{"action":"closed","issue":{"url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2493","repository_url":"https://api.github.com/repos/bcbio/bcbio-nextgen","labels_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2493/labels{/name}","comments_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2493/comments","events_url":"https://api.github.com/repos/bcbio/bcbio-nextgen/issues/2493/events","html_url":"https://github.com/bcbio/bcbio-nextgen/issues/2493","id":354380529,"node_id":"MDU6SXNzdWUzNTQzODA1Mjk=","number":2493,"title":"Mutect2 Gatk4 errors java.lang.StringIndexOutOfBoundsException: String index out of range: 402","user":{"login":"PatrickJReed","id":4350664,"node_id":"MDQ6VXNlcjQzNTA2NjQ=","avatar_url":"https://avatars2.githubusercontent.com/u/4350664?v=4","gravatar_id":"","url":"https://api.github.com/users/PatrickJReed","html_url":"https://github.com/PatrickJReed","followers_url":"https://api.github.com/users/PatrickJReed/followers","following_url":"https://api.github.com/users/PatrickJReed/following{/other_user}","gists_url":"https://api.github.com/users/PatrickJReed/gists{/gist_id}","starred_url":"https://api.github.com/users/PatrickJReed/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PatrickJReed/subscriptions","organizations_url":"https://api.github.com/users/PatrickJReed/orgs","repos_url":"https://api.github.com/users/PatrickJReed/repos","events_url":"https://api.github.com/users/PatrickJReed/events{/privacy}","received_events_url":"https://api.github.com/users/PatrickJReed/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-27T16:08:19Z","updated_at":"2018-08-28T10:12:27Z","closed_at":"2018-08-28T10:12:27Z","author_association":"NONE","body":"I'm running Mutect2 with the latest bcbio development build (as of this morning) and its bugging out. Any help would be appreciated.\r\nHere is my template-\r\ndetails:\r\n- analysis: variant2\r\n  metadata:\r\n    batch:\r\n    phenotype:\r\n    description:\r\n  genome_build: hg38\r\n  algorithm:\r\n    aligner: bwa\r\n    adapters: [truseq,illumina]\r\n    mark_duplicates: true\r\n    recalibrate: false\r\n    realign: false\r\n    effects: vep\r\n    remove_lcr: false\r\n    phasing: false\r\n    tools_on: [bwa-mem, qualimap_full]\r\n    tools_off: [gemini]\r\n    kraken: minikraken\r\n    variantcaller:\r\n      somatic: [vardict, mutect2, strelka2]\r\n      germline: [freebayes, gatk-haplotype]\r\n    ensemble:\r\n       numpass: 1\r\n    svcaller: [cnvkit, manta, delly, lumpy, wham, gridss, metasv]\r\n\r\noutput is as follows-\r\n[2018-08-27T15:49Z] System YAML configuration: /usr/local/share/bcbio/galaxy/bcbio_system.yaml\r\n[2018-08-27T15:49Z] Resource requests: bwa, sambamba, samtools; memory: 3.00, 3.00, 3.00; cores: 16, 16, 16\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 16 cores each with 48.1g of memory reserved for each job\r\n[2018-08-27T15:49Z] Timing: organize samples\r\n[2018-08-27T15:49Z] multiprocessing: organize_samples\r\n[2018-08-27T15:49Z] Using input YAML configuration: /home/ubuntu/efs/SZ_Twins_WGS/config/SZ_Twins_WGS.yaml\r\n[2018-08-27T15:49Z] Checking sample YAML configuration: /home/ubuntu/efs/SZ_Twins_WGS/config/SZ_Twins_WGS.yaml\r\n[2018-08-27T15:49Z] Testing minimum versions of installed programs\r\n[2018-08-27T15:49Z] Timing: alignment preparation\r\n[2018-08-27T15:49Z] multiprocessing: prep_align_inputs\r\n/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py:86: UserWarning: Multiprocessing-backed parallel loops cannot be nested, setting n_jobs=1\r\n  for data in joblib.Parallel(parallel[\"num_jobs\"], batch_size=1)(joblib.delayed(fn)(x) for x in items):\r\n/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py:86: UserWarning: Multiprocessing-backed parallel loops cannot be nested, setting n_jobs=1\r\n  for data in joblib.Parallel(parallel[\"num_jobs\"], batch_size=1)(joblib.delayed(fn)(x) for x in items):\r\n[2018-08-27T15:49Z] Skipping trimming of Pair1_SZ.