{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1674","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1674/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1674/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1674/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1674","id":193840991,"number":1674,"title":"CNVkit deprecated option \"loh\" used","user":{"login":"gabeng","id":1035021,"avatar_url":"https://avatars.githubusercontent.com/u/1035021?v=3","gravatar_id":"","url":"https://api.github.com/users/gabeng","html_url":"https://github.com/gabeng","followers_url":"https://api.github.com/users/gabeng/followers","following_url":"https://api.github.com/users/gabeng/following{/other_user}","gists_url":"https://api.github.com/users/gabeng/gists{/gist_id}","starred_url":"https://api.github.com/users/gabeng/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gabeng/subscriptions","organizations_url":"https://api.github.com/users/gabeng/orgs","repos_url":"https://api.github.com/users/gabeng/repos","events_url":"https://api.github.com/users/gabeng/events{/privacy}","received_events_url":"https://api.github.com/users/gabeng/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-12-06T17:56:01Z","updated_at":"2016-12-06T18:27:05Z","closed_at":"2016-12-06T18:23:11Z","body":"I was just running a number of targeted sequencing samples with the CNVkit option. Then this error appeared. The `loh` option does not seem to be used when assigning batches.\r\nbcbio_nextgen version: 1.0.0\r\ncnvkit version: 0.8.1\r\n\r\nSeems this option was removed from CNVkit in 0.8.0: https://github.com/etal/cnvkit/releases/tag/v0.8.0\r\n\r\n```\r\nCalledProcessError: Command '/home/ubuntu/local/share/bcbio/anaconda/bin/cnvkit.py loh -t -s /bioinf-data/work/structural/14M23_S8/cnvkit/raw/14M2653_S8-sort-chromfilter.cns -o /bioinf-data/work/structural/14M23_S8/cnvkit/raw/tx/tmp6sk4Wq/14M23_S8-sort-loh.pdf /bioinf-data/10112-cnv-testrun-5/work/freebayes/14M23_S8-filter-14M23_S8.vcf.gz\r\nusage: cnvkit.py [-h]\r\n\r\n\r\n                 {batch,target,access,antitarget,coverage,reference,fix,segment,call,diagram,scatter,heatmap,breaks,gainloss,gender,metrics,segmetrics,import-picard,import-seg,import-theta,export,version}\r\n                 ...\r\ncnvkit.py: error: invalid choice: 'loh' (choose from 'batch', 'target', 'access', 'antitarget', 'coverage', 'reference', 'fix', 'segment', 'call', 'diagram', 'scatter', 'heatmap', 'breaks', 'gainloss', 'gender', 'metrics', 'segmetrics', 'import-picard', 'import-seg', 'import-theta', 'export', 'version')\r\n' returned non-zero exit status 2\r\n___________________________________________________________________________\r\nubuntu@ip-172-31-7-159:/bioinf-data/work$ cnvkit.py loh -h\r\nusage: cnvkit.py [-h]\r\n                 {batch,target,access,antitarget,coverage,reference,fix,segment,call,diagram,scatter,heatmap,breaks,gainloss,gender,metrics,segmetrics,import-picard,import-seg,import-theta,export,version}\r\n                 ...\r\ncnvkit.py: error: invalid choice: 'loh' (choose from 'batch', 'target', 'access', 'antitarget', 'coverage', 'reference', 'fix', 'segment', 'call', 'diagram', 'scatter', 'heatmap', 'breaks', 'gainloss', 'gender', 'metrics', 'segmetrics', 'import-picard', 'import-seg', 'import-theta', 'export', 'version')\r\n```"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/265230637","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1674#issuecomment-265230637","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1674","id":265230637,"user":{"login":"gabeng","id":1035021,"avatar_url":"https://avatars.githubusercontent.com/u/1035021?v=3","gravatar_id":"","url":"https://api.github.com/users/gabeng","html_url":"https://github.com/gabeng","followers_url":"https://api.github.com/users/gabeng/followers","following_url":"https://api.github.com/users/gabeng/following{/other_user}","gists_url":"https://api.github.com/users/gabeng/gists{/gist_id}","starred_url":"https://api.github.com/users/gabeng/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gabeng/subscriptions","organizations_url":"https://api.github.com/users/gabeng/orgs","repos_url":"https://api.github.com/users/gabeng/repos","events_url":"https://api.github.com/users/gabeng/events{/privacy}","received_events_url":"https://api.github.com/users/gabeng/received_events","type":"User","site_admin":false},"created_at":"2016-12-06T18:27:05Z","updated_at":"2016-12-06T18:27:05Z","body":"Will try that in a moment. Amazing how quick you are with fixes. Thanks!"}}
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