{"action":"created","issue":{"url":"https://api.github.com/repos/pfaucon/PBSIM-PacBio-Simulator/issues/15","repository_url":"https://api.github.com/repos/pfaucon/PBSIM-PacBio-Simulator","labels_url":"https://api.github.com/repos/pfaucon/PBSIM-PacBio-Simulator/issues/15/labels{/name}","comments_url":"https://api.github.com/repos/pfaucon/PBSIM-PacBio-Simulator/issues/15/comments","events_url":"https://api.github.com/repos/pfaucon/PBSIM-PacBio-Simulator/issues/15/events","html_url":"https://github.com/pfaucon/PBSIM-PacBio-Simulator/issues/15","id":387156682,"node_id":"MDU6SXNzdWUzODcxNTY2ODI=","number":15,"title":"--length-max ignored or toned down?","user":{"login":"FiniDG-HAN","id":31845711,"node_id":"MDQ6VXNlcjMxODQ1NzEx","avatar_url":"https://avatars3.githubusercontent.com/u/31845711?v=4","gravatar_id":"","url":"https://api.github.com/users/FiniDG-HAN","html_url":"https://github.com/FiniDG-HAN","followers_url":"https://api.github.com/users/FiniDG-HAN/followers","following_url":"https://api.github.com/users/FiniDG-HAN/following{/other_user}","gists_url":"https://api.github.com/users/FiniDG-HAN/gists{/gist_id}","starred_url":"https://api.github.com/users/FiniDG-HAN/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/FiniDG-HAN/subscriptions","organizations_url":"https://api.github.com/users/FiniDG-HAN/orgs","repos_url":"https://api.github.com/users/FiniDG-HAN/repos","events_url":"https://api.github.com/users/FiniDG-HAN/events{/privacy}","received_events_url":"https://api.github.com/users/FiniDG-HAN/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-12-04T07:39:02Z","updated_at":"2018-12-11T11:52:13Z","closed_at":null,"author_association":"NONE","body":"I have a question, because I ran the command:\r\n`pbsim --data-type CLR --depth 40 --length-min 500 --length-mean 12000 --length-max 40000 --accuracy-min 0.85 --accuracy-mean 0.87 --model_qc /PBSIM-PacBio-Simulator/data/model_qc_clr /path/to/ref.fasta --prefix /path/to/output/`\r\nand\r\n`pbsim --data-type CLR --depth 40 --length-min 500 --length-mean 12000 --length-max 70000 --accuracy-min 0.85 --accuracy-mean 0.87 --model_qc /PBSIM-PacBio-Simulator/data/model_qc_clr /path/to/ref.fasta --prefix /path/to/output/`\r\n\r\nAnd still (whatever I fill in as --length-max), My largest read is around 26000\r\n\r\nWhat is the reason for this? the ref.fasta I used is only 14 Mb in size, so might that be a reason? Or does PBSIM wants to make a specific read length distribution?"},"comment":{"url":"https://api.github.com/repos/pfaucon/PBSIM-PacBio-Simulator/issues/comments/446175977","html_url":"https://github.com/pfaucon/PBSIM-PacBio-Simulator/issues/15#issuecomment-446175977","issue_url":"https://api.github.com/repos/pfaucon/PBSIM-PacBio-Simulator/issues/15","id":446175977,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0NjE3NTk3Nw==","user":{"login":"FiniDG-HAN","id":31845711,"node_id":"MDQ6VXNlcjMxODQ1NzEx","avatar_url":"https://avatars3.githubusercontent.com/u/31845711?v=4","gravatar_id":"","url":"https://api.github.com/users/FiniDG-HAN","html_url":"https://github.com/FiniDG-HAN","followers_url":"https://api.github.com/users/FiniDG-HAN/followers","following_url":"https://api.github.com/users/FiniDG-HAN/following{/other_user}","gists_url":"https://api.github.com/users/FiniDG-HAN/gists{/gist_id}","starred_url":"https://api.github.com/users/FiniDG-HAN/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/FiniDG-HAN/subscriptions","organizations_url":"https://api.github.com/users/FiniDG-HAN/orgs","repos_url":"https://api.github.com/users/FiniDG-HAN/repos","events_url":"https://api.github.com/users/FiniDG-HAN/events{/privacy}","received_events_url":"https://api.github.com/users/FiniDG-HAN/received_events","type":"User","site_admin":false},"created_at":"2018-12-11T11:52:13Z","updated_at":"2018-12-11T11:52:13Z","author_association":"NONE","body":"After further investigation I think I found the answer. I put my thoughts here for future users.\r\nYou also have a parameter called --length-sd, which is set to default 2300 for CLR data-type. I believe this is the reason."}}
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