{"action":"closed","issue":{"url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/71","repository_url":"https://api.github.com/repos/Ecogenomics/CheckM","labels_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/71/labels{/name}","comments_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/71/comments","events_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/71/events","html_url":"https://github.com/Ecogenomics/CheckM/issues/71","id":169048997,"number":71,"title":"indexed and sorted BAM files as Input files for \"coverage\" command","user":{"login":"minsookim1983","id":20807818,"avatar_url":"https://avatars.githubusercontent.com/u/20807818?v=3","gravatar_id":"","url":"https://api.github.com/users/minsookim1983","html_url":"https://github.com/minsookim1983","followers_url":"https://api.github.com/users/minsookim1983/followers","following_url":"https://api.github.com/users/minsookim1983/following{/other_user}","gists_url":"https://api.github.com/users/minsookim1983/gists{/gist_id}","starred_url":"https://api.github.com/users/minsookim1983/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/minsookim1983/subscriptions","organizations_url":"https://api.github.com/users/minsookim1983/orgs","repos_url":"https://api.github.com/users/minsookim1983/repos","events_url":"https://api.github.com/users/minsookim1983/events{/privacy}","received_events_url":"https://api.github.com/users/minsookim1983/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-08-03T05:09:42Z","updated_at":"2016-08-03T06:05:02Z","closed_at":"2016-08-03T06:05:02Z","body":"Dear Donovan,\r\n\r\nHello, this is Min-Soo Kim who is interested in your CheckM tool. I am trying to produce coverage profile from my data using \"coverage\" command. However, I keep getting errors with .bam files, .bai files or .sorted files as follows:\r\n\"[Error] BAM file is either unsorted or not indexed: DIRECTORY/FILE_NAME.bam\"\r\n\"[Error] BAM file is either unsorted or not indexed: DIRECTORY/FILE_NAME.sorted.bai\"\r\n\"[Error] BAM file is either unsorted or not indexed: DIRECTORY/FILE_NAME.sorted\"\r\n\r\nHere is the processes what I did to get sorted and indexed BAM files,\r\n\r\n1. I used bowtie2 with paired-end read files to generate read-mapping SAM files, and converted to BAM files using samtools-v1.3.1\r\n>samtools view -b INPUT.sam OUTPUT.bam\r\n\r\n2. OUTPUT.bam files were sorted and indexed.\r\n> samtools sort INPUT.bam -o OUTPUT.sorted --output_fomt BAM\r\n> samtools index OUTPUT.sorted\r\n\r\n3. I got .bai files, and put in OUTPUT.sorted.bai files with \"coverage\" command.\r\n> checkm coverage -x fa -a 90 -t 20 BIN_FOLDER/ OUTPUT.file FILE1.sorted.bai FILE2.sorted.bai FILE3.sorted.bai ...\r\n\r\nCould you help me figure out what is wrong with me?\r\nThank you for your help.\r\n\r\nMin-Soo Kim"}}
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