REQUIRED for all errors and issues:
a) GATK4.5.0 and 4.6.0


b) Exact command used:
aclab@aclab:~/tmp2$ gatk VariantRecalibrator \
    -R /project/databases/common/hg19/ucsc/hg19.fa \
    -V cohort.vcf \
    --resource:hapmap,known=false,training=true,truth=true,prior=15.0 /project/databases/common/hg19/GATK/hapmap_3.3.hg19.sites.vcf \
    --resource:omni,known=false,training=true,truth=true,prior=12.0 /project/databases/common/hg19/GATK/1000G_omni2.5.hg19.sites.vcf \
    --resource:1000G,known=false,training=true,truth=false,prior=10.0 /project/databases/common/hg19/GATK/1000G_phase1.snps.high_confidence.hg19.sites.vcf \
    --resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /project/databases/common/hg19/GATK/dbsnp_138.hg19.vcf \
    -an DP -an QD -an FS -an SOR -an MQRankSum -an ReadPosRankSum \
    -mode SNP \
    -O recalibrate_SNP.recal \
    --tranches-file recalibrate_SNP.tranches \
    --rscript-file recalibrate_SNP_plots.R 


c) Entire program log:

aclab@aclab:~/tmp2$ gatk VariantRecalibrator \
    -R /project/databases/common/hg19/ucsc/hg19.fa \
    -V cohort.vcf \
    --resource:hapmap,known=false,training=true,truth=true,prior=15.0 /project/databases/common/hg19/GATK/hapmap_3.3.hg19.sites.vcf \
    --resource:omni,known=false,training=true,truth=true,prior=12.0 /project/databases/common/hg19/GATK/1000G_omni2.5.hg19.sites.vcf \
    --resource:1000G,known=false,training=true,truth=false,prior=10.0 /project/databases/common/hg19/GATK/1000G_phase1.snps.high_confidence.hg19.sites.vcf \
    --resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /project/databases/common/hg19/GATK/dbsnp_138.hg19.vcf \
    -an DP -an QD -an FS -an SOR -an MQRankSum -an ReadPosRankSum \
    -mode SNP \
    -O recalibrate_SNP.recal \
    --tranches-file recalibrate_SNP.tranches \
    --rscript-file recalibrate_SNP_plots.R
Using GATK jar /home/aclab/.local/bin/gatk-package-4.6.0.0-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 /home/aclab/.local/bin/gatk-package-4.6.0.0-local.jar VariantRecalibrator -R /project/databases/common/hg19/ucsc/hg19.fa -V cohort.vcf --resource:hapmap,known=false,training=true,truth=true,prior=15.0 /project/databases/common/hg19/GATK/hapmap_3.3.hg19.sites.vcf --resource:omni,known=false,training=true,truth=true,prior=12.0 /project/databases/common/hg19/GATK/1000G_omni2.5.hg19.sites.vcf --resource:1000G,known=false,training=true,truth=false,prior=10.0 /project/databases/common/hg19/GATK/1000G_phase1.snps.high_confidence.hg19.sites.vcf --resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /project/databases/common/hg19/GATK/dbsnp_138.hg19.vcf -an DP -an QD -an FS -an SOR -an MQRankSum -an ReadPosRankSum -mode SNP -O recalibrate_SNP.recal --tranches-file recalibrate_SNP.tranches --rscript-file recalibrate_SNP_plots.R
09:45:25.395 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/aclab/.local/bin/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
09:45:25.593 INFO  VariantRecalibrator - ------------------------------------------------------------
09:45:25.596 INFO  VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.0.0
09:45:25.596 INFO  VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
09:45:25.596 INFO  VariantRecalibrator - Executing as aclab@aclab on Linux v6.8.0-38-generic amd64
09:45:25.596 INFO  VariantRecalibrator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v21.0.1+12-LTS-29
09:45:25.596 INFO  VariantRecalibrator - Start Date/Time: September 12, 2024, 9:45:25 AM CST
09:45:25.597 INFO  VariantRecalibrator - ------------------------------------------------------------
09:45:25.597 INFO  VariantRecalibrator - ------------------------------------------------------------
09:45:25.598 INFO  VariantRecalibrator - HTSJDK Version: 4.1.1
09:45:25.598 INFO  VariantRecalibrator - Picard Version: 3.2.0
09:45:25.598 INFO  VariantRecalibrator - Built for Spark Version: 3.5.0
