{"action":"created","issue":{"url":"https://api.github.com/repos/Ecogenomics/GroopM/issues/13","labels_url":"https://api.github.com/repos/Ecogenomics/GroopM/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/Ecogenomics/GroopM/issues/13/comments","events_url":"https://api.github.com/repos/Ecogenomics/GroopM/issues/13/events","html_url":"https://github.com/Ecogenomics/GroopM/issues/13","id":101250273,"number":13,"title":"negative dimensions error in groopm core","user":{"login":"koadman","id":242390,"avatar_url":"https://avatars.githubusercontent.com/u/242390?v=3","gravatar_id":"","url":"https://api.github.com/users/koadman","html_url":"https://github.com/koadman","followers_url":"https://api.github.com/users/koadman/followers","following_url":"https://api.github.com/users/koadman/following{/other_user}","gists_url":"https://api.github.com/users/koadman/gists{/gist_id}","starred_url":"https://api.github.com/users/koadman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/koadman/subscriptions","organizations_url":"https://api.github.com/users/koadman/orgs","repos_url":"https://api.github.com/users/koadman/repos","events_url":"https://api.github.com/users/koadman/events{/privacy}","received_events_url":"https://api.github.com/users/koadman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-08-16T10:21:56Z","updated_at":"2015-08-16T11:03:59Z","closed_at":null,"body":"Howdy gents, I have stumbled over the following using groopm core (0.3.4 from pip).\r\n\r\n**On stderr**:\r\n  File \"/shared/homes/117335/bin/groopm\", line 381, in <module>\r\n    GM_parser.parseOptions(args)\r\n  File \"/shared/homes/117335/lib/python2.7/site-packages/groopm/groopm.py\", line 138, in parseOptions\r\n    gf=gf)\r\n  File \"/shared/homes/117335/lib/python2.7/site-packages/groopm/cluster.py\", line 208, in makeCores\r\n    self.initialiseCores(kmerThreshold, coverageThreshold)\r\n  File \"/shared/homes/117335/lib/python2.7/site-packages/groopm/cluster.py\", line 247, in initialiseCores\r\n    putative_clusters = self.findNewClusterCenters(kmerThreshold, coverageThreshold)\r\n  File \"/shared/homes/117335/lib/python2.7/site-packages/groopm/cluster.py\", line 405, in findNewClusterCenters\r\n    coverageThreshold)\r\n  File \"/shared/homes/117335/lib/python2.7/site-packages/groopm/cluster.py\", line 670, in twoWayContraction\r\n    (k_partitions, k_keeps) = self.HP.houghPartition(k_dat[:,0], l_dat)\r\n  File \"/shared/homes/117335/lib/python2.7/site-packages/groopm/cluster.py\", line 1360, in houghPartition\r\n    imgTag=imgTag)\r\n  File \"/shared/homes/117335/lib/python2.7/site-packages/groopm/cluster.py\", line 1503, in recursiveSelect\r\n    (m, ret_point, accumulator) = self.houghTransform(tData.astype(float)[startRange:endRange,:], imShape)\r\n  File \"/shared/homes/117335/lib/python2.7/site-packages/groopm/cluster.py\", line 1730, in houghTransform\r\n    Cs = np_array(range(cols)*d_len)\r\nValueError: negative dimensions are not allowed\r\n\r\n\r\n**Standard output has the following**:\r\n\r\n*******************************************************************************\r\n [[GroopM 0.3.4]] Running in core creation mode...\r\n*******************************************************************************\r\nLoading data from: groopdb\r\n    GroopM DB version (5) up to date\r\n    Loaded indices with condition: length >= 1500\r\n    Working with: 597943 contigs\r\n    Loading coverage profiles\r\n    Loading PCA kmer sigs (42 dimensional space)\r\n    Loading PCA kmer variance (total variance: 0.80)\r\n    Loading contig names\r\n    Loading contig lengths (Total: 1831237672 BP)\r\n    Loading contig GC ratios (Average GC: 0.408)\r\n    Creating color map\r\n    { THIS: 0:47:35.123 || TOTAL: 0:47:35.165 }\r\n    Loading transformed data\r\n    Reticulating splines\r\n    { THIS: 0:06:47.138 || TOTAL: 0:54:22.303 }\r\nCreate cores\r\n     .... .... .... .... .... .... .... .... .... ....\r\n   0 Unexpected error: <type 'exceptions.ValueError'>\r\n\r\n\r\n\r\n**I ran**: \r\ngroopm core -b 500000 groopdb\r\n\r\nThe only possibly unusual issues are that (1) many contigs have no mapped reads, and (2) two earlier attempts at groopm core on the same DB were mercilessly killed by the job scheduler for exceeding RAM limits. "},"comment":{"url":"https://api.github.com/repos/Ecogenomics/GroopM/issues/comments/131524959","html_url":"https://github.com/Ecogenomics/GroopM/issues/13#issuecomment-131524959","issue_url":"https://api.github.com/repos/Ecogenomics/GroopM/issues/13","id":131524959,"user":{"login":"wwood","id":15348,"avatar_url":"https://avatars.githubusercontent.com/u/15348?v=3","gravatar_id":"","url":"https://api.github.com/users/wwood","html_url":"https://github.com/wwood","followers_url":"https://api.github.com/users/wwood/followers","following_url":"https://api.github.com/users/wwood/following{/other_user}","gists_url":"https://api.github.com/users/wwood/gists{/gist_id}","starred_url":"https://api.github.com/users/wwood/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/wwood/subscriptions","organizations_url":"https://api.github.com/users/wwood/orgs","repos_url":"https://api.github.com/users/wwood/repos","events_url":"https://api.github.com/users/wwood/events{/privacy}","received_events_url":"https://api.github.com/users/wwood/received_events","type":"User","site_admin":false},"created_at":"2015-08-16T11:03:59Z","updated_at":"2015-08-16T11:03:59Z","body":"OK, would sending the groopm dB be smaller?\n"}}