ImputePipelinePlugin diploidPath error (without error message), possible bug?
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0
Entering edit mode
8 months ago
dovi ▴ 60

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
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 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)


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


phg tassel • 358 views
3
Entering edit mode
8 months ago
pjb39 ▴ 60

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.

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Entering edit mode

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

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Entering edit mode

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