{"action":"opened","issue":{"url":"https://api.github.com/repos/bioinform/varsim/issues/162","repository_url":"https://api.github.com/repos/bioinform/varsim","labels_url":"https://api.github.com/repos/bioinform/varsim/issues/162/labels{/name}","comments_url":"https://api.github.com/repos/bioinform/varsim/issues/162/comments","events_url":"https://api.github.com/repos/bioinform/varsim/issues/162/events","html_url":"https://github.com/bioinform/varsim/issues/162","id":308883002,"number":162,"title":"WARN [main] (VCFparser.java:189): Unrecognized phasing '.'.","user":{"login":"LeeNicha","id":24719780,"avatar_url":"https://avatars3.githubusercontent.com/u/24719780?v=4","gravatar_id":"","url":"https://api.github.com/users/LeeNicha","html_url":"https://github.com/LeeNicha","followers_url":"https://api.github.com/users/LeeNicha/followers","following_url":"https://api.github.com/users/LeeNicha/following{/other_user}","gists_url":"https://api.github.com/users/LeeNicha/gists{/gist_id}","starred_url":"https://api.github.com/users/LeeNicha/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LeeNicha/subscriptions","organizations_url":"https://api.github.com/users/LeeNicha/orgs","repos_url":"https://api.github.com/users/LeeNicha/repos","events_url":"https://api.github.com/users/LeeNicha/events{/privacy}","received_events_url":"https://api.github.com/users/LeeNicha/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-03-27T09:08:18Z","updated_at":"2018-03-27T09:08:18Z","closed_at":null,"author_association":"NONE","body":"Hi, I got the following error when I tried to simulate normal sample with germline mutations.\r\n----------------------------------------------------------------------------------------------------\r\nFile \"varsim.py\", line 721, in <module>\r\n    disable_vcf2diploid=args.disable_vcf2diploid)\r\n  File \"varsim.py\", line 356, in varsim_main\r\n    processes = monitor_processes(processes)\r\n  File \"varsim.py\", line 141, in monitor_processes\r\n    raise Exception('Aborting... Please check log for details.')\r\nException: Aborting... Please check log for details.\r\n----------------------------------------------------------------------------------------------------\r\n[RandVCF2VCF.tar.gz](https://github.com/bioinform/varsim/files/1851186/RandVCF2VCF.tar.gz)\r\n\r\nThis is my command:\r\npython varsim.py --reference ~/program/automated_wxs_pipeline/database/human_g1k_v37.fasta --vc_in_vcf All.vcf.gz --sv_insert_seq insert_seq.txt --sv_dgv GRCh37_hg19_supportingvariants_2016-05-15.txt --id normal --read_length 101 --vc_num_snp 3000000 --sv_num_ins 0 --sv_num_del 0 --sv_num_dup 0 --sv_num_inv 0 --mean_fragment_size 350 --sd_fragment_size 50 --nlanes 5 --total_coverage 100 --simulator_executable ART/art_bin_VanillaIceCream/art_illumina --out_dir germline/out --log_dir germline/log --work_dir germline/work --simulator art\r\n\r\nThank you in advance for your kind response."}}
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