ISSUE: Rscript produce by VariantCalibration has a  compatibility issue with the scales package version 0.3.0 and later. In these versions, the space argument of pal_gradient_n() only supports "Lab", not "rgb". This means your script needs to be updated to accommodate this change in the scales library requirements.

FIX :

In Rscript  all the parameter instances:

scale_fill_gradient(high = "green", low = "red", space = "rgb")
has to be change to

scale_fill_gradient(high = "green", low = "red", space = "Lab")

Then the script can be re run separately to obtain pdf file with graphs

REQUIRED for all errors and issues:
a) GATK version used: The Genome Analysis Toolkit (GATK) v4.6.0.0
b) Exact command used:

gatk --java-options "-Xmx4G" VariantRecalibrator \
    -R human_g1k_v37.fasta \
    -V allsamples_chr20_snps.vcf.gz \
    --trust-all-polymorphic \
    -tranche 100.0 \
    -tranche 99.95 \
    -tranche 99.9 \
    -tranche 99.8 \
    -tranche 99.6 \
    -tranche 99.5 \
    -tranche 99.4 \
    -tranche 99.3 \
    -tranche 99.0 \
    -tranche 98.0 \
    -tranche 97.0 \
    -tranche 90.0 \
    --resource:1000G,known=false,training=true,truth=true,prior=10.0 ALL.chr20_phase1_release_v3_snps.vcf.gz \
    -an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR \
    -mode SNP \
    --max-gaussians 6 \
    -O recalibrate_SNP.recal \
    --tranches-file recalibrate_SNP.tranches \
    --rscript-file recalibrate_SNP_plots.R

c) Entire program log: 

