I am running GISTIC on a number of copy number segmented data files downloaded/generated from various datasets for comparison. GISTIC works fine for all segmentation files, except for one, where I keep getting the following message.
(base) mh-ikom01:~/GISTIC$ ./run_gistic_ICGC_corrected2 --- creating output directory --- --- running GISTIC --- Setting Matlab MCR root to /home/local/mortenry/GISTIC/MATLAB_Compiler_Runtime GISTIC version 2.0.23 GISTIC 2.0 input error detected: All input data were removed after NaN processing.
However I cannot find any reason why this file won't work, since the structure of the segment file is no different than for the other datasets. I paste in the first few example lines:
First segments of file that works fine!
V219 1 604268 842413 10 -0.0421 V219 1 850905 2814971 217 0.078 V219 1 2832087 4094205 136 0.0446 V219 1 4113823 5630812 86 -0.0101 108415 segments in total
First segments of file that creates error message!
CPCG0368-F1 1 10000 10467 0 0.000959037722634586 CPCG0368-F1 1 11447 177416 165 0.000959037722634586 CPCG0368-F1 1 227417 267718 40 0.000959037722634586 CPCG0368-F1 1 317719 471367 153 0.000959037722634586 CPCG0368-F1 1 521368 564448 43 0.000959037722634586 785129 segments in total
I should mention two things which I corrected to try to make the file run:
First GISTIC could not run becuase of many overlapping segments. I modified the segmentation file to non-overlapping segments, which removed the overlap-error, But instead I got the NaN error.
Since the segments were from WGS data, there were no info on number of markers for each segment. Since I first added a column with "NA"s for markers, and thought that this might be the reason the error. I then replaced this column wuth some marker pseudo-numbers scaled according to the segment length. But I still got the same error message.
I have also read at a previous post on the topic : GISTIC 2.0.23 error However, there seem to be segments defined for all samples, and I have also double-checked that the sample ids are identical for the _segment and _arraylist files. So this does not seem to be the problem.
I'm stuck at the moment, so any help would be appreciated.
Added to the original message: I have done some more checking, and I have been able to generate two segmentation files from the beginning of chr1. Both are subsets from the segmentation file that would not run in the first place. The first segmentation file seem to run fine. The other segmentation file includes one additional segment compared to the first file (the next segment sorted according to position), and generates the error message. I cannot see anything wrong with this segment, so I still cannot figure out why I get an error. I will be happy to provide these two files to work with for anyone who wish to figure this out the problem.