{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/wasabi/issues/3","repository_url":"https://api.github.com/repos/COMBINE-lab/wasabi","labels_url":"https://api.github.com/repos/COMBINE-lab/wasabi/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/wasabi/issues/3/comments","events_url":"https://api.github.com/repos/COMBINE-lab/wasabi/issues/3/events","html_url":"https://github.com/COMBINE-lab/wasabi/issues/3","id":161257713,"number":3,"title":"Salmon Error","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":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2016-06-20T18:07:50Z","updated_at":"2016-06-20T20:45:03Z","closed_at":null,"body":"Using this with some salmon files for import into sleuth.\r\nI get this error:\r\n```\r\nError in setnames(quant, c(\"target_id\", \"length\", \"tpm\", \"est_counts\")) : \r\n  Can't assign 4 names to a 5 column data.table\r\n```\r\nMy data file (quant.sf) looks like this\r\n```\r\nName\tLength\tEffectiveLength\tTPM\tNumReads\r\nENSDART00000171117.1\t11\t11\t0\t0\r\nENSDART00000162914.1\t10\t10\t0\t0\r\nENSDART00000172037.1\t344\t169.752\t4.10497\t9\r\n...\r\n```\r\nAnd I can't get to help\r\n`?prepare_fish_for_sleuth`"},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/wasabi/issues/comments/227263805","html_url":"https://github.com/COMBINE-lab/wasabi/issues/3#issuecomment-227263805","issue_url":"https://api.github.com/repos/COMBINE-lab/wasabi/issues/3","id":227263805,"user":{"login":"rob-p","id":361470,"avatar_url":"https://avatars.githubusercontent.com/u/361470?v=3","gravatar_id":"","url":"https://api.github.com/users/rob-p","html_url":"https://github.com/rob-p","followers_url":"https://api.github.com/users/rob-p/followers","following_url":"https://api.github.com/users/rob-p/following{/other_user}","gists_url":"https://api.github.com/users/rob-p/gists{/gist_id}","starred_url":"https://api.github.com/users/rob-p/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rob-p/subscriptions","organizations_url":"https://api.github.com/users/rob-p/orgs","repos_url":"https://api.github.com/users/rob-p/repos","events_url":"https://api.github.com/users/rob-p/events{/privacy}","received_events_url":"https://api.github.com/users/rob-p/received_events","type":"User","site_admin":false},"created_at":"2016-06-20T20:45:03Z","updated_at":"2016-06-20T20:45:03Z","body":"Hrmm; then it seems something is not being written as expected.  The way you're running `salmon` seems fine, but the output should look something like this:\r\n\r\n```\r\n├── aux\r\n│   ├── expected_bias.gz\r\n│   ├── observed_bias.gz\r\n│   ├── fld.gz\r\n│   └── meta_info.json\r\n├── cmd_info.json\r\n├── libFormatCounts.txt\r\n├── libParams\r\n│   └── flenDist.txt\r\n├── logs\r\n│   └── salmon_quant.log\r\n└── quant.sf\r\n```\r\n\r\nThe `aux` subdirectory of the quantification directory is where `salmon` stores metainformation about the run, and where `wasabi` looks to determine which input routine it should use.  Salmon should complain and exit if it is unable to create this directory, unless something very strange is happening in the underlying filesystem."}}
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