{"action":"created","issue":{"url":"https://api.github.com/repos/koszullab/GRAAL/issues/14","repository_url":"https://api.github.com/repos/koszullab/GRAAL","labels_url":"https://api.github.com/repos/koszullab/GRAAL/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/koszullab/GRAAL/issues/14/comments","events_url":"https://api.github.com/repos/koszullab/GRAAL/issues/14/events","html_url":"https://github.com/koszullab/GRAAL/issues/14","id":308579300,"number":14,"title":"AttributeError: 'int' object has no attribute 'astype'","user":{"login":"bgbrink","id":11661112,"avatar_url":"https://avatars1.githubusercontent.com/u/11661112?v=4","gravatar_id":"","url":"https://api.github.com/users/bgbrink","html_url":"https://github.com/bgbrink","followers_url":"https://api.github.com/users/bgbrink/followers","following_url":"https://api.github.com/users/bgbrink/following{/other_user}","gists_url":"https://api.github.com/users/bgbrink/gists{/gist_id}","starred_url":"https://api.github.com/users/bgbrink/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgbrink/subscriptions","organizations_url":"https://api.github.com/users/bgbrink/orgs","repos_url":"https://api.github.com/users/bgbrink/repos","events_url":"https://api.github.com/users/bgbrink/events{/privacy}","received_events_url":"https://api.github.com/users/bgbrink/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2018-03-26T13:46:55Z","updated_at":"2018-03-28T09:04:59Z","closed_at":null,"author_association":"NONE","body":"When I run GRAAL, I receive the following error:\r\n\r\n```\r\nProcessing...\r\nDescription: convert dense file to COO sparse data.\r\nDone.\r\nstart filtering\r\nnfrags =  [95581]\r\nn init frags =  [95581]\r\nmean sparsity =  0.0021264316\r\nstd sparsity =  0.0022989216\r\nmax_sparsity =  0.059509736\r\ncleaning : start\r\nnumber of fragments to remove =  0\r\nException in thread Thread-2:\r\nTraceback (most recent call last):\r\n  File \"/usr/lib/python2.7/threading.py\", line 801, in __bootstrap_inner\r\n    self.run()\r\n  File \"main_window.py\", line 85, in run\r\n    pyramid = pyr.build_and_filter(self.base_folder, self.size_pyramid, self.factor)\r\n  File \"/home/benedikt/Python/GRAAL/pyramid_sparse.py\", line 69, in build_and_filter\r\n    current_abs_fragments_contacts, pyramid_0)\r\n  File \"/home/benedikt/Python/GRAAL/pyramid_sparse.py\", line 756, in remove_problematic_fragments\r\n    p.render(pt ,'step %s\\nProcessing...\\nDescription: removing bad fragments.' % step)\r\n  File \"/home/benedikt/Python/GRAAL/progressbar.py\", line 61, in render\r\n    self.progress = (bar_width * percent.astype(np.int)) / 100\r\nAttributeError: 'int' object has no attribute 'astype'\r\n```\r\n\r\nThe input data has been generated using the HiC-Box (thanks again for your help there).\r\n\r\nMost likely unrelated: the stdout is spammed with this message as well:\r\n```\r\n*** BUG ***\r\nIn pixman_region32_init_rect: Invalid rectangle passed\r\nSet a breakpoint on '_pixman_log_error' to debug\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/koszullab/GRAAL/issues/comments/376815138","html_url":"https://github.com/koszullab/GRAAL/issues/14#issuecomment-376815138","issue_url":"https://api.github.com/repos/koszullab/GRAAL/issues/14","id":376815138,"user":{"login":"bgbrink","id":11661112,"avatar_url":"https://avatars1.githubusercontent.com/u/11661112?v=4","gravatar_id":"","url":"https://api.github.com/users/bgbrink","html_url":"https://github.com/bgbrink","followers_url":"https://api.github.com/users/bgbrink/followers","following_url":"https://api.github.com/users/bgbrink/following{/other_user}","gists_url":"https://api.github.com/users/bgbrink/gists{/gist_id}","starred_url":"https://api.github.com/users/bgbrink/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bgbrink/subscriptions","organizations_url":"https://api.github.com/users/bgbrink/orgs","repos_url":"https://api.github.com/users/bgbrink/repos","events_url":"https://api.github.com/users/bgbrink/events{/privacy}","received_events_url":"https://api.github.com/users/bgbrink/received_events","type":"User","site_admin":false},"created_at":"2018-03-28T09:04:59Z","updated_at":"2018-03-28T09:04:59Z","author_association":"NONE","body":"I looked a bit more into this this morning. I ran everything again from scratch and this is what I got.\r\n\r\n**Master branch**\r\nComputation runs fine up until here:\r\n```\r\nhere we go\r\n92.65692814897916% ▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣□□ step 9000000\r\nProcessing...\r\nDescription: convert dense file to COO sparse data.\r\nDone.\r\nStart filling the pyramid\r\nhere we go\r\n92.65692814897916% ▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣□□ step 9000000\r\nProcessing...\r\nDescription: loading sparse data into hdf5.\r\nDone.\r\npyramid built.\r\nhere we go\r\n92.65692814897916% ▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣▣□□ step 9000000\r\nProcessing...\r\nDescription: convert dense file to COO sparse data.\r\nDone.\r\nstart filtering\r\nnfrags =  [95581]\r\nException in thread Thread-1:\r\nTraceback (most recent call last):\r\n  File \"/usr/lib/python2.7/threading.py\", line 801, in __bootstrap_inner\r\n    self.run()\r\n  File \"main_window.py\", line 85, in run\r\n    pyramid = pyr.build_and_filter(self.base_folder, self.size_pyramid, self.factor)\r\n  File \"/home/benedikt/Python/GRAAL/pyramid_sparse.py\", line 69, in build_and_filter\r\n    current_abs_fragments_contacts, pyramid_0)\r\n  File \"/home/benedikt/Python/GRAAL/pyramid_sparse.py\", line 585, in remove_problematic_fragments\r\n    sparse_mat_csr = sp.csr_matrix((np_2_scipy_sparse[2,:], np_2_scipy_sparse[0:2,:]), shape=(nfrags, nfrags))\r\n  File \"/usr/local/lib/python2.7/dist-packages/scipy/sparse/compressed.py\", line 51, in __init__\r\n    other = self.__class__(coo_matrix(arg1, shape=shape))\r\n  File \"/usr/local/lib/python2.7/dist-packages/scipy/sparse/coo.py\", line 191, in __init__\r\n    self._check()\r\n  File \"/usr/local/lib/python2.7/dist-packages/scipy/sparse/coo.py\", line 241, in _check\r\n    raise ValueError('negative row index found')\r\nValueError: negative row index found\r\n\r\n```\r\n\r\n**Develop Branch**\r\nI has to make the following changes to get this version to run:\r\n\r\n1. File \"main_window.py\", line 9, changed `wxversion.select(\"2.8\")` to `wxversion.select(\"3.0\")`\r\n2. File \"pyramid_sparse.py\", changed all occurences of `p = ProgressBar('green', width=20, block='▣', empty='□')` to `p = ProgressBar('green', width=20, block='|', empty='-')` in order to avoid SyntaxError: Non-ASCII character\r\n3. Files \"simulation_loader.py\" \"cuda_lib_gl.py\", line 9, changed `import Image` to `from PIL import Image`\r\n\r\nHowever, the end result is exactly the same, computation runs fine until ValueError."}}
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