{"action":"created","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/2041","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/2041/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/2041/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/2041/events","html_url":"https://github.com/vgteam/vg/issues/2041","id":392804423,"node_id":"MDU6SXNzdWUzOTI4MDQ0MjM=","number":2041,"title":"RepresentativeTraversalFinder crashes on cactus graph with failed assertion","user":{"login":"eldariont","id":6477692,"node_id":"MDQ6VXNlcjY0Nzc2OTI=","avatar_url":"https://avatars0.githubusercontent.com/u/6477692?v=4","gravatar_id":"","url":"https://api.github.com/users/eldariont","html_url":"https://github.com/eldariont","followers_url":"https://api.github.com/users/eldariont/followers","following_url":"https://api.github.com/users/eldariont/following{/other_user}","gists_url":"https://api.github.com/users/eldariont/gists{/gist_id}","starred_url":"https://api.github.com/users/eldariont/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eldariont/subscriptions","organizations_url":"https://api.github.com/users/eldariont/orgs","repos_url":"https://api.github.com/users/eldariont/repos","events_url":"https://api.github.com/users/eldariont/events{/privacy}","received_events_url":"https://api.github.com/users/eldariont/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"adamnovak","id":5062495,"node_id":"MDQ6VXNlcjUwNjI0OTU=","avatar_url":"https://avatars1.githubusercontent.com/u/5062495?v=4","gravatar_id":"","url":"https://api.github.com/users/adamnovak","html_url":"https://github.com/adamnovak","followers_url":"https://api.github.com/users/adamnovak/followers","following_url":"https://api.github.com/users/adamnovak/following{/other_user}","gists_url":"https://api.github.com/users/adamnovak/gists{/gist_id}","starred_url":"https://api.github.com/users/adamnovak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamnovak/subscriptions","organizations_url":"https://api.github.com/users/adamnovak/orgs","repos_url":"https://api.github.com/users/adamnovak/repos","events_url":"https://api.github.com/users/adamnovak/events{/privacy}","received_events_url":"https://api.github.com/users/adamnovak/received_events","type":"User","site_admin":false},"assignees":[{"login":"adamnovak","id":5062495,"node_id":"MDQ6VXNlcjUwNjI0OTU=","avatar_url":"https://avatars1.githubusercontent.com/u/5062495?v=4","gravatar_id":"","url":"https://api.github.com/users/adamnovak","html_url":"https://github.com/adamnovak","followers_url":"https://api.github.com/users/adamnovak/followers","following_url":"https://api.github.com/users/adamnovak/following{/other_user}","gists_url":"https://api.github.com/users/adamnovak/gists{/gist_id}","starred_url":"https://api.github.com/users/adamnovak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamnovak/subscriptions","organizations_url":"https://api.github.com/users/adamnovak/orgs","repos_url":"https://api.github.com/users/adamnovak/repos","events_url":"https://api.github.com/users/adamnovak/events{/privacy}","received_events_url":"https://api.github.com/users/adamnovak/received_events","type":"User","site_admin":false}],"milestone":null,"comments":0,"created_at":"2018-12-19T22:35:36Z","updated_at":"2018-12-22T01:01:27Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Hi,\r\n\r\nI was running `toil-vg call` on one of my cactus graph and it crashed:\r\n```\r\nRuntimeError: Docker container for command vg call chunk_S288C.chrXVI_0_aug.vg -t 4 -S SRR4074257.recall.cactus.twoout -z chunk_S288C.chrXVI_0.trans -s chunk_S288C.chrXVI_0.support -b chunk_S288C.chrXVI_0.vg -u -n 0 -r S288C.chrXVI -c S288C.chrXVI -l 954457 -o 0 failed with code 134\r\n```\r\n\r\nI can reproduce the error with the following files and commands on vg v1.12.1-83-g9a00b102 \"Parolise\":\r\n`vg call chunk_S288C.chrI_0_aug.vg -t 4 -S SRR4074257.recall.cactus.twoout -z chunk_S288C.chrI_0.trans -s chunk_S288C.chrI_0.support -b chunk_S288C.chrI_0.vg -u -n 0 -r S288C.chrI -c S288C.chrI -l 219929 -o 0`\r\n\r\nFiles: https://www.dropbox.com/s/gfpdtmymjfjz90z/Archive.zip?dl=0\r\n\r\nResult:\r\n```\r\n...