If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.9.0

b) Exact command used:

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/yangyxt/software/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar VariantRecalibrator -AS -R /paedyl01
/disk1/yangyxt/indexed_genome/ucsc.hg19.fasta -V /staging/wes/backup_gvcfs/all_wes_samples_plus_8_samples_20201201.chr2.HC.vcf.gz -resource:hapmap,known=false,training=true,truth=true,prior=15.0 /home/yjcao/reference/GATKbundle/hg19/hapmap_3.3.hg19.sites.vcf -resource:omi
ni,known=false,training=true,truth=false,prior=12.0 /home/yjcao/reference/GATKbundle/hg19/1000G_omni2.5.hg19.sites.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 /paedyl01/disk1/yangyxt/indexed_genome/1000GENOMES-phase_3.snp.vcf -resource:dbsnp,known
=true,training=false,truth=false,prior=2.0 /home/yjcao/reference/GATKbundle/hg19/dbsnp_138.hg19.vcf -an QD -an FS -an SOR -an ReadPosRankSum -an MQRankSum -an MQ -mode SNP -L chr2 --tmp-dir /staging/test_tmp -tranche 100.0 -tranche 99.9 -tranche 99.5 -tranche 99.0 -tranch
e 95.0 -rscript-file /staging/wes/backup_gvcfs/all_wes_samples_plus_8_samples_20201201.chr2.HC.snps.plots.R --tranches-file /staging/wes/backup_gvcfs/all_wes_samples_plus_8_samples_20201201.chr2.HC.snps.tranches -O /staging/wes/backup_gvcfs/all_wes_samples_plus_8_samples_
20201201.chr2.HC.snps.recal --max-gaussians 6

c) Entire error log:

12:39:50.400 INFO VariantRecalibratorEngine - Evaluating full set of 3660 variants...
12:39:50.617 INFO VariantRecalibrator - Executing: Rscript /staging/wes/backup_gvcfs/all_wes_samples_plus_8_samples_20201201.chr2.HC.snps.plots.R
12:40:05.752 INFO VariantRecalibrator - Executing: Rscript (resource)org/broadinstitute/hellbender/tools/walkers/vqsr/plot_Tranches.R /staging/wes/backup_gvcfs/all_wes_samples_plus_8_samples_20201201.chr2.HC.snps.tranches 2.15
12:40:05.995 INFO VariantRecalibrator - Shutting down engine
[March 10, 2021 at 12:40:05 PM HKT] org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator done. Elapsed time: 2.44 minutes.
Runtime.totalMemory()=5712642048
org.broadinstitute.hellbender.utils.R.RScriptExecutorException:
Rscript exited with 1
Command Line: Rscript -e tempLibDir = '/staging/test_tmp/Rlib.9822744678945799119';source('/staging/test_tmp/plot_Tranches.14952312278913780722.R'); /staging/wes/backup_gvcfs/all_wes_samples_plus_8_samples_20201201.chr2.HC.snps.tranches 2.15
Stdout:
Stderr: Error in read.table(tranchesFile, sep = ",", head = T) :
no lines available in input
Calls: source -> withVisible -> eval -> eval -> read.table
Execution halted

at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:80)
at org.broadinstitute.hellbender.utils.R.RScriptExecutor.getScriptException(RScriptExecutor.java:19)
at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:130)
at org.broadinstitute.hellbender.utils.R.RScriptExecutor.exec(RScriptExecutor.java:126)
at org.broadinstitute.hellbender.tools.walkers.vqsr.VariantRecalibrator.onTraversalSuccess(VariantRecalibrator.java:734)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1051)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
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)

It says no line available for input but I check the tranche file and here I paste the screenshot:

If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
b) What does (......) mean?
c) Why do I see (......)?
d) Where do I find (......)?
e) Will (......) be in future releases?