{"action":"opened","issue":{"url":"https://api.github.com/repos/jts/nanopolish/issues/416","repository_url":"https://api.github.com/repos/jts/nanopolish","labels_url":"https://api.github.com/repos/jts/nanopolish/issues/416/labels{/name}","comments_url":"https://api.github.com/repos/jts/nanopolish/issues/416/comments","events_url":"https://api.github.com/repos/jts/nanopolish/issues/416/events","html_url":"https://github.com/jts/nanopolish/issues/416","id":339169095,"node_id":"MDU6SXNzdWUzMzkxNjkwOTU=","number":416,"title":"Is \"nanopolish variants --consensus\" stuck on something?","user":{"login":"csm1209","id":40922540,"node_id":"MDQ6VXNlcjQwOTIyNTQw","avatar_url":"https://avatars3.githubusercontent.com/u/40922540?v=4","gravatar_id":"","url":"https://api.github.com/users/csm1209","html_url":"https://github.com/csm1209","followers_url":"https://api.github.com/users/csm1209/followers","following_url":"https://api.github.com/users/csm1209/following{/other_user}","gists_url":"https://api.github.com/users/csm1209/gists{/gist_id}","starred_url":"https://api.github.com/users/csm1209/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/csm1209/subscriptions","organizations_url":"https://api.github.com/users/csm1209/orgs","repos_url":"https://api.github.com/users/csm1209/repos","events_url":"https://api.github.com/users/csm1209/events{/privacy}","received_events_url":"https://api.github.com/users/csm1209/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-07-07T19:28:27Z","updated_at":"2018-07-07T19:28:27Z","closed_at":null,"author_association":"NONE","body":"Hello jts,\r\n\r\nThis is my initial command:\r\n\r\n> nanopolish variants --consensus c_cha_polished_assembly.fasta \\\r\n> -w \"tig00000001:1-2911167\" \\\r\n> -r input_reads_nanopolish.fastq.gz \\\r\n> -b c_chang_reads.sorted.bam \\\r\n> -g /mnt/home/nbrnvofj/Canu/c_chang_assembly/c_chang.contigs.fasta\r\n\r\nI ran it and left it overnight (~12 hrs), and it's still stuck on this display:\r\n\r\n> ##fileformat=VCFv4.2\r\n> ##INFO=<ID=TotalReads,Number=1,Type=Integer,Description=\"The number of event-space reads used to call the variant\">\r\n> ##INFO=<ID=SupportFraction,Number=1,Type=Float,Description=\"The fraction of event-space reads that support the variant\">\r\n> ##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description=\"The number of base-space reads that support the variant\">\r\n> ##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description=\"The fraction of base-space reads that support the variant\">\r\n> ##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description=\"The inferred number of copies of the allele\">\r\n> ##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\r\n> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  sample\r\n\r\nI tried tacking on \"--verbose\" and even \"-t 20\" to see if it would give me some indication that it's working but it stays on the same message again and doesn't seem to be doing anything or creating any output.\r\n\r\nIs this normal, am I just being impatient or am I doing something wrong? I should also mention that I did not use \"nanopolish_makerange.py\" to segment my genome. If I need to use this can you show me specifically how I would structure the command? There aren't specific instructions on makerange in the Nanopolish Documentation.\r\n\r\nThank you!!\r\n\r\nCarl\r\n"}}
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