{"action":"created","issue":{"url":"https://api.github.com/repos/nanoporetech/scrappie/issues/18","repository_url":"https://api.github.com/repos/nanoporetech/scrappie","labels_url":"https://api.github.com/repos/nanoporetech/scrappie/issues/18/labels{/name}","comments_url":"https://api.github.com/repos/nanoporetech/scrappie/issues/18/comments","events_url":"https://api.github.com/repos/nanoporetech/scrappie/issues/18/events","html_url":"https://github.com/nanoporetech/scrappie/issues/18","id":337598487,"node_id":"MDU6SXNzdWUzMzc1OTg0ODc=","number":18,"title":"Processing of a whole folder","user":{"login":"phpeters","id":8387095,"node_id":"MDQ6VXNlcjgzODcwOTU=","avatar_url":"https://avatars0.githubusercontent.com/u/8387095?v=4","gravatar_id":"","url":"https://api.github.com/users/phpeters","html_url":"https://github.com/phpeters","followers_url":"https://api.github.com/users/phpeters/followers","following_url":"https://api.github.com/users/phpeters/following{/other_user}","gists_url":"https://api.github.com/users/phpeters/gists{/gist_id}","starred_url":"https://api.github.com/users/phpeters/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/phpeters/subscriptions","organizations_url":"https://api.github.com/users/phpeters/orgs","repos_url":"https://api.github.com/users/phpeters/repos","events_url":"https://api.github.com/users/phpeters/events{/privacy}","received_events_url":"https://api.github.com/users/phpeters/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-07-02T17:14:02Z","updated_at":"2018-07-02T19:11:22Z","closed_at":null,"author_association":"NONE","body":"Hej,\r\n\r\nscrappie works fine for me if I run it on a single fast5-file provided in the program's reads-folder, as well on a single real data file. \r\nBut when I'm trying to run it on a list of files or a folder with fast5 files, it produces a stack of error messages (example A), or processes just one file (example B). So I try to loop through a list of the files, but then I sometimes get a sequence, or I get a different error message (example C).\r\n\r\nI'm a bit puzzled since it works on one file. Any good idea why I can't process more?\r\n\r\nThanks a lot and best regards!\r\nPhilipp\r\n\r\n### example A\r\nscrappie events folder/to/fast5Files/\r\nHDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:\r\nthread 0  #000: ../../src/H5F.c line 1509 in H5Fopen(): unable to open file\r\nthread 0HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:\r\n:\r\n    major: File accessability\r\n    minor: Unable to open file\r\n\r\n### example B\r\nscrappie events file1.fast5 file2.fast5 \r\nHDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0:\r\n  #000: ../../src/H5F.c line 1509 in H5Fopen(): unable to open file\r\n    major: File accessability\r\n    minor: Unable to open file\r\n  #001: ../../src/H5F.c line 1175 in H5F_open(): unable to retrieve VFL class\r\n    major: File accessability\r\n    minor: Can't get value\r\n  #002: ../../src/H5I.c line 1592 in H5I_inc_ref(): invalid type number\r\n    major: Invalid arguments to routine\r\n    minor: Out of range\r\nscrappie: Failed to open \r\n>readFromFile2\r\nAAATATATA....\r\n\r\n### example C\r\nwhile read line; do scrappie events $line; done < listOfFiles\r\nscrappie: Failed to create dataset for event table /software/scrappie/src/fast5_interface.c:201."},"comment":{"url":"https://api.github.com/repos/nanoporetech/scrappie/issues/comments/401905001","html_url":"https://github.com/nanoporetech/scrappie/issues/18#issuecomment-401905001","issue_url":"https://api.github.com/repos/nanoporetech/scrappie/issues/18","id":401905001,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMTkwNTAwMQ==","user":{"login":"tmassingham-ont","id":19410440,"node_id":"MDQ6VXNlcjE5NDEwNDQw","avatar_url":"https://avatars2.githubusercontent.com/u/19410440?v=4","gravatar_id":"","url":"https://api.github.com/users/tmassingham-ont","html_url":"https://github.com/tmassingham-ont","followers_url":"https://api.github.com/users/tmassingham-ont/followers","following_url":"https://api.github.com/users/tmassingham-ont/following{/other_user}","gists_url":"https://api.github.com/users/tmassingham-ont/gists{/gist_id}","starred_url":"https://api.github.com/users/tmassingham-ont/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tmassingham-ont/subscriptions","organizations_url":"https://api.github.com/users/tmassingham-ont/orgs","repos_url":"https://api.github.com/users/tmassingham-ont/repos","events_url":"https://api.github.com/users/tmassingham-ont/events{/privacy}","received_events_url":"https://api.github.com/users/tmassingham-ont/received_events","type":"User","site_admin":false},"created_at":"2018-07-02T19:11:22Z","updated_at":"2018-07-02T19:11:22Z","author_association":"CONTRIBUTOR","body":"Hello.  A lot of problems like these seem to be because many versions of the HDF5 library that are distributed do not support access from multiple threads.  Do you still get problems running Scrappie using `parallel`, as described by example in the documentation?"}}
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