{"action":"created","issue":{"url":"https://api.github.com/repos/csmiller/EMIRGE/issues/27","repository_url":"https://api.github.com/repos/csmiller/EMIRGE","labels_url":"https://api.github.com/repos/csmiller/EMIRGE/issues/27/labels{/name}","comments_url":"https://api.github.com/repos/csmiller/EMIRGE/issues/27/comments","events_url":"https://api.github.com/repos/csmiller/EMIRGE/issues/27/events","html_url":"https://github.com/csmiller/EMIRGE/issues/27","id":173204896,"number":27,"title":"IndexError: Out of bounds on buffer access (axis 1)","user":{"login":"rbeinart","id":12304019,"avatar_url":"https://avatars.githubusercontent.com/u/12304019?v=3","gravatar_id":"","url":"https://api.github.com/users/rbeinart","html_url":"https://github.com/rbeinart","followers_url":"https://api.github.com/users/rbeinart/followers","following_url":"https://api.github.com/users/rbeinart/following{/other_user}","gists_url":"https://api.github.com/users/rbeinart/gists{/gist_id}","starred_url":"https://api.github.com/users/rbeinart/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rbeinart/subscriptions","organizations_url":"https://api.github.com/users/rbeinart/orgs","repos_url":"https://api.github.com/users/rbeinart/repos","events_url":"https://api.github.com/users/rbeinart/events{/privacy}","received_events_url":"https://api.github.com/users/rbeinart/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-08-25T13:36:20Z","updated_at":"2016-08-31T21:33:31Z","closed_at":null,"body":"Hi there,\r\nI'm running Emirge on a dataset that keeps getting to iteration 12 and then failing (see below). I saw someone posted about this error previously, and that it had to do with read length, but the comment below said this should not longer be an issue.\r\n\r\nAny ideas?\r\n\r\nI've run Emirge successfully on other datasets recently, so I'm not sure why this one is a problem.\r\n\r\nThanks!\r\n-Roxanne-\r\n\r\n\r\n\r\n\r\nDONE Reading bam file /n/girguis_lab/Users/rbeinart/Emirge/BC_metatranscriptome_Emirge_output/iter.12/bowtie.iter.12.PE.bam at Tue Aug 23 16:21:28\r\n2016 [1:11:31.149570]...\r\nCalculating likelihood (25714, 8320954) for iteration 13 at Tue Aug 23 16:22:47 2016...\r\n        Calculating Pr(N=n) for iteration 13 at Tue Aug 23 16:22:47 2016...\r\n        Loading probN for resume case from /n/girguis_lab/Users/rbeinart/Emirge/\r\nBC_metatranscriptome_Emirge_output/iter.13/probN.pkl\r\n        DONE calculating Pr(N=n) for iteration 13 at Tue Aug 23 16:22:54 2016 [0:00:06.533856]...\r\nTraceback (most recent call last):\r\n  File \"/n/girguis_lab/Users/rbeinart/Apps/EMIRGE-master/emirge.py\", line 1697, in <module>\r\n    main()\r\n  File \"/n/girguis_lab/Users/rbeinart/Apps/EMIRGE-master/emirge.py\", line 1688, in main\r\n    do_iterations(em, max_iter = options.iterations, save_every = options.save_every)\r\n  File \"/n/girguis_lab/Users/rbeinart/Apps/EMIRGE-master/emirge.py\", line 1444, in do_iterations\r\n    os.path.join(subdir, \"iter.%02d.cons.fasta\"%(em.iteration_i)))\r\n  File \"/n/girguis_lab/Users/rbeinart/Apps/EMIRGE-master/emirge.py\", line 491, in do_iteration\r\n    self.calc_likelihoods()\r\n  File \"/n/girguis_lab/Users/rbeinart/Apps/EMIRGE-master/emirge.py\", line 1141, in calc_likelihoods\r\n    lik_data)\r\n  File \"_emirge.pyx\", line 132, in _emirge._calc_likelihood (_emirge.c:2661)\r\n    s += ( qual2one_minus_p[qualints[i]] * probN_single[pos + i, j] )    # lookup table\r\nIndexError: Out of bounds on buffer access (axis 1)"},"comment":{"url":"https://api.github.com/repos/csmiller/EMIRGE/issues/comments/243909426","html_url":"https://github.com/csmiller/EMIRGE/issues/27#issuecomment-243909426","issue_url":"https://api.github.com/repos/csmiller/EMIRGE/issues/27","id":243909426,"user":{"login":"epruesse","id":2774474,"avatar_url":"https://avatars.githubusercontent.com/u/2774474?v=3","gravatar_id":"","url":"https://api.github.com/users/epruesse","html_url":"https://github.com/epruesse","followers_url":"https://api.github.com/users/epruesse/followers","following_url":"https://api.github.com/users/epruesse/following{/other_user}","gists_url":"https://api.github.com/users/epruesse/gists{/gist_id}","starred_url":"https://api.github.com/users/epruesse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/epruesse/subscriptions","organizations_url":"https://api.github.com/users/epruesse/orgs","repos_url":"https://api.github.com/users/epruesse/repos","events_url":"https://api.github.com/users/epruesse/events{/privacy}","received_events_url":"https://api.github.com/users/epruesse/received_events","type":"User","site_admin":false},"created_at":"2016-08-31T21:33:31Z","updated_at":"2016-08-31T21:33:31Z","body":"Hi Roxane,\r\nsorry for the late reply. \r\nCan you make the input data and parameters you used available to us? It's probably something else than the read length (I assume you already tried running with the max read len parameter set high), but it's much easier to debug and fix with a test case that reproduces it at hand.\r\nThanks,\r\nElmar"}}
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