What's going on here?

Command:

freebayes -f human_g1k_v37.fasta --only-use-input-alleles --variant-input ALL_20160408.1kg_overlap.vcf.gz --gvcf HG01112.bam >HG01112_freebayes_1kg_p3_overlap.vcf

This works if I run an interactive job on my cluster

Once I submit a job with the same command I get this error

ERROR(freebayes): Could not open input BAM files
BamMultiReader::Open: unable to open all files:
    unable to open file: freebayes_HG01112.vcf

This doesn't make any sense. Any help?

I even get this error with the full path to the BAM file. I have cd in to the correct directory so it's not that issue

If I run an interactive job and enter the same commands found in my job submission script it works.