Analysis fails when using bam files as input

[KWollenbergPhylo]

I am trying to run a TBProfiler 4.2.0 analysis on our Linux HPC cluster using trimmed, aligned, and deduplicated bam files as input (-a option). All of my runs have been failing at the delly analysis step. Here is what I am getting in the system error log:

Running command: set -u pipefail; delly call -t DEL -g /sysapps/cluster/software/Anaconda3/5.3.0/envs/tbprofiler-3.0.4-python3/share/tbprofiler/tbdb.fasta ./ExternalData/STaPHIdedup2/STaPHIdedup/ERR5863687_NC_000962.3sort.dedup2.bam -o ./ExternalData/STaPHItbpvar/288d2fa6-85a5-4071-a9ee-2a196d6f4f6a.delly.bcf Can't find ./ExternalData/STaPHItbpvar/288d2fa6-85a5-4071-a9ee-2a196d6f4f6a.delly.bcf

The directory is present and accessable. It appears that delly is failing but I do not get a TBProfiler error log for this. The runs complete if I use the --no_delly option, but then I don't get lineage calls, which I need. I am using bam files as input because about 1/3 of these samples have technical replicates which are merged to create the final bam file for each sample.