\r\n[2018-08-27T15:49Z] Resource requests: ; memory: 1.00; cores: 1\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2018-08-27T15:49Z] Skipping trimming of Pair1_NS.\r\n[2018-08-27T15:49Z] Resource requests: ; memory: 1.00; cores: 1\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2018-08-27T15:49Z] Skipping trimming of Pair2_NS.\r\n[2018-08-27T15:49Z] Resource requests: ; memory: 1.00; cores: 1\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2018-08-27T15:49Z] Skipping trimming of Pair2_SZ.\r\n[2018-08-27T15:49Z] Resource requests: ; memory: 1.00; cores: 1\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2018-08-27T15:49Z] Skipping trimming of Pair3_NS.\r\n[2018-08-27T15:49Z] Resource requests: ; memory: 1.00; cores: 1\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2018-08-27T15:49Z] Skipping trimming of Pair3_SZ.\r\n[2018-08-27T15:49Z] Resource requests: ; memory: 1.00; cores: 1\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2018-08-27T15:49Z] Skipping trimming of Pair6_NT1.\r\n[2018-08-27T15:49Z] Resource requests: ; memory: 1.00; cores: 1\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2018-08-27T15:49Z] Skipping trimming of Pair6_NT2.\r\n[2018-08-27T15:49Z] Resource requests: ; memory: 1.00; cores: 1\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2018-08-27T15:49Z] Skipping trimming of Pair8_NT1.\r\n[2018-08-27T15:49Z] Resource requests: ; memory: 1.00; cores: 1\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2018-08-27T15:49Z] Skipping trimming of Pair8_NT2.\r\n[2018-08-27T15:49Z] Resource requests: ; memory: 1.00; cores: 1\r\n[2018-08-27T15:49Z] Configuring 2 jobs to run, using 1 cores each with 1.00g of memory reserved for each job\r\n[2018-08-27T15:49Z] multiprocessing: disambiguate_split\r\n[2018-08-27T15:49Z] Timing: alignment\r\n[2018-08-27T15:49Z] multiprocessing: process_alignment\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair1_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair2_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_NS with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair3_SZ with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair6_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT1 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] Aligning lane Pair8_NT2 with bwa aligner\r\n[2018-08-27T15:49Z] multiprocessing: delayed_bam_merge\r\n[2018-08-27T15:50Z] Timing: callable regions\r\n[2018-08-27T15:50Z] multiprocessing: prep_samples\r\n[2018-08-27T15:50Z] multiprocessing: postprocess_alignment\r\n[2018-08-27T15:50Z] Pair6_NT2: Assigned coverage as 'genome' with 89.1% genome coverage and 0.0% offtarget coverage\r\n[2018-08-27T15:50Z] Pair1_NS: Assigned coverage as 'genome' with 89.2% genome coverage and 0.0% offtarget coverage\r\n[2018-08-27T15:50Z] Pair1_SZ: Assigned coverage as 'genome' with 89.2% genome coverage and 0.0% offtarget coverage\r\n[2018-08-27T15:50Z] Pair8_NT1: Assigned coverage as 'genome' with 88.2% genome coverage and 0.0% offtarget coverage\r\n[2018-08-27T15:50Z] Pair2_NS: Assigned coverage as 'genome' with 88.3% genome coverage and 0.0% offtarget coverage\r\n[2018-08-27T15:50Z] Pair2_SZ: Assigned coverage as 'genome' with 88.5% genome coverage and 0.0% offtarget coverage\r\n[2018-08-27T15:50Z] Pair3_NS: Assigned coverage as 'genome' with 88.7% genome coverage and 0.0% offtarget