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  • jw457
    Junior Member
    • Jul 2016
    • 3
    #1

    Falcon run error using test data

    I am a beginner of FALCON and try to learn how to use FALCON.

    I try to follow the steps in "Setup: Complete example" (https://github.com/PacificBioscience...mplete-example)

    To do the test on my laptop Ubuntu 14.04 64 bit, I add one line

    job_type=local to the end of fc_run_ecoli.cfg.

    But when I ran the final command

    fc_run.py fc_run_ecoli.cfg

    I got some errors as below. It's difficult for me to figure out what the problem is.

    Could anyone help me out?

    Many thanks in advance

    The error message is pasted as below.
    ============================================================


    $ fc_run.py fc_run_ecoli.cfg
    [INFO]Setup logging from file "None".
    [INFO]fc_run started with configuration fc_run_ecoli.cfg
    [WARNING]HPC.daligner option "-dal" has changed to "-B". Correcting this for you.
    [WARNING]HPC.daligner option "-dal" has changed to "-B". Correcting this for you.
    [INFO] No target specified, assuming "assembly" as target
    /home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.7+git.85e41a6ab3bbeaece25f43e47c8f9a2cb9feb31a-py2.7-linux-x86_64.egg/falcon_kit/run_support.py:320: UserWarning: Unexpected keys in input config: set(['jobqueue'])
    warnings.warn("Unexpected keys in input config: %s" %repr(unused))
    [INFO]# of tasks in complete graph: 1
    [INFO]tick: 1, #updatedTasks: 0, sleep_time=0.000000
    [INFO]tick: 2, #updatedTasks: 0, sleep_time=0.100000
    [INFO]Running task from function task_make_fofn_abs_raw()
    [WARNING]Missing taskObj.generated_script_fn for task. Maybe we did not need it? Skipping and continuing.
    [INFO]Queued 'task:///home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.7+git.85e41a6ab3bbeaece25f43e47c8f9a2cb9feb31a-py2.7-linux-x86_64.egg/falcon_kit/mains/run1.py/task_make_fofn_abs_raw' ...
    [INFO]Success ('done'). Joining 'task:///home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.7+git.85e41a6ab3bbeaece25f43e47c8f9a2cb9feb31a-py2.7-linux-x86_64.egg/falcon_kit/mains/run1.py/task_make_fofn_abs_raw'...
    [INFO]_refreshTargets() finished with no thread running and no new job to submit
    [INFO]# of tasks in complete graph: 2
    [INFO]tick: 1, #updatedTasks: 0, sleep_time=0.000000
    [INFO]tick: 2, #updatedTasks: 0, sleep_time=0.100000
    [INFO]Running task from function task_build_rdb()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/prepare_rdb.sh'
    [INFO]jobid=J3235bdfbe8402f66d51cc320a3c1db1411944218af61981cd2b1186fc885e1e1
    [INFO]starting job Job(jobid='J3235bdfbe8402f66d51cc320a3c1db1411944218af61981cd2b1186fc885e1e1', cmd='/bin/bash prepare_rdb.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J3235bdfbe8402f66d51cc320a3c1db1411944218af61981cd2b1186fc885e1e1', cmd='/bin/bash prepare_rdb.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]Queued 'task:///home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.7+git.85e41a6ab3bbeaece25f43e47c8f9a2cb9feb31a-py2.7-linux-x86_64.egg/falcon_kit/mains/run1.py/task_build_rdb' ...
    [INFO]tick: 4, #updatedTasks: 1, sleep_time=0.100000
    [INFO]tick: 8, #updatedTasks: 1, sleep_time=0.500000
    [INFO]tick: 16, #updatedTasks: 1, sleep_time=1.000000
    [INFO]Success ('done'). Joining 'task:///home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.7+git.85e41a6ab3bbeaece25f43e47c8f9a2cb9feb31a-py2.7-linux-x86_64.egg/falcon_kit/mains/run1.py/task_build_rdb'...
    [INFO]_refreshTargets() finished with no thread running and no new job to submit
    [INFO]Skip LAcheck after daligner? True
    [INFO]# of tasks in complete graph: 63
    [INFO]tick: 1, #updatedTasks: 0, sleep_time=0.000000
    [INFO]tick: 2, #updatedTasks: 0, sleep_time=0.100000
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0039/rj_0039.sh'
    [INFO]jobid=J8807ca796aa04159217f3565ae2fa8955ad03a696a02efebb4685a71f9cfe7c9
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0020/rj_0020.sh'
    [INFO]jobid=J05e63da8ce32343f800e24dc4142e29609f0050f0d933f1c7f5e2eed3ab22df6
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0019/rj_0019.sh'
    [INFO]jobid=J66fa641cb477688bb337e2ca3b08530849dfc71cefede2672cc88f2acd7893b6
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001c/rj_001c.sh'
    [INFO]jobid=Jd713b6ef4e173c9d26f96e686adc26ad258e0cd88af92735908397a99da8769c
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0000/rj_0000.sh'
    [INFO]jobid=Je141468454c0d12b4390457fd61f0148821f38bb772dbb97f87f9f7c4d339f4d
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001a/rj_001a.sh'
    [INFO]jobid=Jb405724ef23dcadaf7d095eb03a7eede1b3a5ed08b64d253904434111a877bd0
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001f/rj_001f.sh'
    [INFO]jobid=Jf80c4acf54fd4c82c3cb1232a34738e60559b03f10d3045811f3d87f185e091c
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0001/rj_0001.sh'
    [INFO]jobid=J84c88f5b21fc8c39c68dc30b5b127c5d97aa7ddfb4174774f2177b5e0698b6ca
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0011/rj_0011.sh'
    [INFO]jobid=Jb2205fb20f574f3a3686a9ecf6fa4d11c7ae61f55bef6b4dd64b4f169a665ed3
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0004/rj_0004.sh'
    [INFO]jobid=Jcec25672550a76c84da2964fa3d5434f294f420853012becc75d85d4464b42a7
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_003a/rj_003a.sh'
    [INFO]jobid=J508a94693abad3b5925283381c1e105f27fb84929ca42b4fc4c58f4996b3f284
