GISTIC2.0 Out put error

[Amelia Jones]

Hi everyone,

When I try to run GISTIC, I run into problems with the output. Using the same inputs, I received 19 outputs in October, but only 2 outputs yesterday.

I don't understand why?

Any ideas?

Best wishes and many thanks.
Amelia

[Ted Liefeld]

Amelia

could you provide the job numbers for both jobs and I will take a look,

Ted

[Amelia Jones]

Ted

I'm sorry I deleted this job after getting the wrong result, but I kept job with another data, and this output also has only 2 files
This is the job ID for which I used data 2 to get the wrong number of files 473601. GISTIC_2.0
This is the job ID I used to get the correct number of files with data 1 472687. GISTIC_2.0

And the strange thing is that no matter what data I use, it always results in a file size of 403kb

Amelia

[Amelia Jones]

Ted

Just now I re-ran the analysis with data 1 and still got the wrong number of file outputs (job ID:474022)

Amelia

在2022年11月4日星期五 UTC+8 22:10:06<lie...@broadinstitute.org> 写道：

[Ted Liefeld]

Amelia,

I just looked at your job and in the stdout.txt file this error was reported;

GISTIC 2.0 input error detected:
116149 segment start or end positions in '/opt/gpcloud/gp_home/users/HongXY09/uploads/tmp/run6218123174912316095.tmp/seg.file/1/tumor_cnv_data_pred.txt' do not match any markers in '/opt/gpcloud/gp_home/users/HongXY09/uploads/tmp/run7693094298813593329.tmp/markers.file/2/hg_marker_file.txt'.
First bad position is 1:3301765 at line 2.

I am not familiar with GISTIC so to understand this error it's best to consult the GISTIC forum (https://groups.google.com/a/broadinstitute.org/g/gistic-forum) where the authors and developers of GISTIC can respond.

Hope this helps,

Ted

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Ted Liefeld                                      UC San Diego

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[Amelia Jones]

Ted,

Thanks so much, I checked the error message you mentioned and I'm guessing it's because I didn't remove the column names when I exported the file in question. After I removed the column names from both files it analysed successfully!

Thank you so much for your help!

Amelia