coverage\r\n[2018-08-27T15:50Z] Pair8_NT2: Assigned coverage as 'genome' with 88.2% genome coverage and 0.0% offtarget coverage\r\n[2018-08-27T15:50Z] Pair6_NT1: Assigned coverage as 'genome' with 89.0% genome coverage and 0.0% offtarget coverage\r\n[2018-08-27T15:50Z] Pair3_SZ: Assigned coverage as 'genome' with 88.7% genome coverage and 0.0% offtarget coverage\r\n[2018-08-27T15:50Z] multiprocessing: combine_sample_regions\r\n[2018-08-27T15:50Z] Identified 328 parallel analysis blocks\r\nBlock sizes:\r\n  min: 492\r\n  5%: 1155.6\r\n  25%: 6910.5\r\n  median: 246006.0\r\n  75%: 17913994.0\r\n  95%: 27521337.549999982\r\n  99%: 43449900.08000002\r\n  max: 58027652\r\nBetween block sizes:\r\n  min: 251\r\n  5%: 262.75\r\n  25%: 297.75\r\n  median: 416.0\r\n  75%: 1003.25\r\n  95%: 4619.5\r\n  99%: 18145.350000000082\r\n  max: 49998\r\n\r\n[2018-08-27T15:50Z] multiprocessing: calculate_sv_bins\r\n[2018-08-27T15:50Z] multiprocessing: calculate_sv_coverage\r\n[2018-08-27T15:50Z] multiprocessing: normalize_sv_coverage\r\n[2018-08-27T15:50Z] Resource requests: cnvkit; memory: 3.00; cores: 16\r\n[2018-08-27T15:50Z] Configuring 1 jobs to run, using 16 cores each with 48.1g of memory reserved for each job\r\n[2018-08-27T15:50Z] Resource requests: cnvkit; memory: 3.00; cores: 16\r\n[2018-08-27T15:50Z] Configuring 1 jobs to run, using 16 cores each with 48.1g of memory reserved for each job\r\n[2018-08-27T15:50Z] Resource requests: cnvkit; memory: 3.00; cores: 16\r\n[2018-08-27T15:50Z] Configuring 1 jobs to run, using 16 cores each with 48.1g of memory reserved for each job\r\n[2018-08-27T15:50Z] Resource requests: cnvkit; memory: 3.00; cores: 16\r\n[2018-08-27T15:50Z] Configuring 1 jobs to run, using 16 cores each with 48.1g of memory reserved for each job\r\n[2018-08-27T15:50Z] Resource requests: cnvkit; memory: 3.00; cores: 16\r\n[2018-08-27T15:50Z] Configuring 1 jobs to run, using 16 cores each with 48.1g of memory reserved for each job\r\n[2018-08-27T15:50Z] Timing: hla typing\r\n[2018-08-27T15:50Z] Resource requests: freebayes, gatk, gatk-haplotype, mutect2, picard, strelka2, vardict; memory: 3.00, 3.50, 3.00, 3.00, 3.00, 3.00, 3.00; cores: 16, 1, 16, 16, 16, 16, 16\r\n[2018-08-27T15:50Z] Configuring 39 jobs to run, using 1 cores each with 3.50g of memory reserved for each job\r\n[2018-08-27T15:50Z] Timing: alignment post-processing\r\n[2018-08-27T15:50Z] multiprocessing: piped_bamprep\r\n[2018-08-27T15:50Z] Timing: variant calling\r\n[2018-08-27T15:50Z] multiprocessing: variantcall_sample\r\n[2018-08-27T15:50Z] MuTect2\r\n[2018-08-27T15:50Z] Using GATK jar /usr/local/share/bcbio/anaconda/share/gatk4-4.0.8.1-0/gatk-package-4.0.8.1-local.jar\r\n[2018-08-27T15:50Z] Running:\r\n[2018-08-27T15:50Z]     java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms681m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/home/ubuntu/efs/SZ_Twins_WGS/work/bcbiotx/tmpjfcKn8 -jar /usr/local/share/bcbio/anaconda/share/gatk4-4.0.8.1-0/gatk-package-4.0.8.1-local.jar Mutect2 -R /usr/local/share/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --annotation ClippingRankSumTest --annotation DepthPerSampleHC --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation FisherStrand --annotation MappingQuality --annotation DepthPerAlleleBySample --annotation Coverage --read-validation-stringency LENIENT -I /home/ubuntu/efs/SZ_Twins_WGS/work/align/Pair3_SZ/Pair3_SZ-sort.bam --tumor-sample Pair3_SZ -I /home/ubuntu/efs/SZ_Twins_WGS/work/align/Pair3_NS/Pair3_NS-sort.bam --normal-sample Pair3_NS -L /home/ubuntu/efs/SZ_Twins_WGS/work/mutect2/chrUn_KI270467v1/Pair3-chrUn_KI270467v1_0_3920-regions.bed --interval-set-rule