I am trying to re-run the CCLE gene-level CNV with Gistic2, there are 1600+ samples in total. But it will show an error when the Gistic2 starts writing the lesion file:
Writing all_lesions file to: /gpfs/data/davolilab/data/CCLE_2019/CCLE_all/all_lesions.conf_99.txt Subscript indices must either be real positive integers or logicals. Error in add_D_peakcalls (line 90) Error in make_all_lesions_file (line 105) Error in write_gistic_outfiles (line 70) 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) MATLAB:badsubscript
I had tried to grep some of the samples (30-50 samples) to run the Gistic2 separately and it goes perfectly. Just want to know why I can't combine all the samples together? Has anyone met this problem before?
Thank you very much.