{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/9","repository_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda","labels_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/9/comments","events_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/9/events","html_url":"https://github.com/PacificBiosciences/pbbioconda/issues/9","id":359197785,"node_id":"MDU6SXNzdWUzNTkxOTc3ODU=","number":9,"title":"falcon_kit.mains.fasta_filter is crashing","user":{"login":"roblehmann","id":3998527,"node_id":"MDQ6VXNlcjM5OTg1Mjc=","avatar_url":"https://avatars2.githubusercontent.com/u/3998527?v=4","gravatar_id":"","url":"https://api.github.com/users/roblehmann","html_url":"https://github.com/roblehmann","followers_url":"https://api.github.com/users/roblehmann/followers","following_url":"https://api.github.com/users/roblehmann/following{/other_user}","gists_url":"https://api.github.com/users/roblehmann/gists{/gist_id}","starred_url":"https://api.github.com/users/roblehmann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/roblehmann/subscriptions","organizations_url":"https://api.github.com/users/roblehmann/orgs","repos_url":"https://api.github.com/users/roblehmann/repos","events_url":"https://api.github.com/users/roblehmann/events{/privacy}","received_events_url":"https://api.github.com/users/roblehmann/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-09-11T19:51:02Z","updated_at":"2018-09-11T19:59:40Z","closed_at":null,"author_association":"NONE","body":"**Operating system**\r\nCentOS Linux release 7.3.1611\r\n\r\n**Package name**\r\npb-assembly installed today via anaconda\r\n\r\n**Describe the bug**\r\ncrashing command: python -m falcon_kit.mains.fasta_filter median -\r\n\r\nFalcon crashes because falcon_kit.mains.fasta_filter does not accept file name input from the standard input, but expects a file path.\r\nFollowing test call works: python -m falcon_kit.mains.fasta_filter median <path-to-fasta-file>\r\n\r\nIs falcon_kit 1.2.2 outdated?\r\n\r\n**Error message**\r\n```\r\n#fc_fasta2fasta < my.input.fofn >| fc.fofn\r\nwhile read fn; do  cat  ${fn} | python -m falcon_kit.mains.fasta_filter median - | fasta2DB -v raw_reads -i${fn##*/}; done < my.input.fofn\r\n+ read fn\r\n+ fasta2DB -v raw_reads -im170528_174820_42276_c101191972550000001823283109291706_s1_p0.1.subreads.fasta\r\n+ python -m falcon_kit.mains.fasta_filter median -\r\n+ cat /home/lehmanr/dataStore/melPacbio/r000112_42276_170525/DAM4_0245/A07_1/Analysis_Results/m170528_174820_42276_c101191972550000001823283109291706_s1_p0.1.subreads.fasta\r\nfalcon-kit 1.2.2\r\npypeflow 2.0.4\r\nTraceback (most recent call last):\r\n  File \"/home/lehmanr/.conda/envs/denovo_asm/lib/python2.7/runpy.py\", line 174, in _run_module_as_main\r\n    \"__main__\", fname, loader, pkg_name)\r\n  File \"/home/lehmanr/.conda/envs/denovo_asm/lib/python2.7/runpy.py\", line 72, in _run_code\r\n    exec code in run_globals\r\n  File \"/home/lehmanr/anaconda_lib/.conda/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/fasta_filter.py\", line 234, in <module>\r\n    main(sys.argv)          # pragma: no cover\r\n  File \"/home/lehmanr/anaconda_lib/.conda/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/fasta_filter.py\", line 231, in main\r\n    args.func(args)\r\n  File \"/home/lehmanr/anaconda_lib/.conda/envs/denovo_asm/lib/python2.7/site-packages/falcon_kit/mains/fasta_filter.py\", line 164, in cmd_run_median_filter\r\n    with open(args.input_path, 'r') as fp_in:\r\nIOError: [Errno 2] No such file or directory: '-'\r\ncat: write error: Broken pipe\r\nStandard input is empty, terminating!\r\n\r\n```\r\n"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/comments/420404668","html_url":"https://github.com/PacificBiosciences/pbbioconda/issues/9#issuecomment-420404668","issue_url":"https://api.github.com/repos/PacificBiosciences/pbbioconda/issues/9","id":420404668,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMDQwNDY2OA==","user":{"login":"gconcepcion","id":4172670,"node_id":"MDQ6VXNlcjQxNzI2NzA=","avatar_url":"https://avatars1.githubusercontent.com/u/4172670?v=4","gravatar_id":"","url":"https://api.github.com/users/gconcepcion","html_url":"https://github.com/gconcepcion","followers_url":"https://api.github.com/users/gconcepcion/followers","following_url":"https://api.github.com/users/gconcepcion/following{/other_user}","gists_url":"https://api.github.com/users/gconcepcion/gists{/gist_id}","starred_url":"https://api.github.com/users/gconcepcion/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gconcepcion/subscriptions","organizations_url":"https://api.github.com/users/gconcepcion/orgs","repos_url":"https://api.github.com/users/gconcepcion/repos","events_url":"https://api.github.com/users/gconcepcion/events{/privacy}","received_events_url":"https://api.github.com/users/gconcepcion/received_events","type":"User","site_admin":false},"created_at":"2018-09-11T19:59:40Z","updated_at":"2018-09-11T19:59:40Z","author_association":"MEMBER","body":"FYI: I am able to replicate this bug - however. In your fc_run.cfg you should use \r\n`pa_fasta_filter_option=streamed-median` \r\ninstead of\r\n`pa_fasta_filter_option=median`\r\n\r\n"}}
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