INTERSECTION --disable-read-filter NotDuplicateReadFilter -ploidy 2 -O /home/ubuntu/efs/SZ_Twins_WGS/work/bcbiotx/tmpjfcKn8/Pair3-chrUn_KI270467v1_0_3920-raw.vcf.gz\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] Genotyping with VarDict: Inference\r\n[2018-08-27T15:50Z] 15:50:40.688 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/bcbio/anaconda/share/gatk4-4.0.8.1-0/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so\r\n[2018-08-27T15:50Z] 15:50:41.400 INFO  Mutect2 - ------------------------------------------------------------\r\n[2018-08-27T15:50Z] 15:50:41.401 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.8.1\r\n[2018-08-27T15:50Z] 15:50:41.401 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/\r\n[2018-08-27T15:50Z] 15:50:41.415 INFO  Mutect2 - Executing as root@ip-172-31-15-89 on Linux v4.4.0-1035-aws amd64\r\n[2018-08-27T15:50Z] 15:50:41.416 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_144-b01\r\n[2018-08-27T15:50Z] 15:50:41.417 INFO  Mutect2 - Start Date/Time: August 27, 2018 3:50:40 PM UTC\r\n[2018-08-27T15:50Z] 15:50:41.417 INFO  Mutect2 - ------------------------------------------------------------\r\n[2018-08-27T15:50Z] 15:50:41.417 INFO  Mutect2 - ------------------------------------------------------------\r\n[2018-08-27T15:50Z] 15:50:41.418 INFO  Mutect2 - HTSJDK Version: 2.16.0\r\n[2018-08-27T15:50Z] 15:50:41.419 INFO  Mutect2 - Picard Version: 2.18.7\r\n[2018-08-27T15:50Z] 15:50:41.419 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2\r\n[2018-08-27T15:50Z] 15:50:41.419 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false\r\n[2018-08-27T15:50Z] 15:50:41.420 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true\r\n[2018-08-27T15:50Z] 15:50:41.420 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false\r\n[2018-08-27T15:50Z] 15:50:41.421 INFO  Mutect2 - Deflater: IntelDeflater\r\n[2018-08-27T15:50Z] 15:50:41.421 INFO  Mutect2 - Inflater: IntelInflater\r\n[2018-08-27T15:50Z] 15:50:41.422 INFO  Mutect2 - GCS max retries/reopens: 20\r\n[2018-08-27T15:50Z] 15:50:41.422 INFO  Mutect2 - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX\r\n[2018-08-27T15:50Z] 15:50:41.422 INFO  Mutect2 - Initializing engine\r\n[2018-08-27T15:50Z] 15:50:44.344 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/ubuntu/efs/SZ_Twins_WGS/work/mutect2/chrUn_KI270467v1/Pair3-chrUn_KI270467v1_0_3920-regions.bed\r\n[2018-08-27T15:50Z] 15:50:44.390 INFO  IntervalArgumentCollection - Processing 3912 bp from intervals\r\n[2018-08-27T15:50Z] 15:50:44.436 INFO  Mutect2 - Done initializing engine\r\n[2018-08-27T15:50Z] 15:50:44.698 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/usr/local/share/bcbio/anaconda/share/gatk4-4.0.8.1-0/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_utils.so\r\n[2018-08-27T15:50Z] 15:50:44.774 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/usr/local/share/bcbio/anaconda/share/gatk4-4.0.8.1-0/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so\r\n[2018-08-27T15:50Z] 15:50:44.989 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions\r\n[2018-08-27T15:50Z] 15:50:44.990 WARN  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM\r\n[2018-08-27T15:50Z] 15:50:44.991 INFO  IntelPairHmm - Available threads: 72\r\n[2018-08-27T15:50Z] 15:50:44.992 INFO  IntelPairHmm - Requested threads: 4\r\n[2018-08-27T15:50Z] 15:50:44.992 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation\r\n[2018-08-27T15:50Z] 15:50:45.396 INFO  ProgressMeter - Starting traversal\r\n[2018-08-27T15:50Z] 15:50:45.423 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute\r\n[2018-08-27T15:51Z] 15:51:19.196 INFO  ProgressMeter - chrUn_KI270467v1:1379              0.6                    10             17.8\r\n[2018-08-27T15:54Z] 15:54:51.875 INFO  ProgressMeter - chrUn_KI270467v1:3202              4.1                    20              4.9\r\n[2018-08-27T15:55Z] 15:55:20.733 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.32201045\r\n[2018-08-27T15:55Z] 15:55:20.735 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 106.656391427\r\n[2018-08-27T15:55Z] 15:55:20.736 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 17.66 sec\r\n[2018-08-27T15:55Z] 15:55:20.737 INFO  Mutect2 - Shutting down engine\r\n[2018-08-27T15:55Z] [August 27, 2018 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 4.67 minutes.\r\n[2018-08-27T15:55Z] Runtime.totalMemory()=691404800\r\n[2018-08-27T15:55Z] java.lang.StringIndexOutOfBoundsException: String index out of range: 402\r\n[2018-08-27T15:55Z] \tat java.lang.String.substring(String.java:1963)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases.annotate(ReferenceBases.java:48)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:270)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.callMutations(SomaticGenotypingEngine.java:176)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.callRegion(Mutect2Engine.java:211)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.apply(Mutect2.java:212)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:291)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)\r\n[2018-08-27T15:55Z] \tat org.broadinstitute.hellbender.Main.main(Main.java:289)\r\n[2018-08-27T15:55Z] Uncaught exception occurred\r\nTraceback (most recent call last):\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py\", line 23, in run\r\n    _do_run(cmd, checks, log_stdout, env=env)\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py\", line 103, in _do_run\r\n    raise subprocess.CalledProcessError(exitcode, error_msg)\r\nCalledProcessError: Command 'set -o pipefail; unset JAVA_HOME && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && gatk --java-options '-Xms681m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/home/ubuntu/efs/SZ_Twins_WGS/work/bcbiotx/tmpjfcKn8' Mutect2 -R /usr/local/share/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --annotation ClippingRankSumTest --annotation DepthPerSampleHC --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation FisherStrand --annotation MappingQuality --annotation DepthPerAlleleBySample --annotation Coverage --read-validation-stringency LENIENT -I /home/ubuntu/efs/SZ_Twins_WGS/work/align/Pair3_SZ/Pair3_SZ-sort.bam --tumor-sample Pair3_SZ -I /home/ubuntu/efs/SZ_Twins_WGS/work/align/Pair3_NS/Pair3_NS-sort.bam --normal-sample Pair3_NS -L /home/ubuntu/efs/SZ_Twins_WGS/work/mutect2/chrUn_KI270467v1/Pair3-chrUn_KI270467v1_0_3920-regions.bed --interval-set-rule INTERSECTION --disable-read-filter NotDuplicateReadFilter -ploidy 2 -O /home/ubuntu/efs/SZ_Twins_WGS/work/bcbiotx/tmpjfcKn8/Pair3-chrUn_KI270467v1_0_3920-raw.vcf.gz && unset JAVA_HOME && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && gatk --java-options '-Xms681m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/home/ubuntu/efs/SZ_Twins_WGS/work/bcbiotx/tmpjfcKn8' FilterMutectCalls --variant /home/ubuntu/efs/SZ_Twins_WGS/work/bcbiotx/tmpjfcKn8/Pair3-chrUn_KI270467v1_0_3920-raw.vcf.gz --output /home/ubuntu/efs/SZ_Twins_WGS/work/bcbiotx/tmpjfcKn8/Pair3-chrUn_KI270467v1_0_3920-raw-filt.vcf.gz\r\nUsing GATK jar /usr/local/share/bcbio/anaconda/share/gatk4-4.0.8.1-0/gatk-package-4.0.8.1-local.jar\r\nRunning:\r\n    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xms681m -Xmx3181m -XX:+UseSerialGC -Djava.io.tmpdir=/home/ubuntu/efs/SZ_Twins_WGS/work/bcbiotx/tmpjfcKn8 -jar /usr/local/share/bcbio/anaconda/share/gatk4-4.0.8.1-0/gatk-package-4.0.8.1-local.jar Mutect2 -R /usr/local/share/bcbio/genomes/Hsapiens/hg38/seq/hg38.fa --annotation ClippingRankSumTest --annotation DepthPerSampleHC --annotation MappingQualityRankSumTest --annotation MappingQualityZero --annotation QualByDepth --annotation ReadPosRankSumTest --annotation RMSMappingQuality --annotation FisherStrand --annotation MappingQuality --annotation DepthPerAlleleBySample --annotation Coverage --read-validation-stringency LENIENT -I /home/ubuntu/efs/SZ_Twins_WGS/work/align/Pair3_SZ/Pair3_SZ-sort.bam --tumor-sample Pair3_SZ -I /home/ubuntu/efs/SZ_Twins_WGS/work/align/Pair3_NS/Pair3_NS-sort.bam --normal-sample Pair3_NS -L /home/ubuntu/efs/SZ_Twins_WGS/work/mutect2/chrUn_KI270467v1/Pair3-chrUn_KI270467v1_0_3920-regions.bed --interval-set-rule INTERSECTION --disable-read-filter NotDuplicateReadFilter -ploidy 2 -O /home/ubuntu/efs/SZ_Twins_WGS/work/bcbiotx/tmpjfcKn8/Pair3-chrUn_KI270467v1_0_3920-raw.vcf.gz\r\n15:50:40.688 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/bcbio/anaconda/share/gatk4-4.0.8.1-0/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so\r\n15:50:41.400 INFO  Mutect2 - ------------------------------------------------------------\r\n15:50:41.401 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.0.8.1\r\n15:50:41.401 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/\r\n15:50:41.415 INFO  Mutect2 - Executing as root@ip-172-31-15-89 on Linux v4.4.0-1035-aws amd64\r\n15:50:41.416 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_144-b01\r\n15:50:41.417 INFO  Mutect2 - Start Date/Time: August 27, 2018 3:50:40 PM UTC\r\n15:50:41.417 INFO  Mutect2 - ------------------------------------------------------------\r\n15:50:41.417 INFO  Mutect2 - ------------------------------------------------------------\r\n15:50:41.418 INFO  Mutect2 - HTSJDK Version: 2.16.0\r\n15:50:41.419 INFO  Mutect2 - Picard Version: 2.18.7\r\n15:50:41.419 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2\r\n15:50:41.419 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false\r\n15:50:41.420 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true\r\n15:50:41.420 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false\r\n15:50:41.421 INFO  Mutect2 - Deflater: IntelDeflater\r\n15:50:41.421 INFO  Mutect2 - Inflater: IntelInflater\r\n15:50:41.422 INFO  Mutect2 - GCS max retries/reopens: 20\r\n15:50:41.422 INFO  Mutect2 - Using google-cloud-java fork https://github.com/broadinstitute/google-cloud-java/releases/tag/0.20.5-alpha-GCS-RETRY-FIX\r\n15:50:41.422 INFO  Mutect2 - Initializing engine\r\n15:50:44.344 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/ubuntu/efs/SZ_Twins_WGS/work/mutect2/chrUn_KI270467v1/Pair3-chrUn_KI270467v1_0_3920-regions.bed\r\n15:50:44.390 INFO  IntervalArgumentCollection - Processing 3912 bp from intervals\r\n15:50:44.436 INFO  Mutect2 - Done initializing engine\r\n15:50:44.698 INFO  NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/usr/local/share/bcbio/anaconda/share/gatk4-4.0.8.1-0/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_utils.so\r\n15:50:44.774 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/usr/local/share/bcbio/anaconda/share/gatk4-4.0.8.1-0/gatk-package-4.0.8.1-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so\r\n15:50:44.989 INFO  IntelPairHmm - Using CPU-supported AVX-512 instructions\r\n15:50:44.990 WARN  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM\r\n15:50:44.991 INFO  IntelPairHmm - Available threads: 72\r\n15:50:44.992 INFO  IntelPairHmm - Requested threads: 4\r\n15:50:44.992 