{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/269","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/269/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/269/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/269/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/269","id":125068591,"number":269,"title":"/bin/bash: bad interpreter: Text file busy","user":{"login":"yfu","id":1415957,"avatar_url":"https://avatars.githubusercontent.com/u/1415957?v=3","gravatar_id":"","url":"https://api.github.com/users/yfu","html_url":"https://github.com/yfu","followers_url":"https://api.github.com/users/yfu/followers","following_url":"https://api.github.com/users/yfu/following{/other_user}","gists_url":"https://api.github.com/users/yfu/gists{/gist_id}","starred_url":"https://api.github.com/users/yfu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yfu/subscriptions","organizations_url":"https://api.github.com/users/yfu/orgs","repos_url":"https://api.github.com/users/yfu/repos","events_url":"https://api.github.com/users/yfu/events{/privacy}","received_events_url":"https://api.github.com/users/yfu/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2016-01-05T22:42:48Z","updated_at":"2016-01-06T00:11:37Z","closed_at":null,"body":"I have run fc_run.py with the same config file and the same input files several times, but every time, it returned the same error: \"/bin/bash: bad interpreter: Text file busy\". And it seems to be non-deterministic: jobs with different numbers giving the same error message.\r\n\r\nI have attached part of the log below:\r\n```\r\n['/data/fuy2/FALCON-integrate/fc_env/bin/fc_run.py', 'fc_run.cfg', 'logging.ini']\r\n2016-01-05 22:35:03,352 - fc_run - INFO - fc_run started with configuration fc_run.cfg\r\n...\r\n2016-01-05 22:35:07,704 - fc_run - WARNING - Call 'bash /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000/rj_0000.sh 1> /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000/rj_0000.sh.log 2>&1' returned 32256.\r\n2016-01-05 22:35:07,704 - fc_run - ERROR - Contents of '/data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000/rj_0000.sh.log':\r\ncd /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000\r\n+ cd /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000\r\ntrap 'touch /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000/job_0000_done.exit' EXIT\r\n+ trap 'touch /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000/job_0000_done.exit' EXIT\r\nls -il rj_0000.sub.sh\r\n+ ls -il rj_0000.sub.sh\r\n772313525 -rw-r--r-- 1 fuy2 UNIXLDAPUsers 3294 Jan  5 17:35 rj_0000.sub.sh\r\nhostname\r\n+ hostname\r\nummsres17\r\nchmod +x rj_0000.sub.sh\r\n+ chmod +x rj_0000.sub.sh\r\ntouch rj_0000.sub.sh\r\n+ touch rj_0000.sub.sh\r\nls -il rj_0000.sub.sh\r\n+ ls -il rj_0000.sub.sh\r\n772313525 -rwxr-xr-x 1 fuy2 UNIXLDAPUsers 3294 Jan  5 17:35 rj_0000.sub.sh\r\ntime ./rj_0000.sub.sh\r\n+ ./rj_0000.sub.sh\r\n/data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000/rj_0000.sh: ./rj_0000.sub.sh: /bin/bash: bad interpreter: Text file busy\r\ntouch /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000/job_0000_done.exit\r\n+ touch /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000/job_0000_done.exit\r\nTraceback (most recent call last):\r\n  File \"/data/fuy2/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 66, in _run_script_local\r\n    system(cmd, check=True)\r\n  File \"/data/fuy2/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.4.0-py2.7-linux-x86_64.egg/falcon_kit/mains/run.py\", line 23, in system\r\n    raise Exception(msg)\r\nException: Call 'bash /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000/rj_0000.sh 1> /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0000/rj_0000.sh.log 2>&1' returned 32256.\r\n2016-01-05 22:35:07,720 - fc_run - WARNING - Call 'bash /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0006/rj_0006.sh 1> /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0006/rj_0006.sh.log 2>&1' returned 32256.\r\n2016-01-05 22:35:07,721 - fc_run - ERROR - Contents of '/data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0006/rj_0006.sh.log':\r\ncd /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0006\r\n+ cd /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0006\r\ntrap 'touch /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0006/job_0006_done.exit' EXIT\r\n+ trap 'touch /data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0006/job_0006_done.exit' EXIT\r\nls -il rj_0006.sub.sh\r\n+ ls -il rj_0006.sub.sh\r\n772313536 -rw-r--r-- 1 fuy2 UNIXLDAPUsers 4804 Jan  5 17:35 rj_0006.sub.sh\r\nhostname\r\n+ hostname\r\nummsres17\r\nchmod +x rj_0006.sub.sh\r\n+ chmod +x rj_0006.sub.sh\r\ntouch rj_0006.sub.sh\r\n+ touch rj_0006.sub.sh\r\nls -il rj_0006.sub.sh\r\n+ ls -il rj_0006.sub.sh\r\n772313536 -rwxr-xr-x 1 fuy2 UNIXLDAPUsers 4804 Jan  5 17:35 rj_0006.sub.sh\r\ntime ./rj_0006.sub.sh\r\n+ ./rj_0006.sub.sh\r\n**/data/fuy2/cl/results/2016-01-05-falcon/ecoli-test/0-rawreads/job_0006/rj_0006.sh: ./rj_0006.sub.sh: /bin/bash: bad interpreter: Text file busy**\r\n```"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/169175055","html_url":"https://github.com/PacificBiosciences/FALCON/issues/269#issuecomment-169175055","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/269","id":169175055,"user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"created_at":"2016-01-06T00:11:37Z","updated_at":"2016-01-06T00:11:37Z","body":"I can work on this tonight. If I come up with a possible solution, will you test it for us on your system?"}}