Open ramaniak opened 5 years ago
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
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
and get the following error:
Could you please let me know what I am missing? thanks Arun