{"action":"created","issue":{"url":"https://api.github.com/repos/jts/nanocorrect/issues/12","labels_url":"https://api.github.com/repos/jts/nanocorrect/issues/12/labels{/name}","comments_url":"https://api.github.com/repos/jts/nanocorrect/issues/12/comments","events_url":"https://api.github.com/repos/jts/nanocorrect/issues/12/events","html_url":"https://github.com/jts/nanocorrect/issues/12","id":93556039,"number":12,"title":"Problem running nanocorrect, no output files","user":{"login":"nickloman","id":116577,"avatar_url":"https://avatars.githubusercontent.com/u/116577?v=3","gravatar_id":"","url":"https://api.github.com/users/nickloman","html_url":"https://github.com/nickloman","followers_url":"https://api.github.com/users/nickloman/followers","following_url":"https://api.github.com/users/nickloman/following{/other_user}","gists_url":"https://api.github.com/users/nickloman/gists{/gist_id}","starred_url":"https://api.github.com/users/nickloman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nickloman/subscriptions","organizations_url":"https://api.github.com/users/nickloman/orgs","repos_url":"https://api.github.com/users/nickloman/repos","events_url":"https://api.github.com/users/nickloman/events{/privacy}","received_events_url":"https://api.github.com/users/nickloman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":9,"created_at":"2015-07-07T15:19:22Z","updated_at":"2015-07-07T16:21:27Z","closed_at":null,"body":"From a discussion I have been having on email with Adam Hargreaves:\r\n\r\n\r\nHave been trying this command:\r\n\r\npython makerange.py Eco6_48hr_just_2D_readsunixfixed.fasta | parallel -v --progress -P8 'python nanocorrect.py Eco6_48hr {} > Eco6_48hr.{}.corrected.fasta'\r\n\r\nI wasn't sure of the -P $(NC_PROCESS) syntax, so played about with it a bit, not sure if the above version is correct.\r\n\r\nThis gave a lot of files as output, lots of lashow.*.out and poa.input.*.fa files along with *.*.corrected.fasta files which all seem to be empty.\r\n\r\nNot sure if this is due to the commands I'm giving or if there's some kind of install issue which is preventing the script running fully.\r\n\r\n==\r\n\r\n\r\nIt was, but not to the actual executable. Have amended and then tried again, this time I get this error:\r\n\r\nIOError: [Errno 2] No such file or directory: 'clustal-16751.out'\r\npython nanocorrect.py Eco6_48hr 16801:16804 > Eco6_48hr.16801:16804.corrected.fasta\r\nTraceback (most recent call last):\r\n  File \"nanocorrect.py\", line 193, in <module>\r\n    (seq, n_reads) = run_poa_and_consensus(overlaps, read_idx)\r\n  File \"nanocorrect.py\", line 158, in run_poa_and_consensus\r\n    consensus =  clustal2consensus(out_fn)\r\n  File \"nanocorrect.py\", line 86, in clustal2consensus\r\n    alignment = AlignIO.read(fn, \"clustal\")\r\n  File \"/usr/local/lib/python2.7/dist-packages/Bio/AlignIO/__init__.py\", line 427, in read\r\n    first = next(iterator)\r\n  File \"/usr/local/lib/python2.7/dist-packages/Bio/AlignIO/__init__.py\", line 350, in parse\r\n    with as_handle(handle, 'rU') as fp:\r\n  File \"/usr/lib/python2.7/contextlib.py\", line 17, in __enter__\r\n    return self.gen.next()\r\n  File \"/usr/local/lib/python2.7/dist-packages/Bio/File.py\", line 90, in as_handle\r\n    with open(handleish, mode, **kwargs) as fp:\r\nIOError: [Errno 2] No such file or directory: 'clustal-16801.out'\r\nlocal:0/337/100%/0.0s\r\n\r\nSome kind of python module missing?\r\n\r\n\r\n==\r\n\r\nCan you check that 'poa' is on the $PATH ? e.g. if you run poa in a terminal does it run?\r\n\r\n\r\n== \r\n\r\nIt was, but not to the actual executable. Have amended and then tried again, this time I get this error:\r\n\r\nIOError: [Errno 2] No such file or directory: 'clustal-16751.out'\r\npython nanocorrect.py Eco6_48hr 16801:16804 > Eco6_48hr.16801:16804.corrected.fasta\r\nTraceback (most recent call last):\r\n  File \"nanocorrect.py\", line 193, in <module>\r\n    (seq, n_reads) = run_poa_and_consensus(overlaps, read_idx)\r\n  File \"nanocorrect.py\", line 158, in run_poa_and_consensus\r\n    consensus =  clustal2consensus(out_fn)\r\n  File \"nanocorrect.py\", line 86, in clustal2consensus\r\n    alignment = AlignIO.read(fn, \"clustal\")\r\n  File \"/usr/local/lib/python2.7/dist-packages/Bio/AlignIO/__init__.py\", line 427, in read\r\n    first = next(iterator)\r\n  File \"/usr/local/lib/python2.7/dist-packages/Bio/AlignIO/__init__.py\", line 350, in parse\r\n    with as_handle(handle, 'rU') as fp:\r\n  File \"/usr/lib/python2.7/contextlib.py\", line 17, in __enter__\r\n    return self.gen.next()\r\n  File \"/usr/local/lib/python2.7/dist-packages/Bio/File.py\", line 90, in as_handle\r\n    with open(handleish, mode, **kwargs) as fp:\r\nIOError: [Errno 2] No such file or directory: 'clustal-16801.out'\r\nlocal:0/337/100%/0.0s\r\n\r\nSome kind of python module missing?"},"comment":{"url":"https://api.github.com/repos/jts/nanocorrect/issues/comments/119259164","html_url":"https://github.com/jts/nanocorrect/issues/12#issuecomment-119259164","issue_url":"https://api.github.com/repos/jts/nanocorrect/issues/12","id":119259164,"user":{"login":"AdamHargreaves","id":13222442,"avatar_url":"https://avatars.githubusercontent.com/u/13222442?v=3","gravatar_id":"","url":"https://api.github.com/users/AdamHargreaves","html_url":"https://github.com/AdamHargreaves","followers_url":"https://api.github.com/users/AdamHargreaves/followers","following_url":"https://api.github.com/users/AdamHargreaves/following{/other_user}","gists_url":"https://api.github.com/users/AdamHargreaves/gists{/gist_id}","starred_url":"https://api.github.com/users/AdamHargreaves/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AdamHargreaves/subscriptions","organizations_url":"https://api.github.com/users/AdamHargreaves/orgs","repos_url":"https://api.github.com/users/AdamHargreaves/repos","events_url":"https://api.github.com/users/AdamHargreaves/events{/privacy}","received_events_url":"https://api.github.com/users/AdamHargreaves/received_events","type":"User","site_admin":false},"created_at":"2015-07-07T16:21:27Z","updated_at":"2015-07-07T16:21:27Z","body":"OK so it is now running!\r\n\r\nSeemed to be the poa-blosum80.mat file you mentioned Jared. The initial directory I had, the text for this file was in red for whatever reason. I re-cloned nanocorrect from GitHub and replaced this file with the newly downloaded version (white text) and it now seems to be running smoothly.\r\n\r\nNo idea what I had done to mess the file up! Thanks very much both of you for your help!"}}