artemis@ATGMBioinfor3:/home/kristy/falcon_run$ sudo fc_run fc_run_ecoli_local.cfg ecoli_files.fofn
[4386]$('lfs setstripe -c 12 /home/kristy/falcon_run')
sh: 1: lfs: not found
[4386]WARNING: Call 'lfs setstripe -c 12 /home/kristy/falcon_run' returned 32512.
ERROR:root:Failed to setup logging from file "ecoli_files.fofn". Using basicConfig().
Traceback (most recent call last):
File "/usr/lib/falcon/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/run_support.py", line 435, in setup_logger_setup_logging(logging_config_fn)
File "/usr/lib/falcon/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/run_support.py", line 430, in _setup_logging
logging.config.fileConfig(logger_fileobj, defaults=defaults, disable_existing_loggers=False)
File "/usr/lib/python2.7/logging/config.py", line 73, in fileConfig
cp.readfp(fname)
File "/usr/lib/python2.7/ConfigParser.py", line 324, in readfp
self._read(fp, filename)
File "/usr/lib/python2.7/ConfigParser.py", line 512, in _read
raise MissingSectionHeaderError(fpname, lineno, line)
MissingSectionHeaderError: File contains no section headers.
file: ecoli_files.fofn, line: 1
'ecoli_testfiles/ecoli.1.fasta\r\n'
/usr/lib/falcon/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/run_support.py:172: UserWarning: Deprecated setting in config: 'pa_concurrent_jobs' -- Prefer da_concurrent_jobs and la_concurrent_jobs separately
warnings.warn("Deprecated setting in config: 'pa_concurrent_jobs' -- Prefer da_concurrent_jobs and la_concurrent_jobs separately")
/usr/lib/falcon/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/run_support.py:176: UserWarning: Deprecated setting in config: 'ovlp_concurrent_jobs' -- Prefer pda_concurrent_jobs and pla_concurrent_jobs separately
warnings.warn("Deprecated setting in config: 'ovlp_concurrent_jobs' -- Prefer pda_concurrent_jobs and pla_concurrent_jobs separately")
/usr/lib/falcon/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/run_support.py:376: UserWarning: Unexpected keys in input config: set(['ovlp_concurrent_jobs', 'pa_concurrent_jobs', 'jobqueue'])
warnings.warn("Unexpected keys in input config: %s" %repr(unused))
WARNING:pypeflow.simple_pwatcher_bridge:In simple_pwatcher_bridge, pwatcher_impl=<module 'pwatcher.fs_based' from '/usr/lib/falcon/pylib/pypeflow-1.0.0-py2.7.egg/pwatcher/fs_based.pyc'>
ERROR:pypeflow.simple_pwatcher_bridge:Task Node(0-rawreads/raw-fofn-abs) failed with exit-code=256
ERROR:pypeflow.simple_pwatcher_bridge:Some tasks are recently_done but not satisfied: set([Node(0-rawreads/raw-fofn-abs)])
ERROR:pypeflow.simple_pwatcher_bridge:ready: set([])
submitted: set([])
Traceback (most recent call last):
File "/usr/lib/falcon/bin/fc_run", line 11, in <module>
load_entry_point('falcon-kit==0.7', 'console_scripts', 'fc_run')()
File "/usr/lib/falcon/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/mains/run1.py", line 466, in main
main1(argv[0], args.config, args.logger)
File "/usr/lib/falcon/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/mains/run1.py", line 137, in main1
input_fofn_plf=input_fofn_plf,
File "/usr/lib/falcon/pylib/falcon_kit-0.7-py2.7-linux-x86_64.egg/falcon_kit/mains/run1.py", line 173, in run
wf.refreshTargets([fofn_abs_task])
File "/usr/lib/falcon/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/simple_pwatcher_bridge.py", line 226, in refreshTargets
self._refreshTargets(updateFreq, exitOnFailure)
File "/usr/lib/falcon/pylib/pypeflow-1.0.0-py2.7.egg/pypeflow/simple_pwatcher_bridge.py", line 292, in _refreshTargets
raise Exception(msg)
Exception: Some tasks are recently_done but not satisfied: set([Node(0-rawreads/raw-fofn-abs)])