{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/pypeFLOW/issues/22","repository_url":"https://api.github.com/repos/PacificBiosciences/pypeFLOW","labels_url":"https://api.github.com/repos/PacificBiosciences/pypeFLOW/issues/22/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/pypeFLOW/issues/22/comments","events_url":"https://api.github.com/repos/PacificBiosciences/pypeFLOW/issues/22/events","html_url":"https://github.com/PacificBiosciences/pypeFLOW/issues/22","id":158477675,"number":22,"title":"FALCON qsub issues","user":{"login":"StefanoLonardi","id":18489339,"avatar_url":"https://avatars.githubusercontent.com/u/18489339?v=3","gravatar_id":"","url":"https://api.github.com/users/StefanoLonardi","html_url":"https://github.com/StefanoLonardi","followers_url":"https://api.github.com/users/StefanoLonardi/followers","following_url":"https://api.github.com/users/StefanoLonardi/following{/other_user}","gists_url":"https://api.github.com/users/StefanoLonardi/gists{/gist_id}","starred_url":"https://api.github.com/users/StefanoLonardi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/StefanoLonardi/subscriptions","organizations_url":"https://api.github.com/users/StefanoLonardi/orgs","repos_url":"https://api.github.com/users/StefanoLonardi/repos","events_url":"https://api.github.com/users/StefanoLonardi/events{/privacy}","received_events_url":"https://api.github.com/users/StefanoLonardi/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/PacificBiosciences/pypeFLOW/labels/question","name":"question","color":"cc317c"}],"state":"open","locked":false,"assignee":{"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},"milestone":null,"comments":6,"created_at":"2016-06-04T00:33:49Z","updated_at":"2016-06-04T19:51:00Z","closed_at":null,"body":"This is a follow-up on an issue I opened in **FALCON**. I was finally able to run **FALCON** on the provided examples synth0 and ecoli using `job_type = local`, but I could not run it when `job_type = torque`. I decided first to see if I can run synth0 on torque, so I changed the `sge_option_... `and `job_type = torque` and `*_concurrent_jobs = 1` in the file `./FALCON-integrate/FALCON-examples/run/synth0/fc_run.cfg` (I removed the #commented lines before posting it below)\r\n\r\n```\r\n[General]\r\nuse_tmpdir = true\r\njob_type = torque\r\ninput_fofn = input.fofn\r\ninput_type = raw\r\ngenome_size = 5000\r\nseed_coverage = 20\r\nlength_cutoff_pr = 1\r\nsge_option_da = -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu\r\nsge_option_la = -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu\r\nsge_option_pda = -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu\r\nsge_option_pla = -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu\r\nsge_option_fc = -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu\r\nsge_option_cns = -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu\r\npa_concurrent_jobs = 1\r\ncns_concurrent_jobs = 1\r\novlp_concurrent_jobs = 1\r\npa_HPCdaligner_option =   -v -B4 -t50 -h1 -e.99 -w1 -l1 -s1000\r\novlp_HPCdaligner_option = -v -B4 -t50 -h1 -e.99 -l1 -s1000\r\npa_DBsplit_option =   -a -x5 -s.065536\r\novlp_DBsplit_option = -a -x5 -s50\r\nfalcon_sense_option = --output_multi --min_idt 0.70 --min_cov 1 --max_n_read 20000 --n_core 0\r\noverlap_filtering_setting = --max_diff 10000 --max_cov 100000 --min_cov 1 --min_len 1 --bestn 1000 --n_core 0\r\n```\r\n\r\nThis is what happens when I run `make test` using torque.\r\n\r\n```\r\n(fc_env) [stelo@head FALCON-integrate]$ make test\r\nln -sf ../../git-sym/git-sym /home/stelo/FALCON-integrate/fc_env/bin/git-sym\r\n. /home/stelo/FALCON-integrate/fc_env/bin/activate; make -C ./FALCON-make/ test\r\nmake[1]: Entering directory `/home/stelo/FALCON-integrate/FALCON-make'\r\nmake -C /home/stelo/FALCON-integrate/FALCON-examples test\r\nmake[2]: Entering directory `/home/stelo/FALCON-integrate/FALCON-examples'\r\npython -c 'import pypeflow.common; print pypeflow.common'\r\n<module 'pypeflow.common' from '/home/stelo/FALCON-integrate/pypeFLOW/pypeflow/common.pyc'>\r\npython -c 'import falcon_kit; print falcon_kit.falcon'\r\n<CDLL '/home/stelo/FALCON-integrate/FALCON/ext_falcon.so', handle e7b060 at 2b68a52b8650>\r\nmake run-synth0\r\nmake[3]: Entering directory `/home/stelo/FALCON-integrate/FALCON-examples'\r\ngit-sym update run/synth0\r\ngit: 'check-ignore' is not a git command. See 'git --help'.