{"action":"opened","issue":{"url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/64","repository_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda","labels_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/64/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/64/comments","events_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/64/events","html_url":"https://github.com/PacificBiosciences/pbbioconda/issues/64","id":392267500,"node_id":"MDU6SXNzdWUzOTIyNjc1MDA=","number":64,"title":"blasr mixed query file types is not allowed","user":{"login":"Phylloxera","id":13121075,"node_id":"MDQ6VXNlcjEzMTIxMDc1","avatar_url":"https://avatars0.githubusercontent.com/u/13121075?v=4","gravatar_id":"","url":"https://api.github.com/users/Phylloxera","html_url":"https://github.com/Phylloxera","followers_url":"https://api.github.com/users/Phylloxera/followers","following_url":"https://api.github.com/users/Phylloxera/following{/other_user}","gists_url":"https://api.github.com/users/Phylloxera/gists{/gist_id}","starred_url":"https://api.github.com/users/Phylloxera/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Phylloxera/subscriptions","organizations_url":"https://api.github.com/users/Phylloxera/orgs","repos_url":"https://api.github.com/users/Phylloxera/repos","events_url":"https://api.github.com/users/Phylloxera/events{/privacy}","received_events_url":"https://api.github.com/users/Phylloxera/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-12-18T17:50:26Z","updated_at":"2018-12-18T17:50:26Z","closed_at":null,"author_association":"NONE","body":"**Operating system**\r\nCentos 7\r\n\r\n**Package name**\r\nblasr 5.3.2-06c9543 (packaged with smrtlink)\r\n\r\n**Conda environment**\r\nn/a... does this mean i should be asking for help elsewhere?\r\n\r\n**Describe the bug**\r\nI am trying to map ccs sequel reads to a eukaryote reference genome. I first tried fastq, then bam, finally consensusreadset.xml following the EXAMPLES here: [https://github.com/PacificBiosciences/blasr/blob/develop/doc/EXAMPLES.md](url). Regardless of the input I try, I get the same error.\r\n\r\n**Error message**\r\nERROR, mixed query file types is not allowed.\r\n\r\n**To Reproduce**\r\n`blasr /path/to/ccs.consensusreadset.xml /path/to/reference.fasta --nproc 40 --stride 5 --useQuality true --bam --out out.bam --sa /path/to/reference.sa`\r\n\r\n**Expected behavior**\r\nRun without error\r\n"}}
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