\r\nS288C.chrI\t23744\t5516691_5514212_5552938_5553675_5540725-5516691_5553675_5540725\tA\tAGG\t4473\tPASS\tDP=301;SVLEN=2;XSEE=9892,9893,9894,4887785;XREF\tGT:DP:XDP:AD:XADL:SB:XAAD\t1/0:301:140,237:120,181:-8.250185:60,60,95,86:181\r\nS288C.chrI\t23741\t5578978_5558693_5533720_5516691-5578978_5558693_4887786_5516691\tTTT\tGCG,GCA\t3402.67\tlowxadl\tDP=271;SVLEN=0,0;XSEE=9890,9891,9892,3945529,3945530,4887786;XREF\tGT:DP:XDP:AD:XADL:SB:XAAD\t1/2:271:140,237:0,181,90:-17.880078:0,0,79,102,39,51:271\r\nS288C.chrI\t23735\t5539370_5561058_5565421\tA\tG\t6762.33\tPASS\tDP=182;SVLEN=0;XSEE=9886,9887,9888,4777338;XREF\tGT:DP:XDP:AD:XADL:SB:XAAD\t1/1:182:140,237:1,181:.:0,1,78,103:181\r\nS288C.chrI\t23732\t5518064_5506440_5549947_5539370\tAG\tTT\t6963.8\tPASS\tDP=186;SVLEN=0;XSEE=9883,9884,9885,9886,3945528,5277386;XREF\tGT:DP:XDP:AD:XADL:SB:XAAD1/1:186:140,237:0,186:.:0,0,69,117:186\r\nS288C.chrI\t23728\t5560953_5550838_5518064\tA\tT\t7219\tPASS\tDP=192;SVLEN=0;XSEE=9881,9882,9883,3945527;XREF\tGT:DP:XDP:AD:XADL:SB:XAAD\t1/1:192:140,237:0,192:.:0,0,83,109:192\r\nS288C.chrI\t23722\t5582180_5573761_5533682_5506174_5503309_5529903_5560953-5582180_5556196_5533682_9879_9880_5560953\tTCGAG\tTCAGC,CCGAG\t2879.8\tlowxadl\tDP=238;SVLEN=0,0;XSEE=9876,9877,9878,9879,9880,9881,3311828,3945524,3945525,3945526,4887788,5089103;XREF\tGT:DP:XDP:AD:XADL:SB:XAAD\t1/2:238:140,237:19,141,78:-11.298452:6,13,64,77,32,46:219\r\nvg: src/traversal_finder.cpp:1146: vg::RepresentativeTraversalFinder::find_traversals(const vg::Snarl&)::<lambda(std::vector<vg::Visit>)>: Assertion `contents.first.count(augmented.graph.get_node(visit.node_id()))' failed.\r\nERROR: Signal 6 occurred. VG has crashed. Run 'vg bugs --new' to report a bug.\r\nStack trace path: /tmp/vg_crash_zg8mUz/stacktrace.txt\r\n```"},"comment":{"url":"https://api.github.com/repos/vgteam/vg/issues/comments/449532888","html_url":"https://github.com/vgteam/vg/issues/2041#issuecomment-449532888","issue_url":"https://api.github.com/repos/vgteam/vg/issues/2041","id":449532888,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0OTUzMjg4OA==","user":{"login":"adamnovak","id":5062495,"node_id":"MDQ6VXNlcjUwNjI0OTU=","avatar_url":"https://avatars1.githubusercontent.com/u/5062495?v=4","gravatar_id":"","url":"https://api.github.com/users/adamnovak","html_url":"https://github.com/adamnovak","followers_url":"https://api.github.com/users/adamnovak/followers","following_url":"https://api.github.com/users/adamnovak/following{/other_user}","gists_url":"https://api.github.com/users/adamnovak/gists{/gist_id}","starred_url":"https://api.github.com/users/adamnovak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/adamnovak/subscriptions","organizations_url":"https://api.github.com/users/adamnovak/orgs","repos_url":"https://api.github.com/users/adamnovak/repos","events_url":"https://api.github.com/users/adamnovak/events{/privacy}","received_events_url":"https://api.github.com/users/adamnovak/received_events","type":"User","site_admin":false},"created_at":"2018-12-22T01:01:27Z","updated_at":"2018-12-22T01:01:27Z","author_association":"CONTRIBUTOR","body":"OK, I've managed to replicate this. It looks like the traversal finder is trying to find a traversal that includes something that isn't actually in the snarl that it is trying to find a traversal of, which it detects is nonsensical.\r\n\r\nTo actually find and fix the problem, I'm going to have to break out just the subgraph of the offending snarl, make a little unit test out of it, and then fix it to pass. Not too hard, but I don't think I'm going to be able to get to it until January, unfortunately."}}
{"actor":{"display_login":"adamnovak"}}