\r\n-> in dir 'run/synth0'\r\n<- back to dir '/home/stelo/FALCON-integrate/FALCON-examples'\r\nsymlink: 'run/synth0/data/ref.fasta'\r\nsymlink: 'run/synth0/data/synth0.fasta'\r\n-> in dir '/home/stelo/FALCON-integrate/FALCON-examples/.git/git-sym-local/links'\r\n<- back to dir '/home/stelo/FALCON-integrate/FALCON-examples'\r\ngit-sym show run/synth0\r\ngit: 'check-ignore' is not a git command. See 'git --help'.\r\n-> in dir 'run/synth0'\r\n<- back to dir '/home/stelo/FALCON-integrate/FALCON-examples'\r\nsymlink: 'run/synth0/data/ref.fasta'\r\nsymlink: 'run/synth0/data/synth0.fasta'\r\n. run/synth0/data/ref.fasta\t.git-sym/synth0.ref.fasta\r\n. run/synth0/data/synth0.fasta\t.git-sym/synth0-circ-20.pb.fasta\r\ngit-sym check run/synth0\r\ngit: 'check-ignore' is not a git command. See 'git --help'.\r\n-> in dir 'run/synth0'\r\n<- back to dir '/home/stelo/FALCON-integrate/FALCON-examples'\r\nsymlink: 'run/synth0/data/ref.fasta'\r\nsymlink: 'run/synth0/data/synth0.fasta'\r\ncd run/synth0; fc_run.py fc_run.cfg logging.ini\r\n[INFO] fc_run started with configuration fc_run.cfg\r\n[INFO]  No target specified, assuming \"assembly\" as target\r\n[INFO] # of tasks in complete graph: 1\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] tick: 2, #updatedTasks: 0, sleep_time=0.100000\r\n[INFO] Running task from function task_make_fofn_abs_raw()\r\n[WARNING] Missing taskObj.generated_script_fn for task. Maybe we did not need it? Skipping and continuing.\r\n[INFO] Queued 'task:///home/stelo/FALCON-integrate/FALCON/falcon_kit/mains/run1.py/task_make_fofn_abs_raw' ...\r\n[INFO] Success ('done'). Joining 'task:///home/stelo/FALCON-integrate/FALCON/falcon_kit/mains/run1.py/task_make_fofn_abs_raw'...\r\n[INFO] _refreshTargets() finished with no thread running and no new job to submit\r\n[INFO] # of tasks in complete graph: 2\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] tick: 2, #updatedTasks: 0, sleep_time=0.100000\r\n[INFO] Running task from function task_build_rdb()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/prepare_rdb.sh'\r\n[INFO] jobid=J50b0079619ed1e0485d3adbd235ca121ef78997c49605faf74557e25fdf6d9f9\r\n[INFO] starting job Job(jobid='J50b0079619ed1e0485d3adbd235ca121ef78997c49605faf74557e25fdf6d9f9', cmd='/bin/bash prepare_rdb.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N J50b0079619ed1e -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/J50b0079619ed1e0485d3adbd235ca121ef78997c49605faf74557e25fdf6d9f9 -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-J50b0079619ed1e0485d3adbd235ca121ef78997c49605faf74557e25fdf6d9f9.bash\r\n102909.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='J50b0079619ed1e0485d3adbd235ca121ef78997c49605faf74557e25fdf6d9f9', cmd='/bin/bash prepare_rdb.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task:///home/stelo/FALCON-integrate/FALCON/falcon_kit/mains/run1.py/task_build_rdb' ...\r\n[INFO] tick: 4, #updatedTasks: 1, sleep_time=0.100000\r\n[INFO] tick: 8, #updatedTasks: 1, sleep_time=0.500000\r\n[INFO] Success ('done'). Joining 'task:///home/stelo/FALCON-integrate/FALCON/falcon_kit/mains/run1.py/task_build_rdb'...\r\n[INFO] _refreshTargets() finished with no thread running and no new job to submit\r\n[INFO] # of tasks in complete graph: 5\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] tick: 2, #updatedTasks: 0, sleep_time=0.100000\r\n[INFO] Running task from function task_run_daligner()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0000/rj_0000.sh'\r\n[INFO] jobid=Je0ddc6198e5f9fba0a27cf615c1a6d1207f2d978a55ab3cfc9fd367beeacb564\r\n[INFO] starting job Job(jobid='Je0ddc6198e5f9fba0a27cf615c1a6d1207f2d978a55ab3cfc9fd367beeacb564', cmd='/bin/bash rj_0000.