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_000c/rj_000c.sh'
    [INFO]jobid=J5c379923f2e6b560757f4c7b660ec599c3fd919e9a565b8db4ee4fa66a4d6c2a
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001d/rj_001d.sh'
    [INFO]jobid=J2af90530a6e0eead2c2f1e1025315ef63004d767510b5ddac5ff9929ecf3a8cb
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0031/rj_0031.sh'
    [INFO]jobid=Jadee82d11758117372cf81007b4fce4952d5aeb9627c483a5e71a9ac09a8436b
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0034/rj_0034.sh'
    [INFO]jobid=J99aa0e314131e9c7e16368163f3559eedac54d245cd95c2e8762224204db71d2
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0025/rj_0025.sh'
    [INFO]jobid=J2e5b557f638c5274433b2a8136eb3e92abe6ce189b72655b1cfcd29485737840
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0024/rj_0024.sh'
    [INFO]jobid=J50d5e1ba639f05a470575601538f23b75b4bec69d39beaf1c5cdc63bfe0fa4f6
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_002e/rj_002e.sh'
    [INFO]jobid=J2ca4ce947c31cb1970bbe25c774645abf8e21cea43e7349a056f4ded6eb4c810
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001e/rj_001e.sh'
    [INFO]jobid=J071b4d0376ddeb15da637507d8e4ef64ff1114431216316344dffae6d109394f
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0029/rj_0029.sh'
    [INFO]jobid=J6a66013e27f72270bc39f9159dc27c2093783389819616f1fee436f785c3763c
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0021/rj_0021.sh'
    [INFO]jobid=J139f747a7a5dc25343ff3f234884847264495b7f4f87ea277cd86a310334ccfe
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0030/rj_0030.sh'
    [INFO]jobid=Jbb84f00a6e4a8640acd4d077964cdee3a1c0df739b5226832a1e6d3c9a72ed08
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0027/rj_0027.sh'
    [INFO]jobid=Jf9bf380651849c039a250f27b67f007f511edd793cbfeda93aac841052957b5f
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_000a/rj_000a.sh'
    [INFO]jobid=J95631df7a717e2cf2bf50671e200cb320cfd64c14476aae7ffb6701f80d5c93d
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001b/rj_001b.sh'
    [INFO]jobid=Jd8ec46878de441fa996a6715e385317750ca68770d51773a6fd51d1b63b558b3
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0009/rj_0009.sh'
    [INFO]jobid=J4da3a028ac80627ae6f4bace7685def91f866cc5e67ec8111b07a0faa9b7094e
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0005/rj_0005.sh'
    [INFO]jobid=Ja0a727b26e96831c31fc3448c246f5c96a649cda68442a79c351dd3de3a58a31
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_000b/rj_000b.sh'
    [INFO]jobid=J324ee6e1d557747580f48dfe1f4412a5db7a73003cd74ce9ea70b8bd99b66dd9
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_002d/rj_002d.sh'
    [INFO]jobid=Jb532810ecc97bf4217bd594bd864a695274071c7616999f91ec83a7060917f83
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0035/rj_0035.sh'
    [INFO]jobid=J39d2c3ec6ab245d35b9a9de1ddcbc7236b79d92bda5e38ef5b5d03f3ff8ac126
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0022/rj_0022.sh'
    [INFO]jobid=Jc23f311141d2a35ccfec00dd5f18a6505baa8de0cfbbb88cf4933f764452e1e8
    [INFO]Running task from function task_run_daligner()
    [INFO]script_fn:'/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0014/rj_0014.sh'
    [INFO]jobid=Jc77b25ec8e099c45dbdd1f0fba4e037a2690022bdf78a61093996f204a5e6608
    [INFO]starting job Job(jobid='Jd713b6ef4e173c9d26f96e686adc26ad258e0cd88af92735908397a99da8769c', cmd='/bin/bash rj_001c.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001c', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jd713b6ef4e173c9d26f96e686adc26ad258e0cd88af92735908397a99da8769c', cmd='/bin/bash rj_001c.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001c', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jadee82d11758117372cf81007b4fce4952d5aeb9627c483a5e71a9ac09a8436b', cmd='/bin/bash rj_0031.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0031', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jadee82d11758117372cf81007b4fce4952d5aeb9627c483a5e71a9ac09a8436b', cmd='/bin/bash rj_0031.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0031', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J2ca4ce947c31cb1970bbe25c774645abf8e21cea43e7349a056f4ded6eb4c810', cmd='/bin/bash rj_002e.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_002e', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J2ca4ce947c31cb1970bbe25c774645abf8e21cea43e7349a056f4ded6eb4c810', cmd='/bin/bash rj_002e.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_002e', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J39d2c3ec6ab245d35b9a9de1ddcbc7236b79d92bda5e38ef5b5d03f3ff8ac126', cmd='/bin/bash rj_0035.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0035', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J39d2c3ec6ab245d35b9a9de1ddcbc7236b79d92bda5e38ef5b5d03f3ff8ac126', cmd='/bin/bash rj_0035.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0035', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J95631df7a717e2cf2bf50671e200cb320cfd64c14476aae7ffb6701f80d5c93d', cmd='/bin/bash rj_000a.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_000a', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J95631df7a717e2cf2bf50671e200cb320cfd64c14476aae7ffb6701f80d5c93d', cmd='/bin/bash rj_000a.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_000a', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J05e63da8ce32343f800e24dc4142e29609f0050f0d933f1c7f5e2eed3ab22df6', cmd='/bin/bash rj_0020.