PHG findPath Error after mapping sequences

Question

[kathrynm]

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

[pjb39]

There is not enough information to diagnose the problem. The error indicates that something unexpected happened but not what or where, just where in the code that the problem was caught. Search for "error" then for "exception" to see if any non-fatal errors show up earlier in the log. If that does not help, I will need to have you e-mail me the entire log file (zipped or gzipped). You can send it to pjb39 at Cornell dot edu.

Answer 1

[pjb39]

Thanks for sending the entire log file. The actual problem was that the graph used for path finding was empty: [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory - After filtering PathFinderForSingleTaxonNodesFactory.myGraph has 0 ranges and 0 taxa I think this happened because the minTaxa parameter was set to 20 but probably should be set to 1 or 2. So change the config file parameter to "minTaxa=1" (or 2). I don't know how many taxa in the graph but judging from the number of nodes it is not very many. Also, you should also change the algorithmType to "algorithmType=classic". There is a bug in the efficient algorithm that will probably cause that to fail.