{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1509","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1509/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1509/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1509/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1509","id":170472499,"number":1509,"title":"Java Version Error","user":{"login":"lsturm1","id":14970970,"avatar_url":"https://avatars.githubusercontent.com/u/14970970?v=3","gravatar_id":"","url":"https://api.github.com/users/lsturm1","html_url":"https://github.com/lsturm1","followers_url":"https://api.github.com/users/lsturm1/followers","following_url":"https://api.github.com/users/lsturm1/following{/other_user}","gists_url":"https://api.github.com/users/lsturm1/gists{/gist_id}","starred_url":"https://api.github.com/users/lsturm1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lsturm1/subscriptions","organizations_url":"https://api.github.com/users/lsturm1/orgs","repos_url":"https://api.github.com/users/lsturm1/repos","events_url":"https://api.github.com/users/lsturm1/events{/privacy}","received_events_url":"https://api.github.com/users/lsturm1/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-08-10T17:25:32Z","updated_at":"2016-08-11T17:54:07Z","closed_at":null,"body":"Hi,\r\n\r\nI have been running tests fine in the past, but right now bcbio will stop a job right after it starts do to the java version we have. \r\n\r\n\"java version 1.7 required for running MuTect and GATK < 3.6. Found version 1.8.0_92\"\r\n\r\nDo I need to have an older version of java in my path or is there some update to bcbio that will fix this?\r\n\r\nThanks,\r\nLuke"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/239238633","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1509#issuecomment-239238633","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1509","id":239238633,"user":{"login":"lsturm1","id":14970970,"avatar_url":"https://avatars.githubusercontent.com/u/14970970?v=3","gravatar_id":"","url":"https://api.github.com/users/lsturm1","html_url":"https://github.com/lsturm1","followers_url":"https://api.github.com/users/lsturm1/followers","following_url":"https://api.github.com/users/lsturm1/following{/other_user}","gists_url":"https://api.github.com/users/lsturm1/gists{/gist_id}","starred_url":"https://api.github.com/users/lsturm1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lsturm1/subscriptions","organizations_url":"https://api.github.com/users/lsturm1/orgs","repos_url":"https://api.github.com/users/lsturm1/repos","events_url":"https://api.github.com/users/lsturm1/events{/privacy}","received_events_url":"https://api.github.com/users/lsturm1/received_events","type":"User","site_admin":false},"created_at":"2016-08-11T17:54:06Z","updated_at":"2016-08-11T17:54:06Z","body":"Thank you! I got the new GATK up and running. I am doing a joint call using gatk haplotype for variant calling, but there is a new issue... Here is the traceback:\r\n\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR --\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR stack trace\r\n[2016-08-11T13:39Z] sh-18-20.local: java.util.NoSuchElementException\r\n[2016-08-11T13:39Z] sh-18-20.local:     at java.util.HashMap$HashIterator.nextNode(HashMap.java:1439)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at java.util.HashMap$KeyIterator.next(HashMap.java:1461)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.redu\\\r\nceNumberOfAlternativeAllelesBasedOnLikelihoods(HaplotypeCallerGenotypingEngine.java:336)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assi\\\r\ngnGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:264)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.\\\r\njava:964)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.\\\r\njava:251)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.ap\\\r\nply(TraverseActiveRegions.java:709)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.ap\\\r\nply(TraverseActiveRegions.java:705)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoSchedu\\\r\nler.java:274)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveReg\\\r\nions.java:274)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveReg\\\r\nions.java:78)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler\\\r\n.java:99)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:311)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:11\\\r\n3)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java\\\r\n:255)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java\\\r\n:157)\r\n[2016-08-11T13:39Z] sh-18-20.local:     at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR -------------------------------------------------------------------------------------\\\r\n-----\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR This might be a bug. Please check the documentation guide to see if this is a known p\\\r\nroblem.\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR If not, please post the error message, with stack trace, to the GATK forum.\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR Visit our website and forum for extensive documentation and answers to\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR commonly asked questions https://www.broadinstitute.org/gatk\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR\r\n[2016-08-11T13:39Z] sh-18-20.local: ##### ERROR MESSAGE: Code exception (see stack trace for error itself)\r\n\r\n\r\nHow should I go about fixing this?\r\n\r\nThank you,\r\nLuke"}}
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