{"action":"created","issue":{"url":"https://api.github.com/repos/ewels/MultiQC/issues/272","repository_url":"https://api.github.com/repos/ewels/MultiQC","labels_url":"https://api.github.com/repos/ewels/MultiQC/issues/272/labels{/name}","comments_url":"https://api.github.com/repos/ewels/MultiQC/issues/272/comments","events_url":"https://api.github.com/repos/ewels/MultiQC/issues/272/events","html_url":"https://github.com/ewels/MultiQC/issues/272","id":167545023,"number":272,"title":"No handlers could be found for logger \"multiqc\"","user":{"login":"royfrancis","id":5083500,"avatar_url":"https://avatars.githubusercontent.com/u/5083500?v=3","gravatar_id":"","url":"https://api.github.com/users/royfrancis","html_url":"https://github.com/royfrancis","followers_url":"https://api.github.com/users/royfrancis/followers","following_url":"https://api.github.com/users/royfrancis/following{/other_user}","gists_url":"https://api.github.com/users/royfrancis/gists{/gist_id}","starred_url":"https://api.github.com/users/royfrancis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/royfrancis/subscriptions","organizations_url":"https://api.github.com/users/royfrancis/orgs","repos_url":"https://api.github.com/users/royfrancis/repos","events_url":"https://api.github.com/users/royfrancis/events{/privacy}","received_events_url":"https://api.github.com/users/royfrancis/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/ewels/MultiQC/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/ewels/MultiQC/milestones/10","html_url":"https://github.com/ewels/MultiQC/milestones/v0.8","labels_url":"https://api.github.com/repos/ewels/MultiQC/milestones/10/labels","id":1798616,"number":10,"title":"v0.8","description":"Issues targeted for a version 0.8 release of MultiQC","creator":{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"open_issues":9,"closed_issues":10,"state":"open","created_at":"2016-05-31T12:18:59Z","updated_at":"2016-07-26T08:43:07Z","due_on":null,"closed_at":null},"comments":4,"created_at":"2016-07-26T08:06:10Z","updated_at":"2016-07-28T09:26:34Z","closed_at":"2016-07-26T08:43:06Z","body":"Hi,\r\nI have tried MultiQC with FastQC output and it works. Now I am trying with Skewer log files and I can't get it to work.\r\n\r\nRunning `multiqc ./path/` returns 'No results found'. So looking into the config, I found\r\n```\r\nskewer:\r\n    contents: COMMAND LINE:\t skewer\r\n```\r\nbut my log file has a full path `/path/path/skewer`. So, I created a multiqc_config.yaml in the working directory and included :\r\n\r\n```\r\nskewer:\r\n    contents: COMMAND LINE:\t /path/path/skewer\r\n```\r\n\r\nand ran `multiqc ./path/` I get this error: `No handlers could be found for logger \"multiqc\"`\r\n\r\nMy log files are named \r\n```\r\na02-trimmed.log\r\nk12-trimmed.log\r\nm13-trimmed.log\r\n...\r\n```\r\n\r\nI have tried many variations\r\n\r\n```\r\nsp:\r\n        skewer:\r\n                contents: COMMAND LINE:\t /path/path/skewer\r\n                fn: trimmed.log\r\n\r\n```\r\n```\r\nsp:\r\n        skewer:\r\n                fn: trimmed.log\r\n\r\n```\r\n```\r\nsp:\r\n        skewer:\r\n                contents: null\r\n                fn: trimmed.log\r\n\r\n```\r\nAlso tried `multiqc -m skewer ./path/`.\r\n\r\nThey all result in the same error."},"comment":{"url":"https://api.github.com/repos/ewels/MultiQC/issues/comments/235845173","html_url":"https://github.com/ewels/MultiQC/issues/272#issuecomment-235845173","issue_url":"https://api.github.com/repos/ewels/MultiQC/issues/272","id":235845173,"user":{"login":"ewels","id":465550,"avatar_url":"https://avatars.githubusercontent.com/u/465550?v=3","gravatar_id":"","url":"https://api.github.com/users/ewels","html_url":"https://github.com/ewels","followers_url":"https://api.github.com/users/ewels/followers","following_url":"https://api.github.com/users/ewels/following{/other_user}","gists_url":"https://api.github.com/users/ewels/gists{/gist_id}","starred_url":"https://api.github.com/users/ewels/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ewels/subscriptions","organizations_url":"https://api.github.com/users/ewels/orgs","repos_url":"https://api.github.com/users/ewels/repos","events_url":"https://api.github.com/users/ewels/events{/privacy}","received_events_url":"https://api.github.com/users/ewels/received_events","type":"User","site_admin":false},"created_at":"2016-07-28T09:26:34Z","updated_at":"2016-07-28T09:26:34Z","body":"Hi @royfrancis,\r\n\r\nAfter briefly panicking that the format of Skewer logs had changed in a recent update, I think I found the cause of the error. It was simply that your input files had the extension `.fq.gz` and the module was only written to handle `.fastq` extensions. I updated the regex and I think it should work now.\r\n\r\nLet me know if you have any problems with this version..\r\n\r\nCheers,\r\n\r\nPhil"}}
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