16:55:17.644 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/workdir/.snakemake/conda/e96e36a8/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
16:55:17.918 INFO  BaseRecalibrator - ------------------------------------------------------------
16:55:17.918 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.4.1
16:55:17.919 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
16:55:17.919 INFO  BaseRecalibrator - Executing as root@0cb88a7b9347 on Linux v4.19.87+ amd64
16:55:17.919 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_192-b01
16:55:17.919 INFO  BaseRecalibrator - Start Date/Time: February 19, 2020 4:55:17 PM UTC
16:55:17.919 INFO  BaseRecalibrator - ------------------------------------------------------------
16:55:17.920 INFO  BaseRecalibrator - ------------------------------------------------------------
16:55:17.920 INFO  BaseRecalibrator - HTSJDK Version: 2.21.0
16:55:17.920 INFO  BaseRecalibrator - Picard Version: 2.21.2
16:55:17.920 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:55:17.920 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:55:17.921 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:55:17.921 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:55:17.921 INFO  BaseRecalibrator - Deflater: IntelDeflater
16:55:17.921 INFO  BaseRecalibrator - Inflater: IntelInflater
16:55:17.921 INFO  BaseRecalibrator - GCS max retries/reopens: 20
16:55:17.921 INFO  BaseRecalibrator - Requester pays: disabled
16:55:17.921 INFO  BaseRecalibrator - Initializing engine
16:55:17.929 INFO  BaseRecalibrator - Shutting down engine
[February 19, 2020 4:55:17 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=516423680
***********************************************************************

A USER ERROR has occurred: Fasta index file file:///workdir/snakemake-testing/kim-wxs-varlociraptor/refs/genome.fasta.fai for reference file:///workdir/snakemake-testing/kim-wxs-varlociraptor/refs/genome.fasta does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /workdir/.snakemake/conda/e96e36a8/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /workdir/.snakemake/conda/e96e36a8/share/gatk4-4.1.4.1-1/gatk-package-4.1.4.1-local.jar BaseRecalibrator -R snakemake-testing/kim-wxs-varlociraptor/refs/genome.fasta -I snakemake-testing/kim-wxs-varlociraptor/dedup/N23.sorted.bam -O /tmp/tmpacd8o2t4/recal_table.grp --known-sites snakemake-testing/kim-wxs-varlociraptor/refs/variation.noiupac.vcf.gz