09:45:25.598 INFO  VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
09:45:25.598 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:45:25.599 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:45:25.599 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:45:25.599 INFO  VariantRecalibrator - Deflater: IntelDeflater
09:45:25.599 INFO  VariantRecalibrator - Inflater: IntelInflater
09:45:25.599 INFO  VariantRecalibrator - GCS max retries/reopens: 20
09:45:25.599 INFO  VariantRecalibrator - Requester pays: disabled
09:45:25.600 INFO  VariantRecalibrator - Initializing engine
09:45:25.747 INFO  FeatureManager - Using codec VCFCodec to read file file:///project/databases/common/hg19/GATK/hapmap_3.3.hg19.sites.vcf
09:45:25.808 INFO  FeatureManager - Using codec VCFCodec to read file file:///project/databases/common/hg19/GATK/1000G_omni2.5.hg19.sites.vcf
09:45:25.830 INFO  FeatureManager - Using codec VCFCodec to read file file:///project/databases/common/hg19/GATK/1000G_phase1.snps.high_confidence.hg19.sites.vcf
09:45:25.902 INFO  FeatureManager - Using codec VCFCodec to read file file:///project/databases/common/hg19/GATK/dbsnp_138.hg19.vcf
09:45:26.034 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/aclab/tmp2/cohort.vcf
09:45:26.075 INFO  VariantRecalibrator - Done initializing engine
09:45:26.104 INFO  TrainingSet - Found hapmap track:    Known = false   Training = true         Truth = true    Prior = Q15.0
09:45:26.104 INFO  TrainingSet - Found omni track:      Known = false   Training = true         Truth = true    Prior = Q12.0
09:45:26.105 INFO  TrainingSet - Found 1000G track:     Known = false   Training = true         Truth = false   Prior = Q10.0
09:45:26.105 INFO  TrainingSet - Found dbsnp track:     Known = true    Training = false        Truth = false   Prior = Q2.0
09:45:26.109 WARN  GATKVariantContextUtils - Can't determine output variant file format from output file extension "recal". Defaulting to VCF.
09:45:26.139 INFO  ProgressMeter - Starting traversal
09:45:26.139 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
09:45:36.622 INFO  ProgressMeter -       chr2:102927726              0.2                  4000          22902.9
09:45:47.935 INFO  ProgressMeter -        chr5:63257124              0.4                  9000          24776.3
09:45:59.798 INFO  ProgressMeter -        chr8:10469817              0.6                 14000          24956.9
09:46:10.213 INFO  ProgressMeter -        chr11:5248243              0.7                 18000          24504.8
09:46:21.664 INFO  ProgressMeter -       chr15:56194877              0.9                 23000          24853.7
09:46:32.815 INFO  ProgressMeter -       chr19:50098018              1.1                 29000          26096.3
09:46:39.437 INFO  ProgressMeter -        chrX:43603391              1.2                 37944          31060.1
09:46:39.437 INFO  ProgressMeter - Traversal complete. Processed 37944 total variants in 1.2 minutes.
09:46:39.447 INFO  VariantDataManager - DP:      mean = 7093.61  standard deviation = 4704.66
09:46:39.457 INFO  VariantDataManager - QD:      mean = 18.43    standard deviation = 7.21
09:46:39.462 INFO  VariantDataManager - FS:      mean = 0.75     standard deviation = 2.27
09:46:39.467 INFO  VariantDataManager - SOR:     mean = 0.75     standard deviation = 0.31
09:46:39.469 INFO  VariantDataManager - MQRankSum:       mean = -0.02    standard deviation = 0.47
09:46:39.472 INFO  VariantDataManager - ReadPosRankSum:          mean = 0.16     standard deviation = 0.66
09:46:39.531 INFO  VariantDataManager - Annotation order is: [DP, QD, MQRankSum, SOR, FS, ReadPosRankSum]
09:46:39.537 INFO  VariantDataManager - Training with 22493 variants after standard deviation thresholding.
09:46:39.541 INFO  GaussianMixtureModel - Initializing model with 100 k-means iterations...
09:46:40.109 INFO  VariantRecalibratorEngine - Finished iteration 0.
