{"action":"created","issue":{"url":"https://api.github.com/repos/binarybottle/mhealthx/issues/5","labels_url":"https://api.github.com/repos/binarybottle/mhealthx/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/binarybottle/mhealthx/issues/5/comments","events_url":"https://api.github.com/repos/binarybottle/mhealthx/issues/5/events","html_url":"https://github.com/binarybottle/mhealthx/issues/5","id":104885789,"number":5,"title":"How to tolerate failed processes?","user":{"login":"binarybottle","id":236532,"avatar_url":"https://avatars.githubusercontent.com/u/236532?v=3","gravatar_id":"","url":"https://api.github.com/users/binarybottle","html_url":"https://github.com/binarybottle","followers_url":"https://api.github.com/users/binarybottle/followers","following_url":"https://api.github.com/users/binarybottle/following{/other_user}","gists_url":"https://api.github.com/users/binarybottle/gists{/gist_id}","starred_url":"https://api.github.com/users/binarybottle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/binarybottle/subscriptions","organizations_url":"https://api.github.com/users/binarybottle/orgs","repos_url":"https://api.github.com/users/binarybottle/repos","events_url":"https://api.github.com/users/binarybottle/events{/privacy}","received_events_url":"https://api.github.com/users/binarybottle/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/binarybottle/mhealthx/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":{"login":"satra","id":184063,"avatar_url":"https://avatars.githubusercontent.com/u/184063?v=3","gravatar_id":"","url":"https://api.github.com/users/satra","html_url":"https://github.com/satra","followers_url":"https://api.github.com/users/satra/followers","following_url":"https://api.github.com/users/satra/following{/other_user}","gists_url":"https://api.github.com/users/satra/gists{/gist_id}","starred_url":"https://api.github.com/users/satra/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/satra/subscriptions","organizations_url":"https://api.github.com/users/satra/orgs","repos_url":"https://api.github.com/users/satra/repos","events_url":"https://api.github.com/users/satra/events{/privacy}","received_events_url":"https://api.github.com/users/satra/received_events","type":"User","site_admin":false},"milestone":null,"comments":6,"created_at":"2015-09-04T12:56:48Z","updated_at":"2015-09-04T15:24:09Z","closed_at":null,"body":"When I run mhealthx on 1,000 audio files, nipype stopped when ffmpeg tried to convert an incomplete file, generating the error below.  How do I make sure that nipype still processes all of the other audio files, and continues on to construct a feature table at the end of the pipeline (with empty cells for failed files)?\r\n\r\n----\r\nException: Subnodes of node: convert_phonation_file failed:\r\nSubnode 954 failed\r\nError:\r\nCommand:\r\nffmpeg -i /Users/arno/mhealthx_cache/mhealthx/retrieve_phonation_file/mapflow/_retrieve_phonation_file954/audio_audio.m4a-2d4631c3-1f7d-4a42-bc5b-4ddb737a9b3b7521126929657780583.tmp.m4a -ac 2 /Users/arno/mhealthx_cache/mhealthx/retrieve_phonation_file/mapflow/_retrieve_phonation_file954/audio_audio.m4a-2d4631c3-1f7d-4a42-bc5b-4ddb737a9b3b7521126929657780583.tmp.m4a.wav\r\nStandard output:\r\nStandard error:\r\nffmpeg version 2.7.2 Copyright (c) 2000-2015 the FFmpeg developers\r\n  built with Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn)\r\n  configuration: \r\n  libavutil      54. 27.100 / 54. 27.100\r\n  libavcodec     56. 41.100 / 56. 41.100\r\n  libavformat    56. 36.100 / 56. 36.100\r\n  libavdevice    56.  4.100 / 56.  4.100\r\n  libavfilter     5. 16.101 /  5. 16.101\r\n  libswscale      3.  1.101 /  3.  1.101\r\n  libswresample   1.  2.100 /  1.  2.100\r\n[mov,mp4,m4a,3gp,3g2,mj2 @ 0x7fbb5182c800] moov atom not found\r\n/Users/arno/mhealthx_cache/mhealthx/retrieve_phonation_file/mapflow/_retrieve_phonation_file954/audio_audio.m4a-2d4631c3-1f7d-4a42-bc5b-4ddb737a9b3b7521126929657780583.tmp.m4a: Invalid data found when processing input\r\nReturn code: 1\r\nInterface CommandLine failed to run. \r\nInterface Function failed to run. \r\n150904-05:33:51,561 workflow INFO:\r\n\t ***********************************\r\n150904-05:33:51,561 workflow ERROR:\r\n\t could not run node: mhealthx.convert_phonation_file\r\n150904-05:33:51,561 workflow INFO:\r\n\t crashfile: /Users/arno/Software/mhealthx/crash-20150904-053350-arno-convert_phonation_file.pklz\r\n150904-05:33:51,561 workflow INFO:\r\n\t ***********************************\r\nTraceback (most recent call last):\r\n  File \"/software/mhealthx/mhealthx/mhealthx\", line 466, in <module>\r\n    Flow.run(plugin=args.plugin)\r\n  File \"/software/miniconda/lib/python2.7/site-packages/nipype/pipeline/engine.py\", line 700, in run\r\n    runner.run(execgraph, updatehash=updatehash, config=self.config)\r\n  File \"/software/miniconda/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py\", line 56, in run\r\n    report_nodes_not_run(notrun)\r\n  File \"/software/miniconda/lib/python2.7/site-packages/nipype/pipeline/plugins/base.py\", line 92, in report_nodes_not_run\r\n    raise RuntimeError(('Workflow did not execute cleanly. '\r\nRuntimeError: Workflow did not execute cleanly. Check log for details\r\n"},"comment":{"url":"https://api.github.com/repos/binarybottle/mhealthx/issues/comments/137765424","html_url":"https://github.com/binarybottle/mhealthx/issues/5#issuecomment-137765424","issue_url":"https://api.github.com/repos/binarybottle/mhealthx/issues/5","id":137765424,"user":{"login":"satra","id":184063,"avatar_url":"https://avatars.githubusercontent.com/u/184063?v=3","gravatar_id":"","url":"https://api.github.com/users/satra","html_url":"https://github.com/satra","followers_url":"https://api.github.com/users/satra/followers","following_url":"https://api.github.com/users/satra/following{/other_user}","gists_url":"https://api.github.com/users/satra/gists{/gist_id}","starred_url":"https://api.github.com/users/satra/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/satra/subscriptions","organizations_url":"https://api.github.com/users/satra/orgs","repos_url":"https://api.github.com/users/satra/repos","events_url":"https://api.github.com/users/satra/events{/privacy}","received_events_url":"https://api.github.com/users/satra/received_events","type":"User","site_admin":false},"created_at":"2015-09-04T15:24:09Z","updated_at":"2015-09-04T15:24:09Z","body":"it does seem that you don't have any cross-file operation. i would not do this with mapnodes, to many failure options. this seems like a simple workflow per file."}}