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation\r\n15:50:45.396 INFO  ProgressMeter - Starting traversal\r\n15:50:45.423 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute\r\n15:51:19.196 INFO  ProgressMeter - chrUn_KI270467v1:1379              0.6                    10             17.8\r\n15:54:51.875 INFO  ProgressMeter - chrUn_KI270467v1:3202              4.1                    20              4.9\r\n15:55:20.733 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.32201045\r\n15:55:20.735 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 106.656391427\r\n15:55:20.736 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 17.66 sec\r\n15:55:20.737 INFO  Mutect2 - Shutting down engine\r\n[August 27, 2018 3:55:20 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 4.67 minutes.\r\nRuntime.totalMemory()=691404800\r\njava.lang.StringIndexOutOfBoundsException: String index out of range: 402\r\n\tat java.lang.String.substring(String.java:1963)\r\n\tat org.broadinstitute.hellbender.tools.walkers.annotator.ReferenceBases.annotate(ReferenceBases.java:48)\r\n\tat org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:270)\r\n\tat org.broadinstitute.hellbender.tools.walkers.mutect.SomaticGenotypingEngine.callMutations(SomaticGenotypingEngine.java:176)\r\n\tat org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2Engine.callRegion(Mutect2Engine.java:211)\r\n\tat org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2.apply(Mutect2.java:212)\r\n\tat org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:291)\r\n\tat org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:267)\r\n\tat org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:979)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:182)\r\n\tat org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:201)\r\n\tat org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)\r\n\tat org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)\r\n\tat org.broadinstitute.hellbender.Main.main(Main.java:289)\r\n' returned non-zero exit status 3\r\nTraceback (most recent call last):\r\n  File \"/usr/local/bin/bcbio_nextgen.py\", line 242, in <module>\r\n    main(**kwargs)\r\n  File \"/usr/local/bin/bcbio_nextgen.py\", line 47, in main\r\n    run_main(**kwargs)\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 45, in run_main\r\n    fc_dir, run_info_yaml)\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 89, in _run_toplevel\r\n    for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py\", line 152, in variant2pipeline\r\n    samples = genotype.parallel_variantcall_region(samples, run_parallel)\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/variation/genotype.py\", line 202, in parallel_variantcall_region\r\n    \"vrn_file\", [\"region\", \"sam_ref\", \"config\"]))\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/split.py\", line 32, in grouped_parallel_split_combine\r\n    final_output = parallel_fn(parallel_name, split_args)\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 28, in run_parallel\r\n    return run_multicore(fn, items, config, parallel=parallel)\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py\", line 86, in run_multicore\r\n    for data in joblib.Parallel(parallel[\"num_jobs\"], batch_size=1)(joblib.delayed(fn)(x) for x in items):\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 812, in __call__\r\n    self.retrieve()\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py\", line 749, in retrieve\r\n    exception = exception_type(report)\r\nTypeError: __init__() takes at least 3 arguments (2 given)"}}
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