I'm running GISTIC2 on Sequenza generated segmentation data from whole exome tumor-normal pairs. I keep encountering the following warning:

Warning: markers on largest gene exceed markers on smallest chromosome: overriding gene-gistic
> In gene_score_permutations at 43
  In compute_stats at 83
  In run_focal_gistic at 201
  In run_gistic20 at 124
  In run_gistic2_from_seg at 249
  In gp_gistic2_from_seg at 97

I'm not really sure what this warning means and if I should be concerned about it affecting my results. According to the GISTIC documentation, the gene-gistic option "calculates the significance of deletions at a gene level instead of a marker level". What effect will this have on my results and should I be concerned?

Here is my GISTIC command:

./gistic2 -b $basedir \
    -seg $segfile \
    -refgene $refgenefile \
    -ta 0.1 \
    -armpeel 1 \
    -brlen 0.7 \
    -cap 1.5 \
    -conf 0.90 \
    -td 0.1 \
    -genegistic 1 \
    -gcm extreme \
    -js 4 \
    -maxseg 2000 \
    -qvt 0.25 \
    -rx 0 \
    -savegene 1 \