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Multi threading in GATK 4 is done with spark now?
In GATK4 noticed I can't use -nt or -nct with tools that support it in GATK 3.x, and I understand that you removed it due to the complexities that it introduced to the code from this discussion: https://github.com/broadinstitute/gatk/issues/2345
So the current solution is to use either a local temporary spark server and "--sparkMaster 'local[N]'", or a permanent local or remote spark server. I tried running HaplotypeCallerSpark locally and it said needed a .2bit reference file?
A USER ERROR has occurred: Bad input: Running this tool with BROADCAST strategy requires a 2bit reference. To create a 2bit reference from an existing fasta file, download faToTwoBit from the link on https://genome.ucsc.edu/goldenPath/help/twoBit.html, then run faToTwoBit in.fasta out.2bit
So I created one with FaToTwoBit but it still didn't work.
Here's the command I used:
gatk-launch HaplotypeCallerSpark -O output.vcf -R human_g1k_v37_decoy.2bit --input input.bam
And the error message:
Exception in thread "main" java.lang.AssertionError: assertion failed: Version must be zero at scala.Predef$.assert(Predef.scala:170) at org.bdgenomics.adam.util.TwoBitFile.readHeader(TwoBitFile.scala:85) at org.bdgenomics.adam.util.TwoBitFile.<init>(TwoBitFile.scala:62) at org.broadinstitute.hellbender.engine.spark.datasources.ReferenceTwoBitSource.<init>(ReferenceTwoBitSource.java:43) at org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource.<init>(ReferenceMultiSource.java:41) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeReference(GATKSparkTool.java:393) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.initializeToolInputs(GATKSparkTool.java:360) at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:351) at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:38) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:116) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:173) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:192) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:131) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:152) at org.broadinstitute.hellbender.Main.main(Main.java:233) 17/08/02 15:27:14 INFO ShutdownHookManager: Shutdown hook called 17/08/02 15:27:14 INFO ShutdownHookManager: Deleting directory /tmp/travis/spark-f911bb61-2fb0-48d1-8c6a-49ff149f14e3
Is it a bug? And (why) do I need a .2bit fasta reference file? Can I shut off the broadcast strategy and skip the need for a .2bit reference file?