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0000', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N Je0ddc6198e5f9f -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/Je0ddc6198e5f9fba0a27cf615c1a6d1207f2d978a55ab3cfc9fd367beeacb564 -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-Je0ddc6198e5f9fba0a27cf615c1a6d1207f2d978a55ab3cfc9fd367beeacb564.bash\r\n102910.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='Je0ddc6198e5f9fba0a27cf615c1a6d1207f2d978a55ab3cfc9fd367beeacb564', cmd='/bin/bash rj_0000.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0000', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/d_0000_raw_reads' ...\r\n[INFO] tick: 4, #updatedTasks: 1, sleep_time=0.100000\r\n[INFO] tick: 8, #updatedTasks: 1, sleep_time=0.500000\r\n[INFO] Success ('done'). Joining 'task://localhost/d_0000_raw_reads'...\r\n[INFO] Running task from function task_run_daligner()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0001/rj_0001.sh'\r\n[INFO] jobid=Jc217ef7ca3b34c549739e5cdffe99f8e95b4829db4d0b564615e9525389c117f\r\n[INFO] starting job Job(jobid='Jc217ef7ca3b34c549739e5cdffe99f8e95b4829db4d0b564615e9525389c117f', cmd='/bin/bash rj_0001.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0001', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N Jc217ef7ca3b34c -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/Jc217ef7ca3b34c549739e5cdffe99f8e95b4829db4d0b564615e9525389c117f -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-Jc217ef7ca3b34c549739e5cdffe99f8e95b4829db4d0b564615e9525389c117f.bash\r\n102911.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='Jc217ef7ca3b34c549739e5cdffe99f8e95b4829db4d0b564615e9525389c117f', cmd='/bin/bash rj_0001.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0001', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/d_0001_raw_reads' ...\r\n[INFO] Success ('done'). Joining 'task://localhost/d_0001_raw_reads'...\r\n[INFO] tick: 16, #updatedTasks: 2, sleep_time=0.000000\r\n[INFO] Running task from function task_daligner_gather()\r\n[INFO] Symlink .las files for further merging:\r\n{'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/m_00001': ['/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0000/L1.1.1.las',\r\n                                                                                '/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0001/L1.1.2.las'],\r\n '/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/m_00002': ['/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0001/L1.2.1.las',\r\n                                                                                '/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/job_0001/L1.2.2.las']}\r\n[WARNING] Missing taskObj.generated_script_fn for task. Maybe we did not need it? Skipping and continuing.\r\n[INFO] Queued 'task://localhost/rda_check' ...\r\n[INFO] Success ('done'). Joining 'task://localhost/rda_check'...\r\n[INFO] _refreshTargets() finished with no thread running and no new job to submit\r\n[INFO] # of tasks in complete graph: 7\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] tick: 2, #updatedTasks: 0, sleep_time=0.100000\r\n[INFO] Running task from function task_run_las_merge()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/m_00002/rp_00002.sh'\r\n[INFO] jobid=J6e6e88137a47843df341207664607ae5d0eb5ec4712e591bf100b965013fc6ff\r\n[INFO] starting job Job(jobid='J6e6e88137a47843df341207664607ae5d0eb5ec4712e591bf100b965013fc6ff', cmd='/bin/bash rp_00002.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/m_00002', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N J6e6e88137a4784 -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/J6e6e88137a47843df341207664607ae5d0eb5ec4712e591bf100b965013fc6ff -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-J6e6e88137a47843df341207664607ae5d0eb5ec4712e591bf100b965013fc6ff.bash\r\n102912.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='J6e6e88137a47843df341207664607ae5d0eb5ec4712e591bf100b965013fc6ff', cmd='/bin/bash rp_00002.