Using GATK jar /home/Bioinformatics/gatk/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 -Xmx4G -jar /home/Bioinformatics/gatk/gatk-package-4.6.0.0-local.jar VariantRecalibrator -R human_g1k_v37.fasta -V allsamples_chr20_snps.vcf.gz --trust-all-polymorphic -tranche 100.0 -tranche 99.95 -tranche 99.9 -tranche 99.8 -tranche 99.6 -tranche 99.5 -tranche 99.4 -tranche 99.3 -tranche 99.0 -tranche 98.0 -tranche 97.0 -tranche 90.0 --resource:1000G,known=false,training=true,truth=true,prior=10.0 ALL.chr20_phase1_release_v3_snps.vcf.gz -an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP --max-gaussians 6 -O recalibrate_SNP.recal --tranches-file recalibrate_SNP.tranches --rscript-file recalibrate_SNP_plots.R
09:38:33.345 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/Bioinformatics/gatk/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
09:38:33.613 INFO  VariantRecalibrator - ------------------------------------------------------------
09:38:33.616 INFO  VariantRecalibrator - The Genome Analysis Toolkit (GATK) v4.6.0.0
09:38:33.616 INFO  VariantRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
09:38:33.616 INFO  VariantRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v21.0.4+7-Ubuntu-1ubuntu224.04
09:38:33.616 INFO  VariantRecalibrator - Start Date/Time: September 27, 2024, 9:38:33 AM CST
09:38:33.616 INFO  VariantRecalibrator - ------------------------------------------------------------
09:38:33.617 INFO  VariantRecalibrator - ------------------------------------------------------------
09:38:33.617 INFO  VariantRecalibrator - HTSJDK Version: 4.1.1
09:38:33.618 INFO  VariantRecalibrator - Picard Version: 3.2.0
09:38:33.618 INFO  VariantRecalibrator - Built for Spark Version: 3.5.0
09:38:33.618 INFO  VariantRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
09:38:33.618 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:38:33.618 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:38:33.618 INFO  VariantRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:38:33.619 INFO  VariantRecalibrator - Deflater: IntelDeflater
09:38:33.619 INFO  VariantRecalibrator - Inflater: IntelInflater
09:38:33.619 INFO  VariantRecalibrator - GCS max retries/reopens: 20
09:38:33.619 INFO  VariantRecalibrator - Requester pays: disabled
09:38:33.620 INFO  VariantRecalibrator - Initializing engine
09:38:33.830 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/BQSR_bam/GVCF_files/ALL.chr20_phase1_release_v3_snps.vcf.gz
09:38:33.869 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/BQSR_bam/GVCF_files/allsamples_chr20_snps.vcf.gz
09:38:33.908 WARN  IndexUtils - Feature file "file:///home/Documents/GVCF_files/ALL.chr20_phase1_release_v3_snps.vcf.gz" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
09:38:33.933 INFO  VariantRecalibrator - Done initializing engine
09:38:33.936 INFO  TrainingSet - Found 1000G track:     Known = false     Training = true     Truth = true     Prior = Q10.0
09:38:33.945 WARN  GATKVariantContextUtils - Can't determine output variant file format from output file extension "recal". Defaulting to VCF.
09:38:34.001 INFO  ProgressMeter - Starting traversal
09:38:34.002 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
09:38:45.175 INFO  ProgressMeter -           20:2838118              0.2                  7000          37600.7
09:38:56.682 INFO  ProgressMeter -           20:5923204              0.4                 15000          39682.5
09:39:07.950 INFO  ProgressMeter -           20:8583414              0.6                 21000          37115.6
09:39:18.212 INFO  ProgressMeter -          20:11237743              0.7                 27000          36643.3
09:39:28.658 INFO  ProgressMeter -          20:13764654              0.9                 33000          36226.6
09:39:39.394 INFO  ProgressMeter -          20:16560330              1.1                 39000          35784.2
09:39:51.369 INFO  ProgressMeter -          20:19358934              1.3                 46000          35674.1
09:40:03.141 INFO  ProgressMeter -          20:22308161              1.5                 51000          34328.4
09:40:14.234 INFO  ProgressMeter -          20:24639363              1.7                 56000          33522.6
09:40:25.649 INFO  ProgressMeter -          20:31556638              1.9                 77000          41380.4
09:40:37.748 INFO  ProgressMeter -          20:35770999              2.1                 82000          39758.9
09:40:48.052 INFO  ProgressMeter -          20:38555808              2.2                 87000          38941.0
09:40:59.734 INFO  ProgressMeter -          20:41335773              2.4                 92000          37877.7
09:41:10.153 INFO  ProgressMeter -          20:44016863              2.6                 97000          37271.6
09:41:20.563 INFO  ProgressMeter -          20:46486269              2.8                102000          36743.5
09:41:32.970 INFO  ProgressMeter -          20:49984023              3.0                109000          36542.8
09:41:43.483 INFO  ProgressMeter -          20:52972517              3.2                116000          36731.9
09:41:53.522 INFO  ProgressMeter -          20:55488739              3.3                122000          36688.1
09:42:04.527 INFO  ProgressMeter -          20:58398890              3.5                128000          36480.2
