bedpe.annot error

[ramaniak]

Hello,
I am trying to run INTEGRATE-Vis and get the following error on a test file I generated.

the command I am running is

 Integrate-vis.py structure -b test.bedpe -s test -d data/ideogram/Ideogram.37.tsv -r data/reference_genome/GRCh37_r75.all.fa -g data/gene_model/Homo_sapiens.GRCh37.75.gtf -m test.chr10.bam -o test -k

and get the following error:

Structure] Running Integrate-vis structure on test ...
[Structure] Making annotation file...

[Domain] Annotating fusion bedpe file...
loading gene annotation file...
177858 complete transcripts loaded.
loading reference...
1	1	249250621
10	249250622	384785368
11	384785369	519791884
12	519791885	653643779
13	653643780	768813657
14	768813658	876163197
15	876163198	978694589
16	978694590	1069049342
17	1069049343	1150244552
18	1150244553	1228321800
19	1228321801	1287450783
2	1287450784	1530650156
20	1530650157	1593675676
21	1593675677	1641805571
22	1641805572	1693110137
3	1693110138	1891132567
4	1891132568	2082286843
5	2082286844	2263202103
6	2263202104	2434317170
7	2434317171	2593455833
8	2593455834	2739819855
9	2739819856	2881033286
loading bedpe file...

[Structure] Setting gene name dictionaries...
[Structure] Plotting figures...

Traceback (most recent call last):
  File "/Users/arun/opt/bin/Integrate-vis.py", line 50, in <module>
    sys.exit(main(sys.argv))
  File "/Users/arun/opt/bin/Integrate-vis.py", line 38, in main
    pa_wrapper.main(argv)
  File "/Users/arun/opt/bin/vis_a_structure.py", line 418, in main
    plot_all()
  File "/Users/arun/opt/bin/vis_a_structure.py", line 363, in plot_all
    f=open(bedpeAnnot, "r")
IOError: [Errno 2] No such file or directory: '/Users/arun/Apps/INTEGRATE-Vis/INTEGRATE-Vis.1.0.0/test/tmp/test.bedpe.annot'

Could you please let me know what I am missing?
thanks
Arun