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/m_00002', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/m_00002_raw_reads' ...\r\n[INFO] tick: 4, #updatedTasks: 1, sleep_time=0.100000\r\n[INFO] Success ('done'). Joining 'task://localhost/m_00002_raw_reads'...\r\n[INFO] tick: 8, #updatedTasks: 1, sleep_time=0.000000\r\n[INFO] Running task from function task_run_las_merge()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/m_00001/rp_00001.sh'\r\n[INFO] jobid=J53c0cde6868f9d2b7ac4c7833461dd3b3c5a245ee70deb86d965712fefb601d1\r\n[INFO] starting job Job(jobid='J53c0cde6868f9d2b7ac4c7833461dd3b3c5a245ee70deb86d965712fefb601d1', cmd='/bin/bash rp_00001.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/m_00001', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N J53c0cde6868f9d -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/J53c0cde6868f9d2b7ac4c7833461dd3b3c5a245ee70deb86d965712fefb601d1 -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-J53c0cde6868f9d2b7ac4c7833461dd3b3c5a245ee70deb86d965712fefb601d1.bash\r\n102913.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='J53c0cde6868f9d2b7ac4c7833461dd3b3c5a245ee70deb86d965712fefb601d1', cmd='/bin/bash rp_00001.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/m_00001', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/m_00001_raw_reads' ...\r\n[INFO] Success ('done'). Joining 'task://localhost/m_00001_raw_reads'...\r\n[INFO] _refreshTargets() finished with no thread running and no new job to submit\r\n[INFO] # of tasks in complete graph: 11\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] tick: 2, #updatedTasks: 0, sleep_time=0.100000\r\n[INFO] Running task from function task_run_consensus()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/preads/c_00002.sh'\r\n[INFO] jobid=Jf1f05abdbfdecf1271387ca867421bad6d8136f8660e94bc14f4a1bb10fa2c20\r\n[INFO] starting job Job(jobid='Jf1f05abdbfdecf1271387ca867421bad6d8136f8660e94bc14f4a1bb10fa2c20', cmd='/bin/bash c_00002.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/preads', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N Jf1f05abdbfdecf -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/Jf1f05abdbfdecf1271387ca867421bad6d8136f8660e94bc14f4a1bb10fa2c20 -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-Jf1f05abdbfdecf1271387ca867421bad6d8136f8660e94bc14f4a1bb10fa2c20.bash\r\n102914.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='Jf1f05abdbfdecf1271387ca867421bad6d8136f8660e94bc14f4a1bb10fa2c20', cmd='/bin/bash c_00002.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/preads', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/ct_00002' ...\r\n[INFO] tick: 4, #updatedTasks: 1, sleep_time=0.100000\r\n[INFO] tick: 8, #updatedTasks: 1, sleep_time=0.500000\r\n[INFO] Success ('done'). Joining 'task://localhost/ct_00002'...\r\n[INFO] Running task from function task_run_consensus()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/preads/c_00001.sh'\r\n[INFO] jobid=J04c86fbdb788b39fb6eb0b1382bd5513f3d1cb6a09b9f0ba8fdb0c91d4d007e1\r\n[INFO] starting job Job(jobid='J04c86fbdb788b39fb6eb0b1382bd5513f3d1cb6a09b9f0ba8fdb0c91d4d007e1', cmd='/bin/bash c_00001.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/preads', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N J04c86fbdb788b3 -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/J04c86fbdb788b39fb6eb0b1382bd5513f3d1cb6a09b9f0ba8fdb0c91d4d007e1 -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-J04c86fbdb788b39fb6eb0b1382bd5513f3d1cb6a09b9f0ba8fdb0c91d4d007e1.bash\r\n102915.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='J04c86fbdb788b39fb6eb0b1382bd5513f3d1cb6a09b9f0ba8fdb0c91d4d007e1', cmd='/bin/bash c_00001.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/preads', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/ct_00001' ...\r\n[INFO] tick: 16, #updatedTasks: 2, sleep_time=0.100000\r\n[INFO] Success ('done'). Joining 'task://localhost/ct_00001'...