Hello,

I am working on the pathfinding step of the PHG pipeline and am currently trying to resolve a related issue regarding the correct parameters, described here . However when I try to rerun only the pathfinding step I run into the same error repeatedly. I have had the same for a few of my samples before, but now it has occurred the last 3-4 times I tried.

My config is the same as in the previous post (only with changed pathMethod, minReads, probCorrect, outVcfFile, debugDir) and I am still using the same sqlite database and PHG v1.4.

The error I get is the following:

[DefaultDispatcher-worker-1] INFO net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM - Getting path for chromosome UN
[DefaultDispatcher-worker-1] INFO net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM - Extracted graph tree for chromosome UN
[DefaultDispatcher-worker-1] INFO net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM - emission probability set up in 0 ms.
[DefaultDispatcher-worker-1] INFO net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM - net.maizegenetics.pangenome.api.HaplotypeEmissionProbability@c87b75a
[DefaultDispatcher-worker-1] INFO net.maizegenetics.pangenome.hapCalling.ConvertReadsToPathUsingHMM - transition probability set up in 0 ms.
[DefaultDispatcher-worker-1] DEBUG net.maizegenetics.pangenome.db_loading.DBLoadingUtils - encodePathARrayFromSet: Extracting the haplotypeIds
[DefaultDispatcher-worker-1] 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:646)
        at net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin$processDBUploading$2.invokeSuspend(BestHaplotypePathPlugin.kt:688)
        at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33)
        at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:106)
        at kotlinx.coroutines.scheduling.CoroutineScheduler.runSafely(CoroutineScheduler.kt:571)
        at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.executeTask(CoroutineScheduler.kt:750)
        at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.runWorker(CoroutineScheduler.kt:678)
        at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.run(CoroutineScheduler.kt:665)
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -

After the pathfinding for the last chromosome is done and it tries do encode and compress the path data to store in the database, it runs into an error. I can see in the PHG code where it occurs and my guess would be it is some issue happening with ByteBuffer.allocate(), but since the exception is null and I am not experienced in java, I have trouble figuring out what could be the underlying cause for it. Has anyone encountered this before or has any ideas?

Help is much apprechiated! Thank you!