{"action":"created","issue":{"url":"https://api.github.com/repos/seqan/seqan/issues/683","labels_url":"https://api.github.com/repos/seqan/seqan/issues/683/labels{/name}","comments_url":"https://api.github.com/repos/seqan/seqan/issues/683/comments","events_url":"https://api.github.com/repos/seqan/seqan/issues/683/events","html_url":"https://github.com/seqan/seqan/issues/683","id":47729606,"number":683,"title":"Implement direct BWT construction","user":{"login":"h-2","id":2996863,"avatar_url":"https://avatars.githubusercontent.com/u/2996863?v=3","gravatar_id":"","url":"https://api.github.com/users/h-2","html_url":"https://github.com/h-2","followers_url":"https://api.github.com/users/h-2/followers","following_url":"https://api.github.com/users/h-2/following{/other_user}","gists_url":"https://api.github.com/users/h-2/gists{/gist_id}","starred_url":"https://api.github.com/users/h-2/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/h-2/subscriptions","organizations_url":"https://api.github.com/users/h-2/orgs","repos_url":"https://api.github.com/users/h-2/repos","events_url":"https://api.github.com/users/h-2/events{/privacy}","received_events_url":"https://api.github.com/users/h-2/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/seqan/seqan/labels/enhancement","name":"enhancement","color":"84b6eb"},{"url":"https://api.github.com/repos/seqan/seqan/labels/feature","name":"feature","color":"009800"}],"state":"open","locked":false,"assignee":{"login":"cpockrandt","id":7328307,"avatar_url":"https://avatars.githubusercontent.com/u/7328307?v=3","gravatar_id":"","url":"https://api.github.com/users/cpockrandt","html_url":"https://github.com/cpockrandt","followers_url":"https://api.github.com/users/cpockrandt/followers","following_url":"https://api.github.com/users/cpockrandt/following{/other_user}","gists_url":"https://api.github.com/users/cpockrandt/gists{/gist_id}","starred_url":"https://api.github.com/users/cpockrandt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cpockrandt/subscriptions","organizations_url":"https://api.github.com/users/cpockrandt/orgs","repos_url":"https://api.github.com/users/cpockrandt/repos","events_url":"https://api.github.com/users/cpockrandt/events{/privacy}","received_events_url":"https://api.github.com/users/cpockrandt/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/seqan/seqan/milestones/4","html_url":"https://github.com/seqan/seqan/milestones/Release%202.1.0","labels_url":"https://api.github.com/repos/seqan/seqan/milestones/4/labels","id":813426,"number":4,"title":"Release 2.1.0","description":"Major release.","creator":{"login":"holtgrewe","id":521780,"avatar_url":"https://avatars.githubusercontent.com/u/521780?v=3","gravatar_id":"","url":"https://api.github.com/users/holtgrewe","html_url":"https://github.com/holtgrewe","followers_url":"https://api.github.com/users/holtgrewe/followers","following_url":"https://api.github.com/users/holtgrewe/following{/other_user}","gists_url":"https://api.github.com/users/holtgrewe/gists{/gist_id}","starred_url":"https://api.github.com/users/holtgrewe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/holtgrewe/subscriptions","organizations_url":"https://api.github.com/users/holtgrewe/orgs","repos_url":"https://api.github.com/users/holtgrewe/repos","events_url":"https://api.github.com/users/holtgrewe/events{/privacy}","received_events_url":"https://api.github.com/users/holtgrewe/received_events","type":"User","site_admin":false},"open_issues":49,"closed_issues":69,"state":"open","created_at":"2014-10-04T10:12:56Z","updated_at":"2015-11-09T16:17:35Z","due_on":"2016-02-29T23:00:00Z","closed_at":null},"comments":15,"created_at":"2014-11-04T16:03:00Z","updated_at":"2015-11-10T06:01:14Z","closed_at":null,"body":"I am trying to build an FM-Index over a 13GB fasta file. After one hour of processing with an average cpu-load of only 52% on one core the indexer used up all of the 260GB of external storage and crashed.\r\n\r\nIs it reasonable to see this as a bug? My math was that even if the full suffix array is built during FM-Index creation (is this necessary?), this will at most be 100GB big (2*4byte per entry, as overloaded by me) -- even if adding the complete FM-Index and its Fibres, disk-usage should be less than 150GB.\r\n\r\nAlso it is very difficult to tell where in the process of index creation it actually crashed, since there is no kind of progress indication. And even had it succeeded the cpu-usage is very sub-optimal. \r\n\r\nPlease don't see this as a rant, but I think we need to seriously improve this. I have been asked whether Lambda can search on 40-60GB of index and I really would not like to add an extra empty hard-drive as system requirement ;)"},"comment":{"url":"https://api.github.com/repos/seqan/seqan/issues/comments/155305768","html_url":"https://github.com/seqan/seqan/issues/683#issuecomment-155305768","issue_url":"https://api.github.com/repos/seqan/seqan/issues/683","id":155305768,"user":{"login":"esiragusa","id":172085,"avatar_url":"https://avatars.githubusercontent.com/u/172085?v=3","gravatar_id":"","url":"https://api.github.com/users/esiragusa","html_url":"https://github.com/esiragusa","followers_url":"https://api.github.com/users/esiragusa/followers","following_url":"https://api.github.com/users/esiragusa/following{/other_user}","gists_url":"https://api.github.com/users/esiragusa/gists{/gist_id}","starred_url":"https://api.github.com/users/esiragusa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/esiragusa/subscriptions","organizations_url":"https://api.github.com/users/esiragusa/orgs","repos_url":"https://api.github.com/users/esiragusa/repos","events_url":"https://api.github.com/users/esiragusa/events{/privacy}","received_events_url":"https://api.github.com/users/esiragusa/received_events","type":"User","site_admin":false},"created_at":"2015-11-10T06:01:14Z","updated_at":"2015-11-10T06:01:14Z","body":"@h-2 you have to merge it against v1.4.2, there are only a couple of new files..."}}