{"action":"created","issue":{"url":"https://api.github.com/repos/chrishah/MITObim/issues/12","labels_url":"https://api.github.com/repos/chrishah/MITObim/issues/12/labels{/name}","comments_url":"https://api.github.com/repos/chrishah/MITObim/issues/12/comments","events_url":"https://api.github.com/repos/chrishah/MITObim/issues/12/events","html_url":"https://github.com/chrishah/MITObim/issues/12","id":103388987,"number":12,"title":"Mirabait fails on iteration 0","user":{"login":"cypridina","id":3123273,"avatar_url":"https://avatars.githubusercontent.com/u/3123273?v=3","gravatar_id":"","url":"https://api.github.com/users/cypridina","html_url":"https://github.com/cypridina","followers_url":"https://api.github.com/users/cypridina/followers","following_url":"https://api.github.com/users/cypridina/following{/other_user}","gists_url":"https://api.github.com/users/cypridina/gists{/gist_id}","starred_url":"https://api.github.com/users/cypridina/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cypridina/subscriptions","organizations_url":"https://api.github.com/users/cypridina/orgs","repos_url":"https://api.github.com/users/cypridina/repos","events_url":"https://api.github.com/users/cypridina/events{/privacy}","received_events_url":"https://api.github.com/users/cypridina/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-08-26T23:51:44Z","updated_at":"2015-08-27T00:57:33Z","closed_at":null,"body":"Earlier today I successfully ran tutorial 3 using MITObim 1.6. I then deleted the iteration files, and tried to run the program on my own data. It failed at iteration 0.\r\n\r\nI switch the call to replicate tutorial 3 again, and I keep getting the same error. See below. Any thoughts? Thanks for all of your help so far!\r\n```\r\nMITObim - mitochondrial baiting and iterative mapping\r\nversion 1.6\r\nauthor: Christoph Hahn, (c) 2012-2013\r\n\r\nquick option selected! -maf option will be ignored (if given)\r\n\r\nFull command run: /PATH/MITObim/MITObim_1.6.pl -strain testpool -ref Tthymallus-COI \r\n-readpool /PATH/MITObim/testdata1/Tthymallus-150bp-300sd50-interleaved.fastq \r\n--quick /PATH/MITObim/testdata1/Tthymallus-COI-partial-HQ961018.fasta -end 100 \r\n--noshow --clean\r\n\r\nAll paramters seem to make sense:\r\nstartiteration: 0\r\nenditeration: 100\r\nstrainname: testpool\r\nrefname: Tthymallus-COI\r\nreadpool: /PATH/MITObim/testdata1/Tthymallus-150bp-300sd50-interleaved.fastq\r\nmaf: 0\r\nquick: /PATH/MITObim/testdata1/Tthymallus-COI-partial-HQ961018.fasta\r\npaired: 0\r\ndenovo: 0 (mapping=0, denovo=1)\r\nnoshow: 1\r\nread trimming: 0 (off=0, on=1)\r\nkmer baiting: 31\r\nplatform: SOLEXA\r\nclean: 1 (off=0, on=1)\r\nproofread: 0\r\n\r\nStarting MITObim\r\n\r\n==============\r\n ITERATION 0\r\n==============\r\nAug 26 16:45:28\r\n\r\n\r\nquick option baits reads from provided reference in iteration 0\r\n\r\nfishing readpool using mirabait (k = 31)\r\n\r\n\r\nmirabait seems to have failed - see detailed output above\r\n> \r\n```\r\n(returns back to command prompt here)"},"comment":{"url":"https://api.github.com/repos/chrishah/MITObim/issues/comments/135223026","html_url":"https://github.com/chrishah/MITObim/issues/12#issuecomment-135223026","issue_url":"https://api.github.com/repos/chrishah/MITObim/issues/12","id":135223026,"user":{"login":"chrishah","id":2293242,"avatar_url":"https://avatars.githubusercontent.com/u/2293242?v=3","gravatar_id":"","url":"https://api.github.com/users/chrishah","html_url":"https://github.com/chrishah","followers_url":"https://api.github.com/users/chrishah/followers","following_url":"https://api.github.com/users/chrishah/following{/other_user}","gists_url":"https://api.github.com/users/chrishah/gists{/gist_id}","starred_url":"https://api.github.com/users/chrishah/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chrishah/subscriptions","organizations_url":"https://api.github.com/users/chrishah/orgs","repos_url":"https://api.github.com/users/chrishah/repos","events_url":"https://api.github.com/users/chrishah/events{/privacy}","received_events_url":"https://api.github.com/users/chrishah/received_events","type":"User","site_admin":false},"created_at":"2015-08-27T00:57:33Z","updated_at":"2015-08-27T00:57:33Z","body":"Hi,\r\n\r\nJust to make sure: Are you running `MITObim_1.6.pl` on purpose? Could it be that in your earlier tests you ran version 1.8? Could you give it a quick try?\r\n\r\nIf that doesn't fix it and/or you are running 1.6 on purpose could you please rerun without the `--noshow` flag and let me know what it says.\r\nThanks!\r\n\r\ncheers,\r\nChristoph"}}