09:42:15.328 INFO  ProgressMeter -          20:60996484              3.7                134000          36326.5
09:42:22.248 INFO  ProgressMeter -          20:62822352              3.8                138228          36336.6
09:42:22.248 INFO  ProgressMeter - Traversal complete. Processed 138228 total variants in 3.8 minutes.
09:42:22.272 INFO  VariantDataManager - QD:      mean = 23.05     standard deviation = 7.40
09:42:22.319 INFO  VariantDataManager - MQRankSum:      mean = 0.01     standard deviation = 0.36
09:42:22.328 INFO  VariantDataManager - ReadPosRankSum:      mean = 0.18     standard deviation = 0.85
09:42:22.338 INFO  VariantDataManager - FS:      mean = 1.57     standard deviation = 2.81
09:42:22.347 INFO  VariantDataManager - SOR:      mean = 1.04     standard deviation = 0.73
09:42:22.467 INFO  VariantDataManager - Annotation order is: [QD, MQRankSum, FS, SOR, ReadPosRankSum]
09:42:22.478 INFO  VariantDataManager - Training with 116863 variants after standard deviation thresholding.
09:42:22.482 INFO  GaussianMixtureModel - Initializing model with 100 k-means iterations...
09:42:25.275 INFO  VariantRecalibratorEngine - Finished iteration 0.
09:42:26.331 INFO  VariantRecalibratorEngine - Finished iteration 5.     Current change in mixture coefficients = 0.27780
09:42:27.230 INFO  VariantRecalibratorEngine - Finished iteration 10.     Current change in mixture coefficients = 0.10889
09:42:28.107 INFO  VariantRecalibratorEngine - Finished iteration 15.     Current change in mixture coefficients = 0.01078
09:42:28.658 INFO  VariantRecalibratorEngine - Convergence after 18 iterations!
09:42:28.814 INFO  VariantRecalibratorEngine - Evaluating full set of 138228 variants...
09:42:29.686 INFO  VariantDataManager - Selected worst 10152 scoring variants --> variants with LOD <= -5.0000.
09:42:29.687 INFO  GaussianMixtureModel - Initializing model with 100 k-means iterations...
09:42:29.780 INFO  VariantRecalibratorEngine - Finished iteration 0.
09:42:29.822 INFO  VariantRecalibratorEngine - Finished iteration 5.     Current change in mixture coefficients = 0.04305
09:42:29.858 INFO  VariantRecalibratorEngine - Finished iteration 10.     Current change in mixture coefficients = 0.00846
09:42:29.895 INFO  VariantRecalibratorEngine - Finished iteration 15.     Current change in mixture coefficients = 0.00272
09:42:29.915 INFO  VariantRecalibratorEngine - Convergence after 17 iterations!
09:42:29.931 INFO  VariantRecalibratorEngine - Evaluating full set of 138228 variants...
09:42:30.562 INFO  TrancheManager - Finding 12 tranches for 138228 variants
09:42:30.677 INFO  TrancheManager -   TruthSensitivityTranche threshold 100.00 => selection metric threshold 0.000
09:42:30.720 INFO  TrancheManager -   Found tranche for 100.000: 0.000 threshold starting with variant 0; running score is 0.000 
09:42:30.721 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=100.00 minVQSLod=-37.4840 known=(0 @ 0.0000) novel=(138228 @ 2.1263) truthSites(116873 accessible, 116873 called), name=anonymous]
09:42:30.721 INFO  TrancheManager -   TruthSensitivityTranche threshold 99.95 => selection metric threshold 0.000
09:42:30.763 INFO  TrancheManager -   Found tranche for 99.950: 0.000 threshold starting with variant 7797; running score is 0.001 
09:42:30.764 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.95 minVQSLod=-1.7719 known=(0 @ 0.0000) novel=(130431 @ 2.1730) truthSites(116873 accessible, 116814 called), name=anonymous]
09:42:30.764 INFO  TrancheManager -   TruthSensitivityTranche threshold 99.90 => selection metric threshold 0.001
09:42:30.786 INFO  TrancheManager -   Found tranche for 99.900: 0.001 threshold starting with variant 8906; running score is 0.001 
09:42:30.786 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.90 minVQSLod=-1.4146 known=(0 @ 0.0000) novel=(129322 @ 2.1794) truthSites(116873 accessible, 116756 called), name=anonymous]
09:42:30.787 INFO  TrancheManager -   TruthSensitivityTranche threshold 99.80 => selection metric threshold 0.002
09:42:30.807 INFO  TrancheManager -   Found tranche for 99.800: 0.002 threshold starting with variant 9853; running score is 0.002 
09:42:30.808 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.80 minVQSLod=-1.0261 known=(0 @ 0.0000) novel=(128375 @ 2.1869) truthSites(116873 accessible, 116639 called), name=anonymous]
09:42:30.808 INFO  TrancheManager -   TruthSensitivityTranche threshold 99.60 => selection metric threshold 0.004
09:42:30.824 INFO  TrancheManager -   Found tranche for 99.600: 0.004 threshold starting with variant 10916; running score is 0.004 
09:42:30.825 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.60 minVQSLod=-0.6283 known=(0 @ 0.0000) novel=(127312 @ 2.1937) truthSites(116873 accessible, 116405 called), name=anonymous]
09:42:30.825 INFO  TrancheManager -   TruthSensitivityTranche threshold 99.50 => selection metric threshold 0.005
09:42:30.847 INFO  TrancheManager -   Found tranche for 99.500: 0.005 threshold starting with variant 11232; running score is 0.005 
09:42:30.847 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.50 minVQSLod=-0.5159 known=(0 @ 0.0000) novel=(126996 @ 2.1962) truthSites(116873 accessible, 116288 called), name=anonymous]
09:42:30.847 INFO  TrancheManager -   TruthSensitivityTranche threshold 99.40 => selection metric threshold 0.006
