{"action":"opened","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1338","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1338/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1338/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1338/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1338","id":148572933,"number":1338,"title":"TypeError when starting detect_sv phase with lumpy","user":{"login":"lbeltrame","id":25192,"avatar_url":"https://avatars.githubusercontent.com/u/25192?v=3","gravatar_id":"","url":"https://api.github.com/users/lbeltrame","html_url":"https://github.com/lbeltrame","followers_url":"https://api.github.com/users/lbeltrame/followers","following_url":"https://api.github.com/users/lbeltrame/following{/other_user}","gists_url":"https://api.github.com/users/lbeltrame/gists{/gist_id}","starred_url":"https://api.github.com/users/lbeltrame/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbeltrame/subscriptions","organizations_url":"https://api.github.com/users/lbeltrame/orgs","repos_url":"https://api.github.com/users/lbeltrame/repos","events_url":"https://api.github.com/users/lbeltrame/events{/privacy}","received_events_url":"https://api.github.com/users/lbeltrame/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-04-15T07:00:23Z","updated_at":"2016-04-15T07:00:23Z","closed_at":null,"body":"This is with latest master:\r\n\r\n```python\r\n[2016-04-15T05:41Z] uni01: ipython: detect_sv\r\n[2016-04-15T05:41Z] uni03: Unexpected error\r\nTraceback (most recent call last):\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py\", line 45, in _setup_logging\r\n    yield config\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/ipythontasks.py\", line 357, in detect_sv\r\n    return ipython.zip_args(apply(structural.detect_sv, *args))\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/__init__.py\", line 140, in detect_sv\r\n    for svdata in caller_fn(items):\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/lumpy.py\", line 144, in run\r\n    gt_vcfs = _filter_by_background([paired.tumor_name], [paired.normal_name], gt_vcfs, paired.tumor_data)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/bcbio/structural/lumpy.py\", line 78, in _filter_by_background\r\n    for rec in inp:\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/vcf/parser.py\", line 583, in next\r\n    samples = self._parse_samples(row[9:], fmt, record)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/vcf/parser.py\", line 448, in _parse_samples\r\n    self.samples, samples, samp_fmt, samp_fmt._types, samp_fmt._nums, site)\r\n  File \"cparse.pyx\", line 78, in vcf.cparse.parse_samples (vcf/cparse.c:1839)\r\n  File \"/storage/rozo/bcbio/anaconda/lib/python2.7/site-packages/vcf/model.py\", line 27, in __init__\r\n    self.gt_alleles = [(al if al != '.' else None) for al in allele_delimiter.split(self.data.GT)]\r\n```\r\n\r\nConfiguration template:\r\n\r\n```yaml\r\ndetails:\r\n  - analysis: variant2\r\n    genome_build: hg19\r\n    algorithm:\r\n        aligner: bwa\r\n        mark_duplicates: true\r\n        recalibrate: false\r\n        realign: false\r\n        variantcaller:\r\n            - mutect\r\n            - vardict\r\n            - freebayes\r\n        platform: illumina\r\n        svcaller:\r\n            - lumpy\r\n            - manta\r\n            - cnvkit\r\n        quality_format: Standard\r\n        ensemble:\r\n            numpass: 1\r\n        remove_lcr: true\r\n        trim_reads: false\r\n        variant_regions: my_regions\r\n        effects: snpeff\r\n        clinical_reporting: true\r\n        mixup_check: qsignature\r\n        merge_bamprep: true\r\n        coverage: my_regions\r\n        tools_on: [qualimap_full, multiqc]\r\n    metadata:\r\n        sex: female\r\nupload:\r\n    dir: ../final/\r\nglobals:\r\n    my_regions: /storage/rozo/projects/OV223/regions/targets.bed\r\n```\r\n"}}