Error while using GATK Haplotypecaller

Question

[Sowmya Pulapet]

Hello, I want to create a single vcf file with 2 bam files using GATK's Haplotypecaller. I used the following command :

gatk HaplotypeCaller -R reference.fa -I all_bams.list --min-base-quality-score 20 -O bulk.vcf

where my all_bams.list looks like this:

bam1.bam
bam2.bam

I am runnnig this command from the same folder where the bam files are present. However I am getting the following error:

java.lang.IllegalStateException: the sample list cannot be null or empty
    at org.broadinstitute.hellbender.utils.Utils.validate(Utils.java:814)
    at org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.<init>(GenotypingEngine.java:69)
    at org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine.<init>(MinimalGenotypingEngine.java:46)
    at org.broadinstitute.hellbender.tools.walkers.genotyper.MinimalGenotypingEngine.<init>(MinimalGenotypingEngine.java:35)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.initializeActiveRegionEvaluationGenotyperEngine(HaplotypeCallerEngine.java:328)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.initialize(HaplotypeCallerEngine.java:227)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.<init>(HaplotypeCallerEngine.java:184)
    at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.onTraversalStart(HaplotypeCaller.java:259)
    at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1083)
    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)

I don't understand what's wrong. Is something wrong with my bam file or should I change all_bams.list?

And if I add path of the bam files in all_bams.list then It throws another error:

A USER ERROR has occurred: Couldn't read file. Error was: /path/to/bam/bam1.bam with exception: Cannot read non-existent file: file:///current/folder/path/to/bam/bam1.bam

Please help me out. Thanks in advance.