{"action":"created","issue":{"url":"https://api.github.com/repos/seqan/slimm/issues/33","repository_url":"https://api.github.com/repos/seqan/slimm","labels_url":"https://api.github.com/repos/seqan/slimm/issues/33/labels{/name}","comments_url":"https://api.github.com/repos/seqan/slimm/issues/33/comments","events_url":"https://api.github.com/repos/seqan/slimm/issues/33/events","html_url":"https://github.com/seqan/slimm/issues/33","id":381352024,"node_id":"MDU6SXNzdWUzODEzNTIwMjQ=","number":33,"title":"--directory option causes a segmentation fault and produce bad profiles","user":{"login":"temehi","id":2938760,"node_id":"MDQ6VXNlcjI5Mzg3NjA=","avatar_url":"https://avatars3.githubusercontent.com/u/2938760?v=4","gravatar_id":"","url":"https://api.github.com/users/temehi","html_url":"https://github.com/temehi","followers_url":"https://api.github.com/users/temehi/followers","following_url":"https://api.github.com/users/temehi/following{/other_user}","gists_url":"https://api.github.com/users/temehi/gists{/gist_id}","starred_url":"https://api.github.com/users/temehi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/temehi/subscriptions","organizations_url":"https://api.github.com/users/temehi/orgs","repos_url":"https://api.github.com/users/temehi/repos","events_url":"https://api.github.com/users/temehi/events{/privacy}","received_events_url":"https://api.github.com/users/temehi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-11-15T21:43:46Z","updated_at":"2018-11-15T22:51:35Z","closed_at":null,"author_association":"COLLABORATOR","body":"Running slimm on a batch BAM/FILES within a dirctory using the `--directory` producess a segmentation fault after processing a couple of files. The profiles generated and aother results are also corrupted except for the first file.\r\n\r\nBut running slimm on individual files one by one works fine and produces the correct result.\r\n\r\n```\r\n[Done!] File took 3 secs to process.\r\n\r\nReading 3 of 8 files ... (simulated_reads.sam)\r\n=================================================================\r\nIntializing coverages for all reference genome ... [0 secs]\r\nAnalysing alignments, reads and references ....... [0 secs]\r\n  345 records processed.\r\n    297 matching reads\r\n    297 uniquily matching reads\r\n  references with reads = 1\r\n  expected bins coverage = 0.00547997\r\n  bins coverage cut-off = 0.016129 (0.95 quantile)\r\n  uniq bins coverage cut-off = 0.00446429 (0.95 quantile)\r\n\r\nFiltering unlikely sequences ..................... [0 secs]\r\n  0 passed the threshould coverage.\r\n  1 ref's couldn't pass the coverage threshould.\r\n  0 ref's couldn't pass the uniq coverage threshould.\r\n  uniquily matching reads increased from 297 to 0\r\n\r\nAssigning reads to Least Common Ancestor (LCA) ... [0 secs]\r\nWriting taxnomic profile(s) ...................... /storage/mi/dadi/workspace/development/slimm/include/seqan/include/seqan/basic/basic_exception.h:363 FAILED!  (Uncaught exception of type std::out_of_range: _Map_base::at)\r\n\r\nstack trace:\r\n  0                      [0x449c19]\r\n  1                      [0x44a1c6]\r\n  2                      [0x47e326]\r\n  3                      [0x47e371]\r\n  4                      [0x471c73]\r\n  5                      [0x4d0e1f]\r\n  6                      [0x41d41c]\r\n  7                      [0x4459b8]\r\n  8                      [0x4230a0]\r\n  9                      [0x404cbf]\r\n 10                      [0x514740]\r\n 11                      [0x4060a7]\r\n\r\n[1]    3361 abort      slimm -v -d -o slimm_reports/ slimm_db_5K.sldb bam_files\r\n➜\r\n```"},"comment":{"url":"https://api.github.com/repos/seqan/slimm/issues/comments/439219387","html_url":"https://github.com/seqan/slimm/issues/33#issuecomment-439219387","issue_url":"https://api.github.com/repos/seqan/slimm/issues/33","id":439219387,"node_id":"MDEyOklzc3VlQ29tbWVudDQzOTIxOTM4Nw==","user":{"login":"temehi","id":2938760,"node_id":"MDQ6VXNlcjI5Mzg3NjA=","avatar_url":"https://avatars3.githubusercontent.com/u/2938760?v=4","gravatar_id":"","url":"https://api.github.com/users/temehi","html_url":"https://github.com/temehi","followers_url":"https://api.github.com/users/temehi/followers","following_url":"https://api.github.com/users/temehi/following{/other_user}","gists_url":"https://api.github.com/users/temehi/gists{/gist_id}","starred_url":"https://api.github.com/users/temehi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/temehi/subscriptions","organizations_url":"https://api.github.com/users/temehi/orgs","repos_url":"https://api.github.com/users/temehi/repos","events_url":"https://api.github.com/users/temehi/events{/privacy}","received_events_url":"https://api.github.com/users/temehi/received_events","type":"User","site_admin":false},"created_at":"2018-11-15T22:51:35Z","updated_at":"2018-11-15T22:51:35Z","author_association":"COLLABORATOR","body":"@fconstancias could you please check with the current version of SLIMM (0.2.4)?\r\nThe problem seemed to be fixed in the current version."}}
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