I am trying to convert 450 K methylation coordinates (Single C location) of given hg19 to GRCH38 following suggestions in previous posts (GRCh37/38(NCBI) vs hg19/hg38(UCSC) and Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api))

using default parameters which are-

Minimum ratio of bases that must remap:0.95:

BED 4 to BED 6 OptionsAllow multiple output regions:off Minimum hit size in query:0;

Minimum chain size in target:0 BED 12 OptionsMin ratio of alignment blocks or exons that must map:1.00If thickStart/thickEnd is not mapped, use the closest mapped base:off

However I get an error :

Deleted in new:
    Sequence intersects no chains
Partially deleted in new:
    Sequence insufficiently intersects one chain
Split in new:
    Sequence insufficiently intersects multiple chains
Duplicated in new:
    Sequence sufficiently intersects multiple chains
Boundary problem:
    Missing start or end base in an exon

Here is one line of input;

chr4    54974682    54974682    +

Any suggestion what is wrong?

Thanks