{"action":"created","issue":{"url":"https://api.github.com/repos/YeoLab/gscripts/issues/66","labels_url":"https://api.github.com/repos/YeoLab/gscripts/issues/66/labels{/name}","comments_url":"https://api.github.com/repos/YeoLab/gscripts/issues/66/comments","events_url":"https://api.github.com/repos/YeoLab/gscripts/issues/66/events","html_url":"https://github.com/YeoLab/gscripts/issues/66","id":65484360,"number":66,"title":"Rna-Seq pipeline breaks while indexing bam file","user":{"login":"shassathe","id":8193946,"avatar_url":"https://avatars.githubusercontent.com/u/8193946?v=3","gravatar_id":"","url":"https://api.github.com/users/shassathe","html_url":"https://github.com/shassathe","followers_url":"https://api.github.com/users/shassathe/followers","following_url":"https://api.github.com/users/shassathe/following{/other_user}","gists_url":"https://api.github.com/users/shassathe/gists{/gist_id}","starred_url":"https://api.github.com/users/shassathe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shassathe/subscriptions","organizations_url":"https://api.github.com/users/shassathe/orgs","repos_url":"https://api.github.com/users/shassathe/repos","events_url":"https://api.github.com/users/shassathe/events{/privacy}","received_events_url":"https://api.github.com/users/shassathe/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-03-31T15:58:12Z","updated_at":"2015-03-31T17:37:59Z","closed_at":null,"body":"RNa-Seq pipeline fails during indexing of bam file. Here's the error:\r\n\r\nsamtools: /home/yeo-lab/software/lib/libz.so.1: no version information available (required by samtools)\r\nsamtools: /home/yeo-lab/software/lib/libz.so.1: no version information available (required by samtools)\r\nSamtools-htslib-API: bam_index_build2() not yet implemented"},"comment":{"url":"https://api.github.com/repos/YeoLab/gscripts/issues/comments/88182652","html_url":"https://github.com/YeoLab/gscripts/issues/66#issuecomment-88182652","issue_url":"https://api.github.com/repos/YeoLab/gscripts/issues/66","id":88182652,"user":{"login":"olgabot","id":806256,"avatar_url":"https://avatars.githubusercontent.com/u/806256?v=3","gravatar_id":"","url":"https://api.github.com/users/olgabot","html_url":"https://github.com/olgabot","followers_url":"https://api.github.com/users/olgabot/followers","following_url":"https://api.github.com/users/olgabot/following{/other_user}","gists_url":"https://api.github.com/users/olgabot/gists{/gist_id}","starred_url":"https://api.github.com/users/olgabot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/olgabot/subscriptions","organizations_url":"https://api.github.com/users/olgabot/orgs","repos_url":"https://api.github.com/users/olgabot/repos","events_url":"https://api.github.com/users/olgabot/events{/privacy}","received_events_url":"https://api.github.com/users/olgabot/received_events","type":"User","site_admin":false},"created_at":"2015-03-31T17:37:59Z","updated_at":"2015-03-31T17:37:59Z","body":"Yep, I'm getting the same error.\r\n\r\n```\r\n$ 'samtools' 'index' '/oasis/tscc/scratch/shsathe/projects/sebastian_data_2/Unaligned_I6/CV-B_MN_UT_no_NHS_2_AGTCAA_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam' '/oasis/tscc/scratch/shsathe/projects/sebastian_data_2/Unaligned_I6/CV-B_MN_UT_no_NHS_2_AGTCAA_L001_R1.polyATrim.adapterTrim.rmRep.sorted.rg.bam.bai'\r\nsamtools: /home/yeo-lab/software/lib/libz.so.1: no version information available (required by samtools)\r\nsamtools: /home/yeo-lab/software/lib/libz.so.1: no version information available (required by samtools)\r\nSamtools-htslib-API: bam_index_build2() not yet implemented\r\nAborted\r\n```\r\n\r\nThis isn't using our own `samtools`, which might be the problem.\r\n\r\n```\r\n$ which samtools\r\n/opt/biotools/samtools/bin/samtools\r\n```"}}