{"action":"closed","issue":{"url":"https://api.github.com/repos/dantaki/SV2/issues/16","repository_url":"https://api.github.com/repos/dantaki/SV2","labels_url":"https://api.github.com/repos/dantaki/SV2/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/dantaki/SV2/issues/16/comments","events_url":"https://api.github.com/repos/dantaki/SV2/issues/16/events","html_url":"https://github.com/dantaki/SV2/issues/16","id":337012976,"node_id":"MDU6SXNzdWUzMzcwMTI5NzY=","number":16,"title":"No error and no output for sv2","user":{"login":"carleshf","id":2046180,"node_id":"MDQ6VXNlcjIwNDYxODA=","avatar_url":"https://avatars0.githubusercontent.com/u/2046180?v=4","gravatar_id":"","url":"https://api.github.com/users/carleshf","html_url":"https://github.com/carleshf","followers_url":"https://api.github.com/users/carleshf/followers","following_url":"https://api.github.com/users/carleshf/following{/other_user}","gists_url":"https://api.github.com/users/carleshf/gists{/gist_id}","starred_url":"https://api.github.com/users/carleshf/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/carleshf/subscriptions","organizations_url":"https://api.github.com/users/carleshf/orgs","repos_url":"https://api.github.com/users/carleshf/repos","events_url":"https://api.github.com/users/carleshf/events{/privacy}","received_events_url":"https://api.github.com/users/carleshf/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-06-29T14:07:52Z","updated_at":"2018-06-29T18:31:42Z","closed_at":"2018-06-29T18:31:42Z","author_association":"NONE","body":"I want to use SV2 to combine the results from `manta`, `lumpy-sv`, `strelka` and `forestsv`. I am calling it (for only two of the four results) as:\r\n\r\n```\r\nsv2 \\\r\n    -bam /media/[...]/WGS/Fibroblast/Fibroblast_bwa_b38_recal_leftalignindels.hasLB.bam \\\r\n    -vcf /media/[...]/lumpy_iPSC/Fibroblast_bwa_b38_recal_leftalignindels.hasLB.svtyper.vcf /media/[...]/iPSC/manta_fibroblast/results/variants/candidateSV.vcf.gz /media/[...]/SV/iPSC/manta_fibroblast/results/variants/candidateSmallIndels.vcf.gz \\\r\n    -genome hg38 \\\r\n    -merge \\\r\n    -hg38 /media/[...]/ref/b38/Homo_sapiens_assembly38.fasta \\\r\n    -odir sv2_fibroblast_manta_lumpy \\\r\n    -log sv2_log\r\n```\r\n\r\nBut the results is:\r\n\r\n```\r\nsv2 version:1.4.3.4    report bugs to <dantaki at ucsd dot edu>       error messages located in sv2_log\r\n\r\n[carleshf@server sv2_fibroblast_manta_lumpy]$ ll\r\ntotal 0\r\n-rw-rw-r--. 1 carleshf carleshf 0 Jun 29  2018 sv2_log\r\n```\r\n\r\nI do not see what I am doing wrong and the program does not provide any output."}}
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