Hello, Everyone
I am running GISTIC for copy number analysis. But, some errors occurred like this.
--- running GISTIC ---
Setting Matlab MCR root to /opt/GISTIC/MATLAB_Compiler_Runtime
GISTIC version 2.0.23
Warning: Shortened 1 segments in '/GISTIC_result/P57/P57_gistic_seg.txt' that overlap by one marker.
[^H> In make_D_from_seg at 268
In run_gistic2_from_seg at 188
In gp_gistic2_from_seg at 97]^H
Warning: Number of markers is less than smooth length for the following chromosomes: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22. These chromosomes will not be smoothed. (Smooth length = 8.)
[^H> In smooth_cbs at 54
In clean_gistic_input at 77
In run_gistic2_from_seg at 238
In gp_gistic2_from_seg at 97]^H
GISTIC 2.0 input error detected:
Only one sample remains after noise filtering.
I made segmentation and marker file from NGS data.
I have been struggling for weeks because of this error.
Hi,
I am also running GISTIC 2.0 for copy number analysis, and the same first warning Warning: Shortened 1 segments in '/GISTIC_result/P57/P57_gistic_seg.txt' that overlap by one marker. [^H> In make_D_from_seg at 268 In run_gistic2_from_seg at 188 In gp_gistic2_from_seg at 97]^H occurred. The GISTIC programming was run in Linux system(Ubuntu), and run successfully even though it reported this warning.
However, I didn't meet other errors or warnings when I run GISTIC2.0. I think the reason of error GISTIC 2.0 input error detected: Only one sample remains after noise filtering. is that your sample names were not consistent with the sample names of NGS data.
In addition, I made the input files(CNV segment fils and marker files) from R package TCGAbiolinks (the former file) and the GDC database: https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files (project name: SNP6 GRCh38 Remapped Probeset File for Copy Number Variation Analysis)(the latter file).
Hope my answer can help you.
