GISTIC errors

[Yura SONG]

Hello,

I faced a set of error during running GISTIC 2.0. I am using Ubuntu 18.10, and the version of MCR is v83.

The command and parameters are as below,

> gp_gistic2_from_seg -v 30 -rx 1 -js 4 -savegene 1 -genepattern 0 -b results_$cohort -seg $segfile -refgene hg19.mat -genegistic 1 -smallmem 0 -broad 1 -brlen 0.7 -conf 0.9 -scent none -qvt 0.25

The segfile is attached.

I run with several different cohorts, and only one gives this error messages, but did not give back any further logs.

Error using genomic_location (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)

If possible, could you give me some pieces of advice to overcome it?

Thanks in advance,

Best,

Yura

[Ted Liefeld]

Hi

I think you might have better luck getting help at the GISTIC forum .  https://groups.google.com/a/broadinstitute.org/g/gistic-forum

Hope this helps,

Ted