{"action":"created","issue":{"url":"https://api.github.com/repos/SouthGreenPlatform/TOGGLE/issues/8","repository_url":"https://api.github.com/repos/SouthGreenPlatform/TOGGLE","labels_url":"https://api.github.com/repos/SouthGreenPlatform/TOGGLE/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/SouthGreenPlatform/TOGGLE/issues/8/comments","events_url":"https://api.github.com/repos/SouthGreenPlatform/TOGGLE/issues/8/events","html_url":"https://github.com/SouthGreenPlatform/TOGGLE/issues/8","id":177174676,"number":8,"title":"BWA ALN driving to a 'EOF error' on some FASTQ","user":{"login":"PWSmit","id":20198953,"avatar_url":"https://avatars.githubusercontent.com/u/20198953?v=3","gravatar_id":"","url":"https://api.github.com/users/PWSmit","html_url":"https://github.com/PWSmit","followers_url":"https://api.github.com/users/PWSmit/followers","following_url":"https://api.github.com/users/PWSmit/following{/other_user}","gists_url":"https://api.github.com/users/PWSmit/gists{/gist_id}","starred_url":"https://api.github.com/users/PWSmit/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PWSmit/subscriptions","organizations_url":"https://api.github.com/users/PWSmit/orgs","repos_url":"https://api.github.com/users/PWSmit/repos","events_url":"https://api.github.com/users/PWSmit/events{/privacy}","received_events_url":"https://api.github.com/users/PWSmit/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-09-15T13:22:19Z","updated_at":"2016-09-15T15:37:55Z","closed_at":null,"body":"Hi, \r\n\r\nI tried to use TOGGLE with the test data provided and with my own files. the EOF error pops-up with every version of BWA I tried. I have tried 7.12, 7.15, 6.2, and 7.13. All of them give me the same error. \r\nSuggestion which version I should use would be appreciated. Thanks! \r\n\r\np.s. the automatic installer, doesn't work. it results in various permission errors and end-up with a practically empty folder... "},"comment":{"url":"https://api.github.com/repos/SouthGreenPlatform/TOGGLE/issues/comments/247364474","html_url":"https://github.com/SouthGreenPlatform/TOGGLE/issues/8#issuecomment-247364474","issue_url":"https://api.github.com/repos/SouthGreenPlatform/TOGGLE/issues/8","id":247364474,"user":{"login":"PWSmit","id":20198953,"avatar_url":"https://avatars.githubusercontent.com/u/20198953?v=3","gravatar_id":"","url":"https://api.github.com/users/PWSmit","html_url":"https://github.com/PWSmit","followers_url":"https://api.github.com/users/PWSmit/followers","following_url":"https://api.github.com/users/PWSmit/following{/other_user}","gists_url":"https://api.github.com/users/PWSmit/gists{/gist_id}","starred_url":"https://api.github.com/users/PWSmit/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/PWSmit/subscriptions","organizations_url":"https://api.github.com/users/PWSmit/orgs","repos_url":"https://api.github.com/users/PWSmit/repos","events_url":"https://api.github.com/users/PWSmit/events{/privacy}","received_events_url":"https://api.github.com/users/PWSmit/received_events","type":"User","site_admin":false},"created_at":"2016-09-15T15:37:55Z","updated_at":"2016-09-15T15:37:55Z","body":"Hi,\n\nThanks for the suggestion.\n\n I used BWA mem directly w/o TOGGLE and it works OK. However, via TOGGLE I end up with the same error using BWA mem. in the terminal, he gives me the same error again as well: \n“use of uninitialized value $waitOutput in numeric ne (!=) at home/manager/TOGGLE/toggleGenerator.pl line 541”. It does produce a SAM file which looks OK to me. \n\nI couldn’t find the reason for the error, but I didn’t wrote the tool :) \nYour help will be greatly appreciated as I have to run 250 isolates and your tool would be great for it! \n\nMany thanks, \n\nPieter\n\n> On Sep 15, 2016, at 3:52 PM, Francois Sabot <notifications@github.com> wrote:\n> \n> Hi\n> Did you try the incriminate file directly using BWA aln w/o TOGGLE ? There is a weird bug in aln (not at all TOGGLE related) that sometimes provokes such issue, but we do not know why.\n> \n> Either, try using bwa mem instead of aln/sampe.\n> \n> For the installer, can you provide me the errors and the config (system, kernel, gcc...) that I can check ?\n> \n> cheers\n> \n> F\n> \n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub <https://github.com/SouthGreenPlatform/TOGGLE/issues/8#issuecomment-247333929>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ATQ2KSD5wPI9Gvblke88eeLfWCzdKwnQks5qqU2NgaJpZM4J929_>.\n> \n\n"}}
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