{"action":"created","issue":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2473","repository_url":"https://api.github.com/repos/bcbio/bcbio-nextgen","labels_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2473/labels{/name}","comments_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2473/comments","events_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2473/events","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2473","id":346972140,"node_id":"MDU6SXNzdWUzNDY5NzIxNDA=","number":2473,"title":"Problems with logs and joint VCF file generation in latest dev build","user":{"login":"amizeranschi","id":11562164,"node_id":"MDQ6VXNlcjExNTYyMTY0","avatar_url":"https://avatars1.githubusercontent.com/u/11562164?v=4","gravatar_id":"","url":"https://api.github.com/users/amizeranschi","html_url":"https://github.com/amizeranschi","followers_url":"https://api.github.com/users/amizeranschi/followers","following_url":"https://api.github.com/users/amizeranschi/following{/other_user}","gists_url":"https://api.github.com/users/amizeranschi/gists{/gist_id}","starred_url":"https://api.github.com/users/amizeranschi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/amizeranschi/subscriptions","organizations_url":"https://api.github.com/users/amizeranschi/orgs","repos_url":"https://api.github.com/users/amizeranschi/repos","events_url":"https://api.github.com/users/amizeranschi/events{/privacy}","received_events_url":"https://api.github.com/users/amizeranschi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-08-02T11:31:48Z","updated_at":"2018-08-03T18:35:31Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nAfter upgrading to the latest development version, the logs and joint VCF file generation don't seem to work properly anymore. Debug messages don't get printed anymore (neither on stdout, nor in the log file), and the `bcbio-nextgen-debug.log` file is pretty much identical with `bcbio-nextgen.log`. The only difference is the resource requests messages which appear in the debug log:\r\n\r\n```\r\n[2018-08-02T10:10Z] Resource requests: bwa, sambamba, samtools; memory: 3.00, 3.00, 3.00; cores: 16, 16, 16\r\n[2018-08-02T10:10Z] Configuring 2 jobs to run, using 16 cores each with 48.1g of memory reserved for each job\r\n```\r\n\r\n```\r\n[2018-08-02T10:10Z] Resource requests: gatk, gatk-haplotype, picard; memory: 3.50, 3.00, 3.00; cores: 1, 16, 16\r\n[2018-08-02T10:10Z] Configuring 32 jobs to run, using 1 cores each with 3.50g of memory reserved for each job\r\n```\r\n\r\n```\r\n[2018-08-02T10:18Z] Resource requests: bcbio_variation, fastqc, gatk, gatk-vqsr, gemini, kraken, preseq, qsignature, sambamba, samtools; memory: 3.00, 3.00, 3.50, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00, 3.00; cores: 16, 16, 1, 16, 16, 16, 16, 16, 16, 16\r\n[2018-08-02T10:18Z] Configuring 2 jobs to run, using 16 cores each with 56.1g of memory reserved for each job\r\n```\r\n\r\n\r\nThe multi-sample `<batch>-gatk-haplotype-joint-annotated.vcf.gz` did not get generated, even though the sample-specific VCF files are where they should be.\r\n\r\nFurthermore, `bcbio-nextgen-commands.log` is completely empty.\r\n\r\nTo test all of this, I've run a simple variant calling job that worked flawlessly a few days ago, before upgrading Bcbio-nextgen.\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/comments/410340311","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2473#issuecomment-410340311","issue_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2473","id":410340311,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMDM0MDMxMQ==","user":{"login":"chapmanb","id":39391,"node_id":"MDQ6VXNlcjM5Mzkx","avatar_url":"https://avatars1.githubusercontent.com/u/39391?v=4","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"created_at":"2018-08-03T18:35:31Z","updated_at":"2018-08-03T18:35:31Z","author_association":"MEMBER","body":"Apologies, I'm not sure what to make of this. That looks like a pretty small update distance between two recent development packages. We haven't overhauled any of the logging in that time so I'm not sure why it disappeared on your runs. A couple of questions to help debug:\r\n\r\n- How are you running bcbio? Single machine? On a cluster?\r\n- Did the run environment change between the working and problem runs?\r\n- Could you provide the configuration input you're using?\r\n\r\nApologies, but I don't know why you'd lose both logging and joint calling so hoping for some baseline or ideas to reproduce what you're seeing. Thanks again for helping to debug."}}
{"actor":{"display_login":"chapmanb"}}