{"action":"created","issue":{"url":"https://api.github.com/repos/bcgsc/abyss/issues/91","labels_url":"https://api.github.com/repos/bcgsc/abyss/issues/91/labels{/name}","comments_url":"https://api.github.com/repos/bcgsc/abyss/issues/91/comments","events_url":"https://api.github.com/repos/bcgsc/abyss/issues/91/events","html_url":"https://github.com/bcgsc/abyss/issues/91","id":124254079,"number":91,"title":"Recipe for target '<name>' failed -- Fails while \"generating adjacency?\"","user":{"login":"mebbert","id":1953713,"avatar_url":"https://avatars.githubusercontent.com/u/1953713?v=3","gravatar_id":"","url":"https://api.github.com/users/mebbert","html_url":"https://github.com/mebbert","followers_url":"https://api.github.com/users/mebbert/followers","following_url":"https://api.github.com/users/mebbert/following{/other_user}","gists_url":"https://api.github.com/users/mebbert/gists{/gist_id}","starred_url":"https://api.github.com/users/mebbert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mebbert/subscriptions","organizations_url":"https://api.github.com/users/mebbert/orgs","repos_url":"https://api.github.com/users/mebbert/repos","events_url":"https://api.github.com/users/mebbert/events{/privacy}","received_events_url":"https://api.github.com/users/mebbert/received_events","type":"User","site_admin":false},"labels":[],"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":4,"created_at":"2015-12-29T19:03:56Z","updated_at":"2015-12-29T22:28:08Z","closed_at":null,"body":"Dear abyss,\r\n\r\nThank you for your help and support. I'm assembling a genome but I get the following error (output truncated):\r\n\r\n    Loaded 2601815360 k-mer\r\n    Minimum k-mer coverage is 2\r\n    Using a coverage threshold of 2...\r\n    The median k-mer coverage is 6\r\n    The reconstruction is 1556402828\r\n    The k-mer coverage threshold is 2.44949\r\n    Setting parameter e (erode) to 2\r\n    Setting parameter E (erodeStrand) to 1\r\n    Setting parameter c (coverage) to 2.44949\r\n    Generating adjacency\r\n    Reaping losing child 0x23b7cf0 PID 45187\r\n    /usr/local/bin/abyss-pe:471: recipe for target '<name>-1.fa' failed\r\n    make: *** [<name>-1.fa] Killed\r\n    Removing child 0x23b7cf0 PID 45187 from chain.\r\n    make: Leaving directory 'path/to/abyss/k29'\r\n\r\nComparing this output to that using the provided test data, it appears abyss is failing while \"generating adjacency.\" I don't see any existing issues on this matter. I also ran it with -d (debug) to see if there were any obvious errors, but I don't see anything.\r\n\r\nAny ideas?\r\n\r\nThanks again!"},"comment":{"url":"https://api.github.com/repos/bcgsc/abyss/issues/comments/167891013","html_url":"https://github.com/bcgsc/abyss/issues/91#issuecomment-167891013","issue_url":"https://api.github.com/repos/bcgsc/abyss/issues/91","id":167891013,"user":{"login":"mebbert","id":1953713,"avatar_url":"https://avatars.githubusercontent.com/u/1953713?v=3","gravatar_id":"","url":"https://api.github.com/users/mebbert","html_url":"https://github.com/mebbert","followers_url":"https://api.github.com/users/mebbert/followers","following_url":"https://api.github.com/users/mebbert/following{/other_user}","gists_url":"https://api.github.com/users/mebbert/gists{/gist_id}","starred_url":"https://api.github.com/users/mebbert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mebbert/subscriptions","organizations_url":"https://api.github.com/users/mebbert/orgs","repos_url":"https://api.github.com/users/mebbert/repos","events_url":"https://api.github.com/users/mebbert/events{/privacy}","received_events_url":"https://api.github.com/users/mebbert/received_events","type":"User","site_admin":false},"created_at":"2015-12-29T22:28:08Z","updated_at":"2015-12-29T22:28:08Z","body":"Without /1 and /2 I got the error `All reads are mateless` and followed the tips here: https://www.biostars.org/p/93814/\r\n\r\nHere is what the read IDs looked like before:\r\n\r\n    @D00723:25:C6C71ANXX:3:1101:1481:2023 1:N:0:13\r\n    ...\r\n\r\n    @D00723:25:C6C71ANXX:3:1101:1481:2023 2:N:0:13\r\n    ...\r\n\r\nI'll rerun and report. Thanks!"}}