09:42:30.870 INFO  TrancheManager -   Found tranche for 99.400: 0.006 threshold starting with variant 11560; running score is 0.006 
09:42:30.870 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.40 minVQSLod=-0.4298 known=(0 @ 0.0000) novel=(126668 @ 2.1984) truthSites(116873 accessible, 116171 called), name=anonymous]
09:42:30.871 INFO  TrancheManager -   TruthSensitivityTranche threshold 99.30 => selection metric threshold 0.007
09:42:30.894 INFO  TrancheManager -   Found tranche for 99.300: 0.007 threshold starting with variant 11874; running score is 0.007 
09:42:30.894 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.30 minVQSLod=-0.3531 known=(0 @ 0.0000) novel=(126354 @ 2.1995) truthSites(116873 accessible, 116054 called), name=anonymous]
09:42:30.894 INFO  TrancheManager -   TruthSensitivityTranche threshold 99.00 => selection metric threshold 0.010
09:42:30.919 INFO  TrancheManager -   Found tranche for 99.000: 0.010 threshold starting with variant 12582; running score is 0.010 
09:42:30.920 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=99.00 minVQSLod=-0.1852 known=(0 @ 0.0000) novel=(125646 @ 2.2028) truthSites(116873 accessible, 115704 called), name=anonymous]
09:42:30.920 INFO  TrancheManager -   TruthSensitivityTranche threshold 98.00 => selection metric threshold 0.020
09:42:30.938 INFO  TrancheManager -   Found tranche for 98.000: 0.020 threshold starting with variant 14674; running score is 0.020 
09:42:30.938 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=98.00 minVQSLod=0.2168 known=(0 @ 0.0000) novel=(123554 @ 2.2108) truthSites(116873 accessible, 114535 called), name=anonymous]
09:42:30.938 INFO  TrancheManager -   TruthSensitivityTranche threshold 97.00 => selection metric threshold 0.030
09:42:30.966 INFO  TrancheManager -   Found tranche for 97.000: 0.030 threshold starting with variant 16512; running score is 0.030 
09:42:30.966 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=97.00 minVQSLod=0.5555 known=(0 @ 0.0000) novel=(121716 @ 2.2143) truthSites(116873 accessible, 113366 called), name=anonymous]
09:42:30.966 INFO  TrancheManager -   TruthSensitivityTranche threshold 90.00 => selection metric threshold 0.100
09:42:30.993 INFO  TrancheManager -   Found tranche for 90.000: 0.100 threshold starting with variant 29727; running score is 0.100 
09:42:30.993 INFO  TrancheManager -   TruthSensitivityTranche is TruthSensitivityTranche targetTruthSensitivity=90.00 minVQSLod=3.1987 known=(0 @ 0.0000) novel=(108501 @ 2.2576) truthSites(116873 accessible, 105185 called), name=anonymous]
09:42:30.997 INFO  VariantRecalibrator - Writing out recalibration table...
09:42:32.459 INFO  VariantRecalibrator - Writing out visualization Rscript file...
09:42:32.498 INFO  VariantRecalibrator - Building QD x MQRankSum plot...
09:42:32.504 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:42:32.672 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:42:32.841 INFO  VariantRecalibrator - Building QD x FS plot...
09:42:32.845 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:42:33.013 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:42:33.147 INFO  VariantRecalibrator - Building QD x SOR plot...
09:42:33.150 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:42:33.305 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:42:33.430 INFO  VariantRecalibrator - Building QD x ReadPosRankSum plot...
09:42:33.431 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:42:33.596 INFO  VariantRecalibratorEngine - Evaluating full set of 3660 variants...
09:42:33.721 INFO  VariantRecalibrator - Building MQRankSum x FS plot...
09:42:33.723 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:33.883 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:34.004 INFO  VariantRecalibrator - Building MQRankSum x SOR plot...
09:42:34.006 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:34.165 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:34.298 INFO  VariantRecalibrator - Building MQRankSum x ReadPosRankSum plot...
09:42:34.299 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:34.459 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:34.574 INFO  VariantRecalibrator - Building FS x SOR plot...
09:42:34.574 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:34.741 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:34.853 INFO  VariantRecalibrator - Building FS x ReadPosRankSum plot...
09:42:34.853 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:35.007 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:35.117 INFO  VariantRecalibrator - Building SOR x ReadPosRankSum plot...
09:42:35.118 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:35.273 INFO  VariantRecalibratorEngine - Evaluating full set of 3600 variants...
09:42:35.386 INFO  VariantRecalibrator - Executing: Rscript /home/BQSR_bam/GVCF_files/recalibrate_SNP_plots.R
09:42:36.651 INFO  VariantRecalibrator - Shutting down engine
[September 27, 2024, 9:42:36 AM CST] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 4.06 minutes.
Runtime.totalMemory()=1105199104
org.broadinstitute.hellbender.utils.R.RScriptExecutorException: 
Rscript exited with 1
Command Line: Rscript -e tempLibDir = '/tmp/Rlib.8182557313761951261';source('/home/BQSR_bam/GVCF_files/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/BQSR_bam/GVCF_files/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)