{"action":"created","issue":{"url":"https://api.github.com/repos/bcgsc/abyss/issues/84","labels_url":"https://api.github.com/repos/bcgsc/abyss/issues/84/labels{/name}","comments_url":"https://api.github.com/repos/bcgsc/abyss/issues/84/comments","events_url":"https://api.github.com/repos/bcgsc/abyss/issues/84/events","html_url":"https://github.com/bcgsc/abyss/issues/84","id":108465049,"number":84,"title":"Error with Assertion `isalpha(seq[0])' failed","user":{"login":"verne91","id":3148255,"avatar_url":"https://avatars.githubusercontent.com/u/3148255?v=3","gravatar_id":"","url":"https://api.github.com/users/verne91","html_url":"https://github.com/verne91","followers_url":"https://api.github.com/users/verne91/followers","following_url":"https://api.github.com/users/verne91/following{/other_user}","gists_url":"https://api.github.com/users/verne91/gists{/gist_id}","starred_url":"https://api.github.com/users/verne91/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/verne91/subscriptions","organizations_url":"https://api.github.com/users/verne91/orgs","repos_url":"https://api.github.com/users/verne91/repos","events_url":"https://api.github.com/users/verne91/events{/privacy}","received_events_url":"https://api.github.com/users/verne91/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/bcgsc/abyss/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":{"login":"benvvalk","id":1652775,"avatar_url":"https://avatars.githubusercontent.com/u/1652775?v=3","gravatar_id":"","url":"https://api.github.com/users/benvvalk","html_url":"https://github.com/benvvalk","followers_url":"https://api.github.com/users/benvvalk/followers","following_url":"https://api.github.com/users/benvvalk/following{/other_user}","gists_url":"https://api.github.com/users/benvvalk/gists{/gist_id}","starred_url":"https://api.github.com/users/benvvalk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benvvalk/subscriptions","organizations_url":"https://api.github.com/users/benvvalk/orgs","repos_url":"https://api.github.com/users/benvvalk/repos","events_url":"https://api.github.com/users/benvvalk/events{/privacy}","received_events_url":"https://api.github.com/users/benvvalk/received_events","type":"User","site_admin":false},"milestone":null,"comments":14,"created_at":"2015-09-26T13:45:25Z","updated_at":"2015-10-13T16:55:14Z","closed_at":null,"body":"Hi everyone,\r\n\r\nWhen I run the ABySS, I got an error with the message of \r\n```\r\nABYSS-P: ../Assembly/LoadAlgorithm.h:48: bool AssemblyAlgorithms::loadSequence(Graph *, std::basic_string<char, std::char_traits<char>, std::allocator<char>> &) [with Graph = NetworkSequenceCollection]: Assertion `isalpha(seq[0])' failed.\r\n```\r\n\r\nSo, how to deal with it?"},"comment":{"url":"https://api.github.com/repos/bcgsc/abyss/issues/comments/147776172","html_url":"https://github.com/bcgsc/abyss/issues/84#issuecomment-147776172","issue_url":"https://api.github.com/repos/bcgsc/abyss/issues/84","id":147776172,"user":{"login":"benvvalk","id":1652775,"avatar_url":"https://avatars.githubusercontent.com/u/1652775?v=3","gravatar_id":"","url":"https://api.github.com/users/benvvalk","html_url":"https://github.com/benvvalk","followers_url":"https://api.github.com/users/benvvalk/followers","following_url":"https://api.github.com/users/benvvalk/following{/other_user}","gists_url":"https://api.github.com/users/benvvalk/gists{/gist_id}","starred_url":"https://api.github.com/users/benvvalk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benvvalk/subscriptions","organizations_url":"https://api.github.com/users/benvvalk/orgs","repos_url":"https://api.github.com/users/benvvalk/repos","events_url":"https://api.github.com/users/benvvalk/events{/privacy}","received_events_url":"https://api.github.com/users/benvvalk/received_events","type":"User","site_admin":false},"created_at":"2015-10-13T16:55:14Z","updated_at":"2015-10-13T16:55:14Z","body":"Interesting.  Doesnt' FASTQValidator tell you where the bad characters are? I thought that was the purpose of the program.\r\n\r\nYou may also be able to run this command to highlight illegal characters in your sequence data and view them in `less`:\r\n```\r\nawk '(NR-1)%4==1' reads1_title.fq | LC_ALL=C egrep --color=always '[^a-zA-Z]' | less -R\r\n```\r\n\r\nAlso, I believe you should be able to attach the file directly to this ticket, if it is not too large (please use gzip).  As Shaun suggested, you can probably just send the first part of the file (e.g. first million records), as long as it reproduces the error.  (Use the `head` program to create a partial file and please test that the partial file still produces the error.)"}}