{"action":"created","issue":{"url":"https://api.github.com/repos/ablab/spades/issues/160","repository_url":"https://api.github.com/repos/ablab/spades","labels_url":"https://api.github.com/repos/ablab/spades/issues/160/labels{/name}","comments_url":"https://api.github.com/repos/ablab/spades/issues/160/comments","events_url":"https://api.github.com/repos/ablab/spades/issues/160/events","html_url":"https://github.com/ablab/spades/issues/160","id":351001768,"node_id":"MDU6SXNzdWUzNTEwMDE3Njg=","number":160,"title":"gmapper: segmentation fault in gfa_arc_rm","user":{"login":"sjackman","id":291551,"node_id":"MDQ6VXNlcjI5MTU1MQ==","avatar_url":"https://avatars3.githubusercontent.com/u/291551?v=4","gravatar_id":"","url":"https://api.github.com/users/sjackman","html_url":"https://github.com/sjackman","followers_url":"https://api.github.com/users/sjackman/followers","following_url":"https://api.github.com/users/sjackman/following{/other_user}","gists_url":"https://api.github.com/users/sjackman/gists{/gist_id}","starred_url":"https://api.github.com/users/sjackman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sjackman/subscriptions","organizations_url":"https://api.github.com/users/sjackman/orgs","repos_url":"https://api.github.com/users/sjackman/repos","events_url":"https://api.github.com/users/sjackman/events{/privacy}","received_events_url":"https://api.github.com/users/sjackman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-08-15T23:23:04Z","updated_at":"2018-08-15T23:50:37Z","closed_at":null,"author_association":"NONE","body":"I'm attempting to align Nanopore reads to a Canu unitigs GFA file. I used `gfak fillseq` to add the sequences to the GFA file, and `sed 's/tig00*//g'` to convert the sequence names to numeric identifiers. The stack dump output by `spades-gmapper … | c++filt` is below.\r\n\r\n```\r\n❯❯❯ spades-gmapper foo.yaml foo.gfa gmapper.gfa -k15 -t16\r\n  0:00:00.000     4M / 4M    INFO    General                 (main.cpp                  : 168)   Starting GFA reader, built from N/A, git revision N/A\r\n  0:00:00.003     4M / 4M    INFO    General                 (main.cpp                  : 182)   Loading de Bruijn graph from foo.gfa\r\nThe program was terminated by segmentation fault\r\n=== Stack Trace ===\r\nspades-gmapper(utils::print_stacktrace()+0x38) [0x4d5988]\r\nspades-gmapper(utils::segfault_handler::handler(int)+0x36) [0x4d5af6]\r\n/gsc/btl/linuxbrew/lib/libc.so.6(+0x33070) [0x7f46355b3070]\r\nspades-gmapper(gfa_arc_rm+0x53) [0x5c81e3]\r\nspades-gmapper(gfa_cleanup+0x9) [0x5c8289]\r\nspades-gmapper(gfa_read+0x15a) [0x5c844a]\r\nspades-gmapper(gfa::GFAReader::GFAReader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xc) [0x56398c]\r\nspades-gmapper(LoadGraph(debruijn_graph::DeBruijnGraph&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x5b) [0x4d1dbb]\r\nspades-gmapper(main+0x2a4) [0x4c9084]\r\n/gsc/btl/linuxbrew/lib/libc.so.6(__libc_start_main+0xf5) [0x7f46355a0825]\r\nspades-gmapper(_start+0x29) [0x4ce349]\r\n```"},"comment":{"url":"https://api.github.com/repos/ablab/spades/issues/comments/413375583","html_url":"https://github.com/ablab/spades/issues/160#issuecomment-413375583","issue_url":"https://api.github.com/repos/ablab/spades/issues/160","id":413375583,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMzM3NTU4Mw==","user":{"login":"sjackman","id":291551,"node_id":"MDQ6VXNlcjI5MTU1MQ==","avatar_url":"https://avatars3.githubusercontent.com/u/291551?v=4","gravatar_id":"","url":"https://api.github.com/users/sjackman","html_url":"https://github.com/sjackman","followers_url":"https://api.github.com/users/sjackman/followers","following_url":"https://api.github.com/users/sjackman/following{/other_user}","gists_url":"https://api.github.com/users/sjackman/gists{/gist_id}","starred_url":"https://api.github.com/users/sjackman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sjackman/subscriptions","organizations_url":"https://api.github.com/users/sjackman/orgs","repos_url":"https://api.github.com/users/sjackman/repos","events_url":"https://api.github.com/users/sjackman/events{/privacy}","received_events_url":"https://api.github.com/users/sjackman/received_events","type":"User","site_admin":false},"created_at":"2018-08-15T23:50:37Z","updated_at":"2018-08-15T23:50:37Z","author_association":"NONE","body":"Ah, the problem appears to be that `gfak fillseq` didn't in fact fill in the sequences, and so they're still `*`. It'd still be good if it didn't segfault."}}
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