\r\n[INFO] Running task from function check_r_cns_task()\r\n[WARNING] Missing taskObj.generated_script_fn for task. Maybe we did not need it? Skipping and continuing.\r\n[INFO] Queued 'task://localhost/cns_check' ...\r\n[INFO] Success ('done'). Joining 'task://localhost/cns_check'...\r\n[INFO] Running task from function task_report_pre_assembly()\r\n[INFO] length_cutoff=2000 from '/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/length_cutoff'\r\n[INFO] Report inputs: {'length_cutoff': 2000, 'i_raw_reads_fofn_fn': '/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/input.fofn', 'i_preads_fofn_fn': '/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/input_preads.fofn', 'genome_length': 5000}\r\n[INFO] stats for raw reads:       FastaStats(nreads=50, total=100000, n50=2000, p95=2000)\r\n[INFO] stats for seed reads:      FastaStats(nreads=50, total=100000, n50=2000, p95=2000)\r\n[INFO] stats for corrected reads: FastaStats(nreads=50, total=99447, n50=1989, p95=1989)\r\n[INFO] Report stats:\r\n{\r\n    \"genome_length\": 5000,\r\n    \"length_cutoff\": 2000,\r\n    \"preassembled_bases\": 99447,\r\n    \"preassembled_coverage\": 19.8894,\r\n    \"preassembled_mean\": 1988.94,\r\n    \"preassembled_n50\": 1989,\r\n    \"preassembled_p95\": 1989,\r\n    \"preassembled_reads\": 50,\r\n    \"preassembled_yield\": 0.99447,\r\n    \"raw_bases\": 100000,\r\n    \"raw_coverage\": 20.0,\r\n    \"raw_mean\": 2000.0,\r\n    \"raw_n50\": 2000,\r\n    \"raw_p95\": 2000,\r\n    \"raw_reads\": 50,\r\n    \"seed_bases\": 100000,\r\n    \"seed_coverage\": 20.0,\r\n    \"seed_mean\": 2000.0,\r\n    \"seed_n50\": 2000,\r\n    \"seed_p95\": 2000,\r\n    \"seed_reads\": 50\r\n}\r\n[WARNING] Missing taskObj.generated_script_fn for task. Maybe we did not need it? Skipping and continuing.\r\n[INFO] Queued 'task://localhost/report_pre_assembly' ...\r\n[INFO] Success ('done'). Joining 'task://localhost/report_pre_assembly'...\r\n[INFO] _refreshTargets() finished with no thread running and no new job to submit\r\n[INFO] # of tasks in complete graph: 11\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] tick: 2, #updatedTasks: 0, sleep_time=0.100000\r\n[INFO] Running task from function task_build_pdb()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/prepare_pdb.sh'\r\n[INFO] jobid=J6520f84e07ad07d6d1ca5c2457459f716986fd3229c6b60d9342264bce371423\r\n[INFO] starting job Job(jobid='J6520f84e07ad07d6d1ca5c2457459f716986fd3229c6b60d9342264bce371423', cmd='/bin/bash prepare_pdb.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N J6520f84e07ad07 -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/J6520f84e07ad07d6d1ca5c2457459f716986fd3229c6b60d9342264bce371423 -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-J6520f84e07ad07d6d1ca5c2457459f716986fd3229c6b60d9342264bce371423.bash\r\n102916.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='J6520f84e07ad07d6d1ca5c2457459f716986fd3229c6b60d9342264bce371423', cmd='/bin/bash prepare_pdb.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/build_pdb' ...\r\n[INFO] tick: 4, #updatedTasks: 1, sleep_time=0.100000\r\n[INFO] tick: 8, #updatedTasks: 1, sleep_time=0.500000\r\n[INFO] Success ('done'). Joining 'task://localhost/build_pdb'...\r\n[INFO] _refreshTargets() finished with no thread running and no new job to submit\r\n[INFO] # of tasks in complete graph: 14\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] tick: 2, #updatedTasks: 0, sleep_time=0.100000\r\n[INFO] Running task from function task_run_daligner()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/job_0000/rj_0000.sh'\r\n[INFO] jobid=Jb4e17fb75d5c877c9ee6ac5c90d0b4699513e122e9b72d86a0f972d747007736\r\n[INFO] starting job Job(jobid='Jb4e17fb75d5c877c9ee6ac5c90d0b4699513e122e9b72d86a0f972d747007736', cmd='/bin/bash rj_0000.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/job_0000', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N Jb4e17fb75d5c87 -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/Jb4e17fb75d5c877c9ee6ac5c90d0b4699513e122e9b72d86a0f972d747007736 -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-Jb4e17fb75d5c877c9ee6ac5c90d0b4699513e122e9b72d86a0f972d747007736.bash\r\n102917.