Closed joachimwolff closed 4 years ago
@gtrichard which version are you using? Are you using the Docker container?
runBrowser --version
indicates 1.0, it was installed the 6th of November 2017.
I think that the error related to the bedfile that is not displayed might be related to this?
INFO:werkzeug:127.0.0.1 - - [09/Feb/2018 14:37:36] "GET /get_image?region=chr2R:1000000-11500000&id=13 HTTP/1.1" 200 -
[2018-02-09 14:37:36,341] ERROR in app: Exception on /get_image [GET]
Traceback (most recent call last):
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/flask/app.py", line 1982, in wsgi_app
response = self.full_dispatch_request()
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/flask/app.py", line 1614, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/flask/app.py", line 1517, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/flask/app.py", line 1612, in full_dispatch_request
rv = self.dispatch_request()
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/flask/app.py", line 1598, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/hicbrowser/views.py", line 369, in get_image
trp_list[img_id].plot(outfile, chromosome, start, end)
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/hicexplorer/trackPlot.py", line 226, in plot
track.plot(axis, label_axis, chrom, start, end)
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/hicexplorer/trackPlot.py", line 1425, in plot
self.process_bed(ax.get_figure().get_figwidth(), start_region, end_region)
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/hicexplorer/trackPlot.py", line 1351, in process_bed
for bed in bed_file_h:
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/hicexplorer/readBed.py", line 105, in next
bed = self.get_bed_interval(line)
File "/data/akhtar/group/richard/Softwares/anaconda2/envs/hicexplorer_submatrices/lib/python2.7/site-packages/hicexplorer/readBed.py", line 250, in get_bed_interval
return self.BedInterval._make(line_values)
File "<string>", line 17, in _make
TypeError: Expected 6 arguments, got 4
Hello,
I have two problems with HiCBrowser and the runBrowser command.
Your search - FBtr0114187 - did not match any gene. Check the browser for examples of valid gene names as they may be an id.
While the
genes= file.bed
in browserConfig.ini has that specific line:211000022278158 591 1036 FBtr0114187 0 + 1036 1036 0 1 445, 0,
Ask you me if you need the browserConfig.ini, region_tracks.ini and the corresponding bed files.
Ping @gtrichard I moved your issue because it was posted in the wrong repository.
Orginal posting: https://github.com/deeptools/HiCExplorer/issues/176