SHMT Trees.tsv export (Picoli Command Error and full SHM trees are not exported)

[singhd6]

Hi I ran the attached script and receiving the follwoing error consistently. Full Trees.tsv files are not created.
SCRIPT3_ANALYZE_SWHK1_SHMTR3_trees.txt
Please copy the following information along with the stacktrace:
Version: 4.7.0; built=Wed Aug 07 15:19:48 EDT 2024; rev=976ba14139; lib=repseqio.v5.1
OS: Linux
Java: 23.0.2
Abs path: /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/SWHK1S9/SHMT_SWHK1_8.8.25/ /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/SWHK1S9/SHMT_SWHK1_8.8.25
Cmd args: exportShmTreesWithNodes /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/SWHK1S9/SHMT_SWHK1_8.8.25/SWHK1_R3.shmt /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/SWHK1S9/SHMT_SWHK1_8.8.25/SWHK1_R1_Trees.tsv
�[31m�[1mpicocli.CommandLine$ExecutionException: Error while running command exportShmTreesWithNodes java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0�[21m�[39m�[0m
�[3m at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$lambda-17(SourceFile:420)�[23m�[0m
�[3m at picocli.CommandLine.execute(CommandLine.java:2088)�[23m�[0m
�[3m at com.milaboratory.mixcr.cli.Main.execute(SourceFile:105)�[23m�[0m
�[3m at com.milaboratory.mixcr.cli.Main.main(SourceFile:101)�[23m�[0m
�[31m�[1mCaused by: java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds for length 0�[21m�[39m�[0m
�[3m at com.milaboratory.o.bS.codeAt(SourceFile:47)�[23m�[0m
�[3m at com.milaboratory.core.sequence.NucleotideSequence.codeAt(SourceFile:31)�[23m�[0m
�[3m at com.milaboratory.core.mutations.Mutations.mutate(SourceFile:170)�[23m�[0m
�[3m at com.milaboratory.o.bP.a(SourceFile:383)�[23m�[0m
�[3m at com.milaboratory.o.zd$a.a(SourceFile:643)�[23m�[0m
�[3m at com.milaboratory.o.ze.invoke(SourceFile:2561)�[23m�[0m
�[3m at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74)�[23m�[0m
�[3m at com.milaboratory.o.zd.b(SourceFile:65)�[23m�[0m
�[3m at com.milaboratory.o.zd.b(SourceFile:236)�[23m�[0m
�[3m at com.milaboratory.o.zd.b(SourceFile:233)�[23m�[0m
�[3m at com.milaboratory.o.zd.c(SourceFile:201)�[23m�[0m
�[3m at com.milaboratory.o.rD.invoke(SourceFile:1274)�[23m�[0m
�[3m at com.milaboratory.o.lK.extractValue(SourceFile:1216)�[23m�[0m
�[3m at com.milaboratory.mixcr.export.FieldWithParameters$create$2.invoke(SourceFile:583)�[23m�[0m
�[3m at com.milaboratory.mixcr.export.FieldWithParameters$create$2.invoke(SourceFile:582)�[23m�[0m
�[3m at com.milaboratory.o.lX.a(SourceFile:25)�[23m�[0m
�[3m at com.milaboratory.o.mB.invoke(SourceFile:1491)�[23m�[0m
�[3m at com.milaboratory.o.lX.a(SourceFile:25)�[23m�[0m
�[3m at com.milaboratory.o.mL.put(SourceFile:40)�[23m�[0m
�[3m at com.milaboratory.mixcr.cli.CommandExportShmTreesTableWithNodes.run1(SourceFile:227)�[23m�[0m
�[3m at com.milaboratory.mixcr.cli.MiXCRCommandWithOutputs.run0(SourceFile:69)�[23m�[0m
�[3m at com.milaboratory.mixcr.cli.MiXCRCommand.run(SourceFile:37)�[23m�[0m
�[3m at picocli.CommandLine.executeUserObject(CommandLine.java:1939)�[23m�[0m
�[3m at picocli.CommandLine.access$1300(CommandLine.java:145)�[23m�[0m
�[3m at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358)�[23m�[0m
�[3m at picocli.CommandLine$RunLast.handle(CommandLine.java:2352)�[23m�[0m
�[3m at picocli.CommandLine$RunLast.handle(CommandLine.java:2314)�[23m�[0m
�[3m at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)�[23m�[0m
�[3m at picocli.CommandLine$RunLast.execute(CommandLine.java:2316)�[23m�[0m
�[3m at com.milaboratory.mixcr.cli.Main.registerLogger$lambda-32(SourceFile:539)�[23m�[0m
�[3m at picocli.CommandLine.execute(CommandLine.java:2078)�[23m�[0m
�[3m ... 2 more�[23m�[0m
�[3m Suppressed: java.lang.IllegalStateException: random access primitivI blocks or primitivI reader not closed�[23m�[0m
�[3m at com.milaboratory.o.EH.a(SourceFile:174)�[23m�[0m
�[3m at com.milaboratory.o.EH.close(SourceFile:287)�[23m�[0m
�[3m at com.milaboratory.o.BO.close(SourceFile)�[23m�[0m
�[3m at kotlin.jdk7.AutoCloseableKt.closeFinally(AutoCloseable.kt:64)�[23m�[0m
�[3m at com.milaboratory.mixcr.cli.CommandExportShmTreesTableWithNodes.run1(SourceFile:131)�[23m�[0m
�[3m ... 13 more�[23m�[0m
Appreciate your response.
Thank you
Divya

[mizraelson]

Hi, can you please try the latest develop version and let me know if you are still experiencing the issue?

