java.lang.RuntimeException: Missing event detected.

[A-legac45]

Hello,

I run mixcr on all my bulk mi laboratories tcr data but I encounter a problem for two of them. Do you know what happen? Does somebody already encounter this message?

Many thanks

My code:

/Users/alegac/opt/anaconda3/pkgs/mixcr-4.4.1-0/bin/mixcr -Xmx15g analyze milab-human-rna-tcr-umi-multiplex /Users/alegac/Documents/bulk_tcr/S1/s1_trimmed_R1.fastq.gz /Users/alegac/Documents/bulk_tcr/S1/s1_trimmed_R2.fastq.gz /Users/alegac/Documents/bulk_tcr/S1/results_01

My error :

Writing pre-clones: 72% ETA: 00:01:20
Writing pre-clones: 82,4% ETA: 00:00:44
Writing pre-clones: 92,7% ETA: 00:00:17
Writing pre-clones: 40,6%
Initialization: progress unknown
4.4.1; built=Thu Jul 06 19:36:41 CEST 2023; rev=f7cd556c6c; lib=repseqio.v3.0.1
picocli.CommandLine$ExecutionException: Error while running command assemble java.lang.RuntimeException: Missing event detected.
at com.milaboratory.mixcr.cli.Main.registerExceptionHandlers$lambda-12(SourceFile:323)
at picocli.CommandLine.execute(CommandLine.java:2088)
at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd$PlanBuilder.executeSteps(SourceFile:470)
at com.milaboratory.mixcr.cli.CommandAnalyze$Cmd.run0(SourceFile:412)
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$lambda-26(SourceFile:426)
at picocli.CommandLine.execute(CommandLine.java:2078)
at com.milaboratory.mixcr.cli.Main.main(SourceFile:98)
Caused by: java.lang.RuntimeException: Missing event detected.
at com.milaboratory.o.hN.a(SourceFile:59)
at com.milaboratory.o.hT$c.accept(SourceFile:1484)
at cc.redberry.pipe.blocks.FilteringPort.take(FilteringPort.java:65)
at cc.redberry.pipe.blocks.O2ITransmitter.run(O2ITransmitter.java:63)
at java.base/java.lang.Thread.run(Thread.java:829)

[mizraelson]

Hi, could you please confirm if the issue still persists with the latest MiXCR version? If it does, would it be possible for you to share the file that's causing the error?

[A-legac45]

I used this version /Users/alegac/opt/anaconda3/pkgs/mixcr-4.4.1-0/bin/

with this command

/Users/alegac/opt/anaconda3/pkgs/mixcr-4.4.1-0/bin/mixcr -Xmx15g analyze milab-human-rna-tcr-umi-multiplex
trimmed_R1.fastq.gz trimmed_R2.fastq.gz /results_01

Yes the issue persist for two of my files all the other 12 do not add any problem

[A-legac45]

results_05.align.report.txt
results_05.refine.report.txt

I can not upload my files there are two big unfortunatly

[mizraelson]

Maybe you can share through Google drive or we can provide an sftp for upload?

[mizraelson]

Could you please try running the problematic files with version 4.4.2 to confirm if the issue still persists?

[A-legac45]

Yes I can try this I will install mixcr4.4.2

[mizraelson]

Great, let me know how it works.

[A-legac45]

It seems to run for one sample at least thanks should I re run all my sample with this version ? What is the main different

[mizraelson]

Shouldn't be much difference in results, but since you encountered the error I would recommend using the latest version for consistency.

[A-legac45]

Ok thanks

[A-legac45]

Unfortunately I do not know why but I works for one sample the update of mixcr but not for the other I still have the same error message when I run this

/Users/alegac/Downloads/mixcr-4.4.2/mixcr -Xmx20g analyze milab-human-rna-tcr-umi-multiplex /Users/alegac/Documents/bulk_tcr/D1454T09/D1454T09_trimmed_R1.fastq.gz /Users/alegac/Documents/bulk_tcr/D1454T09/D1454T09_trimmed_R2.fastq.gz /Users/alegac/Documents/bulk_tcr/D1454T09/results_09 -f

Do you have any idea but my last problem?

[mizraelson]

Hi. Is it possible to share the problematic sample with us, so I can reproduce and investigate?

[A-legac45]

I ask my collegue if I can share and let you know

[A-legac45]

	http://xfer.curie.fr/get/My2aUMCB43v/D1454T09_trimmed_R1.fastq.gz

http://xfer.curie.fr/get/tQXbJ0J9Az5/D1454T09_trimmed_R2.fastq.gz

http://xfer.curie.fr/get/bNw50aOlQ2M/results_09.align.report.txt

http://xfer.curie.fr/get/MlMfKbgd59c/results_09.align.report.json

http://xfer.curie.fr/get/KeJFDbWFFmx/results_09.refine.report.txt

http://xfer.curie.fr/get/CzUGjlKVO1T/results_09.refine.report.json

http://xfer.curie.fr/get/EL5jaDemfb8/results_09.vdjca

http://xfer.curie.fr/get/3iHQ2O2MTCp/results_09.refined.vdjca

MERCI. PAR AVANCE

[mizraelson]

Hi,
I wasn't able to replicate the error on my side. The command finished with no errors.

mixcr -Xmx100G analyze milab-human-rna-tcr-umi-multiplex \
D1454T09_trimmed_R1.fastq.gz \
D1454T09_trimmed_R2.fastq.gz \
output

Archive.zip

Please find the clonotype table attached. All the reports look good. Can you try to run it again?

[A-legac45]

Hi,

Super many thanks

I just try running it one more time

/Users/alegac/Downloads/mixcr-4.4.2/mixcr -Xmx22g analyze milab-human-rna-tcr-umi-multiplex /Users/alegac/Documents/bulk_tcr/D1454T09/D1454T09_trimmed_R1.fastq.gz /Users/alegac/Documents/bulk_tcr/D1454T09/D1454T09_trimmed_R2.fastq.gz /Users/alegac/Documents/bulk_tcr/D1454T09/results_09 -f

I let you know if it work.

[A-legac45]

It works on my side now I just increase the -Xmx to 22g