09:46:40.535 INFO  VariantRecalibratorEngine - Finished iteration 5.    Current change in mixture coefficients = 0.37389
09:46:40.852 INFO  VariantRecalibratorEngine - Finished iteration 10.   Current change in mixture coefficients = 0.38005
09:46:41.166 INFO  VariantRecalibratorEngine - Finished iteration 15.   Current change in mixture coefficients = 0.10071
09:46:41.488 INFO  VariantRecalibratorEngine - Finished iteration 20.   Current change in mixture coefficients = 0.12651
09:46:41.772 INFO  VariantRecalibratorEngine - Finished iteration 25.   Current change in mixture coefficients = 0.13470
09:46:42.040 INFO  VariantRecalibratorEngine - Finished iteration 30.   Current change in mixture coefficients = 0.06206
09:46:42.311 INFO  VariantRecalibratorEngine - Finished iteration 35.   Current change in mixture coefficients = 0.08005
09:46:42.597 INFO  VariantRecalibratorEngine - Finished iteration 40.   Current change in mixture coefficients = 0.15578
09:46:42.901 INFO  VariantRecalibratorEngine - Finished iteration 45.   Current change in mixture coefficients = 0.03912
09:46:43.179 INFO  VariantRecalibratorEngine - Finished iteration 50.   Current change in mixture coefficients = 0.04078
09:46:43.441 INFO  VariantRecalibratorEngine - Finished iteration 55.   Current change in mixture coefficients = 0.02248
09:46:43.705 INFO  VariantRecalibratorEngine - Finished iteration 60.   Current change in mixture coefficients = 0.01155
09:46:43.969 INFO  VariantRecalibratorEngine - Finished iteration 65.   Current change in mixture coefficients = 0.00521
09:46:44.232 INFO  VariantRecalibratorEngine - Finished iteration 70.   Current change in mixture coefficients = 0.00229
09:46:44.286 INFO  VariantRecalibratorEngine - Convergence after 71 iterations!
09:46:44.360 INFO  VariantRecalibratorEngine - Evaluating full set of 35523 variants...
09:46:44.564 INFO  VariantDataManager - Selected worst 1389 scoring variants --> variants with LOD <= -5.0000.
09:46:44.564 INFO  GaussianMixtureModel - Initializing model with 100 k-means iterations...
09:46:44.583 INFO  VariantRecalibratorEngine - Finished iteration 0.
09:46:44.588 INFO  VariantRecalibratorEngine - Finished iteration 5.    Current change in mixture coefficients = 0.01642
09:46:44.593 INFO  VariantRecalibratorEngine - Finished iteration 10.   Current change in mixture coefficients = 0.01483
09:46:44.598 INFO  VariantRecalibratorEngine - Finished iteration 15.   Current change in mixture coefficients = 0.00796
09:46:44.603 INFO  VariantRecalibratorEngine - Finished iteration 20.   Current change in mixture coefficients = 0.00721
09:46:44.608 INFO  VariantRecalibratorEngine - Finished iteration 25.   Current change in mixture coefficients = 0.00486
09:46:44.613 INFO  VariantRecalibratorEngine - Finished iteration 30.   Current change in mixture coefficients = 0.00288
09:46:44.617 INFO  VariantRecalibratorEngine - Convergence after 34 iterations!
09:46:44.622 INFO  VariantRecalibratorEngine - Evaluating full set of 35523 variants...
09:46:44.813 INFO  TrancheManager - Finding 4 tranches for 35523 variants
09:46:44.835 INFO  TrancheManager -   TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
09:46:44.844 INFO  TrancheManager -   Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000 
09:46:44.844 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=100.00 minVQSLod=-39948.0342 known=(28711 @ 2.9919) novel=(6812 @ 2.7528) truthSites(16407 accessible, 16407 called), name=anonymous]
09:46:44.844 INFO  TrancheManager -   TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
09:46:44.850 INFO  TrancheManager -   Found tranche for 99.900: 0.001 threshold starting with variant 1094; running score is 0.001 
09:46:44.850 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.90 minVQSLod=-8.8767 known=(28205 @ 3.0057) novel=(6224 @ 2.6504) truthSites(16407 accessible, 16390 called), name=anonymous]
09:46:44.850 INFO  TrancheManager -   TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
09:46:44.853 INFO  TrancheManager -   Found tranche for 99.000: 0.010 threshold starting with variant 3188; running score is 0.010 
09:46:44.853 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.00 minVQSLod=0.1884 known=(26594 @ 3.0539) novel=(5741 @ 2.6759) truthSites(16407 accessible, 16242 called), name=anonymous]
09:46:44.854 INFO  TrancheManager -   TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
09:46:44.856 INFO  TrancheManager -   Found tranche for 90.000: 0.100 threshold starting with variant 14584; running score is 0.100 
09:46:44.857 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=90.00 minVQSLod=4.7961 known=(19802 @ 3.1178) novel=(1137 @ 2.6548) truthSites(16407 accessible, 14766 called), name=anonymous]
09:46:44.858 INFO  VariantRecalibrator - Writing out recalibration table...