[singhd6]

Hi Mark, can you please provide the exact link for the install of MIXCR/4.7.0-develop version on Linux. The above link latest develop version is for windows. I do not see the latest release of mixcr/4.7.0 - develop version on github via this link https://github.com/milaboratory/mixcr/releases/
Thank you
Divya

[singhd6]

Hi,
Thank you so much for your prompt response. Sure, I will try the develop version of MIXCR and will let you know the results.
Divya

[mizraelson]

Hi, there are no different links for different OS, it's always a jar file that works with any system.

[singhd6]

Hi Mark,
I was bale to export the SHM trees with the develop version. Thanks for your help.
Divya

[singhd6]

Hi,
I have been receiving this particular error for building the SHM tree for one of the subject in all the versions of MIXCR:
picocli.CommandLine$ExecutionException: Error while running command findShmTrees java.lang.IllegalArgumentException: Failed requirement for one of the subjects even with the mixcr/4.7.0-223
Command I ran for creating the clns files and and alleles are as below:
ANALYZE CMMAND:
mixcr analyze neb-mouse-rna-xcr-umi-nebnext
JA_11_S2_R1_001.fastq.gz
JA_11_S2_R2_001.fastq.gz
result/JA_11_S2
FIND ALLELES COMMAND:
mixcr findAlleles
--output-template /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/JA11S2/JA1_SHMT_08132025/JA11.allelic.clns
--export-alleles-mutations /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/JA11S2/JA1_SHMT_08132025/JA11_allele_stats.tsv
/mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/JA11S2/result/JA_11_S2.clns

Error I am receiving is at the step of building SHM trees when I ran the SHM tree build command:

BUILD SHM TREE COMMAND:

mixcr findShmTrees /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/JA11S2/JA1_SHMT_08132025/JA11.allelic.clns /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/JA11S2/JA1_SHMT_08132025/JA11.shmt

ERROR:
[singhd6@cc-dclrilog62 JA11S2]$ mixcr findShmTrees /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/JA11S2/JA1_SHMT_08132025/JA11.allelic.clns /mnt/beegfs/singhd6/Divya_data/vhse q/BCR_Seq_Mouse_GZ/JA11S2/JA1_SHMT_08132025/JA11.shmt
IMPORTANT: MiXCR will use at most 12000MB of RAM,
use -Xmx to change automatically set heap size (i.e. -Xmx50g to set heap size to 50 Gb)
Search for clones with the same targets: 0%
Group clones by the same V, J and CDR3Length: 0%
Group clones by the same V, J and CDR3Length: 43.5% ETA: 00:00:01
Step 1/3, Building initial trees: 0%
Can't apply step BuildingInitialTrees(predictor=ClusterPredictor(commonMutationsCountForClustering=5, maxNDNDistanceForClustering=1.0), algorithm=BronKerboschWithFallback(limit=100000 00, fallback=com.milaboratory.mixcr.trees.CommandFindShmTreesParams$ClusterizationAlgorithm$SingleLinkage@4b6ee3e0)) on VJBase(V=IGLV300, J=IGLJ200, CDR3length=34)
Please copy the following information along with the stacktrace:
Version: 4.7.0-223-develop; built=Wed Jul 23 16:53:11 EDT 2025; rev=2079380cb1; lib=repseqio.v6.3
OS: Linux
Java: 23.0.2
Abs path: /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/JA11S2
Cmd args: findShmTrees /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/JA11S2/JA1_SHMT_08132025/JA11.allelic.clns /mnt/beegfs/singhd6/Divya_data/vhseq/BCR_Seq_Mouse_GZ/JA11S2/ JA1_SHMT_08132025/JA11.shmt
picocli.CommandLine$ExecutionException: Error while running command findShmTrees java.lang.IllegalArgumentException: Failed requirement.
at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$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.Main.main(SourceFile:101)
Caused by: java.lang.IllegalArgumentException: Failed requirement.
at com.milaboratory.core.Range.(SourceFile:62)
at com.milaboratory.core.Range.setLower(SourceFile:122)
at com.milaboratory.o.Ao$b.b(SourceFile:656)
at com.milaboratory.o.Ao$b.a(SourceFile:602)
at com.milaboratory.o.Ao.a(SourceFile:328)
at com.milaboratory.mixcr.trees.SHMTreeBuilderBySteps.a(SourceFile:39376)
at com.milaboratory.mixcr.trees.SHMTreeBuilderBySteps.a(SourceFile:16301)
at com.milaboratory.o.Bx.process(SourceFile:36)
at cc.redberry.pipe.blocks.ParallelProcessor$Worker.run(ParallelProcessor.java:308)
at java.base/java.lang.Thread.run(Thread.java:1575)
Suppressed: java.lang.IllegalStateException: Footer not set
at com.milaboratory.o.CR.close(SourceFile:85)
at kotlin.jdk7.AutoCloseableKt.closeFinally(AutoCloseable.kt:64)
at com.milaboratory.mixcr.cli.CommandFindShmTrees.run1(SourceFile:370)
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)
Thank you so much for your help and time.
Divya