Bam file not being read

[drashwinelkar]

I am running whamg of the docker container : wham:1.8.0.1.2017.05.03--hd28b015_0
I have provided and index and sorted bam file which is the output of bwa mem with the -R option.

I get the following error when I run whamg-
INFO: fasta file: ChAdOx1nCov19_scaffolds_RC.fa
INFO: gathering stats (may take some time) for bam: DNA2_wham_sorted.bam
terminate called after throwing an instance of 'std::out_of_range'
what(): basic_string::substr
Aborted (core dumped)

My read length is 75 bp, paired end sequencing.
I tried switching the docker versions but I get the same error, it must be something with my bam file.
The bam file is perfectly valid for other SV calling tools that need it.

[Zev Kronenberg]

My reply is too late to be useful, but it could be a ref file mismatch?