Gistic error (multiple) source?

[Eric David Elass@UW.Edu]

Hello,

I am attempting to use gistic 2.0 with a .seg file generated from CNVkit. I have tried it a handful of times and continue getting the errors listed below. Likewise, because it appears theres an error with figure production, I am not getting any del_qplot figures in my output. Difficult to find any causes/solutions via googling around. Is it an issue with my .seg file? Any help is appreciated!

INFO: Using cached SIF image Error using ghostscript (line 186) Problem converting PostScript. System returned error: -1.Failed to convert to output format; Ghostscript status: -100.**** Unable to open the initial device, quitting. **** Unable to open the initial device, quitting. Artifex Ghostscript 8.54: **** Could not open temporary file /scratch/genepattern/job_29080006/gs_3q5Jir Error in print>LocalPrint (line 307) Error in print (line 233) Error in save_current_figure (line 38) Error in plot_snp_score (line 492) Error in gistic_plots (line 219) Error in run_focal_gistic (line 347) Error in run_gistic20 (line 124) Error in run_gistic2_from_seg (line 249) Error in gp_gistic2_from_seg (line 97) MATLAB:ghostscript:ProblemConvertingPostScriptSystemReturnedError

[Ted Liefeld]

this might have been caused by an issue we tracked down in another help request (problem with the $TMPDIR changing on the compute env to /scratch and that directory not being mounted to the container running the analysis).  Can you retry the 6.15.30 runs to see if they work now?

Thanks for your patience and help,

Ted

[Eric David Elass@UW.Edu]

Hi,

I actually believe I may have resolved the error. I believe it was caused by creating from .seg files from my cnvkit *.call.cns files rather than the *.cns files themselves. I re-ran the new .seg files and no errors occurred. I appreciate your response though!