{"action":"created","issue":{"url":"https://api.github.com/repos/hall-lab/svtools/issues/247","repository_url":"https://api.github.com/repos/hall-lab/svtools","labels_url":"https://api.github.com/repos/hall-lab/svtools/issues/247/labels{/name}","comments_url":"https://api.github.com/repos/hall-lab/svtools/issues/247/comments","events_url":"https://api.github.com/repos/hall-lab/svtools/issues/247/events","html_url":"https://github.com/hall-lab/svtools/issues/247","id":298539115,"number":247,"title":"KeyError: PE (lmerge step)","user":{"login":"MehmetGoktay","id":8544565,"avatar_url":"https://avatars2.githubusercontent.com/u/8544565?v=4","gravatar_id":"","url":"https://api.github.com/users/MehmetGoktay","html_url":"https://github.com/MehmetGoktay","followers_url":"https://api.github.com/users/MehmetGoktay/followers","following_url":"https://api.github.com/users/MehmetGoktay/following{/other_user}","gists_url":"https://api.github.com/users/MehmetGoktay/gists{/gist_id}","starred_url":"https://api.github.com/users/MehmetGoktay/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MehmetGoktay/subscriptions","organizations_url":"https://api.github.com/users/MehmetGoktay/orgs","repos_url":"https://api.github.com/users/MehmetGoktay/repos","events_url":"https://api.github.com/users/MehmetGoktay/events{/privacy}","received_events_url":"https://api.github.com/users/MehmetGoktay/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":12,"created_at":"2018-02-20T10:20:03Z","updated_at":"2018-03-26T13:39:52Z","closed_at":null,"author_association":"NONE","body":"Hi Dave,\r\n\r\nI try to genotype bunch of samples with svtools lsort, svtools lmerge and svtools genotype.\r\n\r\nI try to genotype around 1.2k samples with svtools. If I downsample this collection for example (100 accessions) I do have no problem. Eveything works properly but today I wanted to genotype everything together (1.2k samples). lsort worked but, I can not do lmerge step. \r\n\r\nI keep having this following error: \r\n\r\n File \"path/miniconda2/bin/svtools\", line 6, in <module>\r\n    sys.exit(svtools.cli.main())\r\n  File \"path/miniconda2/lib/python2.7/site-packages/svtools-0.3.2-py2.7.egg/svtools/cli.py\", line 78, in main\r\n  File \"path/miniconda2/lib/python2.7/site-packages/svtools-0.3.2-py2.7.egg/svtools/lmerge.py\", line 632, in run_from_args\r\n  File \"path/miniconda2/lib/python2.7/site-packages/svtools-0.3.2-py2.7.egg/svtools/lmerge.py\", line 597, in l_cluster_by_line\r\n  File \"path/miniconda2/lib/python2.7/site-packages/svtools-0.3.2-py2.7.egg/svtools/lmerge.py\", line 539, in r_cluster\r\n  File \"path/miniconda2/lib/python2.7/site-packages/svtools-0.3.2-py2.7.egg/svtools/lmerge.py\", line 422, in merge\r\nKeyError: 'PE'\r\n\r\nI m not so sure if there is any problematic sample which causes this or if it is an memory issue. Or something else.\r\n\r\nIf you can give me any idea to solve this problem, it would be awesome.\r\n\r\nBest,\r\nMehmet \r\n"},"comment":{"url":"https://api.github.com/repos/hall-lab/svtools/issues/comments/376169176","html_url":"https://github.com/hall-lab/svtools/issues/247#issuecomment-376169176","issue_url":"https://api.github.com/repos/hall-lab/svtools/issues/247","id":376169176,"user":{"login":"MehmetGoktay","id":8544565,"avatar_url":"https://avatars2.githubusercontent.com/u/8544565?v=4","gravatar_id":"","url":"https://api.github.com/users/MehmetGoktay","html_url":"https://github.com/MehmetGoktay","followers_url":"https://api.github.com/users/MehmetGoktay/followers","following_url":"https://api.github.com/users/MehmetGoktay/following{/other_user}","gists_url":"https://api.github.com/users/MehmetGoktay/gists{/gist_id}","starred_url":"https://api.github.com/users/MehmetGoktay/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MehmetGoktay/subscriptions","organizations_url":"https://api.github.com/users/MehmetGoktay/orgs","repos_url":"https://api.github.com/users/MehmetGoktay/repos","events_url":"https://api.github.com/users/MehmetGoktay/events{/privacy}","received_events_url":"https://api.github.com/users/MehmetGoktay/received_events","type":"User","site_admin":false},"created_at":"2018-03-26T13:39:52Z","updated_at":"2018-03-26T13:39:52Z","author_association":"NONE","body":"Hi Dave,\r\n\r\nI have finished genotyping step and the error still remains. But always same samples give error. I think it somehow related with those accessions. (quality, sequencing tech etc.) \r\n\r\nSo I have removed them and I am good to go. \r\n\r\nThank you very much for your help,\r\nMehmet\r\n\r\n"}}
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