mixcr exportPlots giving error #1562
Comments
LeilaKhajavi
changed the title
|
Hi, am trying to reproduce the error but it seems to work on my side. Can you share the metadata file you use? |
|
I will close this issue for now. Feel free to reopen if the issue is not resolved. |
|
I have same Java error. java 18.0.1.1 2022-04-22 mixcr exportPlots vUsage --metadata metadata.csv postanalysis_IGH.json postanalysis_IGH_vUsage.pdf
Is there any solution to this? |
|
Hi, can you please share the metadata file you are using? You can send to support@milaboratories.com |
|
I have sent an email with the metadata file |
|
I managed to find a solution for now..i was using csv..it was not working..i changed the metadata file to tsv file..it started working. |
|
I had tried CSV and txt... And it didn't work for me
I've since left the project so I don't have access to the metadata file I
had been using
…On Mon, Apr 29, 2024, 19:07 pbpayal ***@***.***> wrote:
I managed to find a solution for now..i was using csv..it was not
working..i changed the metadata file to tsv file..it started working.
—
Reply to this email directly, view it on GitHub
<#1562 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AY4DY375LWSONUXA3FCJRTLY7Z46HAVCNFSM6AAAAABD5STBCGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAOBTGIZTONJSGQ>
.
You are receiving this because you authored the thread.Message ID:
***@***.***>
|
|
Yes, it appeares to be a bug with the format. Currently only |
bash mixcr exportPlots diversity -Xmx90g --metadata metadata.csv --plot-type violin --primary-group event --primary-group-values NO,YES,none --hide-non-significant --p-adjust-method BenjaminiHochberg --method Wilcoxon postanalysis/PostgEvent.json postanalysis/Figures/eventDIVERSITYplots.pdf
09:37:51.048 INFO - Debug mode enabled.
09:37:51.051 INFO - allocation manager type not specified, using netty as the default type
09:37:51.052 INFO - Using DefaultAllocationManager at memory/DefaultAllocationManagerFactory.class
App version: 4.6.0; built=Sat Dec 09 20:48:42 CET 2023; rev=c9fafa41fe; lib=repseqio.v4.0
java.lang.ExceptionInInitializerError
at org.apache.arrow.memory.UnsafeAllocationManager.(UnsafeAllocationManager.java:27)
at org.apache.arrow.memory.DefaultAllocationManagerFactory.(DefaultAllocationManagerFactory.java:26)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:421)
at java.base/java.lang.Class.forName(Class.java:412)
at org.apache.arrow.memory.DefaultAllocationManagerOption.getFactory(DefaultAllocationManagerOption.java:108)
at org.apache.arrow.memory.DefaultAllocationManagerOption.getDefaultAllocationManagerFactory(DefaultAllocationManagerOption.java:98)
at org.apache.arrow.memory.BaseAllocator$Config.getAllocationManagerFactory(BaseAllocator.java:733)
at org.apache.arrow.memory.ImmutableConfig.access$801(ImmutableConfig.java:24)
at org.apache.arrow.memory.ImmutableConfig$InitShim.getAllocationManagerFactory(ImmutableConfig.java:83)
at org.apache.arrow.memory.ImmutableConfig.(ImmutableConfig.java:47)
at org.apache.arrow.memory.ImmutableConfig.(ImmutableConfig.java:24)
at org.apache.arrow.memory.ImmutableConfig$Builder.build(ImmutableConfig.java:485)
at org.apache.arrow.memory.BaseAllocator.(BaseAllocator.java:61)
at org.jetbrains.kotlinx.dataframe.io.Allocator$ROOT$2.invoke(arrow.kt:74)
at org.jetbrains.kotlinx.dataframe.io.Allocator$ROOT$2.invoke(arrow.kt:73)
at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74)
at org.jetbrains.kotlinx.dataframe.io.Allocator.getROOT(arrow.kt:73)
at org.jetbrains.kotlinx.dataframe.io.ArrowKt.readArrowFeather$default(arrow.kt:98)
at org.jetbrains.kotlinx.dataframe.io.ArrowKt.readArrowFeather(arrow.kt:245)
at org.jetbrains.kotlinx.dataframe.io.ArrowFeather.readDataFrame(arrow.kt:57)
at org.jetbrains.kotlinx.dataframe.io.GuessKt.read(guess.kt:117)
at org.jetbrains.kotlinx.dataframe.io.GuessKt.read$default(guess.kt:108)
at org.jetbrains.kotlinx.dataframe.io.GuessKt.read(guess.kt:131)
at org.jetbrains.kotlinx.dataframe.io.GuessKt.read(guess.kt:137)
at org.jetbrains.kotlinx.dataframe.io.GuessKt.read(guess.kt:146)
at org.jetbrains.kotlinx.dataframe.io.GuessKt.read$default(guess.kt:145)
at com.milaboratory.o.vx.a(SourceFile:48)
at com.milaboratory.o.vx.a(SourceFile:39)
at com.milaboratory.mixcr.cli.postanalysis.CommandPaExportPlots$metadataDf$2.invoke(SourceFile:95)
at com.milaboratory.mixcr.cli.postanalysis.CommandPaExportPlots$metadataDf$2.invoke(SourceFile:93)
at kotlin.SynchronizedLazyImpl.getValue(LazyJVM.kt:74)
at com.milaboratory.mixcr.cli.postanalysis.CommandPaExportPlots.getMetadataDf(SourceFile:93)
at com.milaboratory.mixcr.cli.postanalysis.CommandPaExportPlots.validate(SourceFile:103)
at com.milaboratory.mixcr.cli.postanalysis.CommandPaExportPlotsBasicStatistics.validate(SourceFile:172)
at com.milaboratory.mixcr.cli.MiXCRCommand.run(SourceFile:35)
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-27(SourceFile:514)
at picocli.CommandLine.execute(CommandLine.java:2078)
at com.milaboratory.mixcr.cli.Main.main(SourceFile:101)
Caused by: java.lang.RuntimeException: Failed to initialize MemoryUtil.
at org.apache.arrow.memory.util.MemoryUtil.(MemoryUtil.java:136)
... 46 more
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field long java.nio.Buffer.address accessible: module java.base does not "opens java.nio" to unnamed module @6a225c39
at java.base/java.lang.reflect.AccessibleObject.throwInaccessibleObjectException(AccessibleObject.java:391)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:367)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:315)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:183)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:177)
at org.apache.arrow.memory.util.MemoryUtil.(MemoryUtil.java:84)
... 46 more
java --version
openjdk 21.0.2-internal 2024-01-16
OpenJDK Runtime Environment (build 21.0.2-internal-adhoc.conda.src)
OpenJDK 64-Bit Server VM (build 21.0.2-internal-adhoc.conda.src, mixed mode, sharing)
postanalysis overlap to generate json file:
bash mixcr postanalysis overlap --default-downsampling none --default-weight-function read --only-productive --drop-outliers --metadata metadata.csv --group event *.clna postanalysis/PostgEvent.json
I have the latest java version (using Ubuntu 22.04) the postanalysis overlap command worked just great but i cannot generate any of the plots using export plots. Any suggestions? (to note, exportQc works just fine)
The text was updated successfully, but these errors were encountered: