{"action":"created","issue":{"url":"https://api.github.com/repos/fungs/taxator-tk/issues/51","repository_url":"https://api.github.com/repos/fungs/taxator-tk","labels_url":"https://api.github.com/repos/fungs/taxator-tk/issues/51/labels{/name}","comments_url":"https://api.github.com/repos/fungs/taxator-tk/issues/51/comments","events_url":"https://api.github.com/repos/fungs/taxator-tk/issues/51/events","html_url":"https://github.com/fungs/taxator-tk/issues/51","id":150054401,"number":51,"title":"taxator: terminates when running with 24 threads","user":{"login":"fungs","id":8776981,"avatar_url":"https://avatars.githubusercontent.com/u/8776981?v=3","gravatar_id":"","url":"https://api.github.com/users/fungs","html_url":"https://github.com/fungs","followers_url":"https://api.github.com/users/fungs/followers","following_url":"https://api.github.com/users/fungs/following{/other_user}","gists_url":"https://api.github.com/users/fungs/gists{/gist_id}","starred_url":"https://api.github.com/users/fungs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fungs/subscriptions","organizations_url":"https://api.github.com/users/fungs/orgs","repos_url":"https://api.github.com/users/fungs/repos","events_url":"https://api.github.com/users/fungs/events{/privacy}","received_events_url":"https://api.github.com/users/fungs/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/fungs/taxator-tk/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-04-21T12:06:07Z","updated_at":"2016-04-21T15:00:49Z","closed_at":null,"body":"The error message is:\r\n\r\ntaxator: /usr/include/boost/thread/pthread/condition_variable.hpp:125: boost::condition_variable_any::~condition_variable_any(): Assertion `!pthread_mutex_destroy(&internal_mutex)' failed.\r\nTerminated"},"comment":{"url":"https://api.github.com/repos/fungs/taxator-tk/issues/comments/212960762","html_url":"https://github.com/fungs/taxator-tk/issues/51#issuecomment-212960762","issue_url":"https://api.github.com/repos/fungs/taxator-tk/issues/51","id":212960762,"user":{"login":"fungs","id":8776981,"avatar_url":"https://avatars.githubusercontent.com/u/8776981?v=3","gravatar_id":"","url":"https://api.github.com/users/fungs","html_url":"https://github.com/fungs","followers_url":"https://api.github.com/users/fungs/followers","following_url":"https://api.github.com/users/fungs/following{/other_user}","gists_url":"https://api.github.com/users/fungs/gists{/gist_id}","starred_url":"https://api.github.com/users/fungs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fungs/subscriptions","organizations_url":"https://api.github.com/users/fungs/orgs","repos_url":"https://api.github.com/users/fungs/repos","events_url":"https://api.github.com/users/fungs/events{/privacy}","received_events_url":"https://api.github.com/users/fungs/received_events","type":"User","site_admin":false},"created_at":"2016-04-21T15:00:49Z","updated_at":"2016-04-21T15:00:49Z","body":"Thanks, I'm adding your findings when run with one core here:\r\n\r\n```\r\nAn unrecoverable error occurred: std::exception\r\n\r\nHere is some debugging information to locate the problem:\r\n/home/johdro/projects/taxator-tk_default.git/src/fileparser.hh(52): Throw in function FileParser<FactoryType>::RecordType* FileParser<FactoryType>::next() [with FactoryType = AlignmentRecordFactory<AlignmentRecordTaxonomy>; FileParser<FactoryType>::RecordType = AlignmentRecordTaxonomy]\r\nDynamic exception type: boost::exception_detail::clone_impl<Exception>\r\nstd::exception::what: std::exception\r\n[exception_tag_line*] = 2\r\n[exception_tag_taxid*] = 349521\r\n[exception_tag_general*] = bad alignment reference taxon\r\n```\r\n\r\nIn all cases (reduced files, normal file, one core, multiple cores) the alignment file sample.alignments.gz is generated but never with more than 1000 lines (looks like the alignment tool is not running properly or there is some buffer limitation)."}}