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='Jb4e17fb75d5c877c9ee6ac5c90d0b4699513e122e9b72d86a0f972d747007736', cmd='/bin/bash rj_0000.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/job_0000', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/d_0000_preads' ...\r\n[INFO] tick: 4, #updatedTasks: 1, sleep_time=0.100000\r\n[INFO] Success ('done'). Joining 'task://localhost/d_0000_preads'...\r\n[INFO] tick: 8, #updatedTasks: 1, sleep_time=0.000000\r\n[INFO] Running task from function task_daligner_gather()\r\n[INFO] Symlink .las files for further merging:\r\n{'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/m_00001': ['/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/job_0000/preads.1.las']}\r\n[WARNING] Missing taskObj.generated_script_fn for task. Maybe we did not need it? Skipping and continuing.\r\n[INFO] Queued 'task://localhost/pda_check' ...\r\n[INFO] Success ('done'). Joining 'task://localhost/pda_check'...\r\n[INFO] _refreshTargets() finished with no thread running and no new job to submit\r\n[INFO] # of tasks in complete graph: 16\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] tick: 2, #updatedTasks: 0, sleep_time=0.100000\r\n[INFO] Running task from function task_run_las_merge()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/m_00001/rp_00001.sh'\r\n[INFO] jobid=J44d2d2b3515e36ba842d68d1e636f111cebf156c1f4b54b0119ae4885fb3a3f1\r\n[INFO] starting job Job(jobid='J44d2d2b3515e36ba842d68d1e636f111cebf156c1f4b54b0119ae4885fb3a3f1', cmd='/bin/bash rp_00001.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/m_00001', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N J44d2d2b3515e36 -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/J44d2d2b3515e36ba842d68d1e636f111cebf156c1f4b54b0119ae4885fb3a3f1 -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-J44d2d2b3515e36ba842d68d1e636f111cebf156c1f4b54b0119ae4885fb3a3f1.bash\r\n102918.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='J44d2d2b3515e36ba842d68d1e636f111cebf156c1f4b54b0119ae4885fb3a3f1', cmd='/bin/bash rp_00001.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/m_00001', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/m_00001_preads' ...\r\n[INFO] tick: 4, #updatedTasks: 1, sleep_time=0.100000\r\n[INFO] Success ('done'). Joining 'task://localhost/m_00001_preads'...\r\n[INFO] tick: 8, #updatedTasks: 1, sleep_time=0.000000\r\n[INFO] Running task from function check_p_merge_check_task()\r\n[WARNING] Missing taskObj.generated_script_fn for task. Maybe we did not need it? Skipping and continuing.\r\n[INFO] Queued 'task://localhost/pmerge_check' ...\r\n[INFO] Success ('done'). Joining 'task://localhost/pmerge_check'...\r\n[INFO] _refreshTargets() finished with no thread running and no new job to submit\r\n[INFO] # of tasks in complete graph: 18\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] tick: 2, #updatedTasks: 0, sleep_time=0.100000\r\n[INFO] Running task from function task_run_db2falcon()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl/run_db2falcon.sh'\r\n[INFO] jobid=J87fa279521da8203556c24b573441f6e10a97f583be9104082b202112b45ce00\r\n[INFO] starting job Job(jobid='J87fa279521da8203556c24b573441f6e10a97f583be9104082b202112b45ce00', cmd='/bin/bash run_db2falcon.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N J87fa279521da82 -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/J87fa279521da8203556c24b573441f6e10a97f583be9104082b202112b45ce00 -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-J87fa279521da8203556c24b573441f6e10a97f583be9104082b202112b45ce00.bash\r\n102919.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='J87fa279521da8203556c24b573441f6e10a97f583be9104082b202112b45ce00', cmd='/bin/bash run_db2falcon.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/1-preads_ovl', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/db2falcon' ...\r\n[INFO] tick: 4, #updatedTasks: 1, sleep_time=0.100000\r\n[INFO] Success ('done'). Joining 'task://localhost/db2falcon'...