{"action":"created","issue":{"url":"https://api.github.com/repos/MrOlm/drep/issues/25","repository_url":"https://api.github.com/repos/MrOlm/drep","labels_url":"https://api.github.com/repos/MrOlm/drep/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/MrOlm/drep/issues/25/comments","events_url":"https://api.github.com/repos/MrOlm/drep/issues/25/events","html_url":"https://github.com/MrOlm/drep/issues/25","id":304152336,"number":25,"title":"dRep failes with symlinks pointing to the same file","user":{"login":"fungs","id":8776981,"avatar_url":"https://avatars3.githubusercontent.com/u/8776981?v=4","gravatar_id":"","url":"https://api.github.com/users/fungs","html_url":"https://github.com/fungs","followers_url":"https://api.github.com/users/fungs/followers","following_url":"https://api.github.com/users/fungs/following{/other_user}","gists_url":"https://api.github.com/users/fungs/gists{/gist_id}","starred_url":"https://api.github.com/users/fungs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fungs/subscriptions","organizations_url":"https://api.github.com/users/fungs/orgs","repos_url":"https://api.github.com/users/fungs/repos","events_url":"https://api.github.com/users/fungs/events{/privacy}","received_events_url":"https://api.github.com/users/fungs/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-03-11T11:58:46Z","updated_at":"2018-03-19T18:40:06Z","closed_at":"2018-03-19T18:40:06Z","author_association":"NONE","body":"Hi, dRep produces errors when trying to lower the thresholds. I basically want to cluster/dereplicate all bins, regardless of size and completion levels. So I ran `dRep dereplicate -pa 0.8 -sa 0.98 -comp 0 -con 50 -l 20000` which gave the following error in v2.0.5:\r\n\r\n```\r\n2b. Cluster pair-wise MASH clustering\r\nTraceback (most recent call last):\r\n  File \"/home/johdro/.conda/envs/drep/bin/dRep\", line 26, in <module>\r\n    controller.parseArguments(args)\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/drep/controller.py\", line 144, in parseArguments\r\n    self.dereplicate_operation(**vars(args))\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/drep/controller.py\", line 86, in dereplicate_operation\r\n    drep.d_workflows.dereplicate_wrapper(kwargs['work_directory'],**kwargs)\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/drep/d_workflows.py\", line 36, in dereplicate_wrapper\r\n    drep.d_cluster.d_cluster_wrapper(wd, **kwargs)\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/drep/d_cluster.py\", line 75, in d_cluster_wrapper\r\n    data_folder, wd=workDirectory, **kwargs)\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/drep/d_cluster.py\", line 145, in cluster_genomes\r\n    Cdb, cluster_ret = cluster_mash_database(Mdb, **kwargs)\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/drep/d_cluster.py\", line 570, in cluster_mash_database\r\n    linkage_db = db.pivot(\"genome1\",\"genome2\",\"dist\")\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/pandas/core/frame.py\", line 4382, in pivot\r\n    return pivot(self, index=index, columns=columns, values=values)\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/pandas/core/reshape/reshape.py\", line 389, in pivot\r\n    return indexed.unstack(columns)\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/pandas/core/series.py\", line 2224, in unstack\r\n    return unstack(self, level, fill_value)\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/pandas/core/reshape/reshape.py\", line 474, in unstack\r\n    fill_value=fill_value)\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/pandas/core/reshape/reshape.py\", line 116, in __init__\r\n    self._make_selectors()\r\n  File \"/home/johdro/.conda/envs/drep/lib/python3.6/site-packages/pandas/core/reshape/reshape.py\", line 154, in _make_selectors\r\n    raise ValueError('Index contains duplicate entries, '\r\nValueError: Index contains duplicate entries, cannot reshape\r\n```\r\n\r\nIt would be great if dRep could also do ANI clustering and representative picking for smaller bins which usually get sorted out, this is the real challenge in metagenome data.\r\n\r\nBest,\r\nJohannes"},"comment":{"url":"https://api.github.com/repos/MrOlm/drep/issues/comments/374321240","html_url":"https://github.com/MrOlm/drep/issues/25#issuecomment-374321240","issue_url":"https://api.github.com/repos/MrOlm/drep/issues/25","id":374321240,"user":{"login":"MrOlm","id":13424205,"avatar_url":"https://avatars1.githubusercontent.com/u/13424205?v=4","gravatar_id":"","url":"https://api.github.com/users/MrOlm","html_url":"https://github.com/MrOlm","followers_url":"https://api.github.com/users/MrOlm/followers","following_url":"https://api.github.com/users/MrOlm/following{/other_user}","gists_url":"https://api.github.com/users/MrOlm/gists{/gist_id}","starred_url":"https://api.github.com/users/MrOlm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MrOlm/subscriptions","organizations_url":"https://api.github.com/users/MrOlm/orgs","repos_url":"https://api.github.com/users/MrOlm/repos","events_url":"https://api.github.com/users/MrOlm/events{/privacy}","received_events_url":"https://api.github.com/users/MrOlm/received_events","type":"User","site_admin":false},"created_at":"2018-03-19T18:40:06Z","updated_at":"2018-03-19T18:40:06Z","author_association":"OWNER","body":"Great- thanks for suggestion. Will add to my internal \"to-do\" list"}}
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