It looks like the reference genome your sequence data was aligned to is different from the reference genome the known sites you are using were called against. You should check for each file what reference genome was used. You may need to realign your data or liftover your sites so that they become compatible.
Then I suggest you use the same reference genome build(hg38) for the known sites in BQSR, as that is the same reference that was used for alignment.
This is a simple CRLF error. There is one additional line ending character at the end of each contig.
Please refer to this thread for more information on CRLF error @SkyWarrior mentioned. @SkyWarrior please feel free to share your two cents on this if you have seen such an error before.
I have not paid enough attention to the contig lengths. The reference that you are using is HG38 however the reference that this bam file is mapped to is hg19.
Check these 2 dict files