Cross chromosomes error in GISTIC2.0 v. 6.15.30 unsing GenePattern public server

[liat anabel]

Hi all,

I am running GISTIC2.0 on the public GenePattern server. 

When executing one of my SEG files, I encounter the following errors in the stderr file:  

Error using genomic_locattderron (line 63)
crosses chromosomes
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)

I am running the analysis against the reference file Human_Hg19.mat. The SEG file is formatted according to the guidelines provided in the documentation available at https://broadinstitute.github.io/gistic2/.

I have tried changing the confidence level to 0.75 and 0.9, but the error persists in both cases. The job IDs for the failed runs are 621834 and 621830.

I have searched through forums and discussions in the Google Group, but I have not found a solution to this issue.

I have attached the error log and the input file for your reference.

I also asked for help in the GISTIC google group and didn't get any answer yet

I would appreciate any assistance you can provide.

Best regards,
Liat Sinberger

[Andrew Cherniack]

Hi

The issue is with your segfile. Itself, and not the formatting.

To answer it, you are going to have to share your segfile.

Regards

Andrew

[liat anabel]

Thank you for the answer.

I'm attaching here the seq and stderr files.

Best regards,

Liat

[Andrew Cherniack]

I am leaving the Broad at 2. I can zoom with you at 4 if you want.

I will also be at DFCI on Monday..

A

___________________________
Andrew Cherniack, PhD                                               
Senior Group Leader

Broad Institute of Harvard and MIT and

Dana Farber Cancer Institute

email: ache...@broadinstitute.org
___________________________

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[liat anabel]

 Hi, If it's still possible, I would love to have a Zoom meeting at 4.

Liat

[Andrew Cherniack]

Sorry 

That email was meant for someone else

Andrew

___________________________
Andrew Cherniack, PhD                                               
Senior Group Leader

Broad Institute of Harvard and MIT and

Dana Farber Cancer Institute

email: ache...@broadinstitute.org
___________________________

To view this discussion visit https://groups.google.com/d/msgid/genepattern-help/4700a7a9-06d4-4811-ab65-2bd0d033dabdn%40googlegroups.com.

[liat anabel]

Thank you for informing me.

Liat

בתאריך יום ו׳, 31 בינו׳ 2025, 23:31, מאת 'Andrew Cherniack' via GenePattern Help Forum ‏<genepatt...@googlegroups.com>:

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[Andrew Cherniack]

But I did figure out the issue.

Your seg file runs using HG38 but not HG19.

Where did you download your data from, and are you sure it's HG19?

Andrew

___________________________
Andrew Cherniack, PhD                                               
Senior Group Leader

Broad Institute of Harvard and MIT and

Dana Farber Cancer Institute

email: ache...@broadinstitute.org
___________________________

To view this discussion visit https://groups.google.com/d/msgid/genepattern-help/CAJcxt2R%2ByH1q82pDi-THi5HAURgY%2B8AGK10hjThf7akNu9GhqA%40mail.gmail.com.

[liat anabel]

Thank you I will check this.

Best regards,

Liat

בתאריך יום ו׳, 31 בינו׳ 2025, 23:39, מאת 'Andrew Cherniack' via GenePattern Help Forum ‏<genepatt...@googlegroups.com>:

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