserve the incomplete .clna file (about ~4.4 G) and you can download via the link https://cloud.tsinghua.edu.cn/f/dcf7afedec2d457e8ad2/

I hope this incompleted file can help you to address this question and imporve MIXCR, if not, you can contact to me and I will run again to obtain the original .clna file.

[mizraelson]

Hi, what do you mean by incomplete?

[Z-YWJ]

When I download the original file (about ~70G), the download was interrupted due to network issues, so I only get the incomplete .clna file (about ~4.4 G). And when I notice this, I have depleted the original file.