{"action":"created","issue":{"url":"https://api.github.com/repos/mcveanlab/mccortex/issues/37","repository_url":"https://api.github.com/repos/mcveanlab/mccortex","labels_url":"https://api.github.com/repos/mcveanlab/mccortex/issues/37/labels{/name}","comments_url":"https://api.github.com/repos/mcveanlab/mccortex/issues/37/comments","events_url":"https://api.github.com/repos/mcveanlab/mccortex/issues/37/events","html_url":"https://github.com/mcveanlab/mccortex/issues/37","id":150719244,"number":37,"title":"Assert Failed assem2str(): strlen(assem_stop_str[assem]) < size","user":{"login":"tseemann","id":453972,"avatar_url":"https://avatars.githubusercontent.com/u/453972?v=3","gravatar_id":"","url":"https://api.github.com/users/tseemann","html_url":"https://github.com/tseemann","followers_url":"https://api.github.com/users/tseemann/followers","following_url":"https://api.github.com/users/tseemann/following{/other_user}","gists_url":"https://api.github.com/users/tseemann/gists{/gist_id}","starred_url":"https://api.github.com/users/tseemann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tseemann/subscriptions","organizations_url":"https://api.github.com/users/tseemann/orgs","repos_url":"https://api.github.com/users/tseemann/repos","events_url":"https://api.github.com/users/tseemann/events{/privacy}","received_events_url":"https://api.github.com/users/tseemann/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-04-25T01:00:37Z","updated_at":"2016-04-26T15:40:18Z","closed_at":"2016-04-26T15:37:25Z","body":"Any value for `-C <float>` in `contigs` causes assert error:\r\n\r\n```\r\n% mccortex63 contigs -C 0.5 -f -o foo1.fa -p infer.ctp.gz infer.ctx\r\n\r\n[25 Apr 2016 10:59:35-XuR][cmd] mccortex63 contigs -C 0.5 -f -o foo1.fa -p infer.ctp.gz infer.ctx\r\n[25 Apr 2016 10:59:35-XuR][cwd] /mnt/seq/JOBS/MDU/J2016-06490/nullarbor.ST80/2014-23625\r\n[25 Apr 2016 10:59:35-XuR][version] mccortex=86b4ffe zlib=1.2.7 htslib=1.3-37-gfc93dfc ASSERTS=ON hash=Lookup3 CHECKS=ON k=33..63\r\n[25 Apr 2016 10:59:35-XuR] Taking number of kmers as genome size: 2,918,130\r\n[25 Apr 2016 10:59:35-XuR][memory] 202 bits per kmer\r\n[25 Apr 2016 10:59:35-XuR][memory] graph: 94.9MB\r\n[25 Apr 2016 10:59:35-XuR][memory] paths: 30.1MB\r\n[25 Apr 2016 10:59:35-XuR][memory] total: 95.1MB of 377.6GB RAM\r\n[25 Apr 2016 10:59:35-XuR][hasht] Allocating table with 3,932,160 entries, using 60.2MB\r\n[25 Apr 2016 10:59:35-XuR][hasht]  number of buckets: 131,072, bucket size: 30\r\n[25 Apr 2016 10:59:35-XuR][graph] kmer-size: 63; colours: 1; capacity: 3,932,160\r\n[25 Apr 2016 10:59:35-XuR][GPathReader] need 7216 paths 16810 bytes\r\n[25 Apr 2016 10:59:35-XuR][GPathSet] Allocating for 7,216 paths, 7KB colset, 9.4KB seq => 143.3KB total\r\n[25 Apr 2016 10:59:35-XuR][FileFilter] Loading file infer.ctx [1 colour]\r\n[25 Apr 2016 10:59:35-XuR][GReader] 2,918,130 kmers, 58.4MB filesize\r\n[25 Apr 2016 10:59:35-XuR][GReader] Loaded 2,918,130 / 2,918,130 (100.00%) of kmers parsed\r\n[25 Apr 2016 10:59:35-XuR][hasht] buckets: 131,072 [2^17]; bucket size: 30; memory: 60.2MB; occupancy: 2,918,130 / 3,932,160 (74.21%)\r\n[25 Apr 2016 10:59:35-XuR][hasht]  collisions  0: 2901076\r\n[25 Apr 2016 10:59:35-XuR][hasht]  collisions  1: 16416\r\n[25 Apr 2016 10:59:35-XuR][hasht]  collisions  2: 609\r\n[25 Apr 2016 10:59:35-XuR][hasht]  collisions  3: 25\r\n[25 Apr 2016 10:59:35-XuR][hasht]  collisions  4: 3\r\n[25 Apr 2016 10:59:35-XuR][hasht]  collisions  5: 1\r\n[25 Apr 2016 10:59:35-XuR][FileFilter] Loading file infer.ctp.gz [1 colour]\r\n[25 Apr 2016 10:59:35-XuR][GPathSet] Allocating for 32,768 paths, 32KB colset, 384KB seq => 1MB total\r\n[25 Apr 2016 10:59:35-XuR] Loaded 7,216 paths from 1,688 kmers\r\n[25 Apr 2016 10:59:35-XuR][Assemble] Assembling contigs with 2 threads, walking colour 0\r\n[25 Apr 2016 10:59:35-XuR][Assemble] Using missing info check: yes\r\n[25 Apr 2016 10:59:35-XuR][Assemble] Stop traversal if step cummulative confidence < 0.500000\r\n[25 Apr 2016 10:59:35-XuR][Assemble]   Writing contigs to foo1.fa\r\n[25 Apr 2016 10:59:35-XuR][Assemble] Seeding with random kmers...\r\n[src/tools/assemble_stats.c:43] Assert Failed assem2str(): strlen(assem_stop_str[assem]) < size\r\n[25 Apr 2016 10:59:35-XuR] Assert Error\r\nAborted (core dumped)\r\n```"},"comment":{"url":"https://api.github.com/repos/mcveanlab/mccortex/issues/comments/214787069","html_url":"https://github.com/mcveanlab/mccortex/issues/37#issuecomment-214787069","issue_url":"https://api.github.com/repos/mcveanlab/mccortex/issues/37","id":214787069,"user":{"login":"noporpoise","id":1274443,"avatar_url":"https://avatars.githubusercontent.com/u/1274443?v=3","gravatar_id":"","url":"https://api.github.com/users/noporpoise","html_url":"https://github.com/noporpoise","followers_url":"https://api.github.com/users/noporpoise/followers","following_url":"https://api.github.com/users/noporpoise/following{/other_user}","gists_url":"https://api.github.com/users/noporpoise/gists{/gist_id}","starred_url":"https://api.github.com/users/noporpoise/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/noporpoise/subscriptions","organizations_url":"https://api.github.com/users/noporpoise/orgs","repos_url":"https://api.github.com/users/noporpoise/repos","events_url":"https://api.github.com/users/noporpoise/events{/privacy}","received_events_url":"https://api.github.com/users/noporpoise/received_events","type":"User","site_admin":false},"created_at":"2016-04-26T15:40:18Z","updated_at":"2016-04-26T15:40:18Z","body":"Fixed - thanks for all the testing. Much appreciated."}}