**hello,
when i run gatk, the error always occur, like this "java.lang.IllegalArgumentException: samples cannot be empty"
is there mistake in my input file?
thank you for your help !**

**my bam file as following:**
HWI-EAS418:3:37:1070:1462	83	chr20	46689301	255	50M	=	46687222	-2129	CAGCTCCAGGCCGCTCAAGAAGCGGCTGCTCCGCTCCCGGGCTGCGGCCA     0:@2%,6.=:.4=,4+6;B79>=BB=2>7=:9=4(599@BB9BB>BB??A	NH:i:1	HI:i:1	AS:i:99	nM:i:0

**the script is following:**
java -jar /home/H/mutation/gatk/gatk-package-4.1.4.1-local.jar HaplotypeCaller -R /home/H/mutation/ref/ctat_genome_lib_build_dir/ref_genome.fa \
-I /home/H/mutation/ctat-mutations-master/testing/__misc_data/Aligned.sortedByCoord.out.GRCh38.bam \
--recover-dangling-heads true \
--dont-use-soft-clipped-bases \
-stand-call-conf 20.0 -O test.vcf

**the logs are followinig:**
Runtime.totalMemory()=2260729856
java.lang.IllegalArgumentException: samples cannot be empty
	at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:725)
	at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ReferenceConfidenceModel.<init>(ReferenceConfidenceModel.java:116)
	at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.initialize(HaplotypeCallerEngine.java:221)
	at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.<init>(HaplotypeCallerEngine.java:164)
	at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.onTraversalStart(HaplotypeCaller.java:224)
	at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1046)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
	at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
	at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:163)
	at org.broadinstitute.hellbender.Main.mainEntry(Main.java:206)
	at org.broadinstitute.hellbender.Main.main(Main.java:292)


I had the same problem, I had to add the read group @RG tag to the .bam file using

 `samtools addreplacerg -r '@RG\tID:samplename\tSM:samplename'  input.bam -o output.bam`