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0020', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J05e63da8ce32343f800e24dc4142e29609f0050f0d933f1c7f5e2eed3ab22df6', cmd='/bin/bash rj_0020.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0020', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jcec25672550a76c84da2964fa3d5434f294f420853012becc75d85d4464b42a7', cmd='/bin/bash rj_0004.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0004', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jcec25672550a76c84da2964fa3d5434f294f420853012becc75d85d4464b42a7', cmd='/bin/bash rj_0004.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0004', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jc77b25ec8e099c45dbdd1f0fba4e037a2690022bdf78a61093996f204a5e6608', cmd='/bin/bash rj_0014.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0014', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jc77b25ec8e099c45dbdd1f0fba4e037a2690022bdf78a61093996f204a5e6608', cmd='/bin/bash rj_0014.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0014', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J99aa0e314131e9c7e16368163f3559eedac54d245cd95c2e8762224204db71d2', cmd='/bin/bash rj_0034.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0034', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J99aa0e314131e9c7e16368163f3559eedac54d245cd95c2e8762224204db71d2', cmd='/bin/bash rj_0034.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0034', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J2af90530a6e0eead2c2f1e1025315ef63004d767510b5ddac5ff9929ecf3a8cb', cmd='/bin/bash rj_001d.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001d', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J2af90530a6e0eead2c2f1e1025315ef63004d767510b5ddac5ff9929ecf3a8cb', cmd='/bin/bash rj_001d.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001d', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Ja0a727b26e96831c31fc3448c246f5c96a649cda68442a79c351dd3de3a58a31', cmd='/bin/bash rj_0005.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0005', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Ja0a727b26e96831c31fc3448c246f5c96a649cda68442a79c351dd3de3a58a31', cmd='/bin/bash rj_0005.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0005', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J071b4d0376ddeb15da637507d8e4ef64ff1114431216316344dffae6d109394f', cmd='/bin/bash rj_001e.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001e', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J071b4d0376ddeb15da637507d8e4ef64ff1114431216316344dffae6d109394f', cmd='/bin/bash rj_001e.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001e', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J508a94693abad3b5925283381c1e105f27fb84929ca42b4fc4c58f4996b3f284', cmd='/bin/bash rj_003a.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_003a', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J508a94693abad3b5925283381c1e105f27fb84929ca42b4fc4c58f4996b3f284', cmd='/bin/bash rj_003a.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_003a', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jb532810ecc97bf4217bd594bd864a695274071c7616999f91ec83a7060917f83', cmd='/bin/bash rj_002d.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_002d', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jb532810ecc97bf4217bd594bd864a695274071c7616999f91ec83a7060917f83', cmd='/bin/bash rj_002d.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_002d', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J5c379923f2e6b560757f4c7b660ec599c3fd919e9a565b8db4ee4fa66a4d6c2a', cmd='/bin/bash rj_000c.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_000c', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J5c379923f2e6b560757f4c7b660ec599c3fd919e9a565b8db4ee4fa66a4d6c2a', cmd='/bin/bash rj_000c.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_000c', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J8807ca796aa04159217f3565ae2fa8955ad03a696a02efebb4685a71f9cfe7c9', cmd='/bin/bash rj_0039.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0039', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J8807ca796aa04159217f3565ae2fa8955ad03a696a02efebb4685a71f9cfe7c9', cmd='/bin/bash rj_0039.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0039', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jd8ec46878de441fa996a6715e385317750ca68770d51773a6fd51d1b63b558b3', cmd='/bin/bash rj_001b.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001b', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jd8ec46878de441fa996a6715e385317750ca68770d51773a6fd51d1b63b558b3', cmd='/bin/bash rj_001b.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001b', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J50d5e1ba639f05a470575601538f23b75b4bec69d39beaf1c5cdc63bfe0fa4f6', cmd='/bin/bash rj_0024.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0024', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J50d5e1ba639f05a470575601538f23b75b4bec69d39beaf1c5cdc63bfe0fa4f6', cmd='/bin/bash rj_0024.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0024', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J4da3a028ac80627ae6f4bace7685def91f866cc5e67ec8111b07a0faa9b7094e', cmd='/bin/bash rj_0009.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0009', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J4da3a028ac80627ae6f4bace7685def91f866cc5e67ec8111b07a0faa9b7094e', cmd='/bin/bash rj_0009.