{"action":"closed","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/520","repository_url":"https://api.github.com/repos/PacificBiosciences/FALCON","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/520/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/520/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/520/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/520","id":204184436,"number":520,"title":"failed to run FALCON-integrate","user":{"login":"yilunhuangyue","id":16872303,"avatar_url":"https://avatars2.githubusercontent.com/u/16872303?v=3","gravatar_id":"","url":"https://api.github.com/users/yilunhuangyue","html_url":"https://github.com/yilunhuangyue","followers_url":"https://api.github.com/users/yilunhuangyue/followers","following_url":"https://api.github.com/users/yilunhuangyue/following{/other_user}","gists_url":"https://api.github.com/users/yilunhuangyue/gists{/gist_id}","starred_url":"https://api.github.com/users/yilunhuangyue/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yilunhuangyue/subscriptions","organizations_url":"https://api.github.com/users/yilunhuangyue/orgs","repos_url":"https://api.github.com/users/yilunhuangyue/repos","events_url":"https://api.github.com/users/yilunhuangyue/events{/privacy}","received_events_url":"https://api.github.com/users/yilunhuangyue/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2017-01-31T01:55:36Z","updated_at":"2017-03-03T21:42:40Z","closed_at":"2017-03-03T21:42:39Z","body":"Hello, I have installed FALCON-integrate using the easy way, \r\nexport GIT_SYM_CACHE_DIR=~/.git-sym-cache # to speed things up\r\ngit clone git://github.com/PacificBiosciences/FALCON-integrate.git\r\ncd FALCON-integrate\r\ngit checkout master  # or whatever version you want\r\nmake init\r\nsource env.sh\r\nmake config-edit-user\r\nmake -j all\r\n\r\n Everything seems ok in installation and I have do a test using the E.coli data:\r\n\r\nwget https://www.dropbox.com/s/tb78i5i3nrvm6rg/m140913_050931_42139_c100713652400000001823152404301535_s1_p0.1.subreads.fasta\r\nwget https://www.dropbox.com/s/v6wwpn40gedj470/m140913_050931_42139_c100713652400000001823152404301535_s1_p0.2.subreads.fasta\r\nwget https://www.dropbox.com/s/j61j2cvdxn4dx4g/m140913_050931_42139_c100713652400000001823152404301535_s1_p0.3.subreads.fasta.\r\n\r\nIt ran successfully and got the final result p_ctg.fa. But when I used my own data, I met an error like this:\r\n\r\n[INFO]About to submit: Node(0-rawreads/job_37d3)\r\n[INFO]About to submit: Node(0-rawreads/job_1e5e)\r\n[INFO]About to submit: Node(0-rawreads/job_2bcd)\r\n[ERROR]Failed generate_script() for Node(0-rawreads/job_164f)\r\nTraceback (most recent call last):\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/pypeFLOW/pypeflow/simple_pwatcher_bridge.py\", line 344, in execute\r\n    actual_script_fn = self.generate_script()\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/pypeFLOW/pypeflow/simple_pwatcher_bridge.py\", line 392, in generate_script\r\n    open(task_json_fn, 'w').write(task_content)\r\nIOError: [Errno 22] invalid mode ('w') or filename: u'/home02/wuguizhi/JLX/Falcon_test2/0-rawreads/job_164f/task.json'\r\nTraceback (most recent call last):\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/fc_env/bin/fc_run.py\", line 6, in <module>\r\n    exec(compile(open(__file__).read(), __file__, 'exec'))\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/FALCON/src/py_scripts/fc_run.py\", line 5, in <module>\r\n    main(sys.argv)\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/FALCON/falcon_kit/mains/run1.py\", line 461, in main\r\n    main1(argv[0], args.config, args.logger)\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/FALCON/falcon_kit/mains/run1.py\", line 136, in main1\r\n    input_fofn_plf=input_fofn_plf,\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/FALCON/falcon_kit/mains/run1.py\", line 234, in run\r\n    wf.refreshTargets(exitOnFailure=exitOnFailure)\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/pypeFLOW/pypeflow/simple_pwatcher_bridge.py\", line 226, in refreshTargets\r\n    self._refreshTargets(updateFreq, exitOnFailure)\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/pypeFLOW/pypeflow/simple_pwatcher_bridge.py\", line 258, in _refreshTargets\r\n    unsubmitted = set(self.tq.enque(to_submit)) # In theory, this traps exceptions.\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/pypeFLOW/pypeflow/simple_pwatcher_bridge.py\", line 67, in enque\r\n    generated_script_fn = node.execute() # misnomer; this only dumps task.json now\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/pypeFLOW/pypeflow/simple_pwatcher_bridge.py\", line 344, in execute\r\n    actual_script_fn = self.generate_script()\r\n  File \"/home02/wuguizhi/software/FALCON-integrate/pypeFLOW/pypeflow/simple_pwatcher_bridge.py\", line 392, in generate_script\r\n    open(task_json_fn, 'w').write(task_content)\r\nIOError: [Errno 22] invalid mode ('w') or filename: u'/home02/wuguizhi/JLX/Falcon_test2/0-rawreads/job_164f/task.json'\r\n\r\nmy cfg file is like this:\r\n\r\n[General]\r\nuse_tmpdir = True\r\njob_type = local\r\n\r\n\r\ninput_fofn = input.fofn\r\n\r\ninput_type = raw\r\n\r\nlength_cutoff = 14000\r\n\r\nlength_cutoff_pr = 14000\r\n\r\n\r\njobqueue = production\r\nsge_option_da = -pe smp 8 -q %(jobqueue)s\r\nsge_option_la = -pe smp 2 -q %(jobqueue)s\r\nsge_option_pda = -pe smp 8 -q %(jobqueue)s\r\nsge_option_pla = -pe smp 2 -q %(jobqueue)s\r\nsge_option_fc = -pe smp 24 -q %(jobqueue)s\r\nsge_option_cns = -pe smp 8 -q %(jobqueue)s\r\n\r\npa_concurrent_jobs = 36\r\novlp_concurrent_jobs = 36\r\n\r\npa_HPCdaligner_option =  -v -B4 -t16  -e.70 -l1000 -s1000\r\novlp_HPCdaligner_option = -v -B4 -t32  -e.96 -l500 -s1000\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  --max_n_read 200 --n_core 6\r\n\r\noverlap_filtering_setting = --max_diff 100 --max_cov 100 --min_cov 20 --bestn 10 \r\n\r\nThe genome in my case is about 300M and I have 70X sequencing fasta data in all. Is there any wrong in my case. How should I deal with it?\r\nThank you so much~"}}
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