\r\n[INFO] tick: 8, #updatedTasks: 1, sleep_time=0.100000\r\n[INFO] Running task from function task_run_falcon_asm()\r\n[INFO] script_fn:'/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/2-asm-falcon/run_falcon_asm.sh'\r\n[INFO] jobid=Jb93e27ec197b3d278a8f4357145e082e29404b21bd2b9db29623016696a8fca3\r\n[INFO] starting job Job(jobid='Jb93e27ec197b3d278a8f4357145e082e29404b21bd2b9db29623016696a8fca3', cmd='/bin/bash run_falcon_asm.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/2-asm-falcon', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None})\r\n[INFO] !qsub -N Jb93e27ec197b3d -l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu -V -d /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/jobs/Jb93e27ec197b3d278a8f4357145e082e29404b21bd2b9db29623016696a8fca3 -o stdout -e stderr -S /bin/bash /home/stelo/FALCON-integrate/FALCON-examples/run/synth0/mypwatcher/wrappers/run-Jb93e27ec197b3d278a8f4357145e082e29404b21bd2b9db29623016696a8fca3.bash\r\n102920.head\r\n[INFO] Submitted backgroundjob=MetaJobTorque(MetaJob(job=Job(jobid='Jb93e27ec197b3d278a8f4357145e082e29404b21bd2b9db29623016696a8fca3', cmd='/bin/bash run_falcon_asm.sh', rundir='/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/2-asm-falcon', options={'sge_option': '-l nodes=1:ppn=16:nogpu,walltime=4:00:00,mem=50000mb -M stelo@cs.ucr.edu', 'job_type': None}), lang_exe='/bin/bash'))\r\n[INFO] Queued 'task://localhost/falcon' ...\r\n[INFO] tick: 16, #updatedTasks: 2, sleep_time=0.700000\r\n[INFO] Success ('done'). Joining 'task://localhost/falcon'...\r\n[INFO] _refreshTargets() finished with no thread running and no new job to submit\r\nmake[3]: Leaving directory `/home/stelo/FALCON-integrate/FALCON-examples'\r\nmake -C run/synth0 test\r\nmake[3]: Entering directory `/home/stelo/FALCON-integrate/FALCON-examples/run/synth0'\r\n./check.py\r\nshifted by 3269 (rc)\r\nmake[3]: Leaving directory `/home/stelo/FALCON-integrate/FALCON-examples/run/synth0'\r\nmake -C run/synth0 clean\r\nmake[3]: Entering directory `/home/stelo/FALCON-integrate/FALCON-examples/run/synth0'\r\n\\rm -rf 0-*/ 1-*/ 2-*/ *.log mypwatcher/\r\nmake[3]: Leaving directory `/home/stelo/FALCON-integrate/FALCON-examples/run/synth0'\r\nmake -C run/synth0 go0 # still test the old pypeflow too, for now\r\nmake[3]: Entering directory `/home/stelo/FALCON-integrate/FALCON-examples/run/synth0'\r\nfc_run0 fc_run.cfg logging.ini\r\n[INFO] fc_run started with configuration fc_run.cfg\r\n[INFO]  No target specified, assuming \"assembly\" as target\r\n[INFO] # of tasks in complete graph: 1\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] Running task from function task_make_fofn_abs_raw()\r\n[INFO] Queued 'task:///home/stelo/FALCON-integrate/FALCON/falcon_kit/mains/run0.py/task_make_fofn_abs_raw' ...\r\n[INFO] tick: 2, #updatedTasks: 1, sleep_time=0.000000\r\n[INFO] Success ('done'). Joining 'task:///home/stelo/FALCON-integrate/FALCON/falcon_kit/mains/run0.py/task_make_fofn_abs_raw'...\r\n[INFO] _refreshTargets() finished with no thread running and no new job to submit\r\n[INFO] # of tasks in complete graph: 2\r\n[INFO] tick: 1, #updatedTasks: 0, sleep_time=0.000000\r\n[INFO] Running task from function task_build_rdb()\r\n[INFO] Queued 'task:///home/stelo/FALCON-integrate/FALCON/falcon_kit/mains/run0.py/task_build_rdb' ...\r\n[INFO] tick: 2, #updatedTasks: 1, sleep_time=0.000000\r\n[INFO] (torque) '/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/prepare_rdb.sh'\r\n102921.head\r\n[INFO] tick: 4, #updatedTasks: 1, sleep_time=0.200000\r\n[INFO] '/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/rdb_build_done.exit' found.\r\n[WARNING] '/home/stelo/FALCON-integrate/FALCON-examples/run/synth0/0-rawreads/rdb_build_done' is missing. job: 'prepare_rdb.sh-task_build_rdb-task_build_rdb' failed!\r\n[INFO] Failure ('fail'). Joining 'task:///home/stelo/FALCON-integrate/FALCON/falcon_kit/mains/run0.py/task_build_rdb'...\r\n[CRITICAL] Any exception caught in RefreshTargets() indicates an unrecoverable error. Shutting down...