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0009', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jc23f311141d2a35ccfec00dd5f18a6505baa8de0cfbbb88cf4933f764452e1e8', cmd='/bin/bash rj_0022.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0022', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jc23f311141d2a35ccfec00dd5f18a6505baa8de0cfbbb88cf4933f764452e1e8', cmd='/bin/bash rj_0022.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0022', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J2e5b557f638c5274433b2a8136eb3e92abe6ce189b72655b1cfcd29485737840', cmd='/bin/bash rj_0025.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0025', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J2e5b557f638c5274433b2a8136eb3e92abe6ce189b72655b1cfcd29485737840', cmd='/bin/bash rj_0025.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0025', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jb2205fb20f574f3a3686a9ecf6fa4d11c7ae61f55bef6b4dd64b4f169a665ed3', cmd='/bin/bash rj_0011.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0011', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jb2205fb20f574f3a3686a9ecf6fa4d11c7ae61f55bef6b4dd64b4f169a665ed3', cmd='/bin/bash rj_0011.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0011', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jf80c4acf54fd4c82c3cb1232a34738e60559b03f10d3045811f3d87f185e091c', cmd='/bin/bash rj_001f.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001f', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jf80c4acf54fd4c82c3cb1232a34738e60559b03f10d3045811f3d87f185e091c', cmd='/bin/bash rj_001f.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001f', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jbb84f00a6e4a8640acd4d077964cdee3a1c0df739b5226832a1e6d3c9a72ed08', cmd='/bin/bash rj_0030.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0030', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jbb84f00a6e4a8640acd4d077964cdee3a1c0df739b5226832a1e6d3c9a72ed08', cmd='/bin/bash rj_0030.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0030', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J84c88f5b21fc8c39c68dc30b5b127c5d97aa7ddfb4174774f2177b5e0698b6ca', cmd='/bin/bash rj_0001.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0001', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J84c88f5b21fc8c39c68dc30b5b127c5d97aa7ddfb4174774f2177b5e0698b6ca', cmd='/bin/bash rj_0001.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0001', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jf9bf380651849c039a250f27b67f007f511edd793cbfeda93aac841052957b5f', cmd='/bin/bash rj_0027.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0027', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jf9bf380651849c039a250f27b67f007f511edd793cbfeda93aac841052957b5f', cmd='/bin/bash rj_0027.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0027', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Je141468454c0d12b4390457fd61f0148821f38bb772dbb97f87f9f7c4d339f4d', cmd='/bin/bash rj_0000.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0000', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Je141468454c0d12b4390457fd61f0148821f38bb772dbb97f87f9f7c4d339f4d', cmd='/bin/bash rj_0000.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0000', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='Jb405724ef23dcadaf7d095eb03a7eede1b3a5ed08b64d253904434111a877bd0', cmd='/bin/bash rj_001a.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001a', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='Jb405724ef23dcadaf7d095eb03a7eede1b3a5ed08b64d253904434111a877bd0', cmd='/bin/bash rj_001a.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_001a', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J139f747a7a5dc25343ff3f234884847264495b7f4f87ea277cd86a310334ccfe', cmd='/bin/bash rj_0021.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0021', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J139f747a7a5dc25343ff3f234884847264495b7f4f87ea277cd86a310334ccfe', cmd='/bin/bash rj_0021.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0021', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J6a66013e27f72270bc39f9159dc27c2093783389819616f1fee436f785c3763c', cmd='/bin/bash rj_0029.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0029', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J6a66013e27f72270bc39f9159dc27c2093783389819616f1fee436f785c3763c', cmd='/bin/bash rj_0029.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0029', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J66fa641cb477688bb337e2ca3b08530849dfc71cefede2672cc88f2acd7893b6', cmd='/bin/bash rj_0019.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0019', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J66fa641cb477688bb337e2ca3b08530849dfc71cefede2672cc88f2acd7893b6', cmd='/bin/bash rj_0019.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_0019', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]starting job Job(jobid='J324ee6e1d557747580f48dfe1f4412a5db7a73003cd74ce9ea70b8bd99b66dd9', cmd='/bin/bash rj_000b.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_000b', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None})
    [INFO]Submitted backgroundjob=MetaJobLocal(MetaJob(job=Job(jobid='J324ee6e1d557747580f48dfe1f4412a5db7a73003cd74ce9ea70b8bd99b66dd9', cmd='/bin/bash rj_000b.sh', rundir='/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/ecoli_test/0-rawreads/job_000b', options={'sge_option': '-pe smp 8 -q your_queue', 'job_type': None}), lang_exe='/bin/bash'))
