{"action":"created","issue":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/94","labels_url":"https://api.github.com/repos/fidelram/deepTools/issues/94/labels{/name}","comments_url":"https://api.github.com/repos/fidelram/deepTools/issues/94/comments","events_url":"https://api.github.com/repos/fidelram/deepTools/issues/94/events","html_url":"https://github.com/fidelram/deepTools/issues/94","id":101420979,"number":94,"title":"Traceback when running bamCorrelate","user":{"login":"msxakk","id":12625765,"avatar_url":"https://avatars.githubusercontent.com/u/12625765?v=3","gravatar_id":"","url":"https://api.github.com/users/msxakk","html_url":"https://github.com/msxakk","followers_url":"https://api.github.com/users/msxakk/followers","following_url":"https://api.github.com/users/msxakk/following{/other_user}","gists_url":"https://api.github.com/users/msxakk/gists{/gist_id}","starred_url":"https://api.github.com/users/msxakk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/msxakk/subscriptions","organizations_url":"https://api.github.com/users/msxakk/orgs","repos_url":"https://api.github.com/users/msxakk/repos","events_url":"https://api.github.com/users/msxakk/events{/privacy}","received_events_url":"https://api.github.com/users/msxakk/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-08-17T13:29:55Z","updated_at":"2015-08-25T13:40:43Z","closed_at":null,"body":"Hello,\r\nI'm trying to run bamCorrelate and I get the following traceback:\r\n\r\nTraceback (most recent call last):\r\n  File \"/usr/local/bin/bamCorrelate\", line 435, in <module>\r\n    main(ARGS)\r\n  File \"/usr/local/bin/bamCorrelate\", line 350, in main\r\n    stepSize=stepsize)\r\n  File \"/usr/local/lib/python2.7/dist-packages/deeptools/countReadsPerBin.py\", line 305, in getNumReadsPerBin\r\n    numberOfProcessors=numberOfProcessors)\r\n  File \"/usr/local/lib/python2.7/dist-packages/deeptools/mapReduce.py\", line 63, in mapReduce\r\n    bed_interval_tree = BED_to_interval_tree(bedFile)\r\n  File \"/usr/local/lib/python2.7/dist-packages/deeptools/mapReduce.py\", line 191, in BED_to_interval_tree\r\n    from bx.intervals.intersection import IntervalTree, Interval\r\n\r\nI installed numpy and scipy via\r\nsudo apt-get install python-numpy python-scipy \r\n\r\nI aslo tried installing fastinterval via\r\npip install fastinterval \r\n\r\nBoth installation looked successful but I'm still getting this error. Any help? Is it a path issue here?"},"comment":{"url":"https://api.github.com/repos/fidelram/deepTools/issues/comments/134589797","html_url":"https://github.com/fidelram/deepTools/issues/94#issuecomment-134589797","issue_url":"https://api.github.com/repos/fidelram/deepTools/issues/94","id":134589797,"user":{"login":"msxakk","id":12625765,"avatar_url":"https://avatars.githubusercontent.com/u/12625765?v=3","gravatar_id":"","url":"https://api.github.com/users/msxakk","html_url":"https://github.com/msxakk","followers_url":"https://api.github.com/users/msxakk/followers","following_url":"https://api.github.com/users/msxakk/following{/other_user}","gists_url":"https://api.github.com/users/msxakk/gists{/gist_id}","starred_url":"https://api.github.com/users/msxakk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/msxakk/subscriptions","organizations_url":"https://api.github.com/users/msxakk/orgs","repos_url":"https://api.github.com/users/msxakk/repos","events_url":"https://api.github.com/users/msxakk/events{/privacy}","received_events_url":"https://api.github.com/users/msxakk/received_events","type":"User","site_admin":false},"created_at":"2015-08-25T13:40:43Z","updated_at":"2015-08-25T13:40:43Z","body":"I tried installing bx-python and I got the following error:\r\nCommand /usr/bin/python -c \"import setuptools;__file__='/home/msxakk/Downloads/build/bx-python/setup.py';exec(compile(open(__file__).read().replace('\\r\\n', '\\n'), __file__, 'exec'))\" install --single-version-externally-managed --record /tmp/pip-XnOjIY-record/install-record.txt failed with error code 1\r\n\r\nHence repeating bamCorrelate command resulted in the same error. "}}