{"action":"created","issue":{"url":"https://api.github.com/repos/pcingola/SnpEff/issues/83","labels_url":"https://api.github.com/repos/pcingola/SnpEff/issues/83/labels{/name}","comments_url":"https://api.github.com/repos/pcingola/SnpEff/issues/83/comments","events_url":"https://api.github.com/repos/pcingola/SnpEff/issues/83/events","html_url":"https://github.com/pcingola/SnpEff/issues/83","id":77560475,"number":83,"title":"Interval has negative coordinates.","user":{"login":"coolucy","id":12492671,"avatar_url":"https://avatars.githubusercontent.com/u/12492671?v=3","gravatar_id":"","url":"https://api.github.com/users/coolucy","html_url":"https://github.com/coolucy","followers_url":"https://api.github.com/users/coolucy/followers","following_url":"https://api.github.com/users/coolucy/following{/other_user}","gists_url":"https://api.github.com/users/coolucy/gists{/gist_id}","starred_url":"https://api.github.com/users/coolucy/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/coolucy/subscriptions","organizations_url":"https://api.github.com/users/coolucy/orgs","repos_url":"https://api.github.com/users/coolucy/repos","events_url":"https://api.github.com/users/coolucy/events{/privacy}","received_events_url":"https://api.github.com/users/coolucy/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-05-18T08:30:39Z","updated_at":"2015-06-02T14:59:35Z","closed_at":null,"body":"Hi, \r\n\r\ni want to build a database from gff file, but i got the follow error. \r\n##########################################################################\r\nCaused by: java.lang.RuntimeException: Interval has negative coordinates.\r\n Class        : Exon\r\n Start        : -1\r\n End          : 240485\r\n ID           : exon:tetur03g00850.5\r\n Parent class : Transcript\r\n Parent       : scaffold_3:239958-244319, strand: -, id:mRNA:tetur03g00850\r\n   Exons:\r\n   scaffold_3:239958-240111 'exon:tetur03g00850.6', rank: 0, frame: 1, sequence:\r\n##########################################################################\r\n\r\nHowever, when i looked up the line, I couldn't find any nevative corrdinates.\r\n##########################################################################\r\nscaffold_3      EGN exon   240343 240486  .       -       1 ID=exon:tetur03g00850.5;Parent=mRNA:tetur03g00850;Ontology_term=SO:0000004\r\n##########################################################################\r\n\r\nSNPEFF version :  \"4.1d\"\r\ncommand line : \r\njava -Xmx4g -jar $SNPEFF build -gff3 -v Tetur_build\r\n\r\nTo build database i created a folder at /snpEff/data/Tetur/build\r\nand also genes.gff.gz, sequences.fa.gz\r\nand added a genome to the configuration file(http://snpeff.sourceforge.net/SnpEff_manual.html#databases).\r\n\r\nCould you please help me to fix it? \r\n"},"comment":{"url":"https://api.github.com/repos/pcingola/SnpEff/issues/comments/107983959","html_url":"https://github.com/pcingola/SnpEff/issues/83#issuecomment-107983959","issue_url":"https://api.github.com/repos/pcingola/SnpEff/issues/83","id":107983959,"user":{"login":"pcingola","id":1334427,"avatar_url":"https://avatars.githubusercontent.com/u/1334427?v=3","gravatar_id":"","url":"https://api.github.com/users/pcingola","html_url":"https://github.com/pcingola","followers_url":"https://api.github.com/users/pcingola/followers","following_url":"https://api.github.com/users/pcingola/following{/other_user}","gists_url":"https://api.github.com/users/pcingola/gists{/gist_id}","starred_url":"https://api.github.com/users/pcingola/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pcingola/subscriptions","organizations_url":"https://api.github.com/users/pcingola/orgs","repos_url":"https://api.github.com/users/pcingola/repos","events_url":"https://api.github.com/users/pcingola/events{/privacy}","received_events_url":"https://api.github.com/users/pcingola/received_events","type":"User","site_admin":false},"created_at":"2015-06-02T14:59:35Z","updated_at":"2015-06-02T14:59:35Z","body":"Sorry for the long delay answering your email, I was on vacation.\nI'm glad to hear it works OK.\n\n\nOn Tue, May 19, 2015 at 4:05 AM, coolucy <notifications@github.com> wrote:\n\n> I think I found the error.\n> the GFF file had an extra space in front of the start coordinate.\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/pcingola/SnpEff/issues/83#issuecomment-103390381>.\n>\n"}}