    [INFO]Queued 'task://localhost/d_0039_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0020_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0019_raw_reads' ...
    [INFO]Queued 'task://localhost/d_001c_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0000_raw_reads' ...
    [INFO]Queued 'task://localhost/d_001a_raw_reads' ...
    [INFO]Queued 'task://localhost/d_001f_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0001_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0011_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0004_raw_reads' ...
    [INFO]Queued 'task://localhost/d_003a_raw_reads' ...
    [INFO]Queued 'task://localhost/d_000c_raw_reads' ...
    [INFO]Queued 'task://localhost/d_001d_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0031_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0034_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0025_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0024_raw_reads' ...
    [INFO]Queued 'task://localhost/d_002e_raw_reads' ...
    [INFO]Queued 'task://localhost/d_001e_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0029_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0021_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0030_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0027_raw_reads' ...
    [INFO]Queued 'task://localhost/d_000a_raw_reads' ...
    [INFO]Queued 'task://localhost/d_001b_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0009_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0005_raw_reads' ...
    [INFO]Queued 'task://localhost/d_000b_raw_reads' ...
    [INFO]Queued 'task://localhost/d_002d_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0035_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0022_raw_reads' ...
    [INFO]Queued 'task://localhost/d_0014_raw_reads' ...
    [INFO]tick: 4, #updatedTasks: 32, sleep_time=0.100000
    [INFO]tick: 8, #updatedTasks: 32, sleep_time=0.500000
    [ERROR]Task Fred{'URL': 'task://localhost/d_001c_raw_reads'} failed with exit-code=35072
    [ERROR]Task Fred{'URL': 'task://localhost/d_0031_raw_reads'} failed with exit-code=35072
    [ERROR]Task Fred{'URL': 'task://localhost/d_002e_raw_reads'} failed with exit-code=35072
    [ERROR]Task Fred{'URL': 'task://localhost/d_0035_raw_reads'} failed with exit-code=35072
    [ERROR]Task Fred{'URL': 'task://localhost/d_000a_raw_reads'} failed with exit-code=35072
    [ERROR]Task Fred{'URL': 'task://localhost/d_0020_raw_reads'} failed with exit-code=35072
    [ERROR]Task Fred{'URL': 'task://localhost/d_0034_raw_reads'} failed with exit-code=35072
    [ERROR]Task Fred{'URL': 'task://localhost/d_003a_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_002d_raw_reads'} failed with exit-code=35072
    [ERROR]Task Fred{'URL': 'task://localhost/d_0039_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_001b_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_0009_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_0022_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_0025_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_0011_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_001f_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_0030_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_0027_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_0000_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_0021_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_0029_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_0019_raw_reads'} failed with exit-code=256
    [ERROR]Task Fred{'URL': 'task://localhost/d_000b_raw_reads'} failed with exit-code=256
    [INFO]Failure ('fail'). Joining 'task://localhost/d_001c_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0031_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_002e_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0035_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_000a_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0020_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0034_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_003a_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_002d_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0039_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_001b_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0009_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0022_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0025_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0011_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_001f_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0030_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0027_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0000_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0021_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0029_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_0019_raw_reads'...
    [INFO]Failure ('fail'). Joining 'task://localhost/d_000b_raw_reads'...
    [CRITICAL]Any exception caught in RefreshTargets() indicates an unrecoverable error. Shutting down...
    /home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py:537: UserWarning:
    "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"
    "! Please wait for all threads / processes to terminate !"
    "! Also, maybe use 'ps' or 'qstat' to check all threads,!"
    "! processes and/or jobs are terminated cleanly. !"
    "!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!"