\r\n/home/stelo/FALCON-integrate/pypeFLOW/pypeflow/controller.py:537: UserWarning:\r\n            \"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\"\r\n            \"! Please wait for all threads / processes to terminate !\"\r\n            \"! Also, maybe use 'ps' or 'qstat' to check all threads,!\"\r\n            \"! processes and/or jobs are terminated cleanly.        !\"\r\n            \"!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\"\r\n\r\n  warnings.warn(shutdown_msg)\r\n[WARNING] #tasks=1, #alive=0\r\nTraceback (most recent call last):\r\n  File \"/home/stelo/FALCON-integrate/fc_env/bin/fc_run0\", line 9, in <module>\r\n    load_entry_point('falcon-kit', 'console_scripts', 'fc_run0')()\r\n  File \"/home/stelo/FALCON-integrate/FALCON/falcon_kit/mains/run0.py\", line 681, in main\r\n    main1(argv[0], args.config, args.logger)\r\n  File \"/home/stelo/FALCON-integrate/FALCON/falcon_kit/mains/run0.py\", line 512, in main1\r\n    wf.refreshTargets([rdb_build_done])\r\n  File \"/home/stelo/FALCON-integrate/pypeFLOW/pypeflow/controller.py\", line 548, in refreshTargets\r\n    raise Exception('Caused by:\\n' + tb)\r\nException: Caused by:\r\nTraceback (most recent call last):\r\n  File \"/home/stelo/FALCON-integrate/pypeFLOW/pypeflow/controller.py\", line 523, in refreshTargets\r\n    rtn = self._refreshTargets(task2thread, objs = objs, callback = callback, updateFreq = updateFreq, exitOnFailure = exitOnFailure)\r\n  File \"/home/stelo/FALCON-integrate/pypeFLOW/pypeflow/controller.py\", line 740, in _refreshTargets\r\n    raise TaskFailureError(\"Counted %d failure(s) with 0 successes so far.\" %failedJobCount)\r\nTaskFailureError: 'Counted 1 failure(s) with 0 successes so far.'\r\nmake[3]: *** [run0] Error 1\r\nmake[3]: Leaving directory `/home/stelo/FALCON-integrate/FALCON-examples/run/synth0'\r\nmake[2]: *** [test] Error 2\r\nmake[2]: Leaving directory `/home/stelo/FALCON-integrate/FALCON-examples'\r\nmake[1]: *** [test] Error 2\r\nmake[1]: Leaving directory `/home/stelo/FALCON-integrate/FALCON-make'\r\nmake: *** [test] Error 2\r\n```"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/pypeFLOW/issues/comments/223774775","html_url":"https://github.com/PacificBiosciences/pypeFLOW/issues/22#issuecomment-223774775","issue_url":"https://api.github.com/repos/PacificBiosciences/pypeFLOW/issues/22","id":223774775,"user":{"login":"StefanoLonardi","id":18489339,"avatar_url":"https://avatars.githubusercontent.com/u/18489339?v=3","gravatar_id":"","url":"https://api.github.com/users/StefanoLonardi","html_url":"https://github.com/StefanoLonardi","followers_url":"https://api.github.com/users/StefanoLonardi/followers","following_url":"https://api.github.com/users/StefanoLonardi/following{/other_user}","gists_url":"https://api.github.com/users/StefanoLonardi/gists{/gist_id}","starred_url":"https://api.github.com/users/StefanoLonardi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/StefanoLonardi/subscriptions","organizations_url":"https://api.github.com/users/StefanoLonardi/orgs","repos_url":"https://api.github.com/users/StefanoLonardi/repos","events_url":"https://api.github.com/users/StefanoLonardi/events{/privacy}","received_events_url":"https://api.github.com/users/StefanoLonardi/received_events","type":"User","site_admin":false},"created_at":"2016-06-04T19:51:00Z","updated_at":"2016-06-04T19:51:00Z","body":"Well, using `fc_run.py fc_run_ecoli.cfg logging.ini` seems to allow **FALCON** to run a lot longer with  concurrency=2 before failing on ecoli (it behaves now like I had concurrency = 1 before). By restarting it a few times I think I should be able to complete the assembly with concurrency=2.\r\n\r\nThere is a lot of errors `You might have a large clock-skew, or filesystem delays, or just filesystem time-rounding.` in `fc.log`. I asked my sysadmin to look into clock-skew, but I might try to change `ALLOWED_SKEW_S` next. (Thanks a lot for answering on a Saturday)"}}
{"actor":{"display_login":"StefanoLonardi"}}