ImputePipelinePlugin diploidPath error (without error message), possible bug?

Question

[dovi]

Hi everyone, I was testing the new diploid path finding from PHG, unfortunatelly I get the same error over and over. Please find below the last lines of the log together with the error:

[pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all geneotypes in genotype table=38
[pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - refRangeRefRangeIDMap is null, creating new one with size : 39087
[pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - loadAnchorHash: at end, size of refRangeRefRangeIDMap: 39087, number of rs.next processed: 39087
[pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all methods in method table=6
[pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all groups in gamete_groups table=1035
[pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all gametes in gametes table=25
[pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading readMappingHash, size of all read_mappings in read_mapping table=13
[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - null
java.util.NoSuchElementException
    at java.base/java.util.HashMap$HashIterator.nextNode(HashMap.java:1495)
    at java.base/java.util.HashMap$KeyIterator.next(HashMap.java:1516)
    at com.google.common.collect.AbstractMapBasedMultimap$WrappedCollection$WrappedIterator.next(AbstractMapBasedMultimap.java:496)
    at net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath.filteredGraph(FindBestDiploidPath.kt:97)
    at net.maizegenetics.pangenome.hapCalling.DiploidCountsToPath.getDiploidPath(FindBestDiploidPath.kt:50)
    at net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.processKeyfile(DiploidPathPlugin.kt:180)
    at net.maizegenetics.pangenome.hapCalling.DiploidPathPlugin.processData(DiploidPathPlugin.kt:118)
    at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:118)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2005)
    at net.maizegenetics.plugindef.AbstractPlugin.fireDataSetReturned(AbstractPlugin.java:1906)
    at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:122)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2005)
    at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:834)
[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -

I get the error running the ImputePipelinePlugin diploidPath mode (diploidPathTVCF or diploidPath), but whenever I run the non-diploid path (pathToVCF or path) the pipeline runs through without errors. I use the latest docker to skip possible errors due to external software or environment. Unfortunately since I do not get an error message of what is wrong I do not know whether it is a problem from my configuration or just a bug, however since the haploid path seems to work, I think it could be a bug?

The key file _pathKeyFile.txt is the following:

SampleName  ReadMappingIds  LikelyParents
SRR10207657 1   
SRR10207879 2   
SRR10207951 3   
SRR10207952 4   
SRR10207954 5   
SRR10207955 6   
SRR10207956 7   
SRR10207957 8   
SRR10207958 9   
SRR10207959 10  
SRR10207960 11  
SRR10207961 12  
SRR10207962 13

Thanks in advance!

Answer 1

[pjb39]

Hi, The error you have run into is a known bug which has been fixed in a development branch of PHG (PHG-469). The fix will be incorporated into the next PHG release, though I do not have an estimated date for that at this time.

[pjb39]

The new build of the PHG docker contains a fix for this bug.

[dovi]

Thank you for releasing so fast the new version with the fix. I however encountered a new problem in a previous step with this new version, which I posted here: PHG v0.023 (latest) LoadHaplotypesFromGVCFPlugin fails, but v0.022 with same setup not