{"action":"created","issue":{"url":"https://api.github.com/repos/dongjaek/LAST-Plus/issues/8","labels_url":"https://api.github.com/repos/dongjaek/LAST-Plus/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/dongjaek/LAST-Plus/issues/8/comments","events_url":"https://api.github.com/repos/dongjaek/LAST-Plus/issues/8/events","html_url":"https://github.com/dongjaek/LAST-Plus/issues/8","id":107804325,"number":8,"title":"lastdb+ is throwing assertion error","user":{"login":"mhuntemann","id":1672329,"avatar_url":"https://avatars.githubusercontent.com/u/1672329?v=3","gravatar_id":"","url":"https://api.github.com/users/mhuntemann","html_url":"https://github.com/mhuntemann","followers_url":"https://api.github.com/users/mhuntemann/followers","following_url":"https://api.github.com/users/mhuntemann/following{/other_user}","gists_url":"https://api.github.com/users/mhuntemann/gists{/gist_id}","starred_url":"https://api.github.com/users/mhuntemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mhuntemann/subscriptions","organizations_url":"https://api.github.com/users/mhuntemann/orgs","repos_url":"https://api.github.com/users/mhuntemann/repos","events_url":"https://api.github.com/users/mhuntemann/events{/privacy}","received_events_url":"https://api.github.com/users/mhuntemann/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-09-22T21:14:44Z","updated_at":"2015-09-23T03:09:39Z","closed_at":null,"body":"Hi!\r\n\r\nI am trying to rebuild with lastdb+ a protein database that I already built once successfully with the original lastdb. The input fasta file is about 11GB in size.  With the new lastdb+ I am getting an assertion error every time after a couple of minutes and the program exits with 134:\r\n\r\nmarcelh@gpint106:/global/projectb/sandbox/omics/marcelh/NR/nr-20150315$ lastdb+ -p -v last+_nr_db nr.faa\r\nlastdb: reading nr.faa...\r\nlastdb+: MultiSequence.cc:130: void cbrc::MultiSequence::finish(): Assertion `ends.v.back() == seq.v.size()' failed.\r\nAborted\r\nmarcelh@gpint106:/global/projectb/sandbox/omics/marcelh/NR/nr-20150315$ echo $?\r\n134\r\nmarcelh@gpint106:/global/projectb/sandbox/omics/marcelh/NR/nr-20150315$\r\n\r\n\r\nThe program runs fine on the first few sequences of the file though:\r\n\r\nmarcelh@gpint106:/global/projectb/sandbox/omics/marcelh/NR/nr-20150315$ head -100 nr.faa > test.faa\r\nmarcelh@gpint106:/global/projectb/sandbox/omics/marcelh/NR/nr-20150315$ lastdb+ -p -v last+_test_db test.faa\r\nlastdb: reading test.faa...\r\nlastdb: writing...\r\nlastdb: sorting...\r\nlastdb: bucketing...\r\nlastdb: writing...\r\nlastdb: done!\r\nmarcelh@gpint106:/global/projectb/sandbox/omics/marcelh/NR/nr-20150315$ echo $?\r\n0\r\nmarcelh@gpint106:/global/projectb/sandbox/omics/marcelh/NR/nr-20150315$\r\n\r\n\r\nWhat can I do to help debug this?\r\n\r\n\r\nAdditionally, is it possible to create only one big database instead of several partitions?\r\n\r\n\r\nThanks,\r\nMarcel\r\n \r\n\r\n"},"comment":{"url":"https://api.github.com/repos/dongjaek/LAST-Plus/issues/comments/142478515","html_url":"https://github.com/dongjaek/LAST-Plus/issues/8#issuecomment-142478515","issue_url":"https://api.github.com/repos/dongjaek/LAST-Plus/issues/8","id":142478515,"user":{"login":"dongjaek","id":3348514,"avatar_url":"https://avatars.githubusercontent.com/u/3348514?v=3","gravatar_id":"","url":"https://api.github.com/users/dongjaek","html_url":"https://github.com/dongjaek","followers_url":"https://api.github.com/users/dongjaek/followers","following_url":"https://api.github.com/users/dongjaek/following{/other_user}","gists_url":"https://api.github.com/users/dongjaek/gists{/gist_id}","starred_url":"https://api.github.com/users/dongjaek/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dongjaek/subscriptions","organizations_url":"https://api.github.com/users/dongjaek/orgs","repos_url":"https://api.github.com/users/dongjaek/repos","events_url":"https://api.github.com/users/dongjaek/events{/privacy}","received_events_url":"https://api.github.com/users/dongjaek/received_events","type":"User","site_admin":false},"created_at":"2015-09-23T03:09:39Z","updated_at":"2015-09-23T03:09:39Z","body":"I'll push a new version of lastdb+ which should not have this problem when formatting a database tomorrow.\r\nlastal+ should run against any database previously formatted by an earlier version of lastdb, regardless of if it's lastdb+ or not. \r\nRegarding the sorting of the output could you post the first few hundred lines of the output file here or send it to me at david.kim9325@gmail.com ? I'll take a look at it and see where the problem is coming from. Also please use the https://github.com/hallamlab/LAST-Plus version as this branch is my own personal branch for improvements and experiments."}}