GISTIC_2.0 Error

[Debajyoti Kabiraj]

Hi All,

First, I'd like to thank you for creating such an excellent program as GISTIC_2.0. I'm trying this tool for the first time and am having some issues.
Also, I'd want to mention that I'm running GISTIC_2.0 with the IchorCNA output .seg file as the input.
It would be very appreciated if someone could please correct where I am going wrong. 
I've also attached my input seg file.


The Error file shows that

Error using genes_at (line 15) End position is before start position Error in genetables (line 71) Error in write_gistic_outfiles (line 88) 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)

[Ted Liefeld]

Hi, it would help if you could include a jobnumber for the GenePattern server,

Thanks

Ted

[Debajyoti Kabiraj]

Thank you for your response,

My job Id is 590914

I don't know how to get the server name, however, these is status of the job. Please, let me know if this information helps. 

Status
Queue
arn:aws:batch:us-east-1:718039241689:job-queue/gp-cloud-default
Exit Code
255
Status date
Jul 06 02:45:30 PM
Requested resources
job.memory
8 GB
job.cpuCount
1
job.walltime
24:00:00
job.queue
gp-cloud-default
Event log
Added to GenePattern
Jul 06 10:03:53 AM
Submitted to queue
Jul 06 10:03:59 AM
Started running
Jul 06 10:06:56 AM
Finished running
Jul 06 02:45:28 PM
Completed in GenePattern
Jul 06 02:45:32 PM

Regards,

deb

[Andrew Cherniack]

Try adding headers to your seg file.

Standard headers are:  Sample     Chromosome Start End     Num_Probes Segment_Mean

[Andrew Cherniack]

Also, what genome build are you are you using?

Another issue is that your copy number profiles are hyper-segmented. 

I am not familiar with running IchorDNA, but there may be a problem with how your segments were generated.  

[Debajyoti Kabiraj]

Thanks for your valuable responses, after adding the header it's working. 

Best, 

Deb