AssemblyMAFFromAnchorWavePlugin IndexOutOfBoundsException

Question

[ryan]

Hello, I'm attempting to create a test database with a smaller genome just to confirm I can get the pipeline running. I'm using PHG 1.8 with singularity.

I was able to successfully run MakeDefaultDirectoryPlugin, CreateValidIntervalsFilePlugin, and MakeInitialPHGDBPipelinePlugin. Running AssemblyMAFFromAnchorWavePlugin yields an "IndexOutOfBoundsException" error, but the cause is unclear. Independent from PHG plugins I'm able to successfully run the anchorwave gff2seq and minimap2 steps on the reference and query genome I'm practicing with. I'm using arbitrary intervals of 100kb, if that's important.

I can provide further details of the log message if necessary, here's the error:

AssemblyMAFFromAnchorWavePlugin Parameters
outputDir: /phg/outputDir
keyFile: /phg/load_asm_genome_key_file.txt
gffFile: /phg/inputDir/reference/genomic.gff
refFasta: /phg/inputDir/reference/ref.fna
threadsPerRun: 4
numRuns: 2
minimap2Location: minimap2
anchorwaveLocation: anchorwave
refMaxAlignCov: 1
queryMaxAlignCov: 1

[pool-1-thread-1] INFO net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin - processData - call createCDSfromRefData ...
[pool-1-thread-1] INFO net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin - begin Command:anchorwave gff2seq -r /phg/inputDir/reference/ref.fna -i /phg/inputDir/reference/genomic.gff -o /phg/outputDir/refCDS.fa
Value of minimap2Location: minimap2
[pool-1-thread-1] INFO net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin -  Ref minimap Command:minimap2 -x splice -t 4 -k 12 -a -p 0.4 -N20 /phg/inputDir/reference/ref.fna /phg/outputDir/refCDS.fa
[pool-1-thread-1] INFO net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin - Adding entries to the inputChannel:
[pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - Index: 5, Size: 5
java.lang.IndexOutOfBoundsException: Index: 5, Size: 5
    at java.util.ArrayList.rangeCheck(ArrayList.java:657)
    at java.util.ArrayList.get(ArrayList.java:433)
    at net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin$runAnchorWaveMultiThread$4$1.invokeSuspend(AssemblyMAFFromAnchorWavePlugin.kt:224)
    at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33)
    at kotlinx.coroutines.DispatchedTask.run(DispatchedTask.kt:106)
    at kotlinx.coroutines.EventLoopImplBase.processNextEvent(EventLoop.common.kt:279)
    at kotlinx.coroutines.BlockingCoroutine.joinBlocking(Builders.kt:85)
    at kotlinx.coroutines.BuildersKt__BuildersKt.runBlocking(Builders.kt:59)
    at kotlinx.coroutines.BuildersKt.runBlocking(Unknown Source)
    at kotlinx.coroutines.BuildersKt__BuildersKt.runBlocking$default(Builders.kt:38)
    at kotlinx.coroutines.BuildersKt.runBlocking$default(Unknown Source)
    at net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.runAnchorWaveMultiThread(AssemblyMAFFromAnchorWavePlugin.kt:214)
    at net.maizegenetics.pangenome.processAssemblyGenomes.AssemblyMAFFromAnchorWavePlugin.processData(AssemblyMAFFromAnchorWavePlugin.kt:191)
    at net.maizegenetics.plugindef.AbstractPlugin.performFunction(AbstractPlugin.java:111)
    at net.maizegenetics.plugindef.AbstractPlugin.dataSetReturned(AbstractPlugin.java:2017)
    at net.maizegenetics.plugindef.ThreadedPluginListener.run(ThreadedPluginListener.java:29)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)

Thanks, I'm excited to get PHG up and running!

Answer 1

[lcj34]

It looks like something is amiss in your keyfile. Check that all columns have data, and that you have no blank lines in the file, and that the data in all lines is tab-delimited, not space delimited.