{"action":"created","issue":{"url":"https://api.github.com/repos/denovogear/denovogear/issues/279","repository_url":"https://api.github.com/repos/denovogear/denovogear","labels_url":"https://api.github.com/repos/denovogear/denovogear/issues/279/labels{/name}","comments_url":"https://api.github.com/repos/denovogear/denovogear/issues/279/comments","events_url":"https://api.github.com/repos/denovogear/denovogear/issues/279/events","html_url":"https://github.com/denovogear/denovogear/issues/279","id":336345201,"node_id":"MDU6SXNzdWUzMzYzNDUyMDE=","number":279,"title":"Total number of Paired sample sites interrogated: 0","user":{"login":"jiehuang001","id":26947455,"node_id":"MDQ6VXNlcjI2OTQ3NDU1","avatar_url":"https://avatars3.githubusercontent.com/u/26947455?v=4","gravatar_id":"","url":"https://api.github.com/users/jiehuang001","html_url":"https://github.com/jiehuang001","followers_url":"https://api.github.com/users/jiehuang001/followers","following_url":"https://api.github.com/users/jiehuang001/following{/other_user}","gists_url":"https://api.github.com/users/jiehuang001/gists{/gist_id}","starred_url":"https://api.github.com/users/jiehuang001/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jiehuang001/subscriptions","organizations_url":"https://api.github.com/users/jiehuang001/orgs","repos_url":"https://api.github.com/users/jiehuang001/repos","events_url":"https://api.github.com/users/jiehuang001/events{/privacy}","received_events_url":"https://api.github.com/users/jiehuang001/received_events","type":"User","site_admin":false},"labels":[{"id":71314575,"node_id":"MDU6TGFiZWw3MTMxNDU3NQ==","url":"https://api.github.com/repos/denovogear/denovogear/labels/duplicate","name":"duplicate","color":"cccccc","default":true},{"id":977416495,"node_id":"MDU6TGFiZWw5Nzc0MTY0OTU=","url":"https://api.github.com/repos/denovogear/denovogear/labels/works-as-expected","name":"works-as-expected","color":"dddddd","default":false}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2018-06-27T18:46:40Z","updated_at":"2018-06-30T17:06:06Z","closed_at":"2018-06-27T20:36:11Z","author_association":"NONE","body":"**Hi, guys: I previously posted this question. I was really frustrated that it was not resolved, while I thought that my question is very very simple. I hope that this time i will get better luck. Basically, I have a trio, with 3 BAM files for them. I created a sample.ped file with the following content:**\r\n1 18-CG-15-07932_S5_R1_001 0 0 1 0\r\n1 18-CG-15-07931_S4_R1_001 0 0 2 0\r\n1 18-CG-15-07930_S3_R1_001 18-CG-15-07932_S5_R1_001 18-CG-15-07931_S4_R1_001 1 1\r\n\r\n**Then I run DNG with the following commands:**\r\nmodule load samtools/1.8\r\nsamtools mpileup -t DP -gf /share/pkg/bwa/ref/hg19.fa ../bam/18-CG-15-07930_S3_R1_001.bam ../bam/18-CG-15-07931_S4_R1_001.bam ../bam/18-CG-15-07932_S5_R1_001.bam > trio.bcf\r\nmodule load bcftools\r\nbcftools view -Oz -o trio.vcf.gz trio.bcf\r\nmodule load gcc/7.2.0\r\nmodule load python/2.7.13\r\nmodule load denovogear/2018-05-1_6723027\r\ndng dnm auto --rd_cutoff 0 --ped sample.ped --bcf trio.bcf\r\n\r\n**However, instead of getting any output, I got the following LOG file without anything else. Why at the end of this LOG file it says \"Total number of Paired sample sites interrogated: 0\". I am analyzing a trio, not a pair!!!**\r\n\r\n[mpileup] 3 samples in 3 input files\r\n<mpileup> Set max per-file depth to 2666\r\n\r\nCreated SNP lookup table\r\n First mrate: 1 last: 1\r\n First code: 6 last: 6\r\n First target string: AA/AA/AA last: TT/TT/TT\r\n First tref: 0.0002388 last: 0.99301\r\n\r\nCreated indel lookup table First code: 6 last: 6\r\n First target string: RR/RR/RR last: DD/DD/DD\r\n First prior: 0.05 last: 0.114\r\n\r\nCreated paired lookup table\r\n First target string: AA/AA last: TT/TT\r\n First prior 1 last: 1\r\n\r\nTotal number of SNP sites interrogated: 1122103115\r\nTotal number of SNP sites passing read-depth filters: 1122103115\r\nTotal number of INDEL sites interrogated: 604358\r\nTotal number of INDEL sites passing read-depth filters: 587646\r\nTotal number of Paired sample sites interrogated: 0\r\nTotal number of Paired sample sites passing read-depth filters: 0\r\nDone !"},"comment":{"url":"https://api.github.com/repos/denovogear/denovogear/issues/comments/401553744","html_url":"https://github.com/denovogear/denovogear/issues/279#issuecomment-401553744","issue_url":"https://api.github.com/repos/denovogear/denovogear/issues/279","id":401553744,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMTU1Mzc0NA==","user":{"login":"reedacartwright","id":101918,"node_id":"MDQ6VXNlcjEwMTkxOA==","avatar_url":"https://avatars0.githubusercontent.com/u/101918?v=4","gravatar_id":"","url":"https://api.github.com/users/reedacartwright","html_url":"https://github.com/reedacartwright","followers_url":"https://api.github.com/users/reedacartwright/followers","following_url":"https://api.github.com/users/reedacartwright/following{/other_user}","gists_url":"https://api.github.com/users/reedacartwright/gists{/gist_id}","starred_url":"https://api.github.com/users/reedacartwright/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/reedacartwright/subscriptions","organizations_url":"https://api.github.com/users/reedacartwright/orgs","repos_url":"https://api.github.com/users/reedacartwright/repos","events_url":"https://api.github.com/users/reedacartwright/events{/privacy}","received_events_url":"https://api.github.com/users/reedacartwright/received_events","type":"User","site_admin":false},"created_at":"2018-06-30T17:06:06Z","updated_at":"2018-06-30T17:06:06Z","author_association":"CONTRIBUTOR","body":"If you have manually identified sites that are de novos, please post the entire `#CHROM` header line and entire line from those positions so I can manually inspect them an figure out why they weren't being called."}}
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