    warnings.warn(shutdown_msg)
    [ERROR]Task Fred{'URL': 'task://localhost/d_0024_raw_reads'} failed with exit-code=35072
    [WARNING]#tasks=32, #alive=9
    [INFO]Sending signal(9) to pgid=-4083 (pid=4083) based on heartbeat='heartbeat-Jc77b25ec8e099c45dbdd1f0fba4e037a2690022bdf78a61093996f204a5e6608'
    [INFO]Sending signal(9) to pgid=-4070 (pid=4070) based on heartbeat='heartbeat-Jcec25672550a76c84da2964fa3d5434f294f420853012becc75d85d4464b42a7'
    [INFO]Sending signal(9) to pgid=-4105 (pid=4105) based on heartbeat='heartbeat-J2af90530a6e0eead2c2f1e1025315ef63004d767510b5ddac5ff9929ecf3a8cb'
    [INFO]Sending signal(9) to pgid=-4116 (pid=4116) based on heartbeat='heartbeat-Ja0a727b26e96831c31fc3448c246f5c96a649cda68442a79c351dd3de3a58a31'
    [INFO]Sending signal(9) to pgid=-4127 (pid=4127) based on heartbeat='heartbeat-J071b4d0376ddeb15da637507d8e4ef64ff1114431216316344dffae6d109394f'
    [INFO]Sending signal(9) to pgid=-4186 (pid=4186) based on heartbeat='heartbeat-J5c379923f2e6b560757f4c7b660ec599c3fd919e9a565b8db4ee4fa66a4d6c2a'
    [INFO]Sending signal(9) to pgid=-4285 (pid=4285) based on heartbeat='heartbeat-J84c88f5b21fc8c39c68dc30b5b127c5d97aa7ddfb4174774f2177b5e0698b6ca'
    [INFO]Sending signal(9) to pgid=-4312 (pid=4312) based on heartbeat='heartbeat-Jb405724ef23dcadaf7d095eb03a7eede1b3a5ed08b64d253904434111a877bd0'
    [WARNING]Now, #tasks=32, #alive=0
    Traceback (most recent call last):
    File "/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/bin/fc_run.py", line 4, in <module>
    __import__('pkg_resources').run_script('falcon-kit==0.7+git.85e41a6ab3bbeaece25f43e47c8f9a2cb9feb31a', 'fc_run.py')
    File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 719, in run_script
    File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 1504, in run_script
    File "/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.7+git.85e41a6ab3bbeaece25f43e47c8f9a2cb9feb31a-py2.7-linux-x86_64.egg/EGG-INFO/scripts/fc_run.py", line 5, in <module>
    main(sys.argv)
    File "/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.7+git.85e41a6ab3bbeaece25f43e47c8f9a2cb9feb31a-py2.7-linux-x86_64.egg/falcon_kit/mains/run1.py", line 561, in main
    main1(argv[0], args.config, args.logger)
    File "/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.7+git.85e41a6ab3bbeaece25f43e47c8f9a2cb9feb31a-py2.7-linux-x86_64.egg/falcon_kit/mains/run1.py", line 327, in main1
    setNumThreadAllowed=PypeProcWatcherWorkflow.setNumThreadAllowed)
    File "/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/falcon_kit-0.7+git.85e41a6ab3bbeaece25f43e47c8f9a2cb9feb31a-py2.7-linux-x86_64.egg/falcon_kit/mains/run1.py", line 404, in run
    wf.refreshTargets(exitOnFailure=exitOnFailure)
    File "/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py", line 548, in refreshTargets
    raise Exception('Caused by:\n' + tb)
    Exception: Caused by:
    Traceback (most recent call last):
    File "/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py", line 523, in refreshTargets
    rtn = self._refreshTargets(task2thread, objs = objs, callback = callback, updateFreq = updateFreq, exitOnFailure = exitOnFailure)
    File "/home/jiwu2573/files/testing/pacbio/test9/FALCON-integrate/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py", line 740, in _refreshTargets
    raise TaskFailureError("Counted %d failure(s) with 0 successes so far." %failedJobCount)
    TaskFailureError: 'Counted 23 failure(s) with 0 successes so far.'
    Tags: None
  • wdecoster
    Member
    • Oct 2015
    • 97
    #2
    Did you monitor memory usage when running this? That would be my first guess.

