{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/300","repository_url":"https://api.github.com/repos/PacificBiosciences/FALCON","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/300/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/300/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/300/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/300","id":137005316,"number":300,"title":"Solving error to run FALCON ","user":{"login":"lbien","id":14801134,"avatar_url":"https://avatars.githubusercontent.com/u/14801134?v=3","gravatar_id":"","url":"https://api.github.com/users/lbien","html_url":"https://github.com/lbien","followers_url":"https://api.github.com/users/lbien/followers","following_url":"https://api.github.com/users/lbien/following{/other_user}","gists_url":"https://api.github.com/users/lbien/gists{/gist_id}","starred_url":"https://api.github.com/users/lbien/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbien/subscriptions","organizations_url":"https://api.github.com/users/lbien/orgs","repos_url":"https://api.github.com/users/lbien/repos","events_url":"https://api.github.com/users/lbien/events{/privacy}","received_events_url":"https://api.github.com/users/lbien/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2016-02-28T04:20:57Z","updated_at":"2016-02-28T21:36:17Z","closed_at":null,"body":"Hello!\r\n\r\nI installed FALCON-integrate following the manual (https://github.com/PacificBiosciences/FALCON/wiki/Setup%3A-Installation-and-Environment), and ran successfully the example with ecoli_test (https://github.com/PacificBiosciences/FALCON/wiki/Setup%3A-Complete-example), but I haven't succeed to assemble my data. Here is the error I got: \r\n```\r\n2016-02-26 17:56:16,158 - pypeflow.controller - ERROR - Any exception caught in RefreshTargets() indicates an unrecoverable error. Shutting down...\r\nTraceback (most recent call last):\r\n  File \"/home/usr/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py\", line 522, in refreshTargets\r\n    rtn = self._refreshTargets(task2thread, objs = objs, callback = callback, updateFreq = updateFreq, exitOnFailure = exitOnFailure)\r\n  File \"/home/usr/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py\", line 747, in _refreshTargets\r\n    failedJobCount, succeededJobCount))\r\nLateTaskFailureError: 'Counted a total of 2 failure(s) and 4606 success(es).'\r\n2016-02-26 17:56:16,186 - pypeflow.controller - WARNING - #tasks=4608, #alive=0\r\n```\r\n\r\nI used this configuration: \r\n\r\n```\r\ninput_fofn = input.fofn\r\ninput_type = raw\r\nlength_cutoff = 12000\r\nlength_cutoff_pr = 12000\r\n\r\njob_type = local\r\njobqueue = your_queue\r\n\r\nsge_option_da = -pe smp 8 -q jobqueue\r\nsge_option_la = -pe smp 2 -q jobqueue\r\nsge_option_pda = -pe smp 8 -q jobqueue\r\nsge_option_pla = -pe smp 2 -q jobqueue\r\nsge_option_fc = -pe smp 24 -q jobqueue\r\nsge_option_cns = -pe smp 8 -q jobqueue\r\n\r\npa_concurrent_jobs = 32\r\novlp_concurrent_jobs = 32\r\n\r\npa_HPCdaligner_option =  -v -dal4 -t16 -e.70 -l1000 -s1000\r\novlp_HPCdaligner_option = -v -dal4 -t32 -h60 -e.96 -l500 -s1000\r\n\r\npa_DBsplit_option = -x500 -s50\r\novlp_DBsplit_option = -x500 -s50\r\n\r\nfalcon_sense_option = --output_multi --min_idt 0.70 --min_cov 4 --local_match_count_threshold 2 --max_n_read 200 --n_core 6\r\n\r\noverlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20 --bestn 10 --n_core 24\r\n```\r\n\r\nI greatly appreciate your help to run the software. \r\n"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/189949813","html_url":"https://github.com/PacificBiosciences/FALCON/issues/300#issuecomment-189949813","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/300","id":189949813,"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":"2016-02-28T21:36:17Z","updated_at":"2016-02-28T21:36:17Z","body":"`job_type = local`, so this is not (yet) an SGE issue. But you'll need to dive into the log files to see where things went wrong.\r\n\r\n> Counted a total of 2 failure(s) and 4606 success(es).\r\n\r\nYou probably had 2 daligner failures. It is possible -- with a bit of hackery -- to proceed without those, using the 4606 successful jobs.\r\n\r\nYou should see a 4606 files called `0-rawreads/job_*/job_*_done`. You are missing 2. Figure out the job numbers from the logs, and just `touch` them yourself. You might be able to find them by searching for files called `0-rawreads/job_*/job_*_done.exit`. If you find those, then delete the `_*done.exit` files and create the `*_done files. (In other words, `.exit` may or may not exist for failed jobs. It *never* exists for successful jobs.)"}}