Error for gisitic2 (Subscript indices must either be real positive integers or logicals.)

Question

[xzhao.uams]

Hi guys,

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.

Xin

[Ram]

You may have better luck asking gistic forums directly - https://groups.google.com/u/2/a/broadinstitute.org/g/gistic-forum