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Funcotator log4j Error

I am running Funcotator on a full VCF resulting in an empty VCF. I think it is due to an error in the log4j system "No appenders could be found for logger". I have seen this issue reported by other users for other tools but I haven't found a solution. Any idea what is going wrong?

Input:

gatk Funcotator \
-V input.vcf \
-O output.vcf \
-R ucsc.hg19.fasta \
--output-file-format VCF \
--ref-version hg19 \
--data-sources-path ~/Documents/Funcotator_DataSource

Summary:

12:30:56.906 INFO  Funcotator - ------------------------------------------------------------
12:30:56.906 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.0.4.0-0.0.2
12:30:56.906 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
12:30:56.906 INFO  Funcotator - Executing as [email protected] on Linux v4.15.0-20-generic amd64
12:30:56.906 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_121-b15
12:30:56.906 INFO  Funcotator - Start Date/Time: May 29, 2018 12:30:56 PM EDT
12:30:56.906 INFO  Funcotator - ------------------------------------------------------------
12:30:56.906 INFO  Funcotator - ------------------------------------------------------------
12:30:56.906 INFO  Funcotator - HTSJDK Version: 2.14.3
12:30:56.907 INFO  Funcotator - Picard Version: 2.18.2
12:30:56.907 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:30:56.907 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:30:56.907 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:30:56.907 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:30:56.907 INFO  Funcotator - Deflater: IntelDeflater
12:30:56.907 INFO  Funcotator - Inflater: IntelInflater
12:30:56.907 INFO  Funcotator - GCS max retries/reopens: 20
12:30:56.907 INFO  Funcotator - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
12:30:56.907 WARN  Funcotator - 

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: Funcotator is a BETA tool and is not yet ready for use in production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


12:30:56.907 INFO  Funcotator - Initializing engine
12:30:57.099 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/das106/Desktop/Data/SeqData/CCM_01_04/Variants/CCM_01_04_Mutect2_dbsnp.vcf
12:30:57.113 INFO  Funcotator - Done initializing engine
log4j:WARN No appenders could be found for logger (org.broadinstitute.hellbender.tools.funcotator.dataSources.DataSourceUtils).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
12:30:57.122 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/das106/Documents/Funcotator_DataSource/gencode/hg19/gencode.v19.chr_patch_hapl_scaff.annotation.REORDERED.gtf
12:30:57.125 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/das106/Documents/Funcotator_DataSource/clinvar/hg19/clinvar_hgmd.tsv
12:30:57.170 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/das106/Documents/Funcotator_DataSource/oreganno/hg19/oreganno.tsv
12:30:57.182 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/das106/Documents/Funcotator_DataSource/dbsnp/hg19/hg19_All_20170710.vcf.gz
WARNING 2018-05-29 12:30:59 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
WARNING 2018-05-29 12:30:59 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
12:30:59.409 INFO  Funcotator - Shutting down engine
[May 29, 2018 12:30:59 PM EDT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=2258632704
java.lang.IllegalArgumentException: URI is not hierarchical
    at java.io.File.<init>(File.java:418)
    at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.initializeB37SequenceDict(FuncotatorUtils.java:1926)
    at org.broadinstitute.hellbender.tools.funcotator.FuncotatorUtils.isSequenceDictionaryUsingB37Reference(FuncotatorUtils.java:1693)
    at org.broadinstitute.hellbender.tools.funcotator.Funcotator.onTraversalStart(Funcotator.java:374)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:890)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:134)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:179)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:198)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)

Answers

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