{"action":"opened","issue":{"url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/294","repository_url":"https://api.github.com/repos/CGATOxford/UMI-tools","labels_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/294/labels{/name}","comments_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/294/comments","events_url":"https://api.github.com/repos/CGATOxford/UMI-tools/issues/294/events","html_url":"https://github.com/CGATOxford/UMI-tools/issues/294","id":377462612,"node_id":"MDU6SXNzdWUzNzc0NjI2MTI=","number":294,"title":"Error on single-end sam file","user":{"login":"mandiedriskill","id":40249599,"node_id":"MDQ6VXNlcjQwMjQ5NTk5","avatar_url":"https://avatars3.githubusercontent.com/u/40249599?v=4","gravatar_id":"","url":"https://api.github.com/users/mandiedriskill","html_url":"https://github.com/mandiedriskill","followers_url":"https://api.github.com/users/mandiedriskill/followers","following_url":"https://api.github.com/users/mandiedriskill/following{/other_user}","gists_url":"https://api.github.com/users/mandiedriskill/gists{/gist_id}","starred_url":"https://api.github.com/users/mandiedriskill/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mandiedriskill/subscriptions","organizations_url":"https://api.github.com/users/mandiedriskill/orgs","repos_url":"https://api.github.com/users/mandiedriskill/repos","events_url":"https://api.github.com/users/mandiedriskill/events{/privacy}","received_events_url":"https://api.github.com/users/mandiedriskill/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-11-05T15:54:55Z","updated_at":"2018-11-05T15:54:55Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nI am try to run umi_tools dedupe, but I am running into the following error:\r\nTraceback (most recent call last):\r\n\r\n  File \"/Users/mandiedriskill/miniconda3/bin/umi_tools\", line 11, in <module>\r\n    sys.exit(main())\r\n  File \"/Users/mandiedriskill/miniconda3/lib/python3.6/site-packages/umi_tools/umi_tools.py\", line 59, in main\r\n    module.main(sys.argv)\r\n  File \"/Users/mandiedriskill/miniconda3/lib/python3.6/site-packages/umi_tools/dedup.py\", line 146, in main\r\n    raise ValueError(\"Input on standard in not currently supported\")\r\nValueError: Input on standard in not currently supported\r\n\r\nThis is the code and flags I am using:\r\numi_tools dedup --in-sam /Users/mandiedriskill/Desktop/Barkan_Project/view_cp_genome_102617_Total-15Dark_Rep1_mergedAligned.out.sam --out-sam new_test.bam --umi-separator=:\r\n\r\nThe sam file is sorted, but not indexed. \r\nAny help would be appreciate. Thanks"}}
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