Gistic2 output error

Question

[samane.]

I ran gistic2 for TCGA data. but i got these errors. it doe not create gene tables.

Error using genes_at (line 15)
End position is before start position
Error in genetables (line 71)
Error in write_gistic_outfiles (line 88)
Error in run_focal_gistic (line 319)
Error in run_gistic20 (line 124)
Error in run_gistic2_from_seg (line 249)
Error in gp_gistic2_from_seg (line 97)

How can I fix it?

[Abel Sousa]

Hi,

I've got the same error running gistic2. Did you manage to find a solution?

[ATpoint]

Please leave the answer field for answers and use ADD REPLY or ADD COMMENT. Thank you.

[Kevin Blighe]

Please describe that data that you are using as input, and show all steps (code).

[n.verburg]

Hi,

I've got the exact same error message when trying to run GISTIC2 (via broad website) on DNA methylation (EPIC array) derived segmentation file (CHAMP pipeline) of multiple samples:

"Error using genes_at (line 15) End position is before start position Error in genetables (line 71) Error in write_gistic_outfiles (line 88) Error in run_focal_gistic (line 319) Error in run_gistic20 (line 124) Error in run_gistic2_from_seg (line 249) Error in gp_gistic2_from_seg (line 97)"

I've checked the segmentation file and end.position is always higher than the start.position. Using a marker file does not change the error.

Anyone found a solution?

Thanks