GISTIC2.0 Floating point exception error

[Eunice lly]

Hello Gene Pattern team, 

I ran GISTIC2.0 for 3 different cohorts and it was smooth for the first 2. However, for 1 cohort which is also the largest among all, the job terminated before completion. My other cohorts produced 27 output files while this one only produced 19 files. The error report says "float point exception" (see attached image)

Here are my parameters which is the same for the other 2 cohorts and didnt give me any error. 

./gistic2 -b $basedir -seg $segfile -maxspace -refgene $refgenefile -genegistic 1 -smallmem 1 -broad 1 -brlen 0.7 -conf 0.95 -armpeel 1 -savegene 1 -gcm mean -rx 0

Your help is greatly appreciated!

Thank you!

[edh...@cloud.ucsd.edu]

Hi, 

Whats the job id for this job? 

Edwin 

[Eunice lly]

Hi,

I tried several times so they’re:

1382578

1382697

1382781

Thank you!

Eunice 

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[edh...@cloud.ucsd.edu]

Hi Eunice, 

Thanks, the GISTIC forum will provide more information shortly. 

Edwin 

[Eunice lly]

Hi,

Can I follow up on this error?

Thank you!

Eunice 

[edh...@cloud.ucsd.edu]

Hey Eunice, 

What were the input files you used? If there are URL Links to it that would be great. 

Edwin 

[Eunice lly]

Hi Edwin,

Here's the link to my input file https://drive.google.com/file/d/1uLoRqNIhfKYN3caEXHzT9r_vgIfDOZOv/view?usp=sharing

Thanks!

[Andrew Cherniack]

I ran using the default conditions without errors.

What files were you missing in the output?

Andrew

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[Eunice lly]

Hi Andrew, 

I'm missing around 8 files as shown below, left is output for this cohort, right is output from another smaller cohort that I ran without error.

Files such as all_data_by_genes, all_thresholded.by_genes, broad_data_by_genes, broad_significance_results, broad_values_by_arm, focal_data_by_genes, freqarms_vs_ngenes and sample_cutoffs are missing. 

When I ran with the same input file, it was terminated with floating point exception error in the error file.  

Eunice

[Andrew Cherniack]

I was able to run your seg file successfully and generated those files.

I doubt this made a difference by renaming your file TCGA_LUAD_gistic2_segment.seg so that I could look at it in IGV.

Also, what genomic build did you use?

Regards

Andrew

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[Eunice lly]

Hi Andrew, 

Do you mean changing the extension from .txt to .seg?

I'm using hg38. 

Eunice

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[Andrew Cherniack]

yes

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[Eunice lly]

Hi Andrew, 

Here is the .seg file. https://drive.google.com/file/d/1SqXNQ6eQNngyUZIS1o62cIPOxF_Z5455/view?usp=drive_link

Thank you!

Regards,

Eunice

[Andrew Cherniack]

Hi Eunice,

I successfully ran your seg file and got all of the output without error. Have you tried to rerun it recently?

These were my input parameters.

t_amp: 0.1000
 t_del: 0.1000
join_segment_size: 8
 ext: ''
qv_thresh: 0.2500
remove_X: 0
markers: []
max_marker_spacing: 10000
run_broad_analysis: 1
 broad_len_cutoff: 0.7000
ziggs: [1×1 struct]
res: 0.0500
conf_level: 0.9500
 cap: 2.5000
do_gene_gistic: 1
conserve_disk_space: 0
 save_data_files: 0
 use_segarray: 1
write_gene_files: 1
use_two_sided: 0
 do_arbitration: 1
save_seg_data: 0
 fname: ''
 peak_types: {'robust'}
genepattern: 1
arm_peeloff: 1
gene_collapse_method: 'extreme'
sample_center: 'mean'
 alpha: [2.5145 2.1653]
partial_hits: [1 0]
islog: []

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[Eunice lly]

Hi Andrew, 

Thank you for the prompt response. Yes, I rerun it recently and same error occurred. 

My colleague and I tried running in smaller batches with the same parameters that we were using for other cohorts, and the maximum we could run without error is at ~450 samples. Does any of these parameters that you've listed here define the sample size?

Thanks again! 

Regards,

Eunice