GFF liftOver using CrossMap is failing.

Question

[kirannbishwa01]

I am trying to lift over a GFF, GTF using the Chain file generated from VCF. I am using CrossMap as well as liftOver from UCSC.

LiftOver isn't working. CrossMap is giving me an output but it indicates that there are failures. Upon looking at those position in the Chain and original GFF file, I cannot see any pattern to why the Fail - message is rising.

Using liftOver:

$ /home/priyanka/liftOver/liftOver short-GFF.gff BcfOut/MA625-left.chain BcfOut/MA625-left02.gff -errorHelp
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

Using CrossMap:

python /home/priyanka/CrossMap-0.2.7/bin/CrossMap.py gff BcfOut/MA625-left.chain short-GFF.gff > BcfOut/MA625-left.gff

Observed Output:

    1   version-2   gene    1   2541    0.43    -   .   ID=AL1G10010;Name=AL1G10010;Note=Protein_Coding_gene    fail (multpile match to target assembly)
1   version-2   transcript  1   2541    0.43    -   .   ID=AL1G10010.t1;Parent=AL1G10010    fail (multpile match to target assembly)
1   version-2   intron  62  144 0.96    -   .   ID=AL1G10010.t1;Parent=AL1G10010    ->  1   version-2   intron  62  144 0.96    -   .   ID=AL1G10010.t1;Parent=AL1G10010
1   version-2   intron  253 406 1   -   .   ID=AL1G10010.t1;Parent=AL1G10010    ->  1   version-2   intron  253 406 1   -   .   ID=AL1G10010.t1;Parent=AL1G10010
1   version-2   intron  783 1422    1   -   .   ID=AL1G10010.t1;Parent=AL1G10010    fail (multpile match to target assembly)
1   version-2   intron  1643    1802    1   -   .   ID=AL1G10010.t1;Parent=AL1G10010    ->  1   version-2   intron  1641    1800    1   -   .   ID=AL1G10010.t1;Parent=AL1G10010
1   version-2   intron  2036    2123    1   -   .   ID=AL1G10010.t1;Parent=AL1G10010    ->  1   version-2   intron  2034    2121    1   -   .   ID=AL1G10010.t1;Parent=AL1G10010
1   version-2   intron  2348    2443    1   -   .   ID=AL1G10010.t1;Parent=AL1G10010    ->  1   version-2   intron  2346    2441    1   -   .   ID=AL1G10010.t1;Parent=AL1G10010
1   version-2   CDS 1   61  0.75    -   0   ID=AL1G10010.t1;Parent=AL1G10010    ->  1   version-2   CDS 1   61  0.75    -   0   ID=AL1G10010.t1;Parent=AL1G10010
1   version-2   exon    1   61  .   -   .   ID=AL1G10010.t1;Parent=AL1G10010    ->  1   version-2   exon    1   61  .   -   .   ID=AL1G10010.t1;Parent=AL1G10010

Any reason why is this failing ?