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pfenninglab / halLiftover-postprocessing

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find ortholog internal issue #2

Open badoi opened 5 years ago

badoi commented 5 years ago

I'm getting this issue running the post-processing file a couple minutes into running.

` (base) [bnphan@compute-1-13 20190924_mm10ToHg38_halLiftover]$ MOUSEBGGZ='/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/background/mouseDHS/mm10_univ_dhs_ucsc.bed.gz' (base) [bnphan@compute-1-13 20190924_mm10ToHg38_halLiftover]$ MOUSEBG='/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/background/mouseDHS/mm10_univ_dhs_ucsc.bed' (base) [bnphan@compute-1-13 20190924_mm10ToHg38_halLiftover]$ MOUSEBGGZ='/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/background/mouseDHS/mm10_univ_dhs_ucsc.bed.gz' (base) [bnphan@compute-1-13 20190924_mm10ToHg38_halLiftover]$ MOUSEBG='/projects/pfenninggroup/machineLearningForComputationalBiology/gwasEnrichments/background/mouseDHS/mm10_univ_dhs_ucsc.bed' (base) [bnphan@compute-1-13 20190924_mm10ToHg38_halLiftover]$ HALLIFTEDTILE='/home/bnphan/projects/20190924_mm10ToHg38_halLiftover/bed/mm10_univ_dhs_ucsc_halLifted2hg38.bed' (base) [bnphan@compute-1-13 20190924_mm10ToHg38_halLiftover]$ MAXSCOREFILE='/home/bnphan/projects/20190924_mm10ToHg38_halLiftover/bed/mm10_univ_dhs_ucsc_maxScorePosition.bed' (base) [bnphan@compute-1-13 20190924_mm10ToHg38_halLiftover]$ HALLIFTEDSFILE='/home/bnphan/projects/20190924_mm10ToHg38_halLiftover/bed/mm10_univ_dhs_ucsc_maxscorePosition_halLifted2hg38.bed' (base) [bnphan@compute-1-13 20190924_mm10ToHg38_halLiftover]$ OUTFILE='/home/bnphan/projects/20190924_mm10ToHg38_halLiftover/bed/mm10_univ_dhs_ucsc_halLifted2hg38_orthologs.bed' (base) [bnphan@compute-1-13 20190924_mm10ToHg38_halLiftover]$ python /home/bnphan/src/halLiftover-postprocessing/orthologFind.py \

-max_len 1000 -min_len 50 -protect_dist 5 \ -qFile $MOUSEBG \ -tFile $HALLIFTEDTILE \ -sFile $HALLIFTEDSFILE \ -oFile $OUTFILE Traceback (most recent call last): File "/home/bnphan/src/halLiftover-postprocessing/orthologFind.py", line 427, in main(sys.argv[1:]) File "/home/bnphan/src/halLiftover-postprocessing/orthologFind.py", line 421, in main ortholog_find(file_H,max_len,alen,min_len,blen,int(args.protect_dist)); File "/home/bnphan/src/halLiftover-postprocessing/orthologFind.py", line 353, in ortholog_find make_hist(file_H[3],file_H[3],2500) File "/home/bnphan/src/halLiftover-postprocessing/orthologFind.py", line 238, in make_hist plt.figure(1) File "/home/bnphan/miniconda3/lib/python3.7/site-packages/matplotlib/pyplot.py", line 545, in figure **kwargs) File "/home/bnphan/miniconda3/lib/python3.7/site-packages/matplotlib/backend_bases.py", line 3252, in new_figure_manager return cls.new_figure_manager_given_figure(num, fig) File "/home/bnphan/miniconda3/lib/python3.7/site-packages/matplotlib/backends/_backend_tk.py", line 950, in new_figure_manager_given_figure window = tk.Tk(className="matplotlib") File "/home/bnphan/miniconda3/lib/python3.7/tkinter/init.py", line 2023, in init self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: couldn't connect to display "localhost:10.0" `

imk1 commented 4 years ago

Did you ssh in with --x11? If not, try that and see if that solves the problem.