{"action":"created","issue":{"url":"https://api.github.com/repos/vanheeringen-lab/gimmemotifs/issues/70","repository_url":"https://api.github.com/repos/vanheeringen-lab/gimmemotifs","labels_url":"https://api.github.com/repos/vanheeringen-lab/gimmemotifs/issues/70/labels{/name}","comments_url":"https://api.github.com/repos/vanheeringen-lab/gimmemotifs/issues/70/comments","events_url":"https://api.github.com/repos/vanheeringen-lab/gimmemotifs/issues/70/events","html_url":"https://github.com/vanheeringen-lab/gimmemotifs/issues/70","id":384078479,"node_id":"MDU6SXNzdWUzODQwNzg0Nzk=","number":70,"title":"UnboundLocalError: local variable 'valid_bg' referenced before assignment","user":{"login":"mdozmorov","id":864945,"node_id":"MDQ6VXNlcjg2NDk0NQ==","avatar_url":"https://avatars2.githubusercontent.com/u/864945?v=4","gravatar_id":"","url":"https://api.github.com/users/mdozmorov","html_url":"https://github.com/mdozmorov","followers_url":"https://api.github.com/users/mdozmorov/followers","following_url":"https://api.github.com/users/mdozmorov/following{/other_user}","gists_url":"https://api.github.com/users/mdozmorov/gists{/gist_id}","starred_url":"https://api.github.com/users/mdozmorov/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mdozmorov/subscriptions","organizations_url":"https://api.github.com/users/mdozmorov/orgs","repos_url":"https://api.github.com/users/mdozmorov/repos","events_url":"https://api.github.com/users/mdozmorov/events{/privacy}","received_events_url":"https://api.github.com/users/mdozmorov/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-11-25T13:21:54Z","updated_at":"2018-11-26T15:30:44Z","closed_at":"2018-11-26T15:30:44Z","author_association":"NONE","body":"Hi Simon,\r\nI've followed the https://gimmemotifs.readthedocs.io installation instructions. The Conda installation on macOS Sierra 10.12.6 worked fine, environment activated, genome annotations installed. Attempt to run basic analysis results in an error:\r\n```\r\n$ gimme motifs CTCF.bed -g hg19 -n test1\r\nSorry, motif prediction tool MEME is not supported\r\n```\r\nExcluding MEME doesn't help:\r\n```\r\n$ gimme motifs CTCF.bed -g hg19 -n test1 -t Homer,BioProspector\r\nTraceback (most recent call last):\r\n  File \"/Users/mdozmorov/miniconda2/envs/gimme/bin/gimme\", line 513, in <module>\r\n    args.func(args)\r\n  File \"/Users/mdozmorov/miniconda2/envs/gimme/lib/python3.6/site-packages/gimmemotifs/commands/motifs.py\", line 69, in motifs\r\n    gimme_motifs(args.inputfile, args.name, params)\r\n  File \"/Users/mdozmorov/miniconda2/envs/gimme/lib/python3.6/site-packages/gimmemotifs/denovo.py\", line 525, in gimme_motifs\r\n    input_type, background = check_denovo_input(inputfile, params)\r\n  File \"/Users/mdozmorov/miniconda2/envs/gimme/lib/python3.6/site-packages/gimmemotifs/validation.py\", line 60, in check_denovo_input\r\n    if not bg in valid_bg:\r\nUnboundLocalError: local variable 'valid_bg' referenced before assignment\r\n```\r\nThe head of my BED file:\r\n```\r\nchr1 850718 850942\r\nchr1 856275 856499\r\nchr1 862729 862953\r\nchr1 864695 864919\r\nchr1 872641 872865\r\nchr1 889157 889381\r\nchr1 889597 889821\r\nchr1 900920 901144\r\nchr1 907087 907311\r\nchr1 956668 956892\r\n```\r\nWhere to go from there?\r\n\r\nThanks,\r\nMikhail"},"comment":{"url":"https://api.github.com/repos/vanheeringen-lab/gimmemotifs/issues/comments/441680045","html_url":"https://github.com/vanheeringen-lab/gimmemotifs/issues/70#issuecomment-441680045","issue_url":"https://api.github.com/repos/vanheeringen-lab/gimmemotifs/issues/70","id":441680045,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MTY4MDA0NQ==","user":{"login":"mdozmorov","id":864945,"node_id":"MDQ6VXNlcjg2NDk0NQ==","avatar_url":"https://avatars2.githubusercontent.com/u/864945?v=4","gravatar_id":"","url":"https://api.github.com/users/mdozmorov","html_url":"https://github.com/mdozmorov","followers_url":"https://api.github.com/users/mdozmorov/followers","following_url":"https://api.github.com/users/mdozmorov/following{/other_user}","gists_url":"https://api.github.com/users/mdozmorov/gists{/gist_id}","starred_url":"https://api.github.com/users/mdozmorov/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mdozmorov/subscriptions","organizations_url":"https://api.github.com/users/mdozmorov/orgs","repos_url":"https://api.github.com/users/mdozmorov/repos","events_url":"https://api.github.com/users/mdozmorov/events{/privacy}","received_events_url":"https://api.github.com/users/mdozmorov/received_events","type":"User","site_admin":false},"created_at":"2018-11-26T15:30:44Z","updated_at":"2018-11-26T15:30:44Z","author_association":"NONE","body":"Thank you, @simonvh, @jonasungerback, the problem is indeed the misformatted BED file - spaces instead of tabs. Happen sometimes when you got the data from collaborators.\r\n\r\nClosing this issue. @jonasungerback, perhaps you can open a new one for your meme/trawler issue?   "}}
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