gravatar for kathryn.michel

2 hours ago by

Hi PHG team,

I keep getting an error during findPath- I'm using the "new" docker commands and config file parameters.

After all of the sequences are mapped, I get this error:

[DefaultDispatcher-worker-5] DEBUG net.maizegenetics.pangenome.db_loading.DBLoadingUtils - encodePathARrayFromSet: Extracting the haplotypeIds
[DefaultDispatcher-worker-5] DEBUG net.maizegenetics.pangenome.db_loading.DBLoadingUtils - encodePathArrayFromSet: created the compressed path data
[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - DBLoadingUtils:encodePathArrayFromSet: error creating compressed data, null
java.lang.IllegalStateException: DBLoadingUtils:encodePathArrayFromSet: error creating compressed data, null
at net.maizegenetics.pangenome.db_loading.DBLoadingUtils.encodePathArrayFromSet(DBLoadingUtils.java:630)
at net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin$processDBUploading$2.invokeSuspend(BestHaplotypePathPlugin.kt:553)
at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33)
at kotlinx.coroutines.DispatchedTask.run(Dispatched.kt:241)
at kotlinx.coroutines.scheduling.CoroutineScheduler.runSafely(CoroutineScheduler.kt:594)
at kotlinx.coroutines.scheduling.CoroutineScheduler.access$runSafely(CoroutineScheduler.kt:60)
at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.run(CoroutineScheduler.kt:740)
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
BestHaplotypePathPlugin Description...

And then later it says there is no methodID for my pathMethod. Thoughts?
Thanks,
Kathryn



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