{"action":"created","issue":{"url":"https://api.github.com/repos/fxia22/HINGE/issues/50","repository_url":"https://api.github.com/repos/fxia22/HINGE","labels_url":"https://api.github.com/repos/fxia22/HINGE/issues/50/labels{/name}","comments_url":"https://api.github.com/repos/fxia22/HINGE/issues/50/comments","events_url":"https://api.github.com/repos/fxia22/HINGE/issues/50/events","html_url":"https://github.com/fxia22/HINGE/issues/50","id":165660622,"number":50,"title":"seg fault on the ecoli demo","user":{"login":"StefanoLonardi","id":18489339,"avatar_url":"https://avatars.githubusercontent.com/u/18489339?v=3","gravatar_id":"","url":"https://api.github.com/users/StefanoLonardi","html_url":"https://github.com/StefanoLonardi","followers_url":"https://api.github.com/users/StefanoLonardi/followers","following_url":"https://api.github.com/users/StefanoLonardi/following{/other_user}","gists_url":"https://api.github.com/users/StefanoLonardi/gists{/gist_id}","starred_url":"https://api.github.com/users/StefanoLonardi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/StefanoLonardi/subscriptions","organizations_url":"https://api.github.com/users/StefanoLonardi/orgs","repos_url":"https://api.github.com/users/StefanoLonardi/repos","events_url":"https://api.github.com/users/StefanoLonardi/events{/privacy}","received_events_url":"https://api.github.com/users/StefanoLonardi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-07-14T21:15:26Z","updated_at":"2016-07-15T03:13:53Z","closed_at":null,"body":"I was able to compile and install the tool. When I tried to run the demo on ecoli I was able to run everything OK until this point:\r\n\r\n```\r\nstelo@H4:~/HINGE/data$ mkdir log\r\nstelo@H4:~/HINGE/data$ Reads_filter --db ecoli --las ecoli.las -x ecoli --config ~/HINGE/utils/nominal.ini\r\n[2016-07-14 14:06:57.906] [log] [info] Reads filtering\r\n[2016-07-14 14:06:57.906] [log] [info] name of db: ecoli, name of .las file ecoli.las\r\n[2016-07-14 14:06:57.906] [log] [info] name of fasta: , name of .paf file\r\n[2016-07-14 14:06:57.906] [log] [info] Parameters passed in\r\n[filter]\r\nlength_threshold = 1000;\r\nquality_threshold = 0.23;\r\nn_iter = 3; // filter iteration\r\naln_threshold = 1000;\r\nmin_cov = 5;\r\ncut_off = 300;\r\ntheta = 300;\r\nuse_qv = true;\r\n[running]\r\nn_proc = 12;\r\n[draft]\r\nmin_cov = 10;\r\ntrim = 200;\r\nedge_safe = 100;\r\ntspace = 900;\r\nstep = 50;\r\n[consensus]\r\nmin_length = 4000;\r\ntrim_end = 200;\r\nbest_n = 1;\r\nquality_threshold = 0.23;\r\n\r\n[layout]\r\nhinge_slack = 1000\r\nmin_connected_component_size = 8\r\n[2016-07-14 14:06:57.910] [log] [info] Load alignments from ecoli.las\r\n[2016-07-14 14:06:57.910] [log] [info] # Alignments: 15491688\r\n[2016-07-14 14:06:57.910] [log] [info] # Reads: 82590\r\n[2016-07-14 14:07:07.139] [log] [info] Input data finished\r\n[2016-07-14 14:07:07.198] [log] [info] No debug restrictions.\r\n[2016-07-14 14:07:07.247] [log] [info] use_qv_mask set to true\r\n[2016-07-14 14:07:07.247] [log] [info] use_qv_mask set to true\r\n[2016-07-14 14:07:07.247] [log] [info] number processes set to 12\r\n[2016-07-14 14:07:07.247] [log] [info] LENGTH_THRESHOLD = 1000\r\n[2016-07-14 14:07:07.247] [log] [info] QUALITY_THRESHOLD = 0.23\r\n[2016-07-14 14:07:07.247] [log] [info] N_ITER = 3\r\n[2016-07-14 14:07:07.247] [log] [info] ALN_THRESHOLD = 1000\r\n[2016-07-14 14:07:07.247] [log] [info] MIN_COV = 5\r\n[2016-07-14 14:07:07.247] [log] [info] CUT_OFF = 300\r\n[2016-07-14 14:07:07.247] [log] [info] THETA = 300\r\n[2016-07-14 14:07:07.247] [log] [info] EST_COV = 0\r\n[2016-07-14 14:07:07.247] [log] [info] reso = 40\r\n[2016-07-14 14:07:07.247] [log] [info] use_coverage_mask = true\r\n[2016-07-14 14:07:07.247] [log] [info] COVERAGE_FRACTION = 3\r\n[2016-07-14 14:07:07.247] [log] [info] MIN_REPEAT_ANNOTATION_THRESHOLD = 10\r\n[2016-07-14 14:07:07.247] [log] [info] MAX_REPEAT_ANNOTATION_THRESHOLD = 20\r\n[2016-07-14 14:07:07.247] [log] [info] REPEAT_ANNOTATION_GAP_THRESHOLD = 300\r\n[2016-07-14 14:07:07.247] [log] [info] NO_HINGE_REGION = 500\r\n[2016-07-14 14:07:07.247] [log] [info] HINGE_MIN_SUPPORT = 7\r\n[2016-07-14 14:07:07.247] [log] [info] HINGE_BIN_PILEUP_THRESHOLD = 7\r\n[2016-07-14 14:07:07.247] [log] [info] HINGE_READ_UNBRIDGED_THRESHOLD = 6\r\n[2016-07-14 14:07:07.247] [log] [info] HINGE_BIN_LENGTH = 200\r\n[2016-07-14 14:07:07.247] [log] [info] HINGE_TOLERANCE_LENGTH = 100\r\nSegmentation fault (core dumped)\r\n```\r\nFile `log_2016-07-14_14-06.txt` in the directory log is empty"},"comment":{"url":"https://api.github.com/repos/fxia22/HINGE/issues/comments/232850031","html_url":"https://github.com/fxia22/HINGE/issues/50#issuecomment-232850031","issue_url":"https://api.github.com/repos/fxia22/HINGE/issues/50","id":232850031,"user":{"login":"fxia22","id":5158896,"avatar_url":"https://avatars.githubusercontent.com/u/5158896?v=3","gravatar_id":"","url":"https://api.github.com/users/fxia22","html_url":"https://github.com/fxia22","followers_url":"https://api.github.com/users/fxia22/followers","following_url":"https://api.github.com/users/fxia22/following{/other_user}","gists_url":"https://api.github.com/users/fxia22/gists{/gist_id}","starred_url":"https://api.github.com/users/fxia22/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fxia22/subscriptions","organizations_url":"https://api.github.com/users/fxia22/orgs","repos_url":"https://api.github.com/users/fxia22/repos","events_url":"https://api.github.com/users/fxia22/events{/privacy}","received_events_url":"https://api.github.com/users/fxia22/received_events","type":"User","site_admin":false},"created_at":"2016-07-15T03:13:53Z","updated_at":"2016-07-15T03:13:53Z","body":"Hi @StefanoLonardi:\r\n\r\nThis problem is because your .las file contains duplicated records, \r\n\r\nMake sure you run `rm ecoli.*.ecoli.*.las` before running `LAmerge ecoli.las ecoli.*.las`\r\n\r\nIn the log, the number of alignements should be 7745844 rather than 15491688.\r\n\r\nBest,\r\nFei"}}
{"actor":{"display_login":"fxia22"}}