{"action":"created","issue":{"url":"https://api.github.com/repos/nygenome/lancet/issues/22","repository_url":"https://api.github.com/repos/nygenome/lancet","labels_url":"https://api.github.com/repos/nygenome/lancet/issues/22/labels{/name}","comments_url":"https://api.github.com/repos/nygenome/lancet/issues/22/comments","events_url":"https://api.github.com/repos/nygenome/lancet/issues/22/events","html_url":"https://github.com/nygenome/lancet/issues/22","id":335710305,"node_id":"MDU6SXNzdWUzMzU3MTAzMDU=","number":22,"title":"std::bad_alloc error when calling variant using lancet","user":{"login":"Yiming-Shen","id":25326978,"node_id":"MDQ6VXNlcjI1MzI2OTc4","avatar_url":"https://avatars1.githubusercontent.com/u/25326978?v=4","gravatar_id":"","url":"https://api.github.com/users/Yiming-Shen","html_url":"https://github.com/Yiming-Shen","followers_url":"https://api.github.com/users/Yiming-Shen/followers","following_url":"https://api.github.com/users/Yiming-Shen/following{/other_user}","gists_url":"https://api.github.com/users/Yiming-Shen/gists{/gist_id}","starred_url":"https://api.github.com/users/Yiming-Shen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Yiming-Shen/subscriptions","organizations_url":"https://api.github.com/users/Yiming-Shen/orgs","repos_url":"https://api.github.com/users/Yiming-Shen/repos","events_url":"https://api.github.com/users/Yiming-Shen/events{/privacy}","received_events_url":"https://api.github.com/users/Yiming-Shen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-06-26T08:25:26Z","updated_at":"2018-06-28T16:02:48Z","closed_at":null,"author_association":"NONE","body":"Hi, I read your paper of lancet and I am really excited to see the tool being able to reduce STR false positives. \r\nI've just installed lancet on my Linux. But when I ran it on my target sequencing data (BAM files are generated by `bwa mem` algorithm):\r\n`lancet --num-threads 2 --active-region-off --tumor /path/to/the/indexed/tumor-bam --normal /path/to/the/indexed/normal-bam --ref humanhg38.fa --bed target.bed`\r\n\r\nThe log file is written:\r\n\r\n> Loaded 2290 from bedfile\r\n20654 total windows to process\r\nstarting thread 1 on 10324 windows\r\nstarting thread 2 on 10322 windows\r\nProcess reads\r\nProcess reads\r\n\r\nand then it threw error as:\r\n`terminate called after throwing an instance of 'std::bad_alloc'`\r\n`  what():  std::bad_alloc`\r\n and terminated.\r\n\r\nI am no expert in C but I assume this may related to some memory allocation problem.\r\n\r\nI wonder why the error occurred and what your suggestions are to resolve it? \r\n\r\nIf you need any more details please let me know.\r\n\r\nThanks,\r\nYiming"},"comment":{"url":"https://api.github.com/repos/nygenome/lancet/issues/comments/401086364","html_url":"https://github.com/nygenome/lancet/issues/22#issuecomment-401086364","issue_url":"https://api.github.com/repos/nygenome/lancet/issues/22","id":401086364,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMTA4NjM2NA==","user":{"login":"gnarzisi","id":7513490,"node_id":"MDQ6VXNlcjc1MTM0OTA=","avatar_url":"https://avatars3.githubusercontent.com/u/7513490?v=4","gravatar_id":"","url":"https://api.github.com/users/gnarzisi","html_url":"https://github.com/gnarzisi","followers_url":"https://api.github.com/users/gnarzisi/followers","following_url":"https://api.github.com/users/gnarzisi/following{/other_user}","gists_url":"https://api.github.com/users/gnarzisi/gists{/gist_id}","starred_url":"https://api.github.com/users/gnarzisi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gnarzisi/subscriptions","organizations_url":"https://api.github.com/users/gnarzisi/orgs","repos_url":"https://api.github.com/users/gnarzisi/repos","events_url":"https://api.github.com/users/gnarzisi/events{/privacy}","received_events_url":"https://api.github.com/users/gnarzisi/received_events","type":"User","site_admin":false},"created_at":"2018-06-28T16:02:48Z","updated_at":"2018-06-28T16:02:48Z","author_association":"COLLABORATOR","body":"I was able to run Lancet on your small BAMs without any problems. I have attached the output vcf file [test.vcf.zip](https://github.com/nygenome/lancet/files/2146032/test.vcf.zip). I used the exact same command as you:\r\n\r\n```\r\nlancet \r\n   --normal normal.chr1.6181470-6199619.bam \r\n   --tumor tumor.chr1.6181470-6199619.bam \r\n    --reg chr1:6181470-6199619 \r\n    --ref GRCh38.d1.vd1.fa\r\n```\r\n\r\nNot sure why it fails for you on the same data. \r\nCan you run your small test again using the -v option and share the output ? In verbose mode you may be able to identify at what step the code fails to run.\r\n"}}
{"actor":{"display_login":"gnarzisi"}}