{"action":"created","issue":{"url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/79","repository_url":"https://api.github.com/repos/Ecogenomics/CheckM","labels_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/79/labels{/name}","comments_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/79/comments","events_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/79/events","html_url":"https://github.com/Ecogenomics/CheckM/issues/79","id":185657176,"number":79,"title":"Can't find prodigal  on system path","user":{"login":"LovelornPig","id":8847420,"avatar_url":"https://avatars.githubusercontent.com/u/8847420?v=3","gravatar_id":"","url":"https://api.github.com/users/LovelornPig","html_url":"https://github.com/LovelornPig","followers_url":"https://api.github.com/users/LovelornPig/followers","following_url":"https://api.github.com/users/LovelornPig/following{/other_user}","gists_url":"https://api.github.com/users/LovelornPig/gists{/gist_id}","starred_url":"https://api.github.com/users/LovelornPig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LovelornPig/subscriptions","organizations_url":"https://api.github.com/users/LovelornPig/orgs","repos_url":"https://api.github.com/users/LovelornPig/repos","events_url":"https://api.github.com/users/LovelornPig/events{/privacy}","received_events_url":"https://api.github.com/users/LovelornPig/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-10-27T12:41:13Z","updated_at":"2016-10-27T15:37:26Z","closed_at":null,"body":"First, I use virtualenv to active a python2 environment and install checkm by pip.\r\n\r\nThen I create a scrtpt  checkm_metaotu.sh :  \r\n      source  /share/backup/zhujie/software/checkm/activate\r\n      checkm lineage_wf -t 8 -x fa /share/backup/zhujie/biodata/checkm_input_metaotu \r\n /share/backup/zhujie/biodata/checkm_output_metaotu > checkm_metaotu.log 2>&1\r\n\r\nThen I create a qsub script  qsub_checkm_metaotu.sh:\r\n      qsub -cwd -q st.q -l vf=20G,p=8 check_metaotu.sh &\r\n\r\nBut when I run: ./qsub_checkm_metaotu.sh\r\nI got a error in the checkm_metaotu.log:\r\n     *******************************************************\r\n      [CheckM - tree] Placing bins in reference genome tree.\r\n     *******************************************************\r\n      [Error] Make sure prodigal is on your system path.\r\n      Controlled exit resulting from an unrecoverable error or warning.\r\n\r\nIn fact, I already added prodigal path to my ~/.bashrc and source it.\r\nSo, I really want to know what I did wrong.\r\nPlease hele me, thanks very much:)\r\n"},"comment":{"url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/comments/256679054","html_url":"https://github.com/Ecogenomics/CheckM/issues/79#issuecomment-256679054","issue_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/79","id":256679054,"user":{"login":"dparks1134","id":3688336,"avatar_url":"https://avatars.githubusercontent.com/u/3688336?v=3","gravatar_id":"","url":"https://api.github.com/users/dparks1134","html_url":"https://github.com/dparks1134","followers_url":"https://api.github.com/users/dparks1134/followers","following_url":"https://api.github.com/users/dparks1134/following{/other_user}","gists_url":"https://api.github.com/users/dparks1134/gists{/gist_id}","starred_url":"https://api.github.com/users/dparks1134/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dparks1134/subscriptions","organizations_url":"https://api.github.com/users/dparks1134/orgs","repos_url":"https://api.github.com/users/dparks1134/repos","events_url":"https://api.github.com/users/dparks1134/events{/privacy}","received_events_url":"https://api.github.com/users/dparks1134/received_events","type":"User","site_admin":false},"created_at":"2016-10-27T15:37:26Z","updated_at":"2016-10-27T15:37:26Z","body":"I can't say I follow everything you have done, but I would take the error message at face value. Are you sure prodigal and an executable called <code>prodigal</code> is on your path even in the qsub environment? "}}
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