    Comment

    • jw457
      Junior Member
      • Jul 2016
      • 3
      #3
      Thanks for your reply.

      Could you please suggest how to monitor the memory usage on my ubuntu laptop?

      Comment

      • wdecoster
        Member
        • Oct 2015
        • 97
        #4
        I would suggest to install htop (if not already installed) (sudo apt-get install htop). You can use it in a terminal by just typing htop. You will be able to monitor CPU and memory usage of your running processes.

        Comment

        • GenoMax
          Senior Member
          • Feb 2008
          • 7142
          #5
          Since you are running this on a local laptop have you tried to see if PacBio has any instructions on running FALCON without a job scheduler? That may be part of the problem here.

          How much RAM do you have on this laptop?

          Comment

          • gconcepcion
            Member
            • Dec 2010
            • 68
            #6
            Originally posted by jw457 View Post
            Could anyone help me out?
            If you would like direct assistance from the developers, you should visit the FALCON github page:

            Issues · PacificBiosciences/FALCON
            https://github.com/PacificBiosciences/FALCON/issues
            FALCON: experimental PacBio diploid assembler -- Out-of-date -- Please use a binary release: https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries - Issues · PacificBiosciences/FALCON


            But in short, you *are* running locally, this looks like a concurrency issue.

            You should limit the number of concurrent jobs to whatever is reasonable given your laptop configuration.

            Comment

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