for f in MINIMAP BWA ;
do
    ~/gatk-4.2.0.0/gatk HaplotypeCaller --reference  /home/tmichel/projects/rbge/HybSeq_thibauld/reference_genomes/Begonia_loranthoides_scaffold.fasta --input  Hillebrandia_sorted.$f.bam  --output Hillebrandia.$f.g.vcf.gz --emit-ref-confidence GVCF ; 
done

I have used GATK to call variants in BAM files files with both minimap2 and bwa mem with the following script:

~/gatk-4.2.0.0/gatk HaplotypeCaller \
--reference  REF.fasta \
--input  INPUT.bam  \
--output OUTPUT.g.vcf.gz \
--emit-ref-confidence GVCF

But the following error popped:

A USER ERROR has occurred: Argument emit-ref-confidence has a bad value: Can only be used in single sample mode currently. Use the --sample-name argument to run on a single sample out of a multi-sample BAM file.

I have then check the samples names in my BAM file:

 ~/gatk-4.2.0.0/gatk GetSampleName \
        -I INPUT.bam

But the following error popped:

A USER ERROR has occurred: Bad input: The given bam input has no sample names.

It is a bit odd, as I have processed other samples through the PALEOMIX pipeline, using BWA as well for alignement, and never had this issue. Has anyone here experienced the same issue?