{"action":"created","issue":{"url":"https://api.github.com/repos/sanger-pathogens/circlator/issues/51","repository_url":"https://api.github.com/repos/sanger-pathogens/circlator","labels_url":"https://api.github.com/repos/sanger-pathogens/circlator/issues/51/labels{/name}","comments_url":"https://api.github.com/repos/sanger-pathogens/circlator/issues/51/comments","events_url":"https://api.github.com/repos/sanger-pathogens/circlator/issues/51/events","html_url":"https://github.com/sanger-pathogens/circlator/issues/51","id":139543273,"number":51,"title":"disabling mismatch correction in SPAdes","user":{"login":"gedankenstuecke","id":674899,"avatar_url":"https://avatars.githubusercontent.com/u/674899?v=3","gravatar_id":"","url":"https://api.github.com/users/gedankenstuecke","html_url":"https://github.com/gedankenstuecke","followers_url":"https://api.github.com/users/gedankenstuecke/followers","following_url":"https://api.github.com/users/gedankenstuecke/following{/other_user}","gists_url":"https://api.github.com/users/gedankenstuecke/gists{/gist_id}","starred_url":"https://api.github.com/users/gedankenstuecke/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gedankenstuecke/subscriptions","organizations_url":"https://api.github.com/users/gedankenstuecke/orgs","repos_url":"https://api.github.com/users/gedankenstuecke/repos","events_url":"https://api.github.com/users/gedankenstuecke/events{/privacy}","received_events_url":"https://api.github.com/users/gedankenstuecke/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-03-09T10:51:40Z","updated_at":"2016-03-09T11:12:10Z","closed_at":null,"body":"I'm running *circlator* with *SPAdes 3.6.0* and sometimes it crashes with the following error during the contig mismatch correction at the end: \r\n\r\n```\r\nLine 6191, sequence length 17974 vs 1590 from CIGAR\r\nParse error at line 6191: CIGAR and sequence length are inconsistent\r\n\r\n\r\n== Error ==  system call for: \"['/home/bastian/bin/SPAdes-3.5.0-Linux/bin/corrector', '/share/project/circlator_results/03.assemble.tmp.spades.87.7bjtc3gr/mismatch_corrector/contigs/configs/corrector.info', '/share/project/circlator_results/03.assemble.tmp.spades.87.7bjtc3gr/misc/assembled_contigs.fasta']\" finished abnormally, err code: -6\r\n```\r\n\r\nThis leads to the whole `circlator all` crashing in the end, as it happens for each k-mer size. I guess I could just hard-code the corresponding flags into circlator, but I wondered whether disabling this would  \r\n\r\na) be a good idea at all or whether it will lead to my results going down the drain\r\nb) if this should be added as a general option to *circlator* if it's a good idea? "},"comment":{"url":"https://api.github.com/repos/sanger-pathogens/circlator/issues/comments/194244643","html_url":"https://github.com/sanger-pathogens/circlator/issues/51#issuecomment-194244643","issue_url":"https://api.github.com/repos/sanger-pathogens/circlator/issues/51","id":194244643,"user":{"login":"martinghunt","id":4937411,"avatar_url":"https://avatars.githubusercontent.com/u/4937411?v=3","gravatar_id":"","url":"https://api.github.com/users/martinghunt","html_url":"https://github.com/martinghunt","followers_url":"https://api.github.com/users/martinghunt/followers","following_url":"https://api.github.com/users/martinghunt/following{/other_user}","gists_url":"https://api.github.com/users/martinghunt/gists{/gist_id}","starred_url":"https://api.github.com/users/martinghunt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/martinghunt/subscriptions","organizations_url":"https://api.github.com/users/martinghunt/orgs","repos_url":"https://api.github.com/users/martinghunt/repos","events_url":"https://api.github.com/users/martinghunt/events{/privacy}","received_events_url":"https://api.github.com/users/martinghunt/received_events","type":"User","site_admin":false},"created_at":"2016-03-09T11:12:10Z","updated_at":"2016-03-09T11:12:10Z","body":"I have always used spades with --careful (I guess this is the option you want to remove?), so don't know what the effect would be. I suspect that it won't have much effect on Circlataor itself. From the description in the spades help, I guess the percent identity between the spades reassembly and the original contigs could potentially drop a tiny bit. You could compenstate by lowering the minimum identity with --merge_min_id.\r\n\r\nI think it's definitely a good idea to add a circlator option to change it."}}