{"action":"opened","issue":{"url":"https://api.github.com/repos/kundajelab/atac_dnase_pipelines/issues/41","repository_url":"https://api.github.com/repos/kundajelab/atac_dnase_pipelines","labels_url":"https://api.github.com/repos/kundajelab/atac_dnase_pipelines/issues/41/labels{/name}","comments_url":"https://api.github.com/repos/kundajelab/atac_dnase_pipelines/issues/41/comments","events_url":"https://api.github.com/repos/kundajelab/atac_dnase_pipelines/issues/41/events","html_url":"https://github.com/kundajelab/atac_dnase_pipelines/issues/41","id":213750402,"number":41,"title":"ataqc error in hg38: tn5.tagAlign.gz has inconsistent naming convention for record","user":{"login":"jenchien","id":20470722,"avatar_url":"https://avatars2.githubusercontent.com/u/20470722?v=3","gravatar_id":"","url":"https://api.github.com/users/jenchien","html_url":"https://github.com/jenchien","followers_url":"https://api.github.com/users/jenchien/followers","following_url":"https://api.github.com/users/jenchien/following{/other_user}","gists_url":"https://api.github.com/users/jenchien/gists{/gist_id}","starred_url":"https://api.github.com/users/jenchien/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jenchien/subscriptions","organizations_url":"https://api.github.com/users/jenchien/orgs","repos_url":"https://api.github.com/users/jenchien/repos","events_url":"https://api.github.com/users/jenchien/events{/privacy}","received_events_url":"https://api.github.com/users/jenchien/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-03-13T12:19:58Z","updated_at":"2017-03-13T12:19:58Z","closed_at":null,"body":"Hi kundajelab,\r\n\r\nThanks again for updating and maintaining the pipeline. I have got it working on my dataset using hg19, and would like to redo it using hg38. However, it exit with error in the ataqc like below:\r\n\r\n> pybedtools.helpers.BEDToolsError: \r\n\t\tCommand was:\r\n\t\t\r\n\t\t\tbedtools intersect -c -b /osc-fs_home/chang-j/seqdata/EMT/2_WTplus/align/rep2/2_WTplus_rep2.trim.nodup.tn5.tagAlign.gz -a /tmp/pybedtools.KggEsK.tmp\r\n\t\t\r\n\t\tError message was:\r\n\t\t***** WARNING: File /osc-fs_home/chang-j/seqdata/EMT/2_WTplus/align/rep2/2_WTplus_rep2.trim.nodup.tn5.tagAlign.gz has inconsistent naming convention for record:\r\n\t\tGL000008.2\t41\t88\tN\t1000\t+\r\n\t\t\r\n\t\t***** WARNING: File /osc-fs_home/chang-j/seqdata/EMT/2_WTplus/align/rep2/2_WTplus_rep2.trim.nodup.tn5.tagAlign.gz has inconsistent naming convention for record:\r\n\t\tGL000008.2\t41\t88\tN\t1000\t+\r\n\r\nIs it due to the unmatched genome name between ataqc resources data and genome file for aligning? Is there a workaround way? I'm also attaching the full stdout. [atac.bds.log.txt](https://github.com/kundajelab/atac_dnase_pipelines/files/838121/atac.bds.log.txt)\r\n\r\nThank you.\r\n\r\n"}}
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