09:46:45.537 INFO  VariantRecalibrator - Writing out visualization Rscript file...
09:46:45.548 INFO  VariantRecalibrator - Building DP x QD plot...
09:46:45.551 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:45.891 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:46.071 INFO  VariantRecalibrator - Building DP x MQRankSum plot...
09:46:46.074 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:46.384 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:46.535 INFO  VariantRecalibrator - Building DP x SOR plot...
09:46:46.536 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:46.844 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:46.976 INFO  VariantRecalibrator - Building DP x FS plot...
09:46:46.977 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:47.276 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:47.408 INFO  VariantRecalibrator - Building DP x ReadPosRankSum plot...
09:46:47.409 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:46:47.728 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:46:47.854 INFO  VariantRecalibrator - Building QD x MQRankSum plot...
09:46:47.855 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:48.156 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:48.289 INFO  VariantRecalibrator - Building QD x SOR plot...
09:46:48.290 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:48.612 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:48.743 INFO  VariantRecalibrator - Building QD x FS plot...
09:46:48.744 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:49.089 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:49.237 INFO  VariantRecalibrator - Building QD x ReadPosRankSum plot...
09:46:49.238 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:49.594 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:49.742 INFO  VariantRecalibrator - Building MQRankSum x SOR plot...
09:46:49.742 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:50.096 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:50.237 INFO  VariantRecalibrator - Building MQRankSum x FS plot...
09:46:50.238 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:50.542 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:50.669 INFO  VariantRecalibrator - Building MQRankSum x ReadPosRankSum plot...
09:46:50.670 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:50.965 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:51.089 INFO  VariantRecalibrator - Building SOR x FS plot...
09:46:51.090 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:51.394 INFO  VariantRecalibratorEngine - Evaluating full set of 3721 variants...
09:46:51.522 INFO  VariantRecalibrator - Building SOR x ReadPosRankSum plot...
09:46:51.522 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:51.831 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:51.956 INFO  VariantRecalibrator - Building FS x ReadPosRankSum plot...
09:46:51.957 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:52.277 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:46:52.514 INFO  VariantRecalibrator - Executing: Rscript /home/aclab/tmp2/recalibrate_SNP_plots.R
09:46:54.114 INFO  VariantRecalibrator - Shutting down engine
[September 12, 2024, 9:46:54 AM CST] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 1.48 minutes.
Runtime.totalMemory()=3623878656
org.broadinstitute.hellbender.utils.R.RScriptExecutorException: 
Rscript exited with 1
Command Line: Rscript -e tempLibDir = '/tmp/Rlib.16534667698759447733';source('/home/aclab/tmp2/recalibrate_SNP_plots.R');
Stdout: 
Stderr: Error:
! The `space` argument of `pal_gradient_n()` only supports be "Lab" as
  of scales 0.3.0.
Backtrace:
     ▆
  1. ├─base::source("/home/aclab/tmp2/recalibrate_SNP_plots.R")
  2. │ ├─base::withVisible(eval(ei, envir))
  3. │ └─base::eval(ei, envir)
  4. │   └─base::eval(ei, envir)
  5. └─ggplot2::scale_fill_gradient(high = "green", low = "red", space = "rgb")
  6.   ├─ggplot2::continuous_scale(...)
  7.   │ └─ggplot2::ggproto(...)
  8.   │   └─rlang::list2(...)
  9.   └─scales::pal_seq_gradient(low, high, space)
 10.     └─scales::pal_gradient_n(c(low, high), space = space)
 11.       └─lifecycle::deprecate_stop("0.3.0", "pal_gradient_n(space = 'only supports be \"Lab\"')")
 12.         └─lifecycle:::deprecate_stop0(msg)
 13.           └─rlang::cnd_signal(...)
Execution halted

        at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:79)
        at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:18)
        at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:112)
        at org.broadinstitute.hellbender.utils.R.RScriptExecutor.exec(RScriptExecutor.java:125)
        at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.createVisualizationScript(VariantRecalibrator.java:1146)
        at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.onTraversalSuccess(VariantRecalibrator.java:706)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1102)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
        at org.broadinstitute.hellbender.Main.main(Main.java:306)

My R version is 4.3.2