{"action":"created","issue":{"url":"https://api.github.com/repos/tanghaibao/jcvi/issues/14","repository_url":"https://api.github.com/repos/tanghaibao/jcvi","labels_url":"https://api.github.com/repos/tanghaibao/jcvi/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/tanghaibao/jcvi/issues/14/comments","events_url":"https://api.github.com/repos/tanghaibao/jcvi/issues/14/events","html_url":"https://github.com/tanghaibao/jcvi/issues/14","id":161783753,"number":14,"title":"allmaps fails in the final phase","user":{"login":"StefanoLonardi","id":18489339,"avatar_url":"https://avatars.githubusercontent.com/u/18489339?v=3","gravatar_id":"","url":"https://api.github.com/users/StefanoLonardi","html_url":"https://github.com/StefanoLonardi","followers_url":"https://api.github.com/users/StefanoLonardi/followers","following_url":"https://api.github.com/users/StefanoLonardi/following{/other_user}","gists_url":"https://api.github.com/users/StefanoLonardi/gists{/gist_id}","starred_url":"https://api.github.com/users/StefanoLonardi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/StefanoLonardi/subscriptions","organizations_url":"https://api.github.com/users/StefanoLonardi/orgs","repos_url":"https://api.github.com/users/StefanoLonardi/repos","events_url":"https://api.github.com/users/StefanoLonardi/events{/privacy}","received_events_url":"https://api.github.com/users/StefanoLonardi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-06-22T20:55:42Z","updated_at":"2016-06-22T21:54:25Z","closed_at":null,"body":"I am trying to anchor a draft assembly composed of 795 contigs to a genetic map with 36,828 markers in 11 linkage groups.\r\n\r\n**ALLMAPS** works fine solving the optimization problem for each chromosome, then it fails at the end with the following error message.\r\n```\r\nTraceback (most recent call last):\r\n  File \"/usr/lib/python2.7/runpy.py\", line 162, in _run_module_as_main\r\n    \"__main__\", fname, loader, pkg_name)\r\n  File \"/usr/lib/python2.7/runpy.py\", line 72, in _run_code\r\n    exec code in run_globals\r\n  File \"/usr/local/lib/python2.7/dist-packages/jcvi/assembly/allmaps.py\", line 1684, in <module>\r\n    main()\r\n  File \"/usr/local/lib/python2.7/dist-packages/jcvi/assembly/allmaps.py\", line 820, in main\r\n    p.dispatch(globals())\r\n  File \"/usr/local/lib/python2.7/dist-packages/jcvi/apps/base.py\", line 81, in dispatch\r\n    globals[action](sys.argv[2:])\r\n  File \"/usr/local/lib/python2.7/dist-packages/jcvi/assembly/allmaps.py\", line 1331, in path\r\n    build([inputbed, fastafile])\r\n  File \"/usr/local/lib/python2.7/dist-packages/jcvi/assembly/allmaps.py\", line 1451, in build\r\n    fromagp([combined_agp, scaffolds, combined_fasta])\r\n  File \"/usr/local/lib/python2.7/dist-packages/jcvi/formats/chain.py\", line 153, in fromagp\r\n    tSize = componentsizes[tName]\r\nKeyError: 'tig00000085'\r\n```\r\n(the full log is attached)\r\n[log.txt](https://github.com/tanghaibao/jcvi/files/328726/log.txt)\r\n\r\nI want to note that tig00000085 exists in the original scaffold file  `quiver62fast.fasta`, but it seems that **allmaps** overwrites the `quiver62fast.fasta` in this line:\r\n```\r\n11:44:56 [base] cat quiver62fast.chr.fasta quiver62fast.unplaced.fasta >quiver62fast.fasta\r\n```\r\nand in that new file `quiver62fast.fasta` tig00000085 does not exist anymore . Would that explain the KeyError? Why is **allmaps** overwriting the input files? Any advice on how to get rid of the error?"},"comment":{"url":"https://api.github.com/repos/tanghaibao/jcvi/issues/comments/227888870","html_url":"https://github.com/tanghaibao/jcvi/issues/14#issuecomment-227888870","issue_url":"https://api.github.com/repos/tanghaibao/jcvi/issues/14","id":227888870,"user":{"login":"StefanoLonardi","id":18489339,"avatar_url":"https://avatars.githubusercontent.com/u/18489339?v=3","gravatar_id":"","url":"https://api.github.com/users/StefanoLonardi","html_url":"https://github.com/StefanoLonardi","followers_url":"https://api.github.com/users/StefanoLonardi/followers","following_url":"https://api.github.com/users/StefanoLonardi/following{/other_user}","gists_url":"https://api.github.com/users/StefanoLonardi/gists{/gist_id}","starred_url":"https://api.github.com/users/StefanoLonardi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/StefanoLonardi/subscriptions","organizations_url":"https://api.github.com/users/StefanoLonardi/orgs","repos_url":"https://api.github.com/users/StefanoLonardi/repos","events_url":"https://api.github.com/users/StefanoLonardi/events{/privacy}","received_events_url":"https://api.github.com/users/StefanoLonardi/received_events","type":"User","site_admin":false},"created_at":"2016-06-22T21:54:25Z","updated_at":"2016-06-22T21:54:25Z","body":"You are right! Renaming the name of the